Amyris Annual Report 2018

FY2018 Annual Report · Amyris

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Dear Shareholders,

In 2018 we simplified our business and deepened our commitment to leadership in sustainable health
and beauty while accelerating our growth in direct to consumer sales. Today, we are delivering world leading
innovations in clean beauty, zero calorie natural sweetener and cannabinoids. This revenue growth is
recurring and predictable, which enables us to create sustainable value for our shareholders. Each of our
scientific and technology breakthroughs are currently resulting in commercial success. We are on the right
path with the right balance in our goal to improve the health of our planet while delivering profitable
growth as measured by our strong gross margin performance.

This year, we introduced a revolutionary, zero calorie sweetener, naturally made from sugarcane. The
global response from customers to our ingredient has been remarkable. No country or food or beverage
company is immune to the health risks related to added sugar and artificial sweeteners or the financial costs
of healthcare for people living with diabetes or obesity-related conditions.

We have found in consumer testing this year, for our soon to be launched consumer brand called
Purecane™, that people are genuinely delighted to discover a delicious sweetener with no bitter aftertaste,
that is natural, non-GMO, zero calorie and zero glycemic. We are setting a new standard for sugar
reduction and we remain committed to the health and wellness of our planet.

At the start of 2019 we signed a cannabinoid development agreement, which is the largest agreement of
its kind in the world, that we are aware of. This development program is a deep commitment to replace the
need for opioids with a sustainable solution to pain management, anxiety and sleep assistance. We are
doubling down on leading the path to making our planet healthier.

Biossance, our clean beauty skincare brand, remains one of the fastest selling clean beauty brands in
North America with best in class performing products that are clean, safe, non-toxic and sustainably
sourced. From A-list celebrities to social media stars, millions of consumers around the world are buying
Biossance and Amyris produced squalane powered beauty products and telling others how happy they are
with the best performing, most sustainably produced squalane in the world.

As proud as we are of our successes in 2018, we recognize that the year also brought challenges and, in

my view, our financial results did not meet my expectations.

Our shortfall was due to three issues, each of which we have now addressed.

First, after a steep drop in vitamin E pricing and royalty revenue, both of which were outside of our
control, we concluded that the volatility and unpredictable profitability of the vitamin E business made the
business non-strategic to us, given the better margins and growth we are experiencing with our health and
beauty product portfolio. We decided to exit our long-term vitamin E royalty agreement with DSM in
exchange for the net present value paid in upfront cash and consideration valued at around $92 million in
total value.

Second, we observed that the timing and nature of our smaller collaboration agreements had led to
choppy financial flow and complicated our accounting treatment. We decided to focus our attention on
recurring product revenue and larger collaborations.

In 2019, our dependency on future collaboration agreements was largely mitigated with one single large
collaboration with LAVVAN for the development of cannabinoids over a 3 – 5-year term. This agreement is
expected to deliver up to $100 million in the first two years assuming continued execution of milestones.

Finally, the demand for our sweetener ingredient which launched in December 2018, outpaced our

speed to deliver by about 30 – 45 days, which also impacted our year end revenue results.

As we began the process of preparing our Annual Report on Form 10-K for the fiscal year ended 2018
we discovered the need to review the accounting for our partnership with Ginkgo Bioworks in 2017 and
certain material transactions with Royal DSM, a related party, in 2018. This led to a need to restate
financial results for both annual periods to correct certain accounting entries associated with these
transactions. These adjustments had no impact on the value of the original transactions. In all cases we
were paid in full for the items adjusted, and the adjustments were related to movements between P&L
entries and the balance sheet. Through this process, we also encountered significant delays from and a lack

of commitment and resources toward completing our filings on an agreed upon timeline by our prior
auditor, which we subsequently dismissed. Each of these circumstances on their own would be difficult for
our shareholders and Amyris, and in aggregate were more troublesome. With new auditors now in place, we
have put these difficulties behind us and we are thankful for our shareholders’ patience and support and the
unrelenting dedication of our employees.

Even with these challenges, our core products and markets continued to perform very well and today
we are displaying best in class revenue performance with annual product revenue growth rates over 100%. In
clean beauty, our hero ingredient, squalane, is the world’s leading moisturizer. This ingredient is powering
solid growth in our ingredients business, Aprinnova, with broad-based new customer adoption, including
most of the leading world brands. This blockbuster ingredient is also the workhorse behind the success of
Biossance products that consumers love. Still at the relatively early stages of broadening our footprint
within Sephora stores and executing well on geographic expansion, Biossance products are already seeing
solid consumer demand in Canada, Brazil, Mexico, and most recently, Australia and New Zealand.

Similarly, we are successfully attracting the attention of the world with our natural, zero calorie
fermented sugarcane Reb M — which we are branding Purecane. We’ve already garnered the World Food
Innovation Award for our best in show manufacturing innovation and many of the major food and
beverage companies have engaged their R&D teams to begin reformulating their products to replace or
reduce their added sugars with our ingredient.

New product development is where we are really excelling. Global market leaders partner with Amyris
to improve their competitive advantage with innovations for their product portfolios. It is Amyris’s proven
record of success to develop, manufacture at scale and commercialize products that attracted our partner,
LAVVAN, with whom we announced our $300 million partnership to develop cannabinoids this year.
Together, we believe we can provide the market with the highest quality, natural cannabinoids at
significantly reduced cost for a multitude of consumer product and therapeutic applications. In addition to
quickly becoming the leading supplier of the consistently highest purity and highest quality cannabinoids in
the world, we also expect to become a leading brand of consumer solutions for chronic pain management,
anxiety and sleeplessness. We are excited about the unique position we are now in to be able to build on our
strong track record of building leading brands that deliver on the consumer promise of clean, sustainable
ingredients and products that make the world healthier.

Delivering real impact is the work that has gained us the reputation as the leading company in
Synthetic Biology. We are the leading supplier to the world’s best formulators for flavors and fragrances. We
are managing a strong pipeline for new, commercialized molecules We are already the fastest growing
company in our sector and expect to continue the current pace of growth while also leading in reducing our
cash burn and delivering strong gross margin performance.

The challenges we experienced last year allowed us to reflect on and refocus our business. The result is
that we will have a much stronger product portfolio with more predictable revenue growth, allowing us to
manage market expectations more conservatively when providing guidance on financial results. We expect
that taking this approach will help investors see the true value of our business more clearly and as result will
benefit our long-term interests and those of our shareholders.

In closing, we would like to thank our partners, investors and dedicated employees for joining us in the
mission of making our planet healthier by developing and making products that are best performing, lowest
cost, naturally sourced and sustainable for our planet. This is the power of Synthetic Biology and Amyris is
making the technology of this century a reality for our planet. Thank you for your ongoing support of
Amyris’s efforts to Make Good, No Compromise®.

Regards,

John G. Melo
President and Chief Executive Officer

FORWARD-LOOKING STATEMENTS

This annual report contains forward-looking statements reflecting our current expectations that involve
risks and uncertainties. These forward-looking statements include, but are not limited to, statements
concerning our business growth and profitability, revenue and gross margin performance and growth,
reduction in cash operating expenses, milestone payments under our cannabinoid development agreement,
the development, scaling and
geographic expansion of our Biossance consumer skincare brand,
commercialization of our product pipeline and introduction of new products,
including cannabinoid
ingredients, including the cost and quality of such products, our competitive advantage, and similar matters.
The words “anticipates,” “believes,” “estimates,” “expects,” “intends,” “may,” “plans,” “projects,” “will,”
“would” and similar expressions are intended to identify forward-looking statements, although not all
forward-looking statements contain these identifying words. We may not actually achieve the plans,
intentions or expectations disclosed in our forward-looking statements and you should not place undue
reliance on our forward-looking statements. These forward-looking statements involve risks and
uncertainties that could cause our actual results to differ materially from those anticipated or implied in the
forward-looking statements, including, without limitation, the risks set forth in Part 1, Item 1A, “Risk
Factors” of our enclosed Annual Report on Form 10-K for the fiscal year ended December 31, 2018 and in
our other filings with the Securities and Exchange Commission. We do not assume any obligation to update
any forward-looking statements, except as required by law.

Dear Amyris stockholder:

You are cordially invited to attend our 2019 Annual Meeting of Stockholders to be held on Tuesday,
November 19, 2019 at 2:00 p.m. Pacific Time at our headquarters located at 5885 Hollis Street, Suite 100,
Emeryville, California 94608. You can find directions to our headquarters on our company website at
https://amyris.com/contact-us/.

The accompanying Notice of Annual Meeting of Stockholders and Proxy Statement describe the

matters to be voted on at the meeting.

We are using the Internet as our primary means of furnishing proxy materials to our stockholders. As a
result, most stockholders will not receive paper copies of our proxy materials. We will instead send most
stockholders a notice with instructions for accessing the proxy materials and voting over the Internet. The
notice also provides information on how stockholders can obtain paper copies of our proxy materials if
they wish to do so.

Whether or not you plan to attend the annual meeting, please vote as soon as possible. You may vote
over the Internet, by telephone, or, if you receive a paper proxy card or voter instructions form in the mail,
by mailing a completed proxy card or voting instruction form. Voting by any of these methods will ensure
that you are represented at the annual meeting.

On behalf of the Board of Directors, I want to thank you for your continued support of Amyris. We

look forward to seeing you at the meeting.

John Melo
President and Chief Executive Officer

Emeryville, California
October 10, 2019

YOUR VOTE IS IMPORTANT
You are cordially invited to attend the meeting in person. Whether or not you expect to attend the
meeting, please vote as soon as possible in order to ensure your representation at the meeting. You may
submit your proxy and voting instructions over the Internet, by telephone, or, if you receive a paper proxy
card or voter instructions form in the mail, by completing, signing, dating and returning the
accompanying proxy card or voting instruction form as promptly as possible. If your shares are held of
record by a broker, bank or other custodian, nominee, trustee or fiduciary (an “Intermediary”) and you
have not given your Intermediary specific voting instructions, your Intermediary will NOT be able to vote
your shares with respect to most of the proposals, including the election of directors. If you do not
provide voting instructions over the Internet, by telephone, or by returning a completed, signed and dated
proxy card or voting instruction form, your shares will not be voted with respect to those matters. Even if
you have voted by proxy, you may still vote in person if you attend the meeting. Please note, however, that
if your shares are held of record by an Intermediary and you wish to vote at the meeting, you must obtain
a proxy issued in your name from that Intermediary.

AMYRIS, INC.
5885 Hollis Street, Suite 100
Emeryville, California 94608

NOTICE OF ANNUAL MEETING OF STOCKHOLDERS

To Be Held November 19, 2019

The 2019 Annual Meeting of Stockholders of Amyris, Inc. will be held on Tuesday, November 19,
2019 at 2:00 p.m. Pacific Time at our headquarters located at 5885 Hollis Street, Suite 100, Emeryville,
California 94608 for the following purposes:

1. To elect the four Class III directors nominated by our Board of Directors and named herein to

serve on the Board for a three-year term;

2. To ratify the selection of Macias Gini & O’Connell LLP as our independent registered public

accounting firm for the fiscal year ending December 31, 2019;

3. To approve the issuance of shares of our common stock issuable upon the exercise of warrants
and conversion of preferred stock issued to Foris Ventures, LLC in accordance with Nasdaq
Marketplace Rules 5635(b) and 5635(d); and

4. To act upon such other matters as may properly come before the annual meeting or any

adjournments or postponements thereof.

These items of business are more fully described in the Proxy Statement accompanying this Notice of
Annual Meeting of Stockholders. The Board of Directors has fixed the record date for the annual meeting
as September 23, 2019. Only stockholders of record at the close of business on the record date may vote at
the meeting or at any adjournment thereof. A list of stockholders eligible to vote at the meeting will be
available for review for any purpose relating to the meeting during our regular business hours at our
headquarters at 5885 Hollis Street, Suite 100, Emeryville, California 94608 for the ten days prior to the
meeting.

You are cordially invited to attend the meeting in person. Whether or not you expect to attend the
meeting, please vote as soon as possible in order to ensure your representation at the meeting. You may
submit your proxy and voting instructions over the Internet, by telephone, or, if you receive a paper proxy
card or voting instruction form in the mail, by completing, signing, dating and returning the accompanying
proxy card or voting instruction form as promptly as possible. If your shares are held of record by an
Intermediary and you have not given your Intermediary specific voting instructions, your Intermediary will
NOT be able to vote your shares with respect to most of the proposals, including the election of directors. If
you do not provide voting instructions over the Internet, by telephone, or by returning a completed, signed
and dated proxy card or voting instruction form, your shares will not be voted with respect to those matters.
Even if you have voted by proxy, you may still vote in person if you attend the meeting. Please note,
however, that if your shares are held of record by an Intermediary and you wish to vote at the meeting, you
must obtain a proxy issued in your name from that Intermediary.

BY ORDER OF THE BOARD,

Nicole Kelsey
General Counsel and Secretary

Emeryville, California
October 10, 2019

Table of Contents

Information Regarding Solicitation and Voting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Questions and Answers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Forward-Looking Statements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Proposal 1 — Election of Directors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

General . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Vote Required and Board Recommendation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Business Experience and Qualifications of Directors

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Arrangements Concerning Selection of Directors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Independence of Directors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Board Leadership Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Role of the Board in Risk Oversight . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Meetings of the Board and Committees . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Committees of the Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Stockholder Communications with Directors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Proposal 2 — Ratification of Selection of Independent Registered Public Accounting Firm . . . . . . . . . .
General . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vote Required and Board Recommendation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Independent Registered Public Accounting Firm Fee Information . . . . . . . . . . . . . . . . . . . . . . . .
Audit Committee Pre-Approval of Services Performed by our Independent Registered Public

Accounting Firm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Report of the Audit Committee . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Proposal 3 — Approval of the issuance of shares of our common stock issuable upon the exercise of

warrants and conversion of preferred stock issued to Foris Ventures, LLC in accordance with Nasdaq
Marketplace Rules 5635(b) and 5635(d) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
General . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Purpose — Nasdaq Stockholder Approval Requirement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vote Required and Board Recommendation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . .
Potential Adverse Effects — Dilution and Impact on Existing Stockholders
Interests of Certain Persons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Corporate Governance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Corporate Governance Principles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Code of Business Conduct and Ethics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . .
Security Ownership of Certain Beneficial Owners and Management
Delinquent Section 16(a) Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Equity Compensation Plan Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Executive Officers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Executive Compensation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Compensation Discussion and Analysis
Leadership Development and Compensation Committee Report . . . . . . . . . . . . . . . . . . . . . . . . .

Summary Compensation Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Grants of Plan-Based Awards in 2018 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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Narrative Disclosure to Summary Compensation and Grants of Plan-Based Awards Tables . . . . . .

Outstanding Equity Awards as of December 31, 2018 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Option Exercises and Stock Vested During 2018 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Pension Benefits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Non-Qualified Deferred Compensation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Potential Payments upon Termination and upon Termination Following a Change in Control . . . . .

Pay Ratio Disclosure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Agreements with Executive Officers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Limitation of Liability and Indemnification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Director Compensation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Director Compensation for 2018 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Narrative to Director Compensation Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Compensation Committee Interlocks and Insider Participation . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Transactions with Related Persons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Transactions with DSM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Transactions with Foris . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Transactions with Total . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Transactions with Vivo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Reinach Consulting Agreement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Cherry Consulting Agreement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Officer Loans . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Naxyris Loan and Security Agreement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Compensation Arrangements
Indemnification Arrangements
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Executive Compensation and Employment Arrangements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Registration Rights Agreements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Related-Party Transactions Policy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Householding of Proxy Materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Available Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Stockholder Proposals to be Presented at Next Annual Meeting . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Other Matters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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AMYRIS, INC.

PROXY STATEMENT
2019 ANNUAL MEETING OF STOCKHOLDERS

These proxy materials are provided in connection with the solicitation of proxies by the Board of
Directors (the “Board”) of Amyris, Inc., a Delaware corporation (referred to as “Amyris”, the “Company”,
“we”, “us”, or “our”), for our 2019 Annual Meeting of Stockholders to be held at 2:00 p.m. Pacific Time on
Tuesday, November 19, 2019, at our principal executive offices, and for any adjournments or
postponements of the annual meeting. These proxy materials were first sent on or about October 10, 2019
to stockholders entitled to vote at the annual meeting.

INFORMATION REGARDING SOLICITATION AND VOTING

Our principal executive offices are located at 5885 Hollis Street, Suite 100, Emeryville, California
94608, and our telephone number is (510) 450-0761. This Proxy Statement contains important information
for you to consider when deciding how to vote on the matters brought before the meeting. Please read it
carefully.

In accordance with rules and regulations adopted by the U.S. Securities and Exchange Commission
(the “SEC”), we have elected to provide our stockholders with access to our proxy materials over the
Internet. Accordingly, we intend to send a Notice of Internet Availability of Proxy Materials (the “Notice”)
on or about October 10, 2019 to most of our stockholders who owned our common stock at the close of
business on September 23, 2019. The Notice includes instructions on how you can access our annual report
and proxy statement and other soliciting materials on the Internet or, if you wish, request a printed set of
such materials, a list of the matters to be considered at the 2019 annual meeting, and instructions as to how
your shares can be voted. Most stockholders will not receive a printed copy of the proxy materials unless
they request one in the manner set forth in the Notice. This permits us to conserve natural resources and
reduces our printing costs, while giving stockholders a convenient and efficient way to access our proxy
materials and vote their shares.

We will bear the expense of soliciting proxies. In addition to these proxy materials, our directors and
employees (who will receive no compensation in addition to their regular salaries) may solicit proxies in
person, by telephone or by email. We will reimburse Intermediaries for reasonable charges and expenses
incurred in forwarding solicitation materials to their clients.

Who can vote at the meeting?

QUESTIONS AND ANSWERS

The Board set September 23, 2019, as the record date for the meeting. If you owned shares of our
common stock as of the close of business on September 23, 2019, you may attend and vote your shares at
the meeting. Each stockholder is entitled to one vote for each share of common stock held on all matters to
be voted on. As of September 23, 2019, there were 103,400,207 shares of our common stock outstanding
and entitled to vote (as reflected in the records of our stock transfer agent).

Why did I receive a Notice of Internet Availability of Proxy Materials in the mail instead of a full set of proxy
materials?

We are pleased to take advantage of the SEC rule that allows companies to furnish their proxy
materials over the Internet. Accordingly, we have sent to most of our stockholders of record and beneficial
owners a Notice of Internet Availability of Proxy Materials. Instructions on how you can access our annual
report and proxy statement and other soliciting materials on the Internet or, if you wish, request a printed
set of such materials, a list of the matters to be considered at the 2019 annual meeting, and instructions as
to how your shares can be voted may be found in the Notice.

Why did I receive a full set of proxy materials in the mail instead of a Notice of Internet Availability of Proxy
Materials?

Some stockholders may have instructed our transfer agent or their Intermediary to deliver stockholder
communications, such as proxy materials, in paper form. If you would prefer to receive your proxy materials
over the Internet, please follow the instructions provided on your proxy card or voting instruction form to
vote using the Internet and, when prompted, indicate that you agree to receive or access stockholder
communications electronically in future years.

What is the quorum requirement for the meeting?

The holders of a majority of our outstanding shares of common stock as of the record date must be
present in person or represented by proxy at the meeting in order for there to be a quorum, which is
required to hold the meeting and conduct business. If there is no quorum, the holders of a majority of the
shares present at the meeting may adjourn the meeting to another date.

You will be counted as present at the meeting if you are present and entitled to vote in person at the
meeting or you have properly submitted a proxy card or voting instruction form, or voted by telephone or
over the Internet. Both abstentions and broker non-votes (as described below) are counted for the purpose
of determining the presence of a quorum.

As of the record date of September 23, 2019, there were 103,400,207 shares of our common stock
outstanding and entitled to vote (as reflected in the records of our stock transfer agent), which means that
holders of 51,700,104 shares of our common stock must be present in person or by proxy for there to be a
quorum.

What proposals will be voted on at the meeting?

There are six proposals scheduled to be voted on at the meeting:

•

Proposal 1 — Election of the four Class III directors nominated by the Board and named herein
to serve on the Board for a three-year term.

Proposal 2 — Ratification of the selection of Macias Gini & O’Connell LLP as our independent
registered public accounting firm for the fiscal year ending December 31, 2019.

No appraisal or dissenters’ rights exist for any action proposed to be taken at the meeting. We will also
consider any other business that properly comes before the meeting. As of the date of this Proxy Statement,
we are not aware of any other matters to be submitted for consideration at the meeting. If any other matters
are properly brought before the meeting, the persons named in the enclosed proxy card or voting
instruction form will vote the shares they represent using their best judgment.

How does the Board recommend I vote on the proposals?

The Board recommends that you vote:

•

FOR each of the director nominees named in this Proxy Statement; and

FOR the ratification of Macias Gini & O’Connell LLP as our independent registered public
accounting firm for the fiscal year ending December 31, 2019.

FOR the approval of the issuance of shares of our common stock issuable upon the exercise of
warrants and conversion of preferred stock issued to Foris Ventures, LLC in accordance with
Nasdaq Marketplace Rules 5635(b) and 5635(d).

How do I vote my shares in person at the meeting?

If your shares of Amyris common stock are registered directly in your name with our stock transfer
agent, EQ Shareowner Services, you are considered to be the stockholder of record with respect to those
shares. As the stockholder of record, you have the right to vote in person at the meeting.

If your shares are held in a brokerage account or by another Intermediary, you are considered the
beneficial owner of shares held in street name. As the beneficial owner, you are also invited to attend the
meeting. However, since a beneficial owner is not the stockholder of record, you may not vote these shares
in person at the meeting unless you obtain a “legal proxy” from the Intermediary (usually your broker) that
is the record holder of the shares, giving you the right to vote the shares at the meeting. The meeting will be
held on Tuesday, November 19, 2019 at 2:00 p.m. Pacific Time at our headquarters located at 5885 Hollis
Street, Suite 100, Emeryville, California 94608. You can find directions to our headquarters on our
company website at https://amyris.com/contact-us/.

How can I vote my shares without attending the meeting?

Whether you hold shares directly as a registered stockholder of record or beneficially in street name,
you may vote without attending the meeting. You may vote by granting a proxy or, for shares held
beneficially in street name, by submitting voting instructions to your broker, bank or other Intermediary. In
most cases, you will be able to do this by using the Internet, by telephone or by mail.

•

Voting by Internet or telephone. You may submit your proxy over the Internet or by telephone by
following the instructions provided in the Notice, or, if you receive printed proxy materials, by
following the instructions for Internet or telephone voting provided with your proxy materials and
on your proxy card or voting instruction form.

If you receive printed proxy materials, you may submit your proxy by mail by
Voting by mail.
completing, signing, dating and returning your proxy card or, for shares held beneficially in street
name, by following the voting instructions included by your broker or other Intermediary. If you
provide specific voting instructions, your shares will be voted as you have instructed.

Can I vote my shares by filling out and returning the Notice?

No. The Notice will, however, provide instructions on how to vote by Internet, by telephone, by
requesting and returning a paper proxy card or voting instruction form, or by submitting a ballot in person
at the meeting.

What happens if I do not give specific voting instructions?

If you are a stockholder of record and you either indicate when voting on the Internet or by telephone
that you wish to vote as recommended by the Board, or, if you receive printed proxy materials, you sign and
return a proxy card without giving specific voting instructions, then the proxy holders will vote your shares
in the manner recommended by the Board on all matters presented in this Proxy Statement and as the proxy
holders may determine in their discretion with respect to any other matters properly presented for a vote at
the meeting.

If you are a beneficial owner of shares held in street name and do not provide the Intermediary that
holds your shares with specific voting instructions, under stock market rules, the Intermediary that holds
your shares may generally vote at its discretion only on routine matters and cannot vote on non-routine
matters. If the Intermediary that holds your shares does not receive specific instructions from you on how
to vote your shares on a non-routine matter, the Intermediary will inform the inspector of election that it
does not have the authority to vote on this matter with respect to your shares. This is generally referred to as
a “broker non-vote.” For purposes of voting on non-routine matters, broker non-votes will not count as
votes cast on such matters and, therefore, will not affect the outcome of Proposal 1 (which requires a
plurality of votes properly cast in person or by proxy) or Proposal 3 (which requires a majority of votes
properly cast in person or by proxy).

Which proposals are considered “routine” and which are considered “non-routine”?

The ratification of the selection of Macias Gini & O’Connell LLP as our independent registered public
accounting firm for 2019 (Proposal 2) is considered a “routine” matter under applicable rules. The election
of directors (Proposal 1) and the approval of the issuance of shares of our common stock issuable upon the
exercise of warrants and conversion of preferred stock issued to Foris Ventures, LLC in accordance with
Nasdaq Marketplace Rules 5635(b) and 5635(d) (Proposal 3) are considered “non-routine” matters under
applicable rules. An Intermediary cannot vote without instructions on “non-routine” matters, and therefore
we expect there to be broker non-votes on Proposal 1 and Proposal 3.

How are votes counted?

Votes will be counted by the inspector of election appointed for the meeting. The inspector of election
will separately count “For” and “Withhold” votes and any broker non-votes in the election of directors
(Proposal 1). With respect to Proposal 2 and Proposal 3, the inspector of election will separately count
“For” and “Against” votes, abstentions and, with respect to Proposal 3, which is considered a “non-routine”
matter under applicable rules, any broker non-votes. Abstentions will not count toward the vote total for
Proposal 2 or Proposal 3. Broker non-votes will not count toward the vote total for Proposal 1 or
Proposal 3.

What is the vote required to approve each of the Board’s proposals?

•

Proposal 1 — Election of the Board’s four nominees for director. The affirmative vote of a
plurality, or the largest number, of the shares of our common stock present in person or by proxy
at the annual meeting and entitled to vote is required for the election of the directors. This means
that the four director nominees who receive the highest number of ”For” votes (among votes
properly cast in person or by proxy) will be elected to the board. Broker non-votes will not count
toward the vote total for this proposal and therefore will not affect the outcome of this proposal.

Proposal 2 — Ratification of the selection of Macias Gini & O’Connell LLP as our independent
registered public accounting firm for the fiscal year ending December 31, 2019. This proposal must
receive a “For” vote from the holders of a majority of the shares of our common stock properly
casting votes for or against this proposal at the annual meeting in person or by proxy. Abstentions
will not count toward the vote total for this proposal and therefore will not affect the outcome of
this proposal.

Proposal 3 — Approval of the issuance of shares of our common stock issuable upon the exercise of
warrants and conversion of preferred stock issued to Foris Ventures, LLC in accordance with Nasdaq
Marketplace Rules 5635(b) and 5635(d). This proposal must receive a “For” vote from (i) the
holders of a majority of the shares of common stock properly casting votes for or against this
proposal at the annual meeting in person or by proxy (the “Bylaws Standard”) and (ii) a majority
of the total votes of shares of our common stock not owned, directly or indirectly, by Foris
Ventures, LLC or its affiliates (including director John Doerr and Kleiner Perkins Caufield &
Byers), cast in person or by proxy at the annual meeting (the “Disinterested Standard”).
Abstentions and broker non-votes will not count toward the vote total for this proposal and
therefore will not affect the outcome of this proposal.

How can I revoke my proxy and change my vote after I return my proxy card?

You may revoke your proxy and change your vote at any time before the final vote at the meeting. If
you are a stockholder of record, you may do this by signing and submitting a new proxy card with a later
date (if you receive printed proxy materials), by using the Internet or voting by telephone (either of which
must be completed by 11:59 p.m. Pacific Time on November 18, 2019 — your latest telephone or Internet
proxy is counted), or by attending the meeting and voting in person. Attending the meeting alone will not
revoke your proxy unless you specifically request that your proxy be revoked. If you hold shares through an
Intermediary, you must contact that Intermediary directly to revoke any prior voting instructions.

How can I find out the voting results of the meeting?

The preliminary voting results will be announced at the meeting. The final voting results will be
reported in a Current Report on Form 8-K, which we expect to file with the SEC within four business days
after the meeting. If final voting results are not available within four business days after the meeting, we
intend to file a Current Report on Form 8-K reporting the preliminary voting results within that period,
and subsequently report the final voting results in an amendment to the Current Report on Form 8-K
within four business days after the final voting results are known to us.

FORWARD-LOOKING STATEMENTS

This Proxy Statement contains “forward-looking statements” within the meaning of Section 27A of
the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934. These
statements may be identified by their use of such words as “expects,” “anticipates,” “intends,” “hopes,”
“believes,” “could,” “may,” “will,” “projects” and “estimates,” and other similar expressions, but these words
are not the exclusive means of identifying such statements. We caution that a variety of factors, including
but not limited to the following, could cause our results to differ materially from those expressed or implied
in our forward-looking statements: our cash position and ability to fund our operations; difficulties in
predicting future revenues and financial results; the potential loss of, or inability to secure relationships
with, key distributors, customers or partners; our limited operating history and lack of revenues generated
from the sale of our renewable products; our inability to decrease costs to enable sales of our products at
competitive prices; delays in production and commercialization of products due to technical, operational,
cost and counterparty challenges; challenges in developing a customer base in markets with established and
sophisticated competitors; currency exchange rate and commodity price fluctuations; changes in regulatory
schemes governing genetically modified organisms and renewable chemicals; and other risks detailed from
time to time in filings we make with the SEC, including our Annual Reports on Form 10-K, our Quarterly
Reports on Form 10-Q and our Current Reports on Form 8-K. Except as required by law, we assume no
obligation to update any forward-looking information that is included or incorporated by reference in this
Proxy Statement, whether as a result of new information, future events, or otherwise.

PROPOSAL 1 —
ELECTION OF DIRECTORS

General

Under our Certificate of Incorporation and Bylaws, the number of authorized Amyris directors has

been fixed at 12 and the Board is divided into the following three classes with staggered three-year terms:

•

Class I directors, whose term will expire at the annual meeting of stockholders to be held in 2020;

Class II directors, whose term will expire at the annual meeting of stockholders to be held in 2021;
and

Class III directors, whose term will expire at this annual meeting of stockholders and who are
nominated for re-election.

In accordance with our certificate of incorporation, the Board has assigned each member of the Board
to one of the three classes, with the number of directors in each class divided as equally as reasonably
possible. As of the date of this Proxy Statement, there are four Class I seats, four Class II seats, and four
Class III seats constituting the 12 seats on the Board.

Stockholders are being asked to vote for the four Class III nominees listed below to serve until our
2022 Annual Meeting of Stockholders and until each such director’s successor has been elected and
qualified, or until each such director’s earlier death, resignation or removal. The nominees are all current
directors of Amyris.

Vote Required and Board Recommendation

Directors are elected by a plurality of the votes properly cast in person or by proxy. This means that the
four Class III nominees receiving the highest number of affirmative (i.e., “For”) votes will be elected. At the
annual meeting, proxies cannot be voted for a greater number of persons than the four nominees named in
this Proposal 1 and stockholders cannot cumulate votes in the election of directors. Shares represented by
executed proxies will be voted by the proxy holders, if authority to do so is not withheld for any or all of the
nominees, “For” the election of the four nominees named below. If any nominee is unable or declines to
serve as a director at the time of the meeting, the proxies will be voted for a nominee, if any, designated by
the Board to fill the vacancy. As of the date of this Proxy Statement, the Board is not aware that any
nominee up for election is unable or will decline to serve as a director. If you hold shares through a bank,
broker or other Intermediary of record, you must instruct your bank, broker or other Intermediary of
record how to vote so that your vote can be counted on this proposal. Broker non-votes will not count
toward the vote total for this proposal and therefore will not affect the outcome of this proposal.

The Board recommends a vote “FOR” each nominee.

Business Experience and Qualifications of Directors

The following tables and biographies set forth information for each nominee for election at the 2019
annual meeting and for each director of Amyris whose term of office will continue after the 2019 annual
meeting:

Nominees for Class III Directors for a Term Expiring in 2022

Name

John Doerr
Christoph Goppelsroeder

Lisa Qi

Patrick Yang, Ph.D.

Age

68
60

Amyris Offices and Positions

Director, Chair of Nominating and Governance Committee
Director

Director

Director, Member of Leadership Development and
Compensation Committee

John Doerr has been a member of the Board since 2006. Mr. Doerr has been Chairman at Kleiner
Perkins Caufield & Byers (“KPCB”), a venture capital firm, since 1980. Mr. Doerr currently serves on the
board of directors of Alphabet Inc., as well as on the boards of directors of numerous private companies,
and previously served as a director of Zynga, Inc. from April 2013 to May 2017. Mr. Doerr holds a
Bachelor of Science and a Master of Science in electrical engineering and computer science degrees from
Rice University and a Master of Business Administration degree from Harvard University. Mr. Doerr’s
global business leadership as general partner of KPCB, as well as his outside board experience as director of
several public and private companies, enables him to provide valuable insight and guidance to our
management team and the Board.

Christoph Goppelsroeder has been a member of the Board since November 2017. Mr. Goppelsroeder
has served as the President and CEO of DSM Nutritional Products Ltd., a supplier of vitamins,
carotenoids and other nutritional solutions, since 2013 and is a member of the DSM Executive Committee.
Mr. Goppelsroeder has previously worked at Boston Consulting, Syngenta in its seed care business unit,
and F. Hoffman-La Roche in its fine chemicals and vitamins division until the acquisition of such division
by DSM in 2003. Mr. Goppelsroeder holds a degree in engineering from the Swiss Federal Institute of
Technology
from Insead, Fontainebleau.
Mr. Goppelsroeder’s experience in the health and nutrition market enables him to provide the Board with
critical insight into a potential growth area of the Company’s business.

and a Master of Business Administration degree

Lisa Qi has been a member of the Board since May 2019. Ms. Qi is the founder and chief executive
officer of Silver Gift Limited and Daling Xinchao (Beijing) Trading Co., Ltd., which operate the Daling
Family e-commerce platform in China. Ms. Qi brings deep knowledge and significant experience in the
areas of e-commerce, product branding and sales and the management of high-growth companies, which
enables her to make a strategic contribution to the Board and provide guidance to the management team in
these areas.

for

cancer,

immunotherapies

the treatment of

Dr. Patrick Yang has been a member of the Board since July 2014. Dr. Yang is a biotech industry
consultant. He was Executive Vice President of Juno Therapeutics, Inc., a biopharmaceutical company
focused on developing innovative cellular
from
September 2017 to January 2019. From January 2010 through March 2013, Dr. Yang served as Executive
Vice President and Global Head of Technical Operations for F. Hoffmann-La Roche Ltd. (“Roche”), where
he was responsible for Roche’s pharmaceutical and biotech manufacturing operations, process development,
quality, regulatory, supply management and distribution functions. Before joining Roche, Dr. Yang worked
for Genentech Inc., where he most recently served as Executive Vice President of Product Operations, and
was responsible for manufacturing, process development, quality, regulatory affairs and distribution
functions. Prior to joining Genentech Inc., Dr. Yang worked for Merck & Co., where he held several
leadership roles including Vice President of Asia/Pacific Manufacturing Operations and Vice President of
Supply Chain Management. He also previously worked at General Electric Co. and Life Systems, Inc.
Dr. Yang currently serves on the boards of directors of Codexis, Inc. and PharmaEssentia Corporation,
and previously served on the board of directors of Andeavor (formerly Tesoro Corporation) from
December 2010 to September 2018, and Celladon Corporation from March 2014 until May 2015.
Dr. Yang’s experience with the biotechnology industry and operations has enabled him to provide insight
and guidance to our management team and the Board.

Incumbent Class I Directors with a Term Expiring in 2020

Name

Geoffrey Duyk, M.D., Ph.D.

Steven Mills

Carole Piwnica

Age

Amyris Offices and Positions

Director, Interim Chair of the Board and Member of Audit
Committee and Operations and Finance Committee
Director, Chair of Operations and Finance Committee and
Member of Audit Committee and Leadership Development
and Compensation Committee
Director, Chair of Leadership Development and Compensation
Committee and Member of Nominating and Governance
Committee and Operations and Finance Committee

James McCann

Director

Dr. Geoffrey Duyk has been a member of the Board since May 2012 and has served as the interim
Chair of the Board since May 2014. Dr. Duyk previously served on the Board from May 2006 to May 2011.
Dr. Duyk is a partner of Circularis Partners LP, a technology focused investment firm. Previously,
Dr. Duyk served as a partner and managing director of TPG Alternative & Renewable Technologies, a
technology focused investment firm (together with its affiliates, “TPG”), from 2004 to 2017. Prior to TPG,
he served on the board of directors and was President of Research and Development at Exelixis, Inc., a
biopharmaceutical company focusing on drug discovery, from 1996 to 2003. Prior to Exelixis, Dr. Duyk was
Vice President of Genomics and one of the founding scientific staff at Millennium Pharmaceuticals, from
1993 to 1996. Before that, Dr. Duyk was an Assistant Professor at Harvard Medical School in the
Department of Genetics and Assistant Investigator of the Howard Hughes Medical Institute. Dr. Duyk
currently serves on the boards of directors of: Anuvia Plant Nutrients; Concentric Ag Corporation
(formerly Inocucor Technologies, Inc.); and ReGen Holdings Limited as well as on the nonprofit Case
Western Reserve University Board of Trustees. Dr. Duyk is also a member of the Institute Board of
Directors of the Moffitt Cancer Center where he chairs the Research and Development committee.
Dr. Duyk serves as a member of Scientific Advisory Boards for HudsonAlpha, and Lawrence Berkeley
National Laboratory (DOE). Previously, Dr. Duyk served as a member of Scientific Advisory Boards for
Bayer CropSciences, The Jackson Labs as well as numerous NIH advisory committees. He served on the
board of directors of Beta Renewables from 2011 to 2017, Elevance Renewable Sciences from 2007 to 2018,
The American Society of Human Genetics (nonprofit) from 2012 to 2018, EPIRUS Biopharmaceuticals,
Inc. from July 2014 to July 2016, Galleon Pharmaceuticals, Inc. from 2007 to 2016, Genomatica, Inc. from
2012 to 2017, Karos Pharmaceuticals, Inc. from 2010 to 2015, The Wesleyan University Board of Trustees
from 2008 to June 2014, Aerie Pharmaceuticals from August 2005 to June 2017, and DNAnexus, Inc. from
2011 to 2017. Dr. Duyk holds a B.A. in Biology from Wesleyan University and a Ph.D. (Biochemistry) and
M.D. from Case Western Reserve University. Dr. Duyk’s experience with the biotechnology industry
enables him to provide insight and guidance to our management team and Board.

Carole Piwnica has been a member of the Board since September 2009. Ms. Piwnica has been Director
of NAXOS S.A.R.L. (Switzerland) (formerly NAXOS UK), a consulting firm advising private investors,
since January 2008. Previously, Ms. Piwnica served as a director, from 1996 to 2006, and Vice-Chairman of
Governmental Affairs, from 2000 to 2006, of Tate & Lyle Plc, a European food and agricultural ingredients
company. She was a chairman of Amylum Group, a European food ingredient company and affiliate of
Tate & Lyle Plc, from 1996 to 2000. Ms. Piwnica was a member of the board of directors of Aviva plc, a
British insurance company, from May 2003 to December 2011, a member of the Biotech Advisory Council
of Monsanto from May 2006 to October 2009, a member of the board of directors of Dairy Crest from
2007 until 2010, a member of the board of directors of Toepfer Gmbh from 1996 until 2010 and a member
of the board of directors of Louis Delhaize (retail, Belgium) from 2010 until 2013. In 2010, Ms. Piwnica
was appointed as a member of the boards of Eutelsat (satellites, France) and Sanofi (pharmaceuticals,
France). In 2014, she was appointed as a member of the board of Rothschild (financial services, France).
Ms. Piwnica holds a Law degree from the Université Libre de Bruxelles and a Master of Laws degree from
New York University. She was also a member of the bar association of the state of New York, USA from
1985 until 2019 and was a member of the bar association of Paris, France from 1988 until 2013. Based on
her multinational corporate leadership experience and extensive legal and corporate governance experience,
Ms. Piwnica contributes guidance to the management team and the Board in leadership of multinational
agricultural processing businesses and on legal and corporate governance obligations and best practices.

Steven Mills has been a member of the Board since August 2018. Mr. Mills has 40 years of experience
in the fields of accounting, corporate finance, strategic planning, risk management, and mergers and
acquisitions. He served as Chief Financial Officer of Amyris from May 2012 to December 2013. Prior to
joining Amyris, Mr. Mills had a 33-year career at Archer-Daniels-Midland Company (“ADM”), one of the
world’s largest agricultural processors and food ingredient providers. At ADM, he held various senior
executive roles, including Chief Financial Officer, Controller, and head of Global Strategic Planning. Since
2013, Mr. Mills has served as a consultant and advisor to clients in the private equity, agribusiness, and
financial services fields. Mr. Mills currently serves on the boards of Black Hills Corporation (where he also
serves as the chair of the audit committee), Farmers Edge, Inc., Illinois College (where he also serves as the
chairman of the board), and First Illinois Corporation (along with its wholly-owned banking subsidiary,

Hickory Point Bank & Trust). Mr. Mills holds a Bachelor of Science degree in Mathematics from Illinois
College. Mr. Mills’ familiarity with Amyris, as well as his expertise in accounting, finance and management,
enables him to assist our management team and Board build and improve on our business and financial
processes and management.

James McCann has been a member of the Board since May 2019. Mr. McCann is the founder and
chairman of the board of directors of 1-800-FLOWERS.COM, Inc., a floral and gourmet foods gift
retailer and distribution company founded in 1976, and served as chief
executive officer of
1-800-FLOWERS.COM, Inc. from 1976 until June 2016. Mr. McCann also serves on the boards of
directors of International Game Technology PLC (formerly GTECH S.p.A. and Lottomatica Group S.p.A.)
and The Scotts Miracle-Gro Company. Mr. McCann previously served on the board of directors of Willis
Towers Watson PLC (formerly Willis Group Holdings PLC) from 2004 until May 2019. Mr. McCann
brings to the Board extensive experience in business leadership and innovation, which enables him to assist
in the growth and development of our business.

Incumbent Class II Directors with a Term Expiring in 2021

Name

Philip Eykerman

Frank Kung, Ph.D.
John Melo
R. Neil Williams

Age

71
53
66

Amyris Offices and Positions

Director

Director, Member of Operations and Finance Committee
Director, President and Chief Executive Officer
Director, Chair of Audit Committee and Member of
Operations and Finance Committee

Philip Eykerman has been a member of the Board since May 2017. Mr. Eykerman has served as the
Executive Vice-President, Corporate Strategy & Acquisitions of Koninklijke DSM N.V. (together with its
affiliates, “DSM”), a global science-based company in nutrition, health and sustainable living and an entity
with which Amyris has a commercial and financial relationship and which is an owner of greater than
five percent of the Company’s outstanding common stock, since 2011. In this role, he is responsible for
corporate and business group strategy development, budgeting and planning, improvement programs, and
all M&A activities for DSM. In 2015, he was also appointed as a member of the DSM Executive
Committee and at present is also responsible for the DSM Food Specialties as well as DSM Hydrocolloids
activities. Next to these roles within DSM, he is also a Supervisory Board member of ChemicaInvest (DSM/
CVC JV) and Supervisory Board member of AnQore TopCo B.V., and previously served as a member of
the Supervisory Board of Patheon N.V. from March 2014 to August 2017. Before joining DSM,
Mr. Eykerman worked for 14 years at McKinsey & Company of which the last 9 years as a Partner and
leader of McKinsey’s Chemicals Practice in the Benelux and France. Before that, he worked as a process/
project engineer for Fluor Daniel. He holds a master degree in Chemical Engineering from the KU Leuven
(Belgium) and in Refinery Engineering from the Institut Francais du Pétrole (France). Mr. Eykerman’s
experience in corporate strategy, mergers and acquisitions and operations enables him to provide insight to
the Board regarding potential new opportunities for Amyris.

Dr. Frank Kung has been a member of the Board since November 2017. Dr. Kung is a founding
member of Vivo Capital LLC (“Vivo”), a healthcare focused investment firm founded in 1996 in Palo Alto,
California, which is an owner of greater than five percent of the Company’s outstanding common stock.
Dr. Kung started his career in the biotechnology industry in 1979 when he joined Cetus Corporation. He
later co-founded Cetus Immune Corporation in 1981, which was acquired by its parent company in 1983. In
1984 he co-founded Genelabs Technologies, Inc. where he served as Chairman and CEO until 1995. During
his tenure in Genelabs, he brought the company public in 1991, and built it to a 175 employee international
biotech company with operations in the United States, Belgium, Singapore, Switzerland and Taiwan.
Dr. Kung holds a Bachelor of Science degree in chemistry from the National Tsing Hua University in
Taiwan, and a Doctor of Philosophy degree in molecular biology and a Master of Business Administration
degree from the University of California, Berkeley. Dr. Kung currently serves on the board of directors of a
number of emerging healthcare and biotechnology companies. Dr. Kung’s experience in healthcare and
biotechnology and investing in companies enables him to provide the Board and management with
guidance regarding the Company’s business strategy and access to financial markets.

John Melo has nearly three decades of combined experience as an entrepreneur and thought leader in
the global fuels industry and technology innovation. Mr. Melo has served as our Chief Executive Officer
and a director since January 2007 and as our President since June 2008. Before joining Amyris, Mr. Melo
served in various senior executive positions at BP Plc (formerly British Petroleum), one of the world’s
largest energy firms, from 1997 to 2006, most recently as President of U.S. Fuels Operations from 2004 until
December 2006, and previously as Chief Information Officer of the refining and marketing segment from
2001 to 2003, Senior Advisor for e-business strategy to Lord Browne, BP Chief Executive, from 2000 to
2001, and Director of Global Brand Development from 1999 to 2000. Before joining BP, Mr. Melo was
with Ernst & Young, an accounting firm, from 1996 to 1997, and a member of the management teams of
several startup companies,
including Computer Aided Services, a management systems integration
company, and Alldata Corporation, a provider of automobile repair software to the automotive service
industry. Mr. Melo currently serves on the board of directors of Renmatix, Inc., and on the board of the
Industrial action of Bio and also on the board of the California Life Sciences Association. Mr. Melo was
formerly an appointed member to the U.S. section of the U.S.-Brazil CEO Forum. Mr. Melo’s experience as
a senior executive at one of the world’s largest energy companies provides critical leadership in shaping
strategic direction and business transactions, and in building teams to drive innovation.

R. Neil Williams has been a member of the Board since 2013. Mr. Williams served as Executive Vice
President and Chief Financial Officer of Intuit Inc., a business and financial software company, from
January 2008 through January 2018. In such position he was responsible for all financial aspects of Intuit,
including corporate strategy and business development, investor relations, financial operations and real
estate. Before joining Intuit, Mr. Williams was the Executive Vice President and Chief Financial Officer for
Visa U.S.A., Inc. In that role, he led all financial functions for Visa U.S.A., Inc. and its subsidiaries,
including financial planning, business planning and financial monitoring. Mr. Williams concurrently served
as Chief Financial Officer for Inovant LLC, Visa’s global information technology organization, responsible
for global transactions processing and technology development. His previous banking experience includes
senior financial positions at commercial banks in the Southern and Midwest regions of the United States.
Since March 2012, Mr. Williams has also served as a board member and chair of the audit committee of
RingCentral, Inc. He joined the board and audit committee of Oportun, Inc.
in November 2017.
Mr. Williams is a certified public accountant and received his Bachelor’s degree in business administration
from the University of Southern Mississippi. Mr. Williams’ expertise in accounting,
finance and
management enables him to provide important insight and guidance to our management team and Board
and to serve as chair of our Audit Committee.

Arrangements Concerning Selection of Directors

In February 2012, pursuant to a Letter Agreement (the “Letter Agreement”) entered into in
connection with the sale of our common stock to certain investors including Biolding Investment SA
(“Biolding”), Naxyris S.A., an investment vehicle owned by Naxos Capital Partners SCA Sicar (“Naxyris”),
and Maxwell (Mauritius) Pte Ltd (“Maxwell”), we agreed to appoint, and to use reasonable efforts
consistent with the Board’s fiduciary duties to cause the re-nomination by the Board in the future of:

•

One person designated by Biolding to serve as a member of the Board. Pursuant to the Letter
Agreement, Biolding designated His Highness Sheikh Abdullah bin Khalifa Al Thani (“HH”) to
serve as the Biolding representative on the Board, and HH was appointed to the Board in
March 2012. Pursuant to the Letter Agreement, Biolding’s designation rights would terminate
upon a sale of Amyris or Biolding holding less than 173,010 shares of our common stock. On
May 14, 2019, HH resigned from the Board, and in connection therewith Biolding permanently
waived its Board designation right.

One person designated by Naxyris to serve as a member of the Board. Pursuant to the Letter
Agreement, Naxyris designated Ms. Piwnica (who was already on the Board) to serve as the
Naxyris representative on the Board. Naxyris’ designation rights terminate upon a sale of Amyris
or Naxyris holding less than 115,340 shares of our common stock. As of August 30, 2019,
Naxyris beneficially owned 3,743,038 shares of our common stock, representing approximately
3.5% of our outstanding common stock (this includes the assumed exercise of certain warrants
held by Naxyris). Ms. Piwnica is Director of NAXOS S.A.R.L. (Switzerland), a consulting firm

advising private investors and an affiliate of Naxos Capital Partners SCA Sicar, which owns
Naxyris, and receives compensation and benefits from NAXOS S.A.R.L. (Switzerland) pursuant
to its standard compensation policies and practices.

•

initially designated Dr. Nam-Hai Chua to serve as

One person designated by Maxwell to serve as a member of the Board. Pursuant to the Letter
Agreement, Maxwell
the Maxwell
representative on the Board and, following Dr. Chua’s resignation from the Board effective June 7,
2015, Maxwell designated Abraham Klaeijsen to serve as the Maxwell representative on the Board
and he was appointed on June 7, 2015. Mr. Klaeijsen resigned from the Board on November 2,
2017 and Maxwell did not designate a replacement for Mr. Klaeijsen. Maxwell’s designation rights
terminate upon a sale of Amyris or Maxwell holding less than 173,010 shares of our common
stock. As of December 31, 2018, Maxwell’s board designation right had terminated due to
Maxwell holding less than 173,010 shares of our common stock.

In June 2010, we issued 7,101,548 shares of our Series D preferred stock to Total that converted into
643,401 shares of our common stock upon the completion of our initial public offering in September 2010.
In connection with such equity investment, we entered into a letter agreement with Total, pursuant to which
we agreed to appoint a person designated by Total to serve as a member of the Board, and to use reasonable
efforts consistent with the Board’s fiduciary duties to cause the director designated by Total to be
re-nominated by the Board in the future. Pursuant to the letter agreement, Total initially designated
Philippe Boisseau to serve as the Total representative on the Board and, following Mr. Boisseau’s
resignation from the Board in October 2016, Total designated Christophe Vuillez to serve as the Total
representative on the Board. Mr. Vuillez resigned from the Board on May 20, 2019 and Total has not
designated a replacement for Mr. Vuillez. Total’s designation rights terminate upon the earlier of Total
holding less than 321,700 shares of our common stock or a sale of Amyris. As of August 30, 2019, Total
beneficially owned 10,268,173 shares of our common stock, representing approximately 9.9% of our
outstanding common stock (this includes the assumed conversion and exercise of certain convertible
promissory notes and warrants, respectively, held by Total, as described below under “Security Ownership
of Certain Beneficial Owners and Management”).

Pursuant to a Stockholder Agreement entered into in May 2017, and subsequently amended and
restated in August 2017, in connection with the sale of our Series B 17.38% Convertible Preferred Stock and
warrants to DSM (the “DSM Stockholder Agreement”), we agreed to appoint, and to use reasonable
efforts consistent with the Board’s fiduciary duties to cause the re-nomination by the Board in the future of,
two persons designated by DSM to serve as members of the Board. Pursuant to the DSM Stockholder
Agreement, DSM initially designated Mr. Eykerman to serve as a DSM representative on the Board and,
following the amendment and restatement of the DSM Stockholder Agreement in August 2017, DSM
designated Mr. Goppelsroeder to serve as the second DSM representative on the Board. DSM’s designation
rights terminate, with respect to one designee, at such time as DSM beneficially owns less than 10% of our
outstanding common stock and, with respect to both designees, at such time as DSM beneficially owns less
than 4.5% of our outstanding common stock. As of August 30, 2019, DSM beneficially owned 27,001,551
shares of our common stock, representing approximately 23.0% of our outstanding common stock (this
includes the assumed exercise of certain warrants held by DSM, as described below under “Security
Ownership of Certain Beneficial Owners and Management”). Messrs. Eykerman and Goppelsroeder are
to its standard
employees of DSM and receive compensation and benefits from DSM pursuant
compensation policies and practices.

In August 2017, pursuant to a Stockholder Agreement (the “Vivo Stockholder Agreement”) entered
into in connection with the sale of our common stock, Series D Convertible Preferred Stock and warrants
to Vivo, we agreed to appoint, and to use reasonable efforts consistent with the Board’s fiduciary duties to
cause the re-nomination by the Board in the future of, one person designated by Vivo to serve as a member
of the Board. Pursuant to the Vivo Stockholder Agreement, Vivo designated Dr. Kung to serve as the Vivo
representative on the Board. Vivo’s designation rights terminate at such time as Vivo beneficially owns less
than 4.5% of our outstanding common stock. As of August 30, 2019, Vivo beneficially owned 10,725,235
shares of our common stock, representing approximately 9.98% of our outstanding common stock (this
includes the assumed conversion and exercise of certain shares of preferred stock and warrants, respectively,

held by Vivo, as described below under “Security Ownership of Certain Beneficial Owners and
Management”). Dr. Kung is a founding member of Vivo and receives compensation and benefits from Vivo
pursuant to its standard compensation policies and practices.

Mr. Doerr and Dr. Duyk were initially designated to serve on the Board by KPCB and TPG,
respectively, pursuant to a voting agreement as most recently amended and restated on June 21, 2010
(Dr. Duyk resigned from the Board in May 2011 and was re-appointed to the Board in May 2012). As of
the date of this Proxy Statement, notwithstanding the expiration of the voting agreement upon completion
of our initial public offering in September 2010, Mr. Doerr and Dr. Duyk continue to serve on the Board
and we expect each of them to continue to serve as a director until his resignation or until his successor is
duly elected by the holders of our common stock. Mr. Doerr receives compensation and benefits from
KPCB pursuant to its standard compensation policies and practices, and Dr. Duyk retains a carried interest
in certain funds managed by TPG.

Independence of Directors

Under the corporate governance rules of The Nasdaq Stock Market (“Nasdaq”), a majority of the
members of the Board must qualify as “independent,” as affirmatively determined by the Board. The Board
and the Nominating and Governance Committee of the Board consult with our legal counsel to ensure that
the Board’s determinations are consistent with all relevant securities and other laws and regulations
regarding the definition of ”independent,” including those set forth in the applicable Nasdaq rules. The
Nasdaq criteria include various objective standards and a subjective test. A member of the Board is not
considered independent under the objective standards if, for example, he or she is, or at any time during the
past three years was, employed by Amyris, he or she received compensation (other than standard
compensation for Board service) in excess of $120,000 during a period of twelve months within the past
three years, or he or she is an executive officer of any organization to which Amyris made, or from which
Amyris received, payments for property or services (other than payments arising solely from investments in
our securities or payments under non-discretionary charitable contribution matching programs) in the
current or any of the past three fiscal years that exceed 5% of the recipient’s gross revenues for that year, or
$200,000, whichever is more.

The subjective test under the Nasdaq rules for director independence requires that each independent
director not have a relationship which, in the opinion of the Board, would interfere with the exercise of
independent judgment in carrying out the responsibilities of a director. The subjective evaluation of
director independence by the Board was made in the context of the objective standards referenced above. In
making independence determinations, the Board generally considers commercial, financial and professional
services, and other transactions and relationships between Amyris and each director and his or her family
members and affiliated entities.

Based on such criteria, the Board determined that (i) Mr. Melo is not independent because he is an
Amyris employee and (ii) Messrs. Eykerman and Goppelsroeder are not independent because they are each
employees of DSM (with which we have commercial and financial relationships, as described below under
“Transactions with Related Persons”).

For each of

the directors other than Messrs. Melo, Eykerman and Goppelsroeder, the Board
determined that none of the transactions or other relationships of such directors (and their respective
family members and affiliated entities) with Amyris, our executive officers and our independent registered
public accounting firm exceeded Nasdaq objective standards and none would otherwise interfere with the
exercise of independent judgment in carrying out his or her responsibilities as a director. The following is a
description of these relationships:

• Mr. Doerr is a manager of the general partners of entities affiliated with KPCB Holdings, Inc. As
of August 30, 2019, KPCB Holdings, Inc., as nominee for entities affiliated with KPCB, held
278,882 shares of our common stock, which represented approximately 0.3% of our outstanding
common stock. In addition, Mr. Doerr indirectly owns all of the membership interests in Foris
Ventures, LLC (“Foris”), which beneficially owned 21,054,940 shares of our common stock as of
August 30, 2019, representing approximately 19.7% of our outstanding common stock (this
includes the assumed exercise of certain warrants held by Foris, as described below under

“Security Ownership of Certain Beneficial Owners and Management”). We are asking
stockholders to approve the issuance of shares of our common stock issuable upon the exercise of
certain warrants and conversion of certain shares of the Company’s Series B 17.38% Convertible
Preferred Stock held by Foris; see “Proposal 3 — Approval of the issuance of shares of our
common stock issuable upon the exercise of warrants and conversion of preferred stock issued to
Foris Ventures, LLC in accordance with Nasdaq Marketplace Rules 5635(b) and 5635(d)” for
more information. If Proposal 3 had been approved as of August 30, 2019, the number of shares
beneficially owned by Foris would have been 39,705,210 shares, representing approximately 31.7%
of our outstanding common stock. See “Security Ownership of Certain Beneficial Owners and
Management” below for more information.

Dr. Kung is a founding member of Vivo and was designated to serve as a director by Vivo. As of
August 30, 2019, Vivo beneficially owned 10,725,235 shares of our common stock, representing
approximately 9.98% of our outstanding common stock (this includes the assumed conversion
and exercise of certain shares of preferred stock and warrants, respectively, held by Vivo, as
described below under “Security Ownership of Certain Beneficial Owners and Management”). In
addition, Dr. Kung’s daughter is a non-executive employee of Amyris.

Prior to joining the Board, Mr. Mills served as the Chief Financial Officer of Amyris from
May 2012 to December 2013.

•

• Ms. Piwnica was designated to serve as a director by Naxyris. As of August 30, 2019, Naxyris
beneficially owned 3,743,038 shares of our common stock, representing approximately 3.5% of
our outstanding common stock (this includes the assumed exercise of certain warrants held by
Naxyris).

•

Prior to joining the Board, Dr. Yang worked as a consultant to Amyris from September 2013
through July 2014 and received compensation in excess of $120,000 during such period for his
services.

Consistent with these considerations, after a review of all relevant transactions and relationships
between each director, any of his or her family members and affiliated entities, Amyris, our executive
officers and our independent registered public accounting firm, the Board affirmatively determined that a
independent directors, and that the following directors are
majority of
independent: John Doerr, Geoffrey Duyk, Frank Kung, James McCann, Steven Mills, Carole Piwnica, Lisa
Qi, R. Neil Williams and Patrick Yang.

the Board is comprised of

Board Leadership Structure

The Board is composed of our Chief Executive Officer, John Melo, and eleven non-management
directors. Geoffrey Duyk, one of our independent directors, currently serves the principal Board leadership
role as the Board’s interim Chair. The Board expects to appoint an independent director as permanent
Chair. The Board does not have any policy that the Chair must necessarily be separate from the Chief
Executive Officer, but the Board appointed Dr. Duyk as interim Chairman in May 2014 until a permanent
Chair could be identified. Dr. Duyk’s (and his successor’s) responsibilities as Board Chair include working
with management to develop agendas for Board meetings, calling special meetings of the Board, presiding
at executive sessions of independent Board members, gathering input from Board members on Chief
Executive Officer performance and providing feedback to the Chief Executive Officer, gathering input from
Board members after meetings and through an annual self-assessment process and communicating feedback
to the Board and the Chief Executive Officer, as appropriate, and serving as Chief Executive Officer in the
absence of another designated Chief Executive Officer. The Board believes that having an independent
Chair helps reinforce the Board’s independence from management in its oversight of our business and
affairs. In addition, the Board believes that this structure helps to create an environment that is conducive to
objective evaluation and oversight of management’s performance and related compensation, increasing
management accountability and improving the ability of the Board to monitor whether management’s
actions are in our best interests and those of our stockholders. Further, this structure permits our Chief
Executive Officer to focus on the management of our day-to-day operations. Accordingly, we believe our
current Board leadership structure contributes to the effectiveness of the Board as a whole and, as a result,
is the most appropriate structure for us at the present time.

Role of the Board in Risk Oversight

We consider risk as part of our regular evaluation of business strategy and decisions. Assessing and
managing risk is the responsibility of our management, which establishes and maintains risk management
processes, including prioritization processes, action plans and mitigation measures, designed to balance the
risk and benefit of opportunities and strategies. It is management’s responsibility to anticipate, identify and
communicate risks to the Board and/or its committees. The Board as a whole oversees our risk management
systems and processes, as implemented by management and the Board’s committees. As part of its oversight
role, the Board has established an enterprise risk management process that involves management
discussions with and updates to members of the Audit Committee regarding enterprise risk prioritization
and mitigation. In addition, the Board uses its committees to assist in its risk oversight function as follows:

•

The Audit Committee has responsibility for overseeing our financial controls and risk and legal
and regulatory matters.

The Leadership Development and Compensation Committee is responsible for oversight of risk
associated with our compensation programs and plans.

The Nominating and Governance Committee is responsible for oversight of Board processes and
corporate governance related risks.

The Operations and Finance Committee is responsible for oversight of risk associated with our
business operations and financing activities.

The Board receives regular reports from committee Chairs regarding the committees’ activities. In
addition, discussions with the Board regarding our strategic plans and objectives, business results, financial
condition, compensation programs, strategic transactions, and other matters include discussions of the risks
associated with the particular item under consideration.

Meetings of the Board and Committees

During 2018, the Board held five meetings, and its three standing committees during 2018 (the Audit
Committee, Leadership Development and Compensation Committee and Nominating and Governance
Committee) collectively held 17 meetings. Of such meetings, the Audit Committee held nine meetings, the
Leadership Development and Compensation Committee held six meetings and the Nominating and
Governance Committee held two meetings. With the exception of Mr. Eykerman and Mr. Goppelsroeder,
each incumbent director attended at least 75% of the meetings of the Board and of the committees on
which such director served that were held during the period that such director served in 2018. The Board’s
policy is that directors are encouraged to attend our annual meetings of stockholders. No directors attended
our 2018 annual meeting of stockholders.

The following table provides membership and meeting information for the Board and its standing

committees in 2018:

Member of the Board in 2018

Board

Audit
Committee

John Doerr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Leadership
Development
and
Compensation
Committee

Nominating
and
Governance
Committee

Chair

Geoffrey Duyk . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Chair
Philip Eykerman(1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Christoph Goppelsroeder(2) . . . . . . . . . . . . . . . . . . . . . . . .
Frank Kung . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

John Melo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Steven Mills(3) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Carole Piwnica . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Fernando de Castro Reinach(4)
. . . . . . . . . . . . . . . . . . . . .
HH Sheikh Abdullah bin Khalifa Al Thani(5)
. . . . . . . . . . .
Christophe Vuillez(6)
. . . . . . . . . . . . . . . . . . . . . . . . . . . .
R. Neil Williams . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Patrick Yang . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Total meetings in 2018(7) . . . . . . . . . . . . . . . . . . . . . . . . . .

X
X

X
X
X
X
X
X
5

Chair

X
6

(1) Mr. Eykerman attended 3 of 5 Board meetings held during 2018.

(2) Mr. Goppelsroeder attended 3 of 5 Board meetings held during 2018.

(3) Mr. Mills was appointed to the Board and the Audit Committee on August 1, 2018, and was appointed

to the Leadership Development and Compensation Committee on November 6, 2018.

(4) Dr. Reinach resigned from the Board effective August 1, 2018.

(5) HH attended 0 of 5 Board meetings held during 2018. HH resigned from the Board effective May 14,

2019.

(6) Mr. Vuillez attended 3 of 5 Board meetings held during 2018. Mr. Vuillez resigned from the Board

effective May 20, 2019.

(7)

Includes one concurrent meeting of the Board and the Leadership Development and Compensation
Committee.

Committees of the Board

The Board has established an Audit Committee, a Leadership Development and Compensation
Committee, a Nominating and Governance Committee and an Operations and Finance Committee, each as
described below. Members are appointed by the Board to serve on these committees until their resignations
or until otherwise determined by the Board.

Audit Committee

The Audit Committee was established by the Board in accordance with Section 3(a)(58)(A) of the
Securities Exchange Act of 1934 (the “Exchange Act”), and assists the Board in fulfilling the Board’s
oversight of our accounting and system of internal controls, the quality and integrity of our financial
reports, legal and regulatory matters, and the retention, independence and performance of our independent
registered public accounting firm.

Under Nasdaq rules, we must have an audit committee of at least three members, each of whom must
be independent as defined under the rules and regulations of Nasdaq and the Securities and Exchange
Commission (the “SEC”). Our Audit Committee is currently composed of three directors: Dr. Duyk and
Messrs. Mills and Williams. Mr. Williams is the Chair of the Audit Committee. The composition of the
Audit Committee meets the requirements for independence under current Nasdaq and SEC rules and
regulations. The Board has determined that each member of the Audit Committee is independent (as
defined in the relevant Nasdaq and SEC rules and regulations), and is financially literate and able to read
and understand fundamental financial statements, including a company’s balance sheet, income statement
and cash flow statement. In addition, the Board has determined that Mr. Williams is an “audit committee
financial expert” as defined in Item 407(d)(5)(ii) of Regulation S-K promulgated under the Securities Act of
1933, as amended (the “Securities Act”), with employment experience in finance and accounting and other
comparable experience that results in his financial sophistication. Being an “audit committee financial
expert” does not impose on Mr. Williams any duties, obligations or liabilities that are greater than are
generally imposed on him as a member of the Audit Committee and the Board. The Board has adopted a
is posted on our company website at http://
written charter
investors.amyris.com/corporate-governance.

for our Audit Committee that

The Audit Committee performs, among others, the following functions:

•

oversees our accounting and financial reporting processes and audits of our consolidated financial
statements;

oversees our relationship with our independent auditors, including appointing or changing our
independent auditors and ensuring their independence;

oversees IT risk management and cybersecurity matters;

reviews and approves the audit and permissible non-audit services to be provided to us by our
independent auditors;

facilitates communication among our independent auditors, our financial and senior management,
and the Board; and

the adequacy of our accounting and financial reporting
monitors the periodic reviews of
processes and systems of internal control that are conducted by our independent auditors and our
financial and senior management.

In addition, the Audit Committee generally reviews and approves any proposed transaction between
Amyris and any related party, establishes procedures for the receipt, retention and treatment of complaints
received by Amyris regarding accounting, internal accounting controls or auditing matters, and for the
confidential, anonymous submission by Amyris employees of their concerns regarding suspected violations
of laws, governmental rules or regulations, accounting, internal accounting controls or auditing matters, or
company policies (including the administration of our whistleblower policy), and oversees the review of any
complaints and submissions received through the complaint and anonymous reporting procedures.

Leadership Development and Compensation Committee

Under Nasdaq rules, compensation of the executive officers of a company must be determined, or
recommended to the Board for determination, either by independent directors constituting a majority of
the Board’s independent directors in a vote in which only independent directors participate, or by a
compensation committee composed solely of independent directors. Amyris has established the Leadership
Development and Compensation Committee for such matters, which is currently composed of three
directors: Mr. Mills, Ms. Piwnica and Dr. Yang. Ms. Piwnica is the Chair of the Leadership Development
and Compensation Committee. The Board, after consideration of all factors specifically relevant to
determining whether any of Mr. Mills, Ms. Piwnica or Dr. Yang has a relationship to Amyris that is
material to that director’s ability to be independent from management in connection with the duties of a
compensation committee member, including, but not limited to, (i) the source of compensation of such
director, including any consulting, advisory or other compensatory fee paid by Amyris to such director and
(ii) whether such director is affiliated with Amyris, has determined that each member of the Leadership

Development and Compensation Committee is independent (as defined in the relevant Nasdaq and
for our Leadership
SEC rules and regulations). The Board has adopted a written charter
Development
at
and Compensation Committee
http://investors.amyris.com/corporate-governance.

is posted on our

company website

that

The purpose of the Leadership Development and Compensation Committee is to provide guidance
and periodic monitoring for all of our compensation, benefit, perquisite and equity programs. The
Leadership Development and Compensation Committee, through delegation from the Board, has principal
responsibility to evaluate, recommend, approve and review executive officer and director compensation
arrangements, plans, policies and programs maintained by Amyris and to administer our cash-based and
equity-based compensation plans, and may also make recommendations to the Board regarding the Board’s
remaining responsibilities
relating to executive compensation. The Leadership Development and
Compensation Committee discharges the responsibilities of the Board relating to compensation of our
executive officers, and, among other things:

•

reviews and approves the compensation of our executive officers;

reviews and recommends to the Board the compensation of our non-employee directors;

reviews and approves the terms of any compensation agreements with our executive officers;

administers our stock and equity incentive plans;

reviews and makes recommendations to the Board with respect to incentive compensation and
equity incentive plans;

establishes and reviews our overall compensation strategy; and

reviews with the Chief Executive Officer and Board leadership the succession plans for senior
management positions.

The Leadership Development and Compensation Committee also reviews the Compensation
Discussion and Analysis section of our Proxy Statement and recommends to the Board whether it should
be included in the Proxy Statement, has responsibility for the review of our pay ratio disclosure, and
prepares a report of the Leadership Development and Compensation Committee for inclusion in our Proxy
Statement in accordance with SEC rules. The Leadership Development and Compensation Committee has
authority to form and delegate authority to subcommittees, as appropriate.

The Board has established a Management Committee for Employee Equity Awards (“MCEA”),
consisting of our Chief People Officer and our Chief Executive Officer. The MCEA may grant equity
awards to employees who are not officers (as that term is defined in Section 16 of the Securities Exchange
Act of 1934 (the “Exchange Act”) and Rule 16a-1 promulgated under the Exchange Act) of Amyris,
provided that the MCEA is only authorized to grant equity awards that meet grant guidelines approved by
the Board or Leadership Development and Compensation Committee. These guidelines set forth, among
other things, any limit imposed by the Board or Leadership Development and Compensation Committee
on the total number of shares of our common stock that may be subject to equity awards granted to
employees by the MCEA, and any requirements as to the size of an award based on the seniority of an
employee or other factors.

Under its charter, the Leadership Development and Compensation Committee has the authority, at
Amyris’ expense, to retain legal and other consultants, accountants, experts and compensation or other
advisors of its choice to assist the Leadership Development and Compensation Committee in connection
with its functions. During the past fiscal year, the Leadership Development and Compensation Committee
engaged Compensia, Inc. (“Compensia”) as its compensation consultant. Compensia also served as the
Committee’s compensation consultant from 2012 through 2017. Compensia provided the following services
during 2018 (or in connection with 2018 compensation):

•

reviewed and provided recommendations on the composition of Amyris’s compensation peer
group, and provided compensation data relating to executives at the selected peer group
companies;

•

conducted a review of the total compensation arrangements for executive officers of Amyris;

provided advice on executive officers’ compensation, including composition of compensation for
base salary, short-term incentive (cash bonus) plan and long-term incentive (equity) plans;

provided advice on executive officers’ cash bonus plan;

assisted with executive equity program design, including analysis of equity mix, aggregate share
usage and target grant levels;

provided advice and recommendations regarding executive perquisites and Amyris’s executive
severance plan;

updated the Leadership Development and Compensation Committee on emerging trends/best
practices and regulatory requirements in the area of executive and director compensation,
including equity and cash compensation;

provided advice and recommendations regarding certain non-executive employee compensation
arrangements and equity grants; and

assisted with the analysis related to our pay ratio disclosure.

The Leadership Development and Compensation Committee determined that Compensia did not have
any relationships with Amyris or any of its officers or directors or any conflicts of interest that would
impair Compensia’s independence.

The Human Resources, Finance and Legal departments of Amyris work with our Chief Executive
Officer to design and develop new compensation programs applicable to our executive officers and
non-employee directors, to recommend changes to existing compensation programs, to recommend
financial and other performance targets to be achieved under those programs, to prepare analyses of
financial data, to prepare peer group compensation comparisons and other committee briefing materials,
and to implement the decisions of the Leadership Development and Compensation Committee. Members
of these departments and our Chief Executive Officer also meet separately with Compensia to convey
information on proposals that management may make to the Leadership Development and Compensation
Committee, as well as to allow Compensia to collect
information about Amyris to develop its
recommendations. In addition, our Chief Executive Officer conducts reviews of the performance and
compensation of our other executive officers, and based on these reviews and input from Compensia and
our Human Resources department, makes recommendations regarding compensation for such executive
officers directly to the Leadership Development and Compensation Committee.

For the Chief Executive Officer’s compensation, Compensia reviews relevant market data with the
Chair of the Leadership Development and Compensation Committee, as well as the performance of the
Chief Executive Officer, and based on such review makes a recommendation regarding the Chief Executive
Officer’s compensation, which is then presented to the Leadership Development and Compensation
Committee. None of our executive officers participated in the determinations or deliberations of the
Leadership Development and Compensation Committee regarding the amount of any component of his or
her own 2018 compensation.

Operations and Finance Committee

On May 14, 2019, the Board established the Operations and Finance Committee, which is currently
composed of five directors: Dr. Duyk, Dr. Kung, Mr. Mills, Ms. Piwnica and Mr. Williams. Mr. Mills is the
Chair of the Operations and Finance Committee. The Board has determined that each member of the
Operations and Finance Committee is independent (as defined in the relevant Nasdaq and SEC rules and
regulations). The Board has adopted a written charter for our Operations and Finance Committee that is
posted on our company website at http://investors.amyris.com/corporate-governance.

The purpose of the Operations and Finance Committee is to assist the Board with respect to financial

and operational matters and transactions, including:

•

reviewing and approving significant capital expenditures and strategic operational and financing
transactions;

•

overseeing the Company’s capitalization, including the structure and amount of its debt and
equity; and

reviewing the Company’s business operations and plans and operational performance.

Nominating and Governance Committee

Under Nasdaq rules, director nominees must be selected, or recommended for the Board’s selection,
either by independent directors constituting a majority of the Board’s independent directors in a vote in
which only independent directors participate, or by a nominations committee composed solely of
independent directors. Amyris has established the Nominating and Governance Committee for such
matters, which is currently composed of two directors: Mr. Doerr and Ms. Piwnica. Mr. Doerr is the Chair
of the Nominating and Governance Committee. The Board has determined that each member of the
Nominating and Governance Committee is independent (as defined in the relevant Nasdaq and SEC rules
and regulations). The Board has adopted a written charter for our Nominating and Governance Committee
that is posted on our company website at http://investors.amyris.com/corporate-governance.

The purpose of the Nominating and Governance Committee is to ensure that the Board is properly
constituted to meet its fiduciary obligations to stockholders and Amyris, and to assist the Board with
respect to corporate governance matters, including:

•

identifying, considering and nominating candidates for membership on the Board;

developing, recommending and periodically reviewing corporate governance guidelines and
policies for Amyris (including our Corporate Governance Principles, Code of Business Conduct
and Ethics and Insider Trading Policy); and

advising the Board on corporate governance and Board performance matters,
recommendations regarding the structure and composition of the Board and Board committees.

including

The Nominating and Governance Committee also monitors the size,

leadership and committee
structure and composition of the Board and makes any recommendations for changes to the Board, reviews
our narrative disclosures in SEC filings regarding the director nomination process, director qualifications,
Board leadership structure and risk oversight by the Board, considers and approves requested waivers for
our directors or executive officers under our Code of Business Conduct and Ethics, reviews and makes
recommendations to the Board regarding formal procedures for stockholder communications with members
of the Board, and oversees an annual self-assessment process for the Board.

Director Nomination Process

In carrying out its duties to consider and nominate candidates for membership on the Board, the
Nominating and Governance Committee considers a mix of perspectives, qualities and skills that would
contribute to the overall corporate goals and objectives of Amyris and to the effectiveness of the Board.
The Nominating and Governance Committee’s goal is to nominate directors who will provide a balance of
industry, business and technical knowledge, experience and capability. To this end, the Nominating and
including
Governance Committee considers a variety of
demonstrated ability to exercise sound business judgment, relevant industry or business experience,
understanding of and experience with issues and requirements facing public companies, excellence and a
record of professional achievement in the candidate’s field, relevant technical knowledge or aptitude, having
sufficient time and energy to devote to the affairs of Amyris, independence for purposes of compliance with
Nasdaq and SEC rules and regulations, as applicable, and commitment to rigorously represent the
long-term interests of our stockholders. Although the Nominating and Governance Committee uses these
and other criteria to evaluate potential nominees, we have no stated minimum criteria for nominees. While
we do not have a formal policy with regard to the consideration of diversity in identifying director
nominees, the Nominating and Governance Committee strives to nominate directors with a variety of
complementary skills and experience so that, as a group, the Board will possess the appropriate talent, skills
and experience to oversee our business.

for director candidates,

characteristics

The Nominating and Governance Committee generally uses the following processes for identifying and

evaluating nominees for director:

•

In the case of incumbent directors, the Nominating and Governance Committee reviews the
director’s overall service to Amyris during such director’s term,
including performance,
effectiveness, participation and independence.

In seeking to identify new director candidates, the Nominating and Governance Committee may
use its network of contacts to compile a list of potential candidates and may also engage, if
deemed appropriate, a professional search firm. The Nominating and Governance Committee
would conduct any appropriate and necessary inquiries into the backgrounds and qualifications of
possible candidates after considering the structure and needs of the Board. The Nominating and
Governance Committee would then meet to discuss and consider the candidates’ qualifications
and select nominees for recommendation to the Board by majority vote.

The Nominating and Governance Committee will consider director candidates recommended by
stockholders and will use the same criteria to evaluate all candidates. We have not received a
recommendation for a director nominee for the 2019 annual meeting from a stockholder or stockholders.
Stockholders who wish to recommend individuals for consideration by the Nominating and Governance
Committee to become nominees for election to the Board may do so by delivering a written
recommendation to the Nominating and Governance Committee at the following address: Chair of the
Nominating and Governance Committee c/o Secretary of Amyris, Inc. at 5885 Hollis Street, Suite 100,
Emeryville, California 94608. Because we expect to hold our 2020 Annual Meeting of Stockholders (the
“2020 Annual Meeting”) in May 2020, any proposals for inclusion in next year’s proxy materials must be
submitted not earlier than the close of business on the 105th day prior to the 2020 Annual Meeting and not
later than the close of business on the later of (x) the 75th day prior to the 2020 Annual Meeting or (y) the
10th day following the date on which public announcement of the date of the 2020 Annual Meeting is first
made. You are also advised to review our Bylaws, which contain additional requirements about advance
notice of stockholder proposals and director nominations. Submissions must include the full name of the
proposed nominee, a description of the proposed nominee’s business experience and directorships for at
least the previous five years, complete biographical information, a description of the proposed nominee’s
qualifications as a director and a representation that the nominating stockholder is a beneficial or record
owner of our common stock. Any such submission must be accompanied by the written consent of the
proposed nominee to be named as a nominee and to serve as a director if elected.

Stockholder Nominations

Stockholders who wish to nominate persons directly for election to the Board at an annual meeting of
stockholders must meet the deadlines and other requirements set forth in our Bylaws and the rules and
regulations of the SEC. As provided in our certificate of incorporation, subject to the rights of the holders
of any series of preferred stock, any vacancy occurring in the Board can generally be filled only by the
affirmative vote of a majority of the directors then in office. The director appointed to fill the vacancy will
hold office for a term expiring at the annual meeting of stockholders at which the term of office of the class
to which the director has been assigned expires and until such director’s successor shall have been duly
elected and qualified, or until such director’s earlier death, resignation or removal.

Stockholder Communications with Directors

The Board has established a process by which stockholders may communicate with the Board or any of
its members, including the Chair of the Board, or to the independent directors generally. Stockholders and
other interested parties who wish to communicate with the Board or any of the directors may do so by
sending written communications addressed to the Secretary of Amyris at 5885 Hollis Street, Suite 100,
Emeryville, California 94608. The Board has directed that all communications will be compiled by the
Secretary and submitted to the Board or the selected group of directors or individual directors on a
periodic basis. These communications will be reviewed by our Secretary, who will determine whether they
should be presented to the Board. The purpose of this screening is to allow the Board to avoid having to
consider irrelevant or inappropriate communications (such as advertisements and solicitations). The
screening procedure has been approved by a majority of the non-management directors of the Board.

Directors may at any time request that we forward to them immediately all communications received by us
for the Board. All communications directed to the Audit Committee in accordance with the procedures
described above that relate to accounting, internal accounting controls or auditing matters involving Amyris
will be promptly and directly forwarded to all members of the Audit Committee.

PROPOSAL 2 —
RATIFICATION OF SELECTION OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM

General

On July 2, 2019, the Audit Committee selected Macias Gini & O’Connell LLP (“MGO”) as our
independent registered public accounting firm for the fiscal year ending December 31, 2019, and the Board
has directed that management submit the selection of such independent registered public accounting firm
for ratification by our stockholders at the annual meeting. MGO has been engaged as our independent
registered public accounting firm since July 2019. We expect representatives of MGO to be present at the
annual meeting. They will have an opportunity to make a statement if they so desire and will be available to
respond to appropriate questions.

Neither our Bylaws nor other governing documents or applicable law require stockholder ratification
of the selection of our independent registered public accounting firm. However, we are submitting the
selection of MGO to our stockholders for ratification as a matter of good corporate practice. If our
stockholders fail to ratify the selection, the Audit Committee will reconsider whether or not to retain MGO.
Even if the selection is ratified, the Audit Committee in its discretion may direct the selection of a different
independent registered public accounting firm at any time during the year if they determine that such a
change would be in the best interests of Amyris and our stockholders.

Background

On June 9, 2017, PricewaterhouseCoopers LLP (“PwC”) notified us that it declined to stand for
re-election as our independent registered public accounting firm for the 2017 fiscal year. The Audit
Committee conducted a competitive process to determine our independent registered public accounting
firm for the 2017 fiscal year and on June 28, 2017, with the approval of the Audit Committee, we appointed
KPMG LLP (“KPMG”) to serve as our independent registered public accounting firm for the 2017 fiscal
year.

PwC’s audit reports on our consolidated financial statements for the fiscal years ended December 31,
2016 and 2015 contained no adverse opinion or disclaimer of opinion and were not qualified or modified as
to uncertainty, audit scope, or accounting principles, except that PwC’s reports for the fiscal years ended
December 31, 2016, and December 31, 2015 included an explanatory paragraph indicating that there was
substantial doubt about our ability to continue as a going concern.

During our fiscal years ending December 31, 2016 and December 31, 2015, and the subsequent interim
period through June 9, 2017, (i) there were no “disagreements” (within the meaning set forth in
Item 304(a)(1)(iv) of Regulation S-K promulgated under the Securities Exchange Act of 1934
(“Regulation S-K”)) with PwC on any matter of accounting principles or practices, financial statement
disclosure, or auditing scope or procedure, which disagreements, if not resolved to PwC’s satisfaction,
would have caused PwC to make reference to the subject matter of the disagreements in their reports on our
consolidated financial statements for such years; and (ii) there were no “reportable events” (within the
meaning set forth in Item 304(a)(1)(v) of Regulation S-K).

In addition, during our fiscal years ending December 31, 2016 and December 31, 2015, and the
subsequent interim period through June 28, 2017, neither Amyris nor any person on its behalf consulted
with KPMG with respect to either (i) the application of accounting principles to a specified transaction,
either completed or proposed, or the type of audit opinion that might be rendered on our financial
statements, and neither a written report was provided to us nor oral advice was provided that KPMG
concluded was an important factor considered by us in reaching a decision as to the accounting, auditing or
financial reporting issue; or (ii) any matter that was either the subject of a “disagreement” or a “reportable
event” as such terms are described in Items 304(a)(1)(iv) or 304(a)(1)(v), respectively, of Regulation S-K.

On May 15, 2019, we determined, with the approval of the Audit Committee and the Board, to
appoint BDO USA, LLP (“BDO”) to serve as our independent registered public accounting firm for the
fiscal year ending December 31, 2019, and to dismiss KPMG upon completion of its audit of our
consolidated financial statement as of and for the year ended December 31, 2018 and the effectiveness of
internal control over financial reporting as of December 31, 2018, and the issuance of its reports thereon as

well as the re-audit of the consolidated financial statements as of and for the year ended December 31,
2017. Subsequently, On July 3, 2019, (i) BDO resigned as our independent registered public accounting firm
for the fiscal year ending December 31, 2019, prior to performing any substantive work with respect to the
audit work for that year, and (ii) we determined, with the approval of the Audit Committee, to: (A) dismiss
KPMG as our independent registered public accounting firm for the fiscal years ended December 31, 2018
and 2017, (B) appoint MGO as our independent registered public accounting firm for the fiscal years ended
December 31, 2019 and 2018, and (C) appoint BDO as our independent registered public accounting firm
for the re-audit of our consolidated financial statements for the fiscal year ended December 31, 2017. On
July 9, 2019, MGO was formally engaged as our independent registered public accounting firm for the
fiscal years ended December 31, 2019 and 2018. On July 10, 2019, BDO was formally engaged as our
independent registered public accounting firm for the re-audit of our consolidated financial statements for
the fiscal year ended December 31, 2017. The Audit Committee authorized KPMG to respond fully to all
inquiries from BDO and MGO, and BDO to respond fully to all inquiries from MGO.

The audit report of KPMG on our consolidated financial statements as of and for the year ended
December 31, 2017 did not contain any adverse opinion or disclaimer of opinion, nor was it qualified or
modified as to audit scope or accounting principles, except as follows: KPMG’s report on our consolidated
financial statements as of and for the year ended December 31, 2017 contained a separate paragraph stating
that “The accompanying consolidated financial statements have been prepared assuming that the Company
will continue as a going concern. As discussed in Note 1 to the consolidated financial statements, the
Company has suffered recurring losses from operations and has current debt service requirements that raise
substantial doubt about its ability to continue as a going concern. Management’s plans in regard to these
matters are also described in Note 1. The consolidated financial statements do not include any adjustments
that might result from the outcome of this uncertainty.” On April 5, 2019 and May 14, 2019, the Audit
Committee and the Board (upon the recommendation of
the Audit Committee), respectively, after
consultation with senior management and KPMG, concluded that our consolidated financial statements for
the year ended December 31, 2017 and the quarterly and year-to-date periods ended March 31, 2018,
June 30, 2018 and September 30, 2018, respectively, should be restated and should no longer be relied upon.
Further, our disclosures related to such financial statements and related communications issued by or on
behalf of us with respect to such periods, including management’s assessment of internal control over
financial reporting as of December 31, 2017, should also no longer be relied upon. As of July 3, 2019,
KPMG had not completed its audit procedures or issued any reports on our consolidated financial
statements as of and for the year ended December 31, 2018 or our internal control over financial reporting
and disclosure controls and procedures as of December 31, 2018.

there were no “disagreements” or “reportable events,” as

Other than the reportable events disclosed above, during our two most recent fiscal years ended
December 31, 2018 and December 31, 2017, respectively, and the subsequent interim period through July 3,
2019,
such terms are described in
Items 304(a)(1)(iv) and 304(a)(1)(v), respectively, of Regulation S-K and the related instructions thereto,
with KPMG or BDO on any matter of accounting principles or practices, financial statement disclosure, or
auditing scope or procedure, which disagreement(s) or reportable event(s), if not resolved to the satisfaction
of KPMG or BDO, as applicable, would have caused KPMG or BDO, as applicable, to make reference to
the subject matter of the disagreement(s) or reportable event(s) in connection with its report on our
consolidated financial statements for the relevant year.

During our two most recent fiscal years, which ended December 31, 2018 and December 31, 2017, and
the subsequent interim period through July 3, 2019, neither we nor any person on our behalf consulted with
BDO or MGO with respect to either (i) the application of accounting principles to a specified transaction,
either completed or proposed, or the type of audit opinion that might be rendered on our consolidated
financial statements, and neither a written report was provided to us nor oral advice was provided that BDO
or MGO, as applicable, concluded was an important factor in reaching a decision as to any accounting,
auditing or financial reporting issue; or (ii) any matter that was either the subject of a “disagreement” or a
“reportable event,” as such terms are described in Items 304(a)(1)(iv) and 304(a)(1)(v) of Regulation S-K.

Vote Required and Board Recommendation

Ratification of the selection of Macias Gini & O’Connell LLP requires the affirmative vote of the
holders of a majority of the shares of common stock properly casting votes for or against this proposal at

the annual meeting in person or by proxy. Abstentions will not count toward the vote total for this proposal
and therefore will not affect the outcome of this proposal. Shares represented by executed proxies that do
not indicate a vote “For,” “Against” or “Abstain” will be voted by the proxy holders “For” this proposal.

The Board recommends a vote “FOR” this Proposal 2

Independent Registered Public Accounting Firm Fee Information

BDO has served as our independent registered public accounting firm for the fiscal year ended
December 31, 2017 since July 10, 2019, and MGO has served as our independent registered public
accounting firm for the fiscal year ended December 31, 2018 and the fiscal year ending December 31, 2019
since July 9, 2019. The following tables set forth the aggregate fees billed or to be billed to us by BDO and
MGO, respectively, for services performed in or for the fiscal years ended December 31, 2018 and
December 31, 2017 (in thousands):

BDO USA, LLP

Fee Category

Audit Fees . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Audit-Related Fees . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Tax Fees . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
All Other Fees . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Total Fees

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Fiscal Year ended December 31,

2018

$—
—
—
3

$ 3

2017

$2,235
—
—
—

$2,235

The “Audit Fees” category includes aggregate fees billed for the relevant fiscal year for professional
services rendered for the audit of our annual financial statements and review of our unaudited financial
statements included in our Quarterly Reports on Form 10-Q, and for services that are normally provided in
connection with statutory and regulatory filings or engagements for those fiscal years. We did not incur any
fees in this category with respect to BDO for the fiscal year ended December 31, 2018.

The “Tax Fees” category includes aggregate fees billed in the relevant fiscal year for professional
services rendered with respect to tax compliance, tax advice and tax planning. We did not incur any fees in
this category with respect to BDO for the fiscal years ended December 31, 2018 and 2017.

The “All Other Fees” category includes aggregate fees billed in the relevant fiscal year for products and
services other than those reported under the other categories described above. We did not incur any fees in
this category with respect to BDO for the fiscal year ended December 31, 2017.

Macias Gini & O’Connell LLP

Fee Category

Total Fees

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Fiscal Year ended December 31,

2018

$3,150
—
—
—

$3,150

2017

$—
—
—
—

$—

connection with statutory and regulatory filings or engagements for those fiscal years. We did not incur any
fees in this category with respect to MGO for the fiscal year ended December 31, 2017.

The “Tax Fees” category includes aggregate fees billed in the relevant fiscal year for professional
services rendered with respect to tax compliance, tax advice and tax planning. We did not incur any fees in
this category with respect to MGO for the fiscal years ended December 31, 2018 and 2017.

Audit Committee Pre-Approval of Services Performed by our Independent Registered Public Accounting Firm

The Audit Committee’s charter requires it to approve all fees and other compensation paid to, and
pre-approve all audit and non-audit related services provided by, the Company’s independent registered
public accounting firm. The Audit Committee charter permits the Audit Committee to delegate
pre-approval authority to one or more members of the Audit Committee, provided that any pre-approval
decision is reported to the Audit Committee at its next scheduled meeting. The Audit Committee has
delegated such pre-approval authority, for fees of up to $100,000 in the aggregate, to the Chair of the Audit
Committee.

In determining whether to approve audit and non-audit services to be performed by our independent
registered public accounting firm, the Audit Committee takes into consideration the fees to be paid for such
services and whether such fees would affect the independence of the accounting firm in performing its audit
function. In addition, when determining whether to approve non-audit services to be performed by our
independent registered public accounting firm, the Audit Committee considers whether the performance of
such services is compatible with maintaining the independence of the accounting firm in performing its
audit function, and confirms that the non-audit services will not include the prohibited activities set forth in
Section 201 of
for the services described above under
“Audit-Related Fees,” “Tax Fees” and “All Other Fees” (each of which was pre-approved by the Audit
Committee in accordance with its policy), no non-audit services were provided by our independent
registered public accounting firm in 2018 or 2017.

the Sarbanes-Oxley Act of 2002. Except

All fees paid to, and all services provided by, our independent registered public accounting firm during
fiscal years 2018 and 2017 were pre-approved by the Audit Committee in accordance with the pre-approval
procedures described above.

REPORT OF THE AUDIT COMMITTEE*

The Audit Committee has reviewed and discussed with management (i) our restated audited
consolidated financial statements for the fiscal year ended December 31, 2017 and (ii) our audited
consolidated financial statements for the fiscal year December 31, 2018. The Audit Committee has also
discussed with BDO USA, LLP and Macias Gini & O’Connell LLP, our independent registered public
accounting firms for the fiscal year ended December 31, 2017 and the fiscal year ended December 31, 2018,
respectively, the matters required to be discussed by Public Company Accounting Oversight Board Auditing
Standard No. 1301 (Communications with Audit Committees), as amended.

The Audit Committee has received and reviewed the written disclosures and the letters from each of
BDO USA, LLP and Macias Gini & O’Connell LLP required by applicable requirements of the Public
Company Accounting Oversight Board regarding such firms’ respective communications with the Audit
Committee concerning independence, and has discussed with such firms their independence.

Based on the review and discussions referred to above, the Audit Committee recommended to the
Board that the restated audited consolidated financial statements for the fiscal year ended December 31,
2017 and the audited consolidated financial statements for the fiscal year December 31, 2018 be included in
our Annual Report on Form 10-K for the fiscal year ended December 31, 2018 for filing with the Securities
and Exchange Commission.

Amyris, Inc. Audit Committee of the Board

R. Neil Williams (Chair)
Geoffrey Duyk
Steven Mills

The material in this report is not “soliciting material,” is not deemed “filed” with the Securities and
Exchange Commission and is not to be incorporated by reference into any filing of Amyris under the
Securities Act or the Exchange Act, whether made before or after the date hereof and irrespective of any
general incorporation language in any such filing.

PROPOSAL 3 —
APPROVAL OF THE ISSUANCE OF SHARES OF OUR COMMON STOCK ISSUABLE UPON THE EXERCISE OF WARRANTS AND
CONVERSION OF PREFERRED STOCK ISSUED TO FORIS VENTURES, LLC IN ACCORDANCE WITH NASDAQ MARKETPLACE
RULES 5635(B) AND 5635(D)

General

We are asking stockholders to approve the issuance of shares of our common stock issuable upon the
exercise of warrants and conversion of preferred stock issued to Foris Ventures, LLC in accordance with
Nasdaq Marketplace Rules 5635(b) and 5635(d), as described in more detail below.

Background

During 2019, we have engaged in the following issuances of equity securities to Foris Ventures, LLC
(“Foris”), an entity affiliated with director John Doerr of Kleiner Perkins Caufield & Byers, a current
stockholder, and an owner of greater than five percent of our outstanding common stock, par value
$0.0001 per share (the “Common Stock”):

On April 16, 2019, we issued and sold to Foris 6,732,369 shares of Common Stock at a price of
$2.87 per share, the closing bid price of the Common Stock on the Nasdaq Global Select Market on
April 12, 2019, as well as a warrant to purchase up to 5,424,804 shares of Common Stock at an exercise
price of $2.87 per share, with an exercise term of two years from issuance, pursuant to a Securities Purchase
Agreement, dated April 15, 2019, between us and Foris, for aggregate proceeds to us of $20.0 million (the
“April Investment”). The securities were sold in a private placement pursuant to the exemption from
registration under Section 4(a)(2) of the Securities Act of 1933, as amended (the “Securities Act”), and
Regulation D promulgated under the Securities Act.

On April 26, 2019, we issued and sold to Foris 2,832,440 shares of Common Stock at a price of
$5.12 per share, the closing price of the Common Stock on the Nasdaq Global Select Market on April 23,
2019, as well as a warrant to purchase up to 3,983,230 shares of Common Stock at an exercise price of
$5.12 per share, with an exercise term of two years from issuance, pursuant to a Security Purchase
Agreement, dated April 24, 2019, between us and Foris, for aggregate proceeds to us of $15.0 million. The
to the exemption from registration under
securities were sold in a private placement pursuant
Section 4(a)(2) of the Securities Act and Regulation D promulgated under the Securities Act.

On May 14, 2019 we issued and sold to Foris 1,122,460 shares of Common Stock at a price of
$4.60 per share, as well as a warrant to purchase 352,638 shares of Common Stock at an exercise price of
$4.56 per share, the closing price of the Common Stock on the Nasdaq Global Select Market on
May 9, 2019, with an exercise term of two years from issuance (the “Exchange Warrant”), in exchange for
the surrender and cancellation of $5.0 million principal amount of our 6.50% Convertible Senior Notes due
2019 held by Foris, pursuant to an Exchange Agreement, dated May 10, 2019, between us and Foris. The
to the exemption from registration under
securities were sold in a private placement pursuant
Section 3(a)(9) of the Securities Act.

On August 14, 2019, in connection with the entry by us and Foris into the Amendment No 5 and
Waiver to the Loan and Security Agreement, dated June 29, 2018, by and among us, certain of our
subsidiaries and Foris, as successor in interest to GACP Finance Co., LLC, we issued to Foris a warrant to
purchase up to 1,438,829 shares of Common Stock at an exercise price of $2.87 per share, with an exercise
term of two years from issuance. The warrant was issued in a private placement pursuant to the exemption
from registration under Section 4(a)(2) of the Securities Act and Regulation D promulgated under the
Securities Act.

On August 28, 2019, in connection with the entry by us and Foris into a credit agreement to make
available to us an unsecured credit facility in an aggregate principal amount of $19.0 million, which we
borrowed in full on August 28, 2019, we (i) issued to Foris a warrant to purchase up to 4,871,795 shares of
Common Stock at an exercise price of $3.90 per share, with an exercise term of two years from issuance and
(ii) amended the warrants issued to Foris on April 26, 2019 and May 14, 2019 to reduce the exercise price of
such warrants to $3.90 per share.

The exercise price of the warrants described above (collectively, the “Foris Warrants”) is subject to
standard adjustments but does not contain any anti-dilution protection, and the Foris Warrants only permit
“cashless” or “net” exercise after the six-month anniversary of issuance, and only to the extent that there is
not an effective registration statement covering the resale of the applicable shares of Common Stock
underlying the Foris Warrant being exercised.

In addition, each Foris Warrant provides that we may not effect any exercise of such Foris Warrant to
the extent that, after giving effect to such exercise, Foris, together with its affiliates, would beneficially own
in excess of 19.99% of the number of shares of Common Stock outstanding after giving effect to such
exercise, unless we have obtained stockholder approval to exceed such limit. In addition, Foris has agreed
not to exercise any warrant or any other convertible security to the extent that, after giving effect to such
exercise, Foris, together with its affiliates, would beneficially own in excess of 19.99% of the number of
shares of Common Stock outstanding after giving effect to such exercise or conversion, unless we have
obtained stockholder approval to exceed such limit.

We are asking our stockholders to approve allowing Foris to exercise its outstanding warrants, which
would result in Foris beneficially owning in excess of 19.99% of the number of shares of Common Stock
outstanding.

For more information regarding these transactions, please see below under “Transactions with Related

Persons — Agreements with Foris”.

In addition to the warrants listed above, Foris holds the following warrants to purchase our Common

Stock as of August 30, 2019:

Warrant to purchase 4,877,386 shares of Common Stock at an exercise price of $2.87 per share,

exercisable until May 17, 2020

Warrant to purchase 64,103 shares of Common Stock at an exercise price of $0.15 per share,

exercisable until July 29, 2020

Warrant to purchase 152,381 shares of Common Stock at an exercise price of $0.15 per share,

exercisable until February 12, 2021

In addition, as of August 30, 2019, Foris held 6,376.2787 shares of our Series B 17.38% Convertible
Preferred Stock (“Series B Preferred Stock”), which are convertible into 1,012,071 shares of Common
Stock, the conversion of which is subject to a beneficial ownership limitation of 9.99% of the Company’s
outstanding common stock (the “Series B Beneficial Ownership Limitation”). Pursuant to the Certificate of
Designation of Preferences, Rights and Limitations relating to the Series B Preferred Stock (the “Series B
Certificate of Designation”), the shares of Series B Preferred Stock held by Foris automatically converted to
common stock on October 9, 2017, subject to the Series B Beneficial Ownership Limitation. Such
automatic conversion of the Series B Preferred Stock will be held in abeyance to the extent such conversion
would cause Foris to beneficially own in excess of the Series B Beneficial Ownership Limitation, until Foris
is able to receive such shares without exceeding the Series B Beneficial Ownership Limitation. We intend to
amend the Series B Certificate of Designation to remove the Series B Beneficial Ownership Limitation;
provided, that the conversion of the shares of Series B Preferred Stock held by Foris will continue to be
subject to a 19.99% beneficial ownership limitation unless Proposal 3 is approved. All beneficial ownership
information contained in this Proxy Statement that assumes that Proposal 3 is approved also assumes that
the Series B Beneficial Ownership Limitation is removed.

As of August 30, 2019, Foris held (i) 17,527,973 shares of Common Stock, (ii) warrants to purchase up
to an aggregate of 21,165,166 shares of Common Stock at a weighted average exercise price of $3.29 per
share, with expiration dates ranging from July 29, 2020 to August 28, 2021 and (iii) 6,376.2787 shares of
Series B Preferred Stock, which are convertible into 1,012,071 shares of Common Stock. Foris is currently
our largest shareholder on the basis of shares issued and outstanding, and is our second largest shareholder
on a beneficial ownership basis.

In addition, as of August 30, 2019, affiliates of Foris, including director John Doerr and Kleiner

Perkins Caufield & Byers, beneficially owned an aggregate of 295,246 shares of Common Stock.

Currently, due to the beneficial ownership limitations described above, Foris beneficially owns 19.99%
of the outstanding Common Stock. Assuming the full exercise of all Foris warrants currently outstanding
for cash as of August 30, 2019 and the conversion of its shares of Series B Preferred Stock, after giving
effect to such exercises and conversion, Foris, together with its affiliates, would beneficially own an
aggregate of 39,984,057 shares of Common Stock, representing approximately 31.9% of the Common
Stock outstanding after giving effect to such exercise and conversion, and would become our largest
shareholder on a beneficial ownership basis. By approving this Proposal 3, stockholders would be approving
the exercise by Foris of all of its currently outstanding warrants and the conversion of its outstanding
Series B Preferred Stock, which would cause Foris to beneficially own in excess of 20% of our Common
Stock outstanding and become our largest shareholder on a beneficial ownership basis. If Proposal 3 is not
approved, Foris would continue to beneficially own 19.99% of our Common Stock and would be restricted
from exercising its outstanding warrants or outstanding Series B Preferred Stock until such time as the
exercise of such warrants or the conversion of such Series B Preferred Stock would not cause Foris to
exceed 19.99% of the number of shares of Common Stock outstanding after giving effect to such exercise
or conversion.

Purpose — Nasdaq Stockholder Approval Requirement

Our Common Stock is listed on The Nasdaq Stock Market (“Nasdaq”) and trades under the ticker
symbol AMRS. Nasdaq Marketplace Rule 5635(b) requires stockholder approval of security issuances
when the issuance or potential issuance will result in a change of control of the Company. Nasdaq has
generally taken the position that any issuance that results in an investor or group of investors obtaining
a 20% or greater interest or a right to acquire that interest on a post-transaction basis, and that ownership
position would be the largest position in the Company, would be presumed to be a change of control.
Assuming the full exercise of the warrants currently held by Foris and the full exercise of Foris’s shares of
Series B Preferred Stock, Foris (and certain of its affiliates, including director John Doerr) would own
greater than 20% of the voting power of the Company on a post-transaction basis and be the Company’s
the
largest shareholder. By approving Proposal 3, you are approving the proposal for purposes of
requirements under Nasdaq Marketplace Rule 5635(b), which would result in Foris (and certain of its
affiliates, including director John Doerr) obtaining a greater than 20% beneficial ownership interest in the
Company on a post-transaction basis, which ownership position will be the largest ownership position
(both on an issued and outstanding basis and a beneficial ownership basis) in the Company.

Nasdaq Marketplace Rule 5635(d) requires stockholder approval in connection with a transaction
other than a public offering involving the sale or issuance by the issuer of common stock (or securities
convertible into or exchangeable for common stock) equal to 20% or more of the common stock or 20% or
more of the voting power outstanding before the issuance for a price that is less than the lower of: (i) the
closing price of the Common Stock immediately preceding the signing of the binding agreement for the
issuance of such securities; or (ii) the average closing price of the Common Stock for the five trading days
immediately preceding the signing of the binding agreement for the issuance of such securities (the
“Minimum Price”). Based on Nasdaq Marketplace Rule 5635(d), the issuance of the Exchange Warrant,
when taken together with other transactions aggregated for such purpose, may be deemed to involve the
issuance of securities convertible into more than 20% of our Common Stock at a discount to the Minimum
Price.

We are requesting in this Proposal 3 that our stockholders approve the issuance of the Common Stock
issuable upon exercise of the warrants, including the Exchange Warrant, and conversion of the Series B
Preferred Stock currently held by Foris in accordance with Nasdaq Marketplace Rules 5635(b) and (d). The
issuance and sale of the shares of Common Stock underlying such warrants and shares of Series B
Preferred Stock are intended to be exempt from the registration requirements of the Securities Act pursuant
to the Regulation D “safe harbor” provisions of the Securities Act.

Vote Required and Board Recommendation

This proposal must receive a “For” vote from (i) the holders of a majority of the shares of common
stock properly casting votes for or against this proposal at the annual meeting in person or by proxy (the
“Bylaws Standard”) and (ii) a majority of the total votes of shares of our common stock not owned,

directly or indirectly, by Foris Ventures, LLC or its affiliates (including director John Doerr and Kleiner
Perkins Caufield & Byers), cast in person or by proxy at the annual meeting (the “Disinterested Standard”).
Shares represented by executed proxies that do not indicate a vote “For,” “Against” or “Abstain” will be
voted by the proxy holders “For” this proposal. If you own shares through a bank, broker or other
Intermediary, you must instruct your bank, broker or other Intermediary how to vote in order for them to
vote your shares so that your vote can be counted on this proposal. Abstentions and broker non-votes will
not count toward the vote total for this proposal and therefore will not affect the outcome of this proposal.

The Board recommends a vote “FOR” this Proposal 3

The Board determined that Proposal 3 is advisable and in the best interest of our stockholders and

recommended that our stockholders vote in favor of Proposal 3.

In reaching its determination to approve Proposal 3, the Board, with advice from our management and

legal advisors, considered a number of factors, including:

•

the fact that the proceeds from the warrant and preferred stock issuances and the relationship with
Foris will enable us to advance our strategic direction;

the warrants were offered as an inducement for Foris to participate in financing transactions with
us, and it was the determination of the Board that such financing transactions were important
events to strengthen our balance sheet;

our financial condition, results of operations, cash flow and liquidity, including our outstanding
debt obligations, which required us to raise additional capital for ongoing cash needs;

the fact that our management explored financing options with other potential investors and are
not aware of an ability for us to obtain the financing needed for our ongoing cash needs on
comparable or better terms to the transactions with Foris, or at all;

the fact that John Doerr, one of our directors, indirectly owns all of the membership interests in
Foris; and

the fact that our stockholders who did not participate in the financing transactions may be diluted
and the value of our Common Stock may be diluted upon the exercise of the warrants and the
conversion of the Series B Preferred Stock held by Foris.

In view of the variety of factors considered in connection with the evaluation of Proposal 3, the Board
did not find it practicable to, and did not, quantify or otherwise attempt to assign any relative weight to the
various factors considered. In addition, in considering the various factors, individual members of the Board
may have assigned different weights to different factors.

After evaluating these factors for and against the exercise of the warrants and conversion of shares of
Series B Preferred Stock, and the corresponding beneficial ownership of Foris in excess of 19.99% of our
Common Stock, and based upon their knowledge of our business, financial condition and prospects,
potential financing alternatives (or lack thereof), and the views of our management, the Board concluded
that such exercise and conversion, and such corresponding increase in beneficial ownership by Foris, is in
our best interest and in the best interests of our stockholders, and recommends that all stockholders vote
“FOR” the approval of Proposal 3.

Potential Adverse Effects — Dilution and Impact on Existing Stockholders

The issuance of shares of Common Stock upon exercise of the warrants and conversion of the Series B
Preferred Stock currently held by Foris would have a dilutive effect on current stockholders in that
the percentage ownership of the Company held by such current stockholders will decline as a result of the
issuance of the Common Stock upon such exercise or conversion. This means also that our current
stockholders other than Foris will own a smaller interest in us as a result of such issuance and therefore
have less ability to influence significant corporate decisions requiring stockholder approval. Issuance of
Common Stock upon exercise of the warrants and conversion of the Series B Preferred Stock currently held
by Foris could also have a dilutive effect on book value per share and any future earnings per share.
Dilution of equity interests could also cause prevailing market prices for our Common Stock to decline.

Due to potential adjustments to the number of shares of Common Stock issuable upon exercise of the
warrants and conversion of the Series B Preferred Stock issued to Foris, the exact magnitude of the dilutive
effect of the issuance of shares of Common Stock upon exercise of the warrants and conversion of the
Series B Preferred Stock currently held by Foris cannot be conclusively determined. However, the dilutive
effect may be material to current stockholders of the Company.

As a result of such potential issuance, Foris may be able to control or significantly influence our
management and affairs and matters requiring stockholder approval, including the election of directors and
the approval of significant corporate transactions, such as mergers, consolidations or the sale of all or
substantially all of our assets, and may not act in the best interests of our other stockholders. Consequently,
this concentration of ownership may have the effect of delaying or preventing a change of control, or a
change in our management or board of directors, or discouraging a potential acquirer from making a
tender offer or otherwise attempting to obtain control of our company, even if such actions would benefit
our other stockholders.

Interests of Certain Persons

When you consider the Board’s recommendation to vote in favor of Proposal 3, you should be aware
that director John Doerr is affiliated with Foris as well as Kleiner Perkins Caufield & Byers, a current
stockholder, and may have interests that may be different from, or in addition to, the interests of other of
our stockholders. The beneficial ownership of Foris and its affiliates, including Mr. Doerr and Kleiner
Perkins Caufield & Byers, is set forth above. Foris currently holds warrants and shares of Series B Preferred
Stock that will not be exercisable or convertible, respectively, if Proposal 3 is not approved. Foris will not, as
a result of the exercise of its outstanding warrants and conversion of its shares of Series B Preferred Stock,
acquire rights to a majority of the voting power of the Company.

The transactions involving the issuance of the warrants and shares of Series B Preferred Stock
currently held by Foris were separately approved by the Audit Committee, the Operations and Finance
Committee or a Special Committee of the Board, and Mr. Doerr was not a member of, nor participated in,
any meetings of such committees.

Corporate Governance Principles

CORPORATE GOVERNANCE

The Board has adopted written Corporate Governance Principles to provide the Board and its
committees with operating principles designed to enhance the effectiveness of the Board and its committees,
to establish good Board and committee governance, and to establish the responsibilities of management
and the Board in supporting the Board’s activities. The Corporate Governance Principles set forth a
framework for Amyris’s governance practices, including composition of the Board, director nominee
selection, Board membership criteria, director compensation, Board education, meeting responsibilities,
independent directors, standing Board
access to information and employees, executive sessions of
committees and their functions, and responsibilities of management.

Code of Business Conduct and Ethics

We have adopted a Code of Business Conduct and Ethics that applies to all directors, officers and
employees of Amyris as required by Nasdaq governance rules. Our Code of Business Conduct and Ethics
includes a section entitled “Code of Ethics for Chief Executive Officer and Senior Financial Officers,”
providing additional principles for ethical leadership and a requirement that such individuals foster a
culture throughout Amyris that helps ensure the fair and timely reporting of our financial results and
condition. Our Code of Business Conduct and Ethics is available on the corporate governance section of
our website at http://investors.amyris.com/corporate-governance. Stockholders may also obtain a printed
copy of our Code of Business Conduct and Ethics and our Corporate Governance Principles by writing to
the Secretary of Amyris at 5885 Hollis Street, Suite 100, Emeryville, California 94608. If we make any
substantive amendment to a provision of our Code of Business Conduct and Ethics that applies to our
principal executive officer, principal financial officer, principal accounting officer or controller, or persons
performing similar functions, or if we grant any waiver from any of such provisions to any such person, we
will promptly disclose the nature of the amendment or waiver on the corporate governance section of our
website at http://investors.amyris.com/corporate-governance.

SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT

The following table sets forth information with respect to the beneficial ownership of our common

stock, as of August 30, 2019, by:

•

each person, or group of affiliated persons, who is known by us to beneficially own more than 5%
of our voting securities;

each of our directors;

each of our named executive officers; and

all of our directors and named executive officers as a group.

Beneficial ownership is determined in accordance with the rules of the Securities and Exchange
Commission (the “SEC”) and generally includes any shares over which the individual or entity has sole or
shared voting power or investment power. These rules also treat as outstanding all shares of capital stock
that a person would receive upon the exercise of any option, warrant or right or through the conversion of
a security held by that person that are immediately exercisable or convertible or exercisable or convertible
within 60 days of the date as of which beneficial ownership is determined. These shares are deemed to be
outstanding and beneficially owned by the person holding those options, warrants or rights or convertible
securities for the purpose of computing the number of shares beneficially owned and the percentage
ownership of
that person, but they are not treated as outstanding for the purpose of computing
the percentage ownership of any other person. The information does not necessarily indicate beneficial
ownership for any other purpose. Except as indicated in the footnotes to the below table and pursuant to
applicable community property laws, to our knowledge the persons named in the table below have sole
voting and investment power with respect to all shares of common stock attributed to them in the table.

Information with respect to beneficial ownership has been furnished to us by each director and named
executive officer and certain stockholders, and derived from publicly-available SEC beneficial ownership
reports on Forms 3 and 4 and Schedules 13D and 13G filed by covered beneficial owners of our common
stock. Percentage ownership of our common stock in the table is based on 103,185,068 shares of our
common stock outstanding on August 30, 2019 (as reflected in the records of our stock transfer agent).
Except as otherwise set forth below, the address of the beneficial owner is c/o Amyris, Inc., 5885 Hollis
Street, Suite 100, Emeryville, California 94608.

The number and percent of shares owned by Foris Ventures, LLC and director John Doerr do not
include any shares issuable upon the exercise of the warrants or conversion of the shares of preferred stock
that will be exercisable and convertible, respectively, if Proposal 3 is approved.

Name and Address of Beneficial Owner

5% Stockholders
DSM International B.V(1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Foris Ventures, LLC(2)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vivo Capital LLC(3) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Total Raffinage Chimie(4) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Loyola Capital Management, LLC(5) . . . . . . . . . . . . . . . . . . . . . . . . . . .
Directors and Named Executive Officers
John Melo(6) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
John Doerr(2)(7) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Geoffrey Duyk(8) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Philip Eykerman(9)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Christoph Goppelsroeder(10) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Frank Kung(3)(11) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
James McCann(12) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Number of Shares
Beneficially Owned (#)

Percent
of Class (%)

27,001,551
21,054,940
10,725,235
10,268,173
8,300,000

909,575
21,333,787
8,932
12,848
0
10,731,784

1,240

23.0
19.7
9.98
9.9
8.0

*
19.99
*
*
*
9.99

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Name and Address of Beneficial Owner
Steven Mills(13)
Carole Piwnica(14)
Lisa Qi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
R. Neil Williams(15) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Patrick Yang(16) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Kathleen Valiasek(17)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Joel Cherry(18) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Eduardo Alvarez(19) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Nicole Kelsey(20)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
All Directors and Named Executive Officers as a Group (16 Persons)(21)
. .

Number of Shares
Beneficially Owned (#)

Percent
of Class (%)

16,048
15,797

0
14,597

68,997
275,646
323,621
366,876
128,592
34,208,340

*
*

*
*
*
*
*
30.4

* Represents beneficial ownership of less than 1%.

(1)

(2)

Includes 13,994,198 shares of common stock issuable upon exercise of certain warrants held by DSM
International B.V. (together with its affiliates, “DSM”). DSM International B.V. is a wholly owned
subsidiary of Koninklijke DSM N.V. Accordingly, Koninklijke DSM N.V. may be deemed to share
beneficial ownership of the securities held of record by DSM International B.V. Koninklijke DSM N.V.
is a publicly traded company with securities listed on the Amsterdam Stock Exchange. The address for
DSM International B.V. is HET Overloon 1, 6411 TE Heerlen, Netherlands.

Includes 3,526,967 shares of common stock issuable upon exercise of certain warrants held by Foris.
Foris also holds (i) warrants to purchase 17,638,199 shares of common stock, the exercise of which is
subject to (A) a beneficial ownership limitation of 19.99% of the Company’s outstanding common
stock and/or (B) the approval of the Company’s stockholders and (ii) shares of the Company’s Series B
17.38% Convertible Preferred Stock (the “Series B Preferred Stock”), which are convertible into
1,012,071 shares of common stock, the conversion of which is subject to a beneficial ownership
limitation of 9.99% of the Company’s outstanding common stock (the “Series B Beneficial Ownership
Limitation”). Pursuant to the Certificate of Designation of Preferences, Rights and Limitations
relating to the Series B Preferred Stock (the “Series B Certificate of Designation”), the shares of
Series B Preferred Stock held by Foris automatically converted to common stock on October 9, 2017,
subject to the Series B Beneficial Ownership Limitation. Such automatic conversion of the Series B
Preferred Stock will be held in abeyance to the extent such conversion would cause Foris to beneficially
own in excess of the Series B Beneficial Ownership Limitation, until Foris is able to receive such shares
without exceeding the Series B Beneficial Ownership Limitation. We intend to amend the Series B
Certificate of Designation to remove the Series B Beneficial Ownership Limitation; provided, that the
conversion of the shares of Series B Preferred Stock held by Foris will continue to be subject to a
19.99% beneficial ownership limitation unless Proposal 3 is approved. All beneficial ownership
information contained in this Proxy Statement that assumes that Proposal 3 is approved also assumes
that the Series B Beneficial Ownership Limitation is removed. We are asking stockholders to approve
the issuance of the shares of common stock issuable upon the exercise of such warrants and
conversion of such shares of Series B Preferred Stock; see “Proposal 3 — Approval of the issuance of
shares of our common stock issuable upon the exercise of warrants and conversion of preferred stock
issued to Foris Ventures, LLC in accordance with Nasdaq Marketplace Rules 5635(b) and 5635(d)” for
more information. If Proposal 3 had been approved as of August 30, 2019, the number of shares
beneficially owned by Foris, and the Percent of Class, would have been 39,705,210 shares and
approximately 31.7%, respectively. Foris is indirectly owned by director John Doerr, who shares voting
and investment control over the shares held by Foris. The address for Foris is 751 Laurel Street #717,
San Carlos, California 94070.

(3)

exercise of certain warrants held by Vivo. Vivo holds additional shares of Series D Preferred Stock,
which are currently convertible into 1,150,618 shares of common stock, and additional warrants, which
are currently exercisable for 4,991,953 shares of common stock, the conversion and exercise,
respectively, of which is subject to a beneficial ownership limitation of 9.99% of the Company’s
outstanding common stock. For purposes of this table, the shares beneficially owned by Vivo have
been allocated between the number of shares issuable upon the conversion of shares of Series D
Preferred Stock and the exercise of warrants based on the respective number of shares issuable upon
such conversion or exercise. Director Frank Kung is a founding member of Vivo and a voting member
of the general partner of Vivo entities that hold our common stock, Series D Preferred Stock and
warrants, and may be deemed to share voting and dispositive power over the shares held by such
entities. The address for Vivo is 505 Hamilton Avenue, Suite 207, Palo Alto, California 94301.

(4)

Includes (i) 172,820 shares of common stock issuable upon conversion of certain convertible
promissory notes held by Total Raffinage Chimie (“Total”) and (ii) 141,881 shares of common stock
issuable upon exercise of certain warrants held by Total. The address for Total is 2, Place Jean Millier,
La Défense 6, 92400 Courbevoie, France.

(5) The address for Loyola Capital Management, LLC is 222 E. Wisconsin Avenue, Suite 201, Lake Forest,

Illinois 60045.

(6) Shares beneficially owned by Mr. Melo include (i) 559,863 restricted stock units, all of which were
unvested as of August 30, 2019, and (ii) 214,693 shares of common stock issuable upon exercise of
stock options that were exercisable within 60 days of August 30, 2019.

(7) Shares beneficially owned by Mr. Doerr include (i) 21,054,940 shares of common stock beneficially
owned by Foris, in which Mr. Doerr indirectly owns all of the membership interests, (ii) 567 shares of
common stock held by The Vallejo Ventures Trust U/T/A 2/12/96, of which Mr. Doerr is a trustee,
(iii) 278,882 shares of common stock held by entities affiliated with Kleiner Perkins Caufield & Byers
of which Mr. Doerr is an affiliate, excluding 16,399 shares over which Mr. Doerr has no voting or
investment power and (iv) 10,265 shares of common stock issuable upon exercise of stock options that
were exercisable within 60 days of August 30, 2019. We are asking stockholders to approve the issuance
of shares of common stock issuable upon the exercise of certain warrants and conversion of certain
shares of Series B Preferred Stock held by Foris; see “Proposal 3 — Approval of the issuance of shares
of our common stock issuable upon the exercise of warrants and conversion of preferred stock issued
to Foris Ventures, LLC in accordance with Nasdaq Marketplace Rules 5635(b) and 5635(d)” for more
information. If Proposal 3 had been approved as of August 30, 2019, the number of shares beneficially
owned by John Doerr, and the Percent of Class, would have been 39,984,057 shares and approximately
31.9%, respectively.

(8) Shares beneficially owned by Dr. Duyk include 4,666 shares of common stock issuable upon exercise of

stock options that were exercisable within 60 days of August 30, 2019.

(9) Shares beneficially owned by Mr. Eykerman include (i) 666 restricted stock units, all of which were
unvested as of August 30, 2019, and (ii) 7,449 shares of common stock issuable upon exercise of stock
options that were exercisable within 60 days of August 30, 2019. Mr. Eykerman was appointed to the
Board on May 18, 2017 as the designee of DSM. Mr. Eykerman disclaims beneficial ownership of all
shares of Amyris common stock that are or may be beneficially owned by DSM or any of its affiliates.

(10) Mr. Goppelsroeder was appointed to the Board on November 2, 2017 as the designee of DSM.
Mr. Goppelsroeder does not beneficially own any shares of Amyris common stock directly and
disclaims beneficial ownership of all shares of Amyris common stock that are or may be beneficially
owned by DSM or any of its affiliates.

August 30, 2019. Dr. Kung was appointed to the Board on November 2, 2017 as the designee of Vivo.
Dr. Kung disclaims beneficial ownership over shares of Amyris common stock that are or may be
beneficially owned by Vivo except to the extent of his pecuniary interest therein.

(12) Shares beneficially owned by Mr. McCann include 750 shares of common stock issuable upon exercise

of stock options that were exercisable within 60 days of August 30, 2019.

(13) Shares beneficially owned by Mr. Mills include 3,466 shares of common stock issuable upon exercise of

stock options that were exercisable within 60 days of August 30, 2019.

(14) Shares beneficially owned by Ms. Piwnica include 10,265 of common stock issuable upon exercise of
stock options that were exercisable within 60 days of August 30, 2019. Ms. Piwnica is Director of
NAXOS S.A.R.L. (Switzerland), a consulting firm advising private investors, and was designated to
serve as our director by Naxyris S.A., an investment vehicle owned by Naxos Capital Partners SCA
Sicar. NAXOS S.A.R.L.
is affiliated with Naxos Capital Partners SCA Sicar.
Ms. Piwnica disclaims beneficial ownership of all shares of Amyris common stock that are or may be
beneficially owned by Naxyris S.A.

(Switzerland)

(15) Shares beneficially owned by Mr. Williams include 9,465 shares of common stock issuable upon

exercise of stock options that were exercisable within 60 days of August 30, 2019.

(16) Shares beneficially owned by Dr. Yang include 17,065 shares of common stock issuable upon exercise

of stock options that were exercisable within 60 days of August 30, 2019.

(17) Shares beneficially owned by Ms. Valiasek include (i) 138,599 restricted stock units, all of which were
unvested as of August 30, 2019, and (ii) 49,123 shares of common stock issuable upon exercise of stock
options that were exercisable within 60 days of August 30, 2019.

(18) Shares beneficially owned by Dr. Cherry include (i) 149,910 restricted stock units, all of which were
unvested as of August 30, 2019, and (ii) 81,650 shares of common stock issuable upon exercise of stock
options that were exercisable within 60 days of August 30, 2019. Dr. Cherry resigned from the
Company effective June 7, 2019. In connection with his termination of employment, Dr. Cherry agreed
to provide certain consulting services to the Company for a period of one year following the
termination of his employment with the Company (which term may be extended by the mutual
agreement of the parties). In exchange for, and as a result of, such services, Dr. Cherry’s outstanding
equity awards will continue to remain outstanding and vest in accordance with, and subject to, the
applicable equity plan and the relevant award agreements during the term of his consulting agreement
with the Company.

(19) Shares beneficially owned by Mr. Alvarez include (i) 285,000 restricted stock units, all of which were
unvested as of August 30, 2019, and (ii) 30,000 shares of common stock issuable upon exercise of stock
options that were exercisable within 60 days of August 30, 2019.

(20) Shares beneficially owned by Ms. Kelsey include (i) 73,666 restricted stock units, all of which were
unvested as of August 30, 2019, and (ii) 23,958 shares of common stock issuable upon exercise of stock
options that were exercisable within 60 days of August 30, 2019.

(21) Shares beneficially owned by all of our named executive officers and directors as a group include the

shares of common stock described in footnotes 6 through 20 above.

DELINQUENT SECTION 16(A) REPORTS

Section 16(a) of the Exchange Act requires our executive officers and directors, and any person or
entity who beneficially owns more than ten percent of a registered class of our common stock or other
equity securities, to file with the SEC certain reports of ownership and changes in ownership of our
securities. Based solely on review of such filed reports and written representations by our executive officers
and directors that no other reports were required, we believe that, during 2018, no reporting person failed
to file the forms required by Section 16(a) of the Exchange Act on a timely basis, except that Nicole Kelsey,
our General Counsel and Secretary, filed one Form 4 late with respect to the vesting of a restricted stock
unit award in August 2018.

EQUITY COMPENSATION PLAN INFORMATION

The following table shows certain information concerning our common stock reserved for issuance in
connection with our 2005 Stock Option/Stock Issuance Plan, our 2010 Equity Incentive Plan and our 2010
Employee Stock Purchase Plan as of December 31, 2018:

Number of
securities to be
issued upon
exercise of
outstanding
options, warrants
and rights

Weighted-average
exercise price of
outstanding
options, warrants
and rights

Number of
securities to be
issued upon vesting
of outstanding
restricted stock
units

Number of
securities remaining
available for future
issuance under
equity
compensation
plans(1)(2)

Plan Category

Equity compensation plans approved

by security holders. . . . . . . . . . . . .

5,390,270

$11.55

5,294,803

2,559,213

Equity compensation plans not

approved by security holders . . . . .

—

Total. . . . . . . . . . . . . . . . . . . . . . . .

5,390,270

$ —

$11.55

—

5,294,803

2,559,213

(1)

Includes 2,359,750 shares reserved for future issuance under our 2010 Equity Incentive Plan and
199,463 shares reserved for future issuance under our 2010 Employee Stock Purchase Plan. No shares
are reserved for future issuance under our 2005 Stock Option/Stock Issuance Plan other than shares
issuable upon exercise of equity awards outstanding under such plan.

(2) Effective January 1, 2019, the number of shares available for future issuance under our 2010 Equity
Incentive Plan increased by 3,828,241 shares pursuant to the automatic increase provision contained in
the 2010 Equity Incentive Plan and the number of shares available for future issuance under our 2010
Employee Stock Purchase Plan increased by 382,824 shares, in each case pursuant to automatic
increase provisions contained in the respective plans, as discussed in more detail below.

Our 2010 Equity Incentive Plan includes all shares of our common stock reserved for issuance under
our 2005 Stock Option/Stock Issuance Plan immediately prior to our initial public offering that were not
subject to outstanding grants as of the completion of such offering. In addition, any shares of our common
stock (i) issuable upon exercise of stock options granted under our 2005 Stock Option/Stock Issuance Plan
that cease to be subject to such options and (ii) issued under our 2005 Stock Option/Stock Issuance Plan
that are forfeited or repurchased by us at the original issue price, will become part of our 2010 Equity
Incentive Plan reserve.

The number of shares available for grant and issuance under our 2010 Equity Incentive Plan is
increased on January 1 of each year during the term of the plan by an amount equal to the lesser
of (1) five percent (5%) of our shares outstanding on the immediately preceding December 31 and (2) a
number of shares as may be determined by the Board or the Leadership Development and Compensation
Committee of the Board in their discretion. In addition, shares will again be available for grant and
issuance under our 2010 Equity Incentive Plan that are:

•

subject to issuance upon exercise of an option or stock appreciation right granted under our 2010
Equity Incentive Plan and that cease to be subject to such award for any reason other than the
award’s exercise;

•

subject to an award granted under our 2010 Equity Incentive Plan and that are subsequently
forfeited or repurchased by us at the original issue price;

surrendered pursuant to an exchange program; or

subject to an award granted under our 2010 Equity Incentive Plan that otherwise terminates
without shares being issued.

The number of shares reserved for issuance under our 2010 Employee Stock Purchase Plan is increased
on January 1 of each year during the term of the plan by an amount equal to the lesser of (1) one percent
(1%) of our shares outstanding on the immediately preceding December 31 and (2) a number of shares as
may be determined by the Board or the Leadership Development and Compensation Committee of the
Board in their discretion, provided that the aggregate number of shares issued over the term of our 2010
Employee Stock Purchase Plan shall not exceed 1,666,666 shares.

The following table provides the names, ages and offices of each of our current executive officers:

EXECUTIVE OFFICERS

Name

John Melo

Eduardo Alvarez

Kathleen Valiasek

Nicole Kelsey

Jonathan Wolter

John Melo

Age

Director, President and Chief Executive Officer

Position

Chief Operating Officer

Chief Business Officer

General Counsel and Secretary

Interim Chief Financial Officer

See above under “Proposal 1 — Election of Directors — Business Experience and Qualifications of

Directors.”

Eduardo Alvarez

Eduardo Alvarez has served as our Chief Operating Officer since October 2017. Mr. Alvarez has over
30 years of global operations experience both running and advising growth companies. Previously, he
served as Global Operations Strategy Leader for PricewaterhouseCoopers LLP (PwC). During his tenure,
Mr. Alvarez co-led the integration of his prior company, Booz & Company, following its acquisition by
PwC. In that role, he grew operations into a global practice with $1.5 billion in revenue and 4,000
employees. Mr. Alvarez’s assignments focused on delivering structural cost improvements while also driving
sustained revenue growth. His experience also includes roles at Booz Allen Hamilton, General Electric and
AT&T. Alvarez holds a Master of Business Administration from Harvard Business School, a Master of
Science in Mechanical Engineering in computer control and manufacturing from the University of
California, Berkeley, and a Bachelor of Science degree in mechanical engineering from the University of
Michigan. Mr. Alvarez is a board member of The Chicago Council of Global Affairs.

Kathleen Valiasek

Kathleen Valiasek has served as our Chief Business Officer since June 2019 and previously served as
our Chief Financial Officer from January 2017 to June 2019. Prior to joining us, Ms. Valiasek served as
Chief Executive Officer of a finance and strategic consulting firm she founded in 1994, and in this capacity
she worked closely with the senior management teams of fast-growing companies including start-ups,
venture-backed and Fortune 500 companies. Prior to this, she served in key venture capital, real estate
development and accounting roles. Ms. Valiasek holds a Bachelor of Business Administration degree from
the University of Massachusetts, Amherst.

Nicole Kelsey

Nicole Kelsey has served as our General Counsel and Secretary since August 2017. Her areas of
expertise range from U.S. securities laws, to international M&A and corporate governance. Prior to joining
Amyris, she served as General Counsel and Secretary of Criteo, a global leader in commerce marketing
based in Paris, for over three years. Prior to joining Criteo, Ms. Kelsey was the senior securities lawyer for
Medtronic, a global leader in medical technology; she served as head M&A attorney for CIT Group, Inc.;
was the general counsel of a private merchant bank; and worked for the international conglomerate
Vivendi. Before going in-house, Ms. Kelsey practiced with the law firms of White & Case and Willkie,
Farr & Gallagher, in Paris and New York. A Fulbright scholar, Ms. Kelsey holds a J.D. from Northwestern
University and a B.A. from The Ohio State University.

Jonathan Wolter

controller with KPMG Consulting, where he also served as CFO of the firm’s Latin America operations.
Previously, Mr. Wolter held CFO and controller roles with public and private companies and also served as
senior audit manager with Arthur Andersen & Co. His experience spans the biotechnology, technology,
electronics, manufacturing, engineering and banking sectors.

EXECUTIVE COMPENSATION

Compensation Discussion and Analysis

The following discussion describes and analyzes the compensation policies, arrangements and decisions
for our named executive officers in 2018 and should be read in conjunction with the compensation tables
contained elsewhere in this Proxy Statement. We believe our existing compensation policies, arrangements
and decisions are consistent with our compensation philosophy and objectives discussed below and align
the interests of our named executive officers with our short-term and long-term business objectives. During
2018, our named executive officers were:

•

John Melo, our President and Chief Executive Officer (our “CEO”)

Kathleen Valiasek, our Chief Financial Officer (Ms. Valiasek assumed the newly created role of
Chief Business Officer to lead the CBD business and other business development efforts while
continuing to lead the financing and investor relation activities effective June 3, 2019.)

Joel Cherry, our President, Research and Development (Dr. Cherry resigned from the Company
effective June 7, 2019.)

Eduardo Alvarez, our Chief Operating Officer

Nicole Kelsey, our General Counsel and Secretary

Compensation Philosophy and Objectives and Elements of Compensation

The primary objectives of our executive compensation program in 2018 were to:

•

Attract, retain, and motivate highly talented employees that are key to our success;

Reinforce our core values and foster a sense of ownership, urgency and entrepreneurial spirit;

Link compensation to individual, team, and company performance (as appropriate by employee
level);

Emphasize performance-based compensation for individuals who can most directly impact
stockholder value; and

Provide exceptional pay for delivering exceptional results.

Our success depends, among other things, on attracting and retaining executive officers with experience
and skills in a number of different areas as we continue to drive improvements in our technology platform
and production process, pursue and establish key commercial relationships, develop and commercialize
products and establish a reliable supply chain and manufacturing organization.

Our business continues to be in an early stage of development, with cash management being one key
consideration for our strategy and operations. Accordingly, for 2018, we intended to provide a competitive
compensation program that would enable us to attract and retain the top executives and employees
necessary to develop our business, while being prudent in the management of our cash and equity. Based on
this approach, we continued to aim to balance and reward annual and long-term performance with a total
compensation package that included a mix of both cash and equity. Our compensation program was
intended to align the interests of our executive officers, key employees and stockholders and to drive the
creation of stockholder value by providing long-term incentives through equity-based awards.

Our intent and philosophy in designing compensation packages at the time of hiring of new executives
is based on providing compensation that we believe is sufficient to enable us to attract the necessary talent
to grow our business, within prudent limitations as discussed above. Compensation of our executive officers
after the initial period following their hiring is influenced by the amounts of compensation that we initially
agreed to pay them, as well as by our evaluation of their subsequent performance, changes in their levels of
responsibility, retention considerations, prevailing market conditions, our financial condition and prospects,
and our attempt to maintain an appropriate level of internal pay parity in the compensation of existing
executive officers relative to the compensation paid to more recently hired executives.

We compensate our executive officers with a combination of salaries, cash bonuses and equity awards.
We believe this combination of cash and equity compensation, subject to strategic allocation among such
components, is largely consistent with the forms of compensation provided by other companies with which
we compete for executive talent, and, as such, matches the expectations of our executive officers and the
market for executive talent. We also believe that this combination provides appropriate incentive levels to
retain our executives, reward them for performance in the short term and induce them to contribute to the
creation of value in Amyris over the long term. We view the different components of our executive
compensation program as distinct, each serving particular functions in furthering our compensation
philosophy and objectives, and, together, providing a holistic approach to achieving such philosophy and
objectives.

Base Salary. We believe that we must maintain base salary levels that are sufficiently competitive to
position us to attract and retain the executive officers we need and that it is important for our executive
officers to perceive that over time they will continue to have the opportunity to earn a salary that they
regard as competitive. The Leadership Development and Compensation Committee of our Board (the
“LDCC” or the “Committee”) reviews and adjusts, as appropriate, the base salaries of our executive
officers on an annual basis, and makes decisions with respect to the base salaries of new executives at the
time of hire. In making such determinations, the Committee considers several factors, including our overall
financial performance, the individual performance of the executive officer in question (including, for
executives other than our CEO, the recommendation of our CEO based on a performance evaluation of the
executive officer in question), the executive officer’s potential to contribute to our annual and longer-term
strategic goals, the executive officer’s scope of responsibilities, qualifications and experience, competitive
market practices for base salary, prevailing market conditions and internal pay parity.

Cash Bonuses. We believe the ability to earn cash bonuses should provide incentives to our executive
officers to effectively pursue goals established by our Board and should be regarded by our executive
officers as appropriately rewarding effective performance against these goals. For 2018, the LDCC adopted
a cash bonus plan for our executive officers, the details of which are described below under “2018
Compensation.” The 2018 cash bonus plan included company performance goals and individual
performance goals and was structured to motivate our executive officers to achieve our short-term financial
and operational goals and to reward exceptional company and individual performance. In particular, our
2018 cash bonus plan was designed to provide incentives to our executive officers to achieve 2018 company
financial and operational targets on a quarterly and annual basis, together with various key individual
operational objectives that were considered for annual performance achievement. In general, target bonuses
for our executive officers are initially set in their offer letters based on similar factors to those described
above with respect to the determination of base salary. For subsequent years, target bonuses for our
executive officers may be adjusted by the LDCC based on various factors, including any modifications to
base salary, competitive market practices and the other considerations described above with respect to
adjustments in base salary. Certain bonuses paid to our executive officers under our 2018 cash bonus plan
were granted in the discretion of the Committee notwithstanding the Company’s failure to meet stated
performance goals. See “2018 Compensation — Cash Bonuses” below for more information.

Equity Awards. Our equity awards are designed to be sufficiently competitive to allow us to attract
and retain talented and experienced executives. In 2018, we granted both stock option and restricted stock
unit (“RSU”) awards to our executive officers. Stock option awards for executive officers are granted with
an exercise price equal to the fair market value of our common stock on the date of grant; accordingly, such
stock option awards will have value to our executive officers only if the market price of our common stock
increases after the date of grant. RSU awards represent the right to receive full-value shares of our common
stock without payment of any exercise or purchase price. In 2018 we continued a practice that began in
2016 to place a greater emphasis on RSU awards, as compared to stock options, to increase the perceived
value of equity awards granted to our executive officers. The relative weighting between the stock option
and RSU awards granted to our executive officers is based on the LDCC’s review of market practices. In
2018, the LDCC approved special equity awards to our CEO consisting of a stock option subject to
performance-based vesting conditions and RSUs with time-based vesting, as described in more detail below
under “2018 Compensation — Equity Awards — 2018 CEO Equity Awards.”

to the award after one year, and monthly thereafter, subject to continued service through each vesting date.
Our RSU awards have generally been granted with three-year vesting schedules, vesting as to 1/3rd of
the units subject to the award annually, subject to continued service through each vesting date. We believe
such vesting schedules are generally consistent with the option and RSU award granting practices of our
peer group companies. In 2018, we granted stock option and/or RSU awards with non-standard vesting
terms to certain of our executive officers, including our CEO, the details of which are described below
under “2018 Compensation — Equity Awards.”

We grant equity awards to our executive officers in connection with their hiring, or, as applicable, their
promotion from other roles at the Company. The size of initial equity awards is determined based on the
executive’s position with us and takes into consideration the executive’s base salary and other compensation
as well as an analysis of the grant and compensation practices of our peer group companies in connection
with establishing our overall compensation policies. The initial equity awards are generally intended to
provide the executive with an incentive to build value in the Company over an extended period of time,
while remaining consistent with our overall compensation philosophy. Insofar as we have to date incurred
operating losses and consumed substantial amounts of cash in our operations, and to compensate for cash
salaries and cash bonus opportunities that were, in certain cases, lower than those offered by competing
employers, we have sought to attract executives to join us by granting equity awards that would have the
potential to provide significant value if we are successful.

We grant additional equity awards in recognition of commendable performance, in connection with
significant changes in responsibilities, and/or in order to better ensure appropriate retention and incentive
opportunities from time to time. Further, equity awards are a component of the annual compensation
package of our executive officers. In 2018, the LDCC granted equity awards based on input from
management regarding performance, to satisfy our retention objectives and other considerations. In
approving such awards, the LDCC took into account various factors, including the responsibilities, past
performance and anticipated future contribution of the executive officer, his or her overall compensation
package, his or her existing equity holdings and practice at our peer group companies.

Role of Stockholder Say-on-Pay Votes. At our 2011, 2014 and 2017 annual meetings of stockholders,
our stockholders voted, on an advisory basis, on the compensation of our named executive officers
(commonly referred to as a “stockholder say-on-pay vote”). A majority of the votes cast were voted in favor
of the non-binding advisory resolutions approving the compensation of our named executive officers as
summarized in our 2011, 2014 and 2017 proxy statements. In 2017, 99% of the votes cast on the stockholder
say-on-pay proposal approved, on a non-binding advisory basis, the compensation of our named executive
officers as summarized in our 2017 proxy statement. The LDCC believes that this affirms our stockholders’
support of our approach to executive compensation, and, accordingly, did not materially change its
approach to executive compensation in 2018 and does not intend to do so in 2019. In addition, in 2017 our
stockholders approved, and our Board subsequently adopted, a three-year interval for conducting future
stockholder say-on-pay votes. Accordingly, our stockholders will again vote, on an advisory basis, on the
compensation of our named executive officers at our 2020 annual meeting of stockholders.

Compensation Policies and Practices as They Relate to Risk Management

The LDCC has determined, through discussions with management and Compensia at Committee
meetings held in February 2018 and November 2018, that our policies and practices of compensating our
employees, including our executive officers, are not reasonably likely to have a material risk to us. The
assessments conducted by the Committee focused on the key terms of our bonus plans and equity
compensation programs in 2018, and our plans for such programs in 2019. Among other things, the
Committee focused on whether our compensation programs created incentives for risk-taking behavior and
whether existing risk mitigation features and policies were sufficient in light of the overall structure and
composition of our compensation programs. Among other things, the Committee considered the following
aspects of our overall compensation program:

•

Our base salaries are generally high enough to provide our employees with sufficient income so
that they are not dependent on bonus income to meet their basic cost of living.

Cash bonus targets are typically 10 – 20% of an employee’s base salary (40 – 100% for our

•

executive officers), which we believe provides balanced incentives for performance, but does not
encourage excessive risk taking to achieve such goals. For 2019, most employees were removed
from participation in the Company’s 2019 cash bonus plan and received an increase in their base
salary in consideration of such removal. Executive officers (including our named executive
officers) will continue to participate in the Company’s 2019 cash bonus plan.

emphasized

For key employees, our 2018 cash bonus plan (as discussed in more detail below under “2018
Compensation — Cash Bonuses”)
individual
performance objectives and provided for a maximum total bonus funding available for payout of
165% of target funding, with payouts ranging from 0% to 255% of an individual’s annual target
bonus depending on company and individual performance. Our 2019 cash bonus plan applies only
to certain key employees (including our executive officers) and provides for a maximum total
bonus funding available for payout of 150% of target funding, with payouts ranging from 0% to
225% of an individual’s annual target bonus depending on company and individual performance.

performance

company

over

Generally, we do not provide commission or similar compensation programs to our employees.
However, starting in 2016 we implemented a cash incentive plan for certain employees involved in
sales activities. In 2018, we implemented additional incentive plans for certain employees involved
in business development activity. The incentive plans in 2018 for these employees provided what
the employee’s cash
we viewed as moderate leverage,
compensation was base salary and approximately 30 – 40% was commission-based, depending on
the nature of the role.
For our executive officers, in 2018 we targeted the 50th percentile of our competitive market for
total cash compensation and between the 50th and 75th percentiles of our competitive market
(subject to company performance and affordability within dilution constraints) for equity
compensation, which typically was to vest over three to four years, providing our executives with
significant incentives for our longer-term success. For 2019, we are maintaining the same targets
as 2018 for total cash and equity compensation for our executive officers.

in which approximately 60 – 70% of

Based on these considerations, the Committee determined that our compensation programs, including
our executive and non-executive compensation programs, provide an appropriate balance of incentives and
do not encourage our executives or other employees to take excessive risks or otherwise create risks that are
likely to have a material adverse effect on us.

In connection with an annual

Role of Compensation Consultant.

review of our executive
compensation program for 2018, the LDCC retained Compensia, a national compensation consulting firm,
to provide advice and guidance on our executive compensation policies and practices and relevant
the executive compensation practices of similarly situated companies. In 2018,
information about
Compensia assisted in the preparation of materials for executive compensation proposals in advance of
Committee meetings, including 2018 compensation levels for our executive officers and the design of our
cash bonus, equity, severance and change of control programs and other executive benefit programs.
Compensia also reviewed and advised the LDCC on materials relating to executive compensation prepared
by management for Committee consideration. In addition, in the fourth quarter of 2017, Compensia
assisted the LDCC in developing our compensation peer group for 2018 (as discussed below). The LDCC
retained Compensia again in the fourth quarter of 2018 to provide assistance with respect to our 2019
compensation planning, including updates to our compensation peer group.

Compensia, under the direction of the LDCC, may continue to periodically conduct a review of the
competitiveness of our executive compensation programs, including base salaries, cash bonus opportunities,
equity awards and other executive benefits, by analyzing the compensation practices of companies in our
compensation peer group, as well as data from third-party compensation surveys. Generally, the LDCC uses
the results of such analyses to assess the competitiveness of our executive officers’ total compensation, and
to determine whether each component of such total compensation is properly aligned with reasonable and
responsible practices among our peer companies.

The LDCC also retained Compensia for assistance in reviewing and making recommendations to our
Board regarding the compensation program for our non-employee directors when it was originally adopted
in late 2010 and again when such program was subsequently amended in December 2015 and
November 2016, and to provide market data and materials to the Committee.

In September 2017 and November 2018, the LDCC reviewed the independence of Compensia under
applicable compensation consultant independence rules and standards and determined that Compensia had
no conflict of interest with Amyris.

Compensation Decision Process

Under the charter of the LDCC, our Board has delegated to the Committee the authority and
responsibility to discharge the responsibilities of the Board relating to the compensation of our executive
officers. This includes, among other things, review and approval of the compensation of our executive
officers and of
the terms of any compensation agreements with our executive officers. For more
information regarding the functions and composition of the LDCC, please refer to “Proposal 1 — Election
of Directors — Committees of the Board” above.

In general, the LDCC is responsible for the design, implementation and oversight of our executive
compensation program. In accordance with its charter, the Committee determines the annual compensation
of our CEO and other executive officers and reports its compensation decisions to our Board. The
Committee also administers our equity compensation plans, including our 2010 Equity Incentive Plan (the
“2010 EIP”) and 2010 Employee Stock Purchase Plan. Generally, our Human Resources, Finance and
Legal departments work with our Chief Executive Officer to design and develop new compensation
programs applicable to our executive officers and non-employee directors, to recommend changes to
existing compensation programs, to recommend financial and other performance targets to be achieved
under those programs, to prepare analyses of financial data, to prepare peer compensation comparisons
and other committee briefing materials, and to implement the decisions of the Committee. Members of
these departments and our Chief Executive Officer also meet separately with Compensia to convey
information on proposals that management may make to the LDCC, as well as to allow Compensia to
collect information about Amyris to develop its recommendations. In addition, our Chief Executive Officer
conducts reviews of the performance and compensation of our other executive officers, and based on these
reviews and input from Compensia and our Human Resources department, makes recommendations
regarding compensation for such executive officers directly to the Committee. For our CEO’s compensation,
Compensia reviews relevant market data with the Chair of the LDCC, as well as the performance of our
CEO, and based on such review makes a recommendation regarding our CEO’s compensation, which is
then presented to the LDCC. None of our executive officers participated in the determinations or
deliberations of the LDCC regarding the amount of any component of his or her own 2018 compensation.

Use of Competitive Data. To monitor the competitiveness of our executive officers’ compensation, in
November 2017 the LDCC approved a compensation peer group (the “Peer Group”) to be used in
connection with its 2018 compensation discussions that analyzed the compensation of executive officers in
comparable positions at similarly-situated companies. The data gathered from the Peer Group was used as a
reference in setting executive pay levels (including cash and equity compensation), non-employee director
compensation, incentive plan practices, severance and change-in-control practices, equity utilization and
pay/performance alignment. The Peer Group was composed of a cross-section of publicly-traded,
U.S.-based companies of similar size to us (based on revenue, enterprise value, number of employees and
R&D expenditures) from related industries (biotechnology, oil, gas and consumable fuels, chemicals, food
products, personal products and household products). Based on these criteria, the following companies
were included in the Peer Group approved by the LDCC for use in assessing the market position of our
executive compensation for 2018:

•

American Vanguard

Balchem

BioAmber

Codexis

Innospec

Intrexon

2018 Peer Group

•

Kraton Performance Polymers

Landec

Renewable Energy Group

Rentech

Senomyx

TerraVia Holdings (formerly Solazyme)

Yield10 Bioscience (formerly Metabolix)

In November 2018, the LDCC conducted a review of the Peer Group for 2019. Similar to our
approach for developing the 2018 Peer Group, we identified potential peers by screening publicly-traded,
U.S.-based companies of similar size to us (based on revenue, enterprise value, number of employees and
R&D expenditures) from related industries (biotechnology and pharmaceuticals, life sciences tools and
services, oil, gas and consumable fuels, chemicals, food products, personal products and household
products). Based on such analysis, the LDCC removed BioAmber, Kraton, Renewable Energy Group,
Rentech, Senomyx, TerraVia Holdings and Yield10 Bioscience from the Peer Group for 2019 due to their
financial profile, relevance and/or recent acquisition, and added Calyxt, Cambrex, e.l.f. Beauty, Hawkins,
Innophos Holdings, International Flavors & Fragances, Medifast, Phibro Animal Health, Sensient
Technologies, Trecora Resources and USANA Health Sciences.

In addition to reviewing the compensation practices of the Peer Group, the LDCC looks to the
collective experience and judgment of its members and advisors, as well as relevant industry survey data, in
determining total compensation and the various compensation components provided to our executive
officers. While the LDCC does not believe that the Peer Group data is appropriate as a stand-alone tool for
setting executive compensation due to the unique nature of our business, it believes that this information is
a valuable reference source during its decision-making process.

Target Compensation Levels. For 2018 the LDCC generally targeted the 50th percentile of our
competitive market for total cash compensation (base salary and target cash bonus), as determined based
on the Peer Group, supplemented by data from relevant industry surveys. The Committee chose the 50th
percentile for total cash compensation in part because we are still
in the early stages of product
development and therefore need to conserve our cash while we ramp up our operations. Equity has been a
critical and prominent component in our overall compensation package and we believe that it will remain
an important tool for attracting, retaining and motivating our key talent by providing an opportunity for
wealth creation as a result of our long-term success, particularly while we are growing our business. As a
result, for 2018 the LDCC targeted equity compensation levels between the 50th and the 75th percentile
(subject to company performance and affordability within dilution constraints) of our competitive market
for equity compensation based on the Peer Group, supplemented by data from relevant industry surveys,
and taking into consideration the LDCC approved targeted annual burn rate.

To this end, the LDCC approved annual equity awards for Ms. Valiasek, Dr. Cherry and Ms. Kelsey in
May 2018 based primarily on the foregoing strategy. In addition, in April 2018 the LDCC approved special
equity awards for our CEO, the details of which are described below under “2018 Compensation — Equity
Awards — 2018 CEO Equity Awards” and in May 2018 the LDCC approved an equity award for
Mr. Alvarez of 250,000 RSUs in accordance with the terms of his employment offer letter with the
Company entered into in October 2017. Each of such awards was conditioned on the approval by our
stockholders of certain amendments to the 2010 EIP to, among other things,
increase the annual
thereunder, which amendments were approved by our stockholders in
per-participant award limit
May 2018. In determining the size of the annual equity grants and the 2018 CEO Equity Awards, the
LDCC considered the retention value of existing awards held by our named executive officers (taking into
account option exercise prices and the prevailing market value of our common stock), the executives’
overall compensation packages, practice at peer companies and the responsibilities, performance,
anticipated future contributions and retention risk of our named executive officers. In 2018, the equity
awards granted to certain of our executive officers were larger than in prior years, in part due to the low
retention value of existing awards held by such officers.

For 2019, we expect to continue to target the same percentiles for execution compensation as we have
in 2018, as determined based on the Peer Group, supplemented by data from relevant industry surveys,
which approach the LDCC approved in November 2018.

2018 Compensation

Background.

In designing the compensation program and making decisions for our executive officers
for 2018, the Committee sought to balance achievement of critical operational goals with retention of key
personnel, including our executive officers. Accordingly, the Committee focused in particular on providing a
strong equity compensation program in order to provide strong retention incentives through challenging
periods. It also focused on cash management in setting target total cash compensation (and associated
salary and bonus target levels) for our executive officers. Another key theme for 2018 was establishing
strong incentives to drive our performance, including continued emphasis on company performance goals
over individual goals in the 2018 cash bonus plan and on equity compensation for longer-term upside
potential and sharing in company growth.

Base Salaries.

In February 2018, the LDCC reviewed the base salaries, bonus targets and target total
cash compensation of our executive officers against the Peer Group, as supplemented by relevant industry
survey data, and, as a result of such analysis, as well as consideration of the factors described above under
“Compensation Philosophy and Objectives and Elements of Compensation — Base Salary,” determined
that no base salary adjustments were needed to ensure competitive base salaries for our executive officers.

Cash Bonuses. The LDCC adopted a 2018 cash bonus plan for our executive officers in
February 2018. Under the plan, our executive officers were eligible for bonuses based on the achievement of
company metrics for each quarter in 2018, with a portion of their target bonus allocated to annual company
and individual performance. The 2018 cash bonus plan was intended to provide a balanced focus on both
our long-term strategic goals and shorter-term quarterly operational goals. The 2018 cash bonus plan
provided for funding and payout of cash bonus awards based on our quarterly and annual performance
during 2018 under pre-established metrics set by the LDCC for each quarter and for the year. Payouts, if
any, under the 2018 cash bonus plan were made following a review of our results and performance each
quarter and, for the annual component, a review occurred in February 2019 with respect to the annual
performance of the Company as well as each individual’s performance. The 2018 cash bonus plan provided
for a 50% weighting for quarterly achievement (with each quarter worth 12.5% of the total bonus fund for
the year) and 50% for full year 2018 achievement.

The total funding possible under the 2018 cash bonus plan was based on a cash value (or the “target
bonus fund”) determined by the executive officers’ target bonus levels. Target bonus levels for our executive
officers in 2018 varied by individual, but were generally set between 40% and 100% of their annual base
salary. In February and May 2018, the LDCC reviewed our executive officers’ bonus targets as part of its
review of target total cash compensation for similar roles among executive officers at companies in the Peer
Group, as supplemented by relevant industry survey data, and, as a result of such analysis, as well as
the factors described above under “Compensation Philosophy and Objectives and
consideration of
Elements of Compensation — Cash Bonuses,” approved increases to the target bonus level for one of our
executive officers, Ms. Valiasek, from 40% to 50% of annual base salary effective January 1, 2018 and from
50% to 80% of annual base salary effective April 1, 2018.

The quarterly and annual funding of the 2018 cash bonus plan was based on achievement of the
following company performance metrics for the applicable quarter and full year 2018, respectively (as
determined by the LDCC and, in the case of quarterly funding, as applicable for the quarter based on our
operating plan): GAAP revenue (weighted 50%), gross margin (weighted 50%) and earnings before interest,
tax, depreciation and amortization (“EBITDA”) (providing an additional valuation metric at -/+20% for the
annual bonus funding). For each quarterly period and for the annual period under the 2018 cash bonus
plan, “threshold,” “target” and “superior” performance levels were set for each applicable performance
metric, which performance levels were intended to capture the relative difficulty of achievement of that
metric.

threshold level, 70% funding would occur. For a weighted average achievement between the funding
threshold level and “target” level, a pro rata increase in funding would occur up to 100% of the target bonus
fund allocated to such period. For weighted average achievement above the target level, an increase in
funding of 1.67% of the target bonus fund for every 1% above target performance would occur up to 150%
of the target bonus fund for the applicable bonus plan period, provided that the annual bonus funding
would be subject to further adjustment based on the achievement of an annual EBITDA target, which
could increase the annual bonus funding up to 180% of target.

Any payouts for the quarterly bonus periods would be the same as the funded level (provided the
recipient meets eligibility requirements), subject to the final discretion of the Committee. Payouts for the
annual bonus period would be made from the aggregate funded amount in the discretion of the Committee
based on company and individual performance, and could range from 0% to 200% of an individual’s funded
amount for the annual bonus period. The Committee chose to emphasize company performance goals for
the quarterly and annual bonus plan periods given the critical importance of our short term strategic goals,
but also to retain reasonable incentives and rewards for exceptional individual performance, recognizing the
value of such incentives and rewards to our operational performance and to individual retention. For 2018,
the LDCC set the following target bonus levels for our named executive officers:

Name

John Melo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Kathleen Valiasek(1)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Joel Cherry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Eduardo Alvarez . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Nicole Kelsey . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Target Bonus
($)

600,000
304,500
187,500
400,000
158,000

(1) Ms. Valiasek’s target bonus level was increased from 40% to 50% of annual base salary effective
January 1, 2018 and from 50% to 80% of annual base salary effective April 1, 2018. Ms. Valiasek
assumed the newly created role of Chief Business Officer to lead the CBD business and other business
development efforts while continuing to lead the financing and investor relation activities effective
June 3, 2019.

Based on the foregoing bonus plan structure, individual bonuses were awarded each quarter based on
the LDCC’s assessment of company achievement, and with respect to the annual bonus, the LDCC’s
assessment of company achievement as well as each executive officer’s contributions to such achievement,
his or her progress toward achieving his or her individual goals, and his or her demonstrating our core
values. Actual payment of any bonuses with respect to 2018 remained subject to the final discretion of the
Committee. In 2018, the Committee exercised its discretion under the bonus plan to pay awards to certain
of our named executive officers with respect
to the third quarter and annual period of 2018,
notwithstanding the Company’s failure to achieve the funding threshold level under the bonus plan for such
periods. The Committee determined that such bonus awards were consistent with the spirit of the bonus
plan and were appropriate in light of the Company’s progress towards its goals and objectives.

Company Performance Goals. Company performance during 2018 was measured and weighted
against quarterly and annual targets established for GAAP revenue and gross margin and an annual target
established for EBITDA. The quarterly and annual weighting and achievement for each applicable metric
are described below.

These targets were initially discussed with our Board and the LDCC in the second half of 2017. The
annual and first quarter targets were adopted in February 2018, and the second, third and fourth quarter
targets were adopted at subsequent meetings of the Committee during 2018. The applicable targets were
discussed and evaluated each quarter in 2018 and in February 2019 based on quarterly and annual
performance (in February 2019, the LDCC discussed and evaluated the fourth quarter as well as the full
year 2018 results) and continued development of our business and operating plans for 2018 and beyond. In
November 2018, the Committee modified the annual target for GAAP revenue based on a change to our
2018 operating plan. Achievement levels were determined in the discretion of the LDCC following each
period under the 2018 cash bonus plan.

Degree of Difficulty in Achieving Performance Goals. The LDCC considered the likelihood of
achievement when recommending and approving, respectively, the Company and individual performance
goals and bonus plan structures for each of the 2018 cash bonus plan periods, but it did not undertake a
detailed statistical analysis of the difficulty of achievement of each measure. For 2018, the Committee
considered the 70% weighted average achievement level to be attainable with normal effort, 100% to be
challenging but achievable with significant effort, requiring circumstances to align as predicted, and any
amounts in excess of 100% to be difficult to achieve, requiring additional sources of revenue, breakthroughs
in technology, manufacturing operations, process development or business development, and exceptional
levels of effort on the part of the executive team, as well as favorable external conditions.

2018 Quarterly and Annual Bonus Plan Funding and Award Decisions.

In each of May 2018,
August 2018, November 2018 and February 2019, the LDCC determined that our quarterly and annual
performance goals were achieved as follows:

Company Performance Goal

Weighted
Achievement
Level

Funding
Level

Weight

GAAP Revenue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

50%

62%

Gross Margin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Total Q1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

50%

51%
100.0% 113%

121.7%

Q2
GAAP Revenue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Gross Margin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Total Q2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Q3
GAAP Revenue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Gross Margin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Total Q3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

50%
50%
100.0%

0%
65%
65%

0%
0%
0%

75.0%(1)

Q4
GAAP Revenue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Gross Margin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Total Q4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

50%
50%

43%
57%
100.0% 100%

100.0%

ANNUAL
50%
GAAP Revenue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Gross Margin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
50%
EBITDA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . +/-20%
100.0%
Total Annual

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

0%
62%
-20%
50%

71.2%(2)

(1)

(2)

In November 2018, the LDCC approved bonus funding for the third quarter of 2018 at 75% of target
for all eligible employees, except our CEO, notwithstanding the Company’s failure to meet the funding
threshold for such quarter.

In February 2019, the LDCC approved bonus funding for the annual period of 2018 at 71.2% of target
for all eligible employees, notwithstanding the Company’s failure to meet the funding threshold for
such period.

March 31, 2018, June 30, 2018 and September 30, 2018 (the “2018 10-Qs”), respectively. We have restated
such financial statements in our Annual Report on Form 10-K for the fiscal year ended December 31, 2018.
The LDCC is in the process of reviewing its determinations regarding the achievement of our quarterly and
annual performance goals under the 2018 cash bonus plan in light of such restatement.

Individual Performance Goals.

For the annual portion of the 2018 cash bonus plan tied to individual performance, the Committee

considered several factors, including the following:

•

For our CEO, the achievement of growing GAAP revenue, gross margin and EBITDA, improving
employee engagement, maintaining a safe work environment, executive leadership and living our
values.

For Ms. Valiasek, the achievement of meeting quarterly financial targets, developing a corporate
tax strategy and debt reduction plan,
improving finance department performance, executive
leadership and living our values.

For Dr. Cherry, the achievement of assisting in developing new technology projects, managing
operating expenses, growing our technology leadership, improving R&D employee engagement,
meeting technical targets, executive leadership and living our values.

For Mr. Alvarez, the achievement of meeting our production and fulfillment plan, managing
costs, overseeing construction of a new production facility in Brazil, taking on additional
operational roles and accountabilities, executive leadership and living our values.

For Ms. Kelsey, the achievement of managing legal elements of global expansion, developing a
corporate intellectual property policy, improving board organization and financial disclosure
processes, improving legal department performance, executive leadership and living our values.

The Committee considered a variety of factors in determining, in its discretion, to award payouts
under the 2018 cash bonus plan. In addition to the levels of company achievement (for the quarterly and
annual portions) and individual performance (for the annual portion) categories, the Committee considered
our cash needs as well as the level of performance of each named executive officer in achieving company
results and their respective assigned individual goals. Based on the foregoing, and taking into account the
factors described above, the Committee approved the following cash bonus awards under the 2018 cash
bonus plan:

Name

2018
Cumulative
Quarterly Bonus
Payouts
($)

2018
Annual
Portion Bonus
Payout
($)

2018
Aggregate
Annual and
Quarterly Bonus
Payouts
($)

John Melo . . . . . . . . . . . . . . . .
Kathleen Valiasek . . . . . . . . . . .
Joel Cherry . . . . . . . . . . . . . . . .
Eduardo Alvarez . . . . . . . . . . . .
Nicole Kelsey . . . . . . . . . . . . . .

166,275
105,447
69,542
148,350
58,601

192,240
97,562
73,425
156,640
50,624

358,515
203,009
142,967
304,990
109,225

Annual Bonus
Target
($)

600,000
304,500
187,500
400,000
158,000

2018
Actual
Bonus Earned
as a % of
Target Bonus

60
67
76
76
69

We believe that the payment of these awards was appropriate because the 2018 cash bonus plan
appropriately held our named executive officers accountable for achievement of company and individual
goals, and the payouts were reasonable and appropriate in light of our progress towards our business
objectives.

In April 2019, we announced that we would restate our interim condensed consolidated financial
statements for the quarterly and year-to-date periods ended March 31, 2018, June 30, 2018 and
September 30, 2018, included in the 2018 10-Qs. We have restated such financial statements in our Annual
Report on Form 10-K for the fiscal year ended December 31, 2018. The LDCC is in the process of
reviewing its determinations regarding the awards paid to our named executive officers under the 2018 cash
bonus plan in light of such restatement.

In addition to the payments under our 2018 cash bonus plan noted above, in October 2018 the
Company paid a discretionary cash retention bonus to Dr. Cherry in the amount of $50,000, which bonus
payment was ratified and approved by the LDCC in February 2019.

Equity Awards.

In May 2018, the LDCC approved annual equity awards for Ms. Valiasek, Dr. Cherry
and Ms. Kelsey (the “Focal Awards”), as well as an equity award for Mr. Alvarez of 250,000 RSUs in
accordance with the terms of his employment offer letter with the Company entered into in October 2017
(the “Alvarez 2018 Award”). In addition, in April 2018 the LDCC approved special equity awards for our
CEO, as described below (the “CEO Equity Awards”). The Focal Awards, the Alvarez 2018 Award and the
CEO Equity Awards consisted of the stock option and RSU awards set forth in the “Grants of Plan-Based
Awards in 2018” table below. Each of such awards was conditioned on the approval by our stockholders of
certain amendments to the 2010 EIP to, among other things, increase the annual per-participant award limit
thereunder, which amendments were approved by our stockholders in May 2018.

With respect to the Focal Awards, the LDCC determined the allocation of equity awards between stock
options and RSUs after consultation with Compensia, in evaluating the practices of our competitive market
(including the Peer Group) and in consultation with management, taking into consideration, among other
things, the appropriate balance between rewarding previous performance, retention objectives, upside value
potential tied to our and the executive officer’s future performance and the mix of the executive officer’s
current equity holdings. The size of the Focal Awards varied among the applicable named executive officers
based on the value of unvested equity awards already held by him or her, his or her relative contributions
during 2017 and anticipated levels of responsibility for key corporate objectives in 2018. Notwithstanding
our target of between the 50th and the 75th percentile of our competitive market for equity compensation,
the value of the Focal Awards was above the 75th percentile of our competitive market in consideration of
the low retention value of existing awards held by such officers.

The allocation and size of the Alvarez 2018 Award was determined by his employment offer letter with
the Company entered into in October 2017. Please see “2018 CEO Equity Awards” below for details
regarding the determination of the allocation and size of the CEO Equity Awards.

Please see the “Grants of Plan-Based Awards in 2018” table below for more information regarding the
award types and sizes, grant dates, exercise prices and vesting schedules of the Focal Awards, the Alvarez
2018 Award and the CEO Equity Awards.

2018 CEO Equity Awards

Because of the direct relationship between the value of our equity awards and the fair market value of
our common stock, and in order to incentivize our CEO in a manner that aligns his interests with our
long-term strategic direction and the interests of our stockholders and reduces the possibility of business
decisions that favor short-term results at the expense of long-term value creation, in April 2018 the LDCC
approved, with the support of the Board, a grant to our CEO of (i) an option to purchase 3,250,000 shares
of our common stock, such award being subject to performance-based vesting conditions as described
below (the “CEO Performance Option”), and (ii) 700,000 RSUs with the terms described below (the “CEO
RSU” and together with the CEO Performance Option, the “CEO Equity Awards”). The grant of the CEO
Equity Awards was contingent upon approval by our stockholders of both the CEO Equity Awards and
certain amendments to the 2010 EIP to, among other things, increase the annual per-participant award limit
thereunder, which approvals were obtained at our 2018 annual meeting of stockholders held on May 22,
2018. In accordance with our policy regarding equity award grant dates, the CEO Equity Awards were
granted on May 29, 2018, the first business day of the week following the week in which such awards were
approved, with the exercise price of the CEO Performance Option being set at $5.08 per share, the closing
price of our common stock on Nasdaq on such date, in accordance with the terms of the 2010 EIP.

CEO Performance Option. The CEO Performance Option is a performance-based nonqualified stock
option and therefore the CEO will receive compensation from such stock option only to the extent that the
Company achieves the applicable performance milestones.

provided: (i) the Board or the LDCC certify that both the EBITDA Milestone and the Stock Price
Milestone (collectively, the “Milestones”) for such Tranche have been met and (ii) Mr. Melo remains our
CEO on the applicable vesting date. Any Milestone may be met before, at or after the applicable Earliest
Vesting Date for a Tranche provided that the Milestone is met during its applicable Measurement Period.
The EBITDA Measurement Period starts January 1, 2018 and ends December 31, 2021. The Stock Price
Measurement Period starts January 1, 2018 and ends December 31, 2022. In the event that either the
EBITDA Milestone or the Stock Price Milestone is not yet achieved for a Tranche, no shares attributable to
such Tranche will be eligible to vest on such Tranche’s Earliest Vesting Date; provided, however, the
Milestones will remain eligible to be achieved during the remaining EBITDA Measurement Period and
Stock Price Measurement Period, as applicable. For clarity, upon the achievement of both the applicable
EBITDA Milestone and Stock Price Milestone for a Tranche, the shares attributable to such Tranche may
not vest until such Tranche’s Earliest Vesting Date, and only if Mr. Melo remains the CEO on such date.
More than one Tranche may vest simultaneously provided that: the Earliest Vesting Date for each
applicable Tranche has occurred, the requisite EBITDA Milestone and Stock Price Milestone for each
applicable Tranche have been met and Mr. Melo continues as the CEO through the applicable date of
vesting. The table below sets forth the number of shares, EBITDA Milestone, Stock Price Milestone and
Earliest Vesting Date for each Tranche:

Tranche

Number of
Shares

EBITDA Milestone
($M)

Stock Price
Milestone

Earliest Vesting Date

1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

750,000
750,000
750,000
1,000,000

$ 10
$ 60
$ 80
$100

$15
$20
$25
$30

July 1, 2019
July 1, 2020
July 1, 2021
July 1, 2022

EBITDA Milestone. The EBITDA Milestone for a Tranche is achieved if Amyris’s EBITDA (as
described below) equals or exceeds the EBITDA Milestone set forth in the table above for such Tranche for
any fiscal year during the EBITDA Measurement Period. The EBITDA Measurement Period starts
January 1, 2018 and ends December 31, 2021. The Board or the LDCC will measure and certify the level of
achievement of the EBITDA Milestone as of the end of each fiscal year within the EBITDA Measurement
Period.

For purposes of the EBITDA Milestone, “EBITDA” shall mean Amyris’s net (loss) income attributable
to common stockholders for the relevant fiscal year during the EBITDA Measurement Period as
determined in accordance with U.S. Generally Accepted Accounting Principles (“GAAP”) and as reported
by Amyris in its audited financial statements contained in its Annual Report on Form 10-K for the relevant
fiscal year filed with the SEC, plus interest expense (benefit), provision for income taxes, depreciation and
amortization for the same fiscal year as reflected in the audited financial statements. For the avoidance of
doubt, there will be no adjustment to the reported net (loss) income attributable to common stockholders
for stock based compensation in determining EBITDA.

In the event of unusual non-recurring events such as acquisition activities or divestitures of significant
assets or changes in applicable accounting rules, as a result of which the calculation of Amyris’s EBITDA
during the EBITDA Measurement Period is increased or decreased by 10% or more in determining
Amyris’s audited financial statements contained in its Annual Report on Form 10-K filed with the SEC for
the most recently completed fiscal year, the Board or, if the Board delegates authority to the LDCC, the
LDCC may provide for one or more equitable adjustments to the EBITDA Milestones to preserve the
original intent regarding the EBITDA Milestones at the time of the initial award grant.

As of the date of this Proxy Statement, none of the EBITDA Milestones for any of the Tranches had

been achieved.

Global Select Market for a thirty (30)-consecutive day period ending on the date on which the 180-day
average stock price set forth in the table is achieved for the applicable Tranche equals or exceeds the Stock
Price Milestone for the applicable Tranche during the Stock Price Measurement Period. The Stock Price
Measurement Period starts January 1, 2018 and ends December 31, 2022.

The Stock Price Milestone will be adjusted to reflect events such as a stock split or recapitalization in
order to prevent diminution or enlargement of the benefits or potential benefits intended to be made
available under the CEO Performance Option.

The LDCC considers the Stock Price Milestone to be a challenging hurdle and included the EBITDA
Milestone to promote Amyris’s continued focus on growth, sustainability and profitability. The LDCC
selected EBITDA (as defined above) as the appropriate measure because it believes EBITDA is a metric
that is commonly used for companies at this stage of development and because many of Amyris’s
stockholders use it to evaluate Amyris’s performance and viability. It is a measure of cash generation from
operations that does not disincentivize Amyris from making additional investments to grow further. The
EBITDA Milestone is designed to ensure that Amyris maintains operating discipline but does not represent
Amyris’s target EBITDA for any future period. The LDCC included the Stock Price Milestone to drive
sustained, long-term stockholder returns, and to further align Mr. Melo’s compensation opportunity to
long-term stockholder interests. In establishing the EBITDA Milestone and Stock Price Milestone, the
LDCC carefully considered a variety of factors, including Amyris’ growth trajectory and internal growth
plans. The LDCC also reviewed special CEO equity awards approved by other public companies as a
reference point for setting the magnitude and terms of the CEO Performance Option and CEO RSU.

As of the date of this Proxy Statement, none of the Stock Price Milestones for any of the Tranches had

been achieved.

Term. The term of the CEO Performance Option is ten years from the date of the grant, unless
Mr. Melo’s employment with Amyris is terminated prior to such date. Accordingly, Mr. Melo will have
ten years from the date of grant to exercise any portion of the CEO Performance Option that has vested on
or prior to such date, provided that he remains employed at Amyris.

Post-Exercise Holding Period. Mr. Melo must hold at least fifty percent (50%) of the shares he
acquires upon exercise of the CEO Performance Option (net of any shares sold to pay the exercise price and
any tax withholding obligations with respect to the CEO Performance Option) for two years post-exercise.

The LDCC selected a two-year holding period in order to further align Mr. Melo’s interests with
Amyris stockholders’ interests for two years following the exercise of any portion of the CEO Performance
Option. Such alignment ensures that Mr. Melo will be focused on sustaining Amyris’ success both before
and after he exercises his CEO Performance Option.

Employment Requirement for Continued Vesting. Mr. Melo must continue to be employed as
Amyris’ CEO upon each vesting date in order for the corresponding Tranche to vest under the CEO
Performance Option. If Mr. Melo is still employed at Amyris in a role other than CEO, he will no longer be
able to vest under the CEO Performance Option but can continue to hold any unexercised, vested portion
of the CEO Performance Option for the full term of the CEO Performance Option.

Termination of Employment. Except in the context of a change of control of Amyris, there will be
no acceleration of vesting of the CEO Performance Option if the employment of Mr. Melo is terminated,
or if he dies or becomes disabled. In other words, termination of Mr. Melo’s employment with Amyris will
preclude his ability to earn any then-unvested portion of the CEO Performance Option following the date
of his termination.

Change of Control of Amyris.

If Amyris experiences a change of control, such as a merger with or
purchase by another company, vesting under the CEO Performance Option will not automatically
accelerate.

Company’s stockholders in the change of control equals or exceeds the applicable Stock Price Milestone. To
the extent a Stock Price Milestone for a Tranche is achieved upon a change of control, the shares specified
for such Tranche will be subject to time-based vesting (the “COC Time-Based Options”), and such COC
Time-Based Options shall vest upon the later of the date of the change of control and the Earliest Vesting
Date applicable to such Tranche, subject to Mr. Melo remaining the CEO on each such vesting date. To the
extent a Stock Price Milestone for a Tranche is not achieved as a result of the change of control, such
Tranche will be forfeited automatically as of the immediately prior to closing of the change of control and
never shall become vested. Notwithstanding the foregoing, if Mr. Melo is terminated without cause or
resigns for good reason in connection with the change of control, any then unvested COC Time-Based
Options will accelerate, subject to Mr. Melo’s satisfaction of certain terms and conditions, including, but
not limited to delivery of a release of claims, pursuant to the Severance Plan (as defined below), the terms
of which are described below under “Severance Plan” and “Potential Payments upon Termination and upon
Termination Following a Change in Control.”

In addition, if the successor or acquiring corporation (if any) of Amyris refuses to assume, convert,
replace or substitute the CEO Performance Option in connection with a change of control, 100% of
Mr. Melo’s COC Time-Based Options shall accelerate and become vested effective immediately prior to the
change of control.

The treatment of the CEO Performance Option upon a change of control is intended to align
Mr. Melo’s interests with Amyris’s other stockholders with respect to evaluating potential change of control
offers.

Clawback.

In the event of a restatement of Amyris’s financial statements previously filed with the
SEC as a result of material noncompliance with financial reporting requirements (“restated financial
results”), Amyris will require forfeiture (or repayment, as applicable) of
the CEO
Performance Option in excess of what would have been earned or paid based on the restated financial
results.

the portion of

CEO RSU. The CEO RSU will vest in four equal annual installments on July 1 of each of 2019, 2020,
2021 and 2022, subject to Mr. Melo’ s continued service on each vesting date. This four-year vesting
schedule is longer than our typical three-year vesting schedule for RSUs granted to our executive officers
and is intended to further align Mr. Melo’s compensation opportunity to long-term stockholder interests
and to promote retention and continuity in our business. Other than the vesting schedule, the terms of the
CEO RSU are identical to other RSU awards granted to our executive officers.

Severance Plan.

In November 2013, the LDCC adopted the Amyris, Inc. Executive Severance Plan
(or the “Severance Plan”). The Severance Plan had an initial term of 36 months and thereafter will be
automatically extended for successive additional one-year periods unless we provide six months’ notice of
non-renewal prior to the end of the applicable term. In May 2016, May 2017 and February 2018, the LDCC
reviewed the terms of the Severance Plan and elected to allow it to automatically renew upon the expiration
of its initial term in November 2016 and renewal terms in November 2017 and November 2018, respectively.
The LDCC adopted the Severance Plan to provide a consistent and updated severance framework for our
executive officers that aligns with peer practices. The terms of the Severance Plan, including the potential
amounts payable under the Severance Plan and related defined terms, are described in detail below under
“Potential Payments upon Termination and upon Termination Following a Change in Control.” All of our
named executive officers, and all senior level employees of Amyris that are eligible to participate in the
Severance Plan (or, collectively,
the “participants”), have entered into participation agreements to
participate in the Severance Plan. Generally, the benefits under the Severance Plan supersede and replace
any rights the participants have in connection with any change of control or severance benefits contained in
such participants’ employment offer letters, equity award agreements or any other agreement that
specifically relates to accelerated vesting of equity awards; provided, that (i) our CEO is entitled to the
rights and benefits provided for in the CEO Performance Option in connection with a change of control of
Amyris, as described above and (ii) in the event of any conflict between the terms of the CEO Performance
Option and Mr. Melo’s participation agreement or the Severance Plan relating to accelerated vesting of
equity awards, the terms of the CEO Performance Option would govern and control. In addition,
Mr. Alvarez’s participation agreement provides that in the event that prior to full vesting of Mr. Alvarez’s

new hire equity awards, including the Alvarez 2018 Award (collectively, the “Alvarez New Hire Awards”),
Mr. Alvarez’s employment with the Company terminates in circumstances entitling him to severance
benefits under the Severance Plan, whether or not in connection with a change of control, then upon such
termination the vesting and exercisability of each Alvarez New Hire Award will be automatically
accelerated in full and the forfeiture provisions and/or company right of repurchase of each Alvarez New
Hire Award will automatically lapse accordingly.

We believe that the Severance Plan appropriately balances our need to offer a competitive level of
severance protection to our executive officers and to induce them to remain in our employ through the
potentially disruptive conditions that may exist around the time of a change of control, while not unduly
rewarding executive officers for a termination of their employment.

Other Executive Benefits and Perquisites. We provide the following benefits to our executive officers

on the same basis as other eligible employees:

•

health insurance;

time off and sick days;

life insurance and supplemental life insurance;

short-term and long-term disability; and

a Section 401(k) plan with an employer matching contribution.

We believe that these benefits are generally consistent with those offered by other companies with

which we compete for executive talent.

Some of the executive officers whom we have hired, including Mr. Alvarez and Ms. Kelsey, held
positions in locations outside of Northern California at the time they agreed to join us. We have agreed in
these instances to pay certain relocation and travel expenses to these executive officers, including housing
and rental car expenses. The amounts of relocation and travel expenses paid to our named executive officers
are included in the “All Other Compensation” column of the “Summary Compensation Table” below and
the related footnotes. Given the high cost of living in the San Francisco Bay Area relative to most other
metropolitan areas in the United States, we believe that for us not to be limited to hiring executives located
near our headquarters in Emeryville, California, we must be willing to offer to pay an agreed upon amount
of relocation costs.

Other Compensation Practices and Policies. The following additional compensation practices and

policies apply to our executive officers in 2018:

Timing of Equity Awards. The timing of equity awards has been determined by our Board or the
LDCC based on our Board’s or the LDCC’s view at the time regarding the adequacy of executive equity
interests in us for purposes of retention and motivation.

In March 2018 and November 2018, our Board and the LDCC, respectively, ratified our existing policy
regarding equity award grant dates, fixing grant dates in an effort to ensure the integrity of the equity award
granting process. This policy took effect beginning with equity awards granted after the original adoption of
the policy in March 2011. Under the policy, equity awards are generally granted on the following schedule:

•

For equity awards to ongoing employees, the grant date is set as the first business day of the week
following the week in which the award is approved; and

For equity awards to new hires, the grant date is set as the first business day of the week following
the later of the week in which the award is approved or the week in which the new hire commences
his or her employment.

employees”). Remuneration in excess of $1 million is exempt from this deduction limit if it qualifies as
“performance-based compensation” within the meaning of Section 162(m) with respect to taxable years
beginning on or before December 31, 2017 and payable pursuant to a binding written agreement in effect on
November 2, 2017.

To date, the Committee has not taken the deductibility limit imposed by Section 162(m) into
consideration in setting compensation. However, the 2010 EIP includes various provisions designed to allow
us to qualify stock options and other equity awards as “performance-based compensation” under
Section 162(m), including a limitation on the maximum number of shares subject to awards that may be
granted to an individual under the 2010 EIP in any one year. Among other requirements, for certain awards
granted under the 2010 EIP to qualify as fully deductible performance-based compensation under
Section 162(m), our stockholders were required to re-approve the 2010 EIP on or before the first annual
meeting of stockholders at which directors were to be elected that occurred after the close of the third
calendar year following the calendar year of our initial public offering. We sought and received such
approval at our 2012 annual meeting of stockholders. Section 162(m) also requires re-approval of the 2010
EIP by stockholders after five years if the LDCC has retained discretion to select the criteria used to set
performance goals under the 2010 EIP from year to year. The 2010 EIP permits the LDCC to choose from
among several objective performance measures as
the granting and/or vesting
of ”performance-based” equity compensation under the 2010 EIP. Accordingly, we sought and received
such approval at our 2017 annual meeting of stockholders.

the basis

for

The exemption from Section 162(m)’s deduction limit for “performance-based compensation” has been
repealed, effective for taxable years beginning after December 31, 2017, such that compensation paid to our
covered employees in excess of $1 million will not be deductible unless it qualifies for transition relief
applicable to certain arrangements in place as of November 2, 2017. The LDCC cannot determine with
certainty how the deduction limit of Section 162(m) may impact our executive compensation programs in
future years. While the LDCC has not adopted a formal policy regarding tax deductibility of
the
compensation paid to our executive officers, tax deductibility under Section 162(m) is a factor in its
compensation deliberations. However, because of ambiguities and uncertainties as to the application and
interpretation of Section 162(m) and the regulations issued thereunder, including the uncertain scope of the
transition relief for certain arrangements in place as of November 2, 2017 under the legislation repealing
Section 162(m)’s exemption from the deduction limit, no assurance can be given that compensation
intended to satisfy the requirements for exemption from Section 162(m) in fact will. The LDCC seeks to
balance the cost and benefit of tax deductibility with our executive compensation goals designed to
promote long-term stockholder interests, and therefore may, in its discretion, authorize compensation
payments that do not consider the deductibility limit imposed by Section 162(m) when it believes that such
payments are appropriate to attract and retain executive talent and to be in the best interests of the
Company and our stockholders. Accordingly, we expect that a portion of our future cash compensation
and equity awards to our executive officers will not be deductible under Section 162(m).

For example, with respect to the CEO Performance Option and CEO RSU described above, we expect
that Mr. Melo always will be a covered employee for purposes of Section 162(m) of the Code. Therefore, in
any given year in which Mr. Melo exercises all or part of the CEO Performance Option, or vests and is
settled in any portion of the CEO RSU, we will be able to take a tax deduction of only $1,000,000 or less,
regardless of the amount of compensation recognized by Mr. Melo from the exercise of the CEO
Performance Option or settlement of the CEO RSU.

interim condensed consolidated financial statements for the quarterly and year-to-date periods ended
March 31, 2018, June 30, 2018 and September 30, 2018. In addition, we have restated our audited
consolidated financial statements for the year ended December 31, 2017, which are contained in our Annual
Report on Form 10-K for the fiscal year ended December 31, 2018. The LDCC is in the process of
evaluating whether adjustments or recoveries of 2017 or 2018 awards or payments are appropriate based
upon the facts and circumstances surrounding such restatements.

Stock Ownership Policy. We have not established stock ownership or similar guidelines with regard to
our executive officers. All of our executive officers currently have a direct or indirect, through their stock
option holdings, equity interest in our company and we believe that they regard the potential returns from
these interests as a significant element of their potential compensation for services to us.

Insider Trading Policy and Hedging Prohibition. We have adopted an Insider Trading Policy that,
among other things, prohibits our employees, officers and directors from trading in our securities while in
possession of material, non-public information. In addition, under our Insider Trading Policy, our
employees, officers and directors may not acquire, sell or trade in any interest or position relating to the
future price of our securities (such as a put option, a call option or a short sale).

Leadership Development and Compensation Committee Report*

The Leadership Development and Compensation Committee has reviewed and discussed with
management the “Compensation Discussion and Analysis” contained in this Proxy Statement. Based on
this review and discussion, the Leadership Development and Compensation Committee recommended to
the Board that the Compensation Discussion and Analysis be included in this Proxy Statement.

Amyris, Inc. Leadership Development and Compensation Committee of the Board

Carole Piwnica (Chair)
Steven Mills
Patrick Yang

Summary Compensation Table

The following table sets forth information regarding compensation earned by our named executive
officers in 2018 and, where the individual was a named executive officer for the relevant prior year, 2017 and
2016.

Name and Principal

Position
John Melo

President and Chief
Executive Officer

Kathleen Valiasek(9)
Chief Financial
Officer

Joel Cherry(16)

President, Research
and Development

Eduardo Alvarez

Chief Operating
Officer

Nicole Kelsey

General Counsel
and Secretary

Year
2018
2017
2016

2018
2017

2018
2017
2016

2018
2017

Salary
($)
600,000
579,167(5)
550,000

Bonus
($)
192,240(3)
640,000(6)

—

Stock
Awards
($)(1)

Option
Awards
($)(1)

3,556,000 5,122,500
43,930
162,350

147,465
250,750

Non-Equity
Incentive Plan
Compensation
($)(2)
166,275
581,948
333,056

All Other
Compensation
($)

Total
($)

997(4) 9,638,012
934(7) 1,993,444
468(8) 1,296,624

420,000
398,686(12)(13)

129,062(10) 1,016,000
45,000(14)
137,623

370,650
126,996

73,947
163,085

5,500(11) 2,015,159
4,310(15) 875,700

375,000
370,937(19)
358,750

400,000
91,026(24)

141,004(17) 1,079,500
118,718
118,000

—
—

138,994
35,489
76,400

51,963
181,331
93,256

194,140(22) 1,270,000
202,300

—

— 110,850
91,026

62,886

6,520(18) 1,792,981
7,500(20) 713,975
7,760(21) 654,166

2,437(23) 1,977,427
396(25) 447,634

395,000
158,760(28)

65,437(26)
—

508,000
52,290

185,325
17,077

43,788
67,465

5,500(27) 1,203,050
237,570(29) 533,162

(1) The amounts in the “Stock Awards” and “Option Awards” columns reflect the aggregate grant date
fair value of such awards computed in accordance with FASB ASC Topic 718, excluding the effect of
estimated forfeitures. The assumptions made in the valuation of the awards are discussed in Note 12,
“Stock-based Compensation” of ”Notes to Consolidated Financial Statements” in our Annual Report
on Form 10-K for the fiscal year ended December 31, 2018. See the “Grants of Plan-Based Awards in
2018” table for additional information regarding stock and option awards granted to our named
executive officers in 2018. These amounts do not correspond to the actual value that may be recognized
by our named executive officers.

(2) As required under applicable rules of the Securities and Exchange Commission, payments under our
2018 cash bonus plan are included in the column entitled “Non-Equity Incentive Plan Compensation,”
as they were based upon the satisfaction of pre-established performance targets, the outcome of which
was substantially uncertain.

(3)

Includes a cash bonus payment in the amount of $192,240 under our 2018 cash bonus plan for the
annual period approved by the LDCC in its discretion, notwithstanding the Company’s failure to meet
the funding threshold for such period. See “Executive Compensation — Compensation Discussion and
Analysis — 2018 Compensation — Cash Bonuses” above for more information.

(4)

Includes $997 for taxes associated with long term disability insurance.

(5) Mr. Melo’s annual base salary was increased from $550,000 to $600,000 effective June 1, 2017.

(6)

Includes certain discretionary cash bonuses paid to Mr. Melo in an aggregate amount of $500,000 in
recognition of exceptional individual performance, as well as a discretionary cash bonus paid to
Mr. Melo in the amount of $140,000 in recognition of the value lost on the voiding of certain equity
awards granted to him in November 2015 that, when aggregated with other equity awards granted to
him in 2015, inadvertently exceeded the annual per-participant award limit contained in the 2010 EIP.

(7)

Includes $934 for taxes associated with long term disability insurance premiums.

(8)

Includes $468 for taxes associated with long term disability insurance premiums.

(9) Ms. Valiasek assumed the newly created role of Chief Business Officer to lead the CBD business and
other business development efforts while continuing to lead the financing and investor relation
activities effective June 3, 2019.

(10) Includes certain cash bonus payments in an aggregate amount of $129,062 under our 2018 cash bonus
plan for the third quarter and annual period approved by the LDCC in its discretion, notwithstanding
such periods. See “Executive
the Company’s
Compensation — Compensation Discussion and Analysis — 2018 Compensation — Cash Bonuses”
above for more information.

funding threshold for

to meet

failure

the

(11) Includes $5,500 for Section 401(k) plan employer matching contribution.

(12) Ms. Valiasek joined us on January 4, 2017. The amount shown in the “Salary” column for 2017

represents a partial year’s salary based on her January 4, 2017 start date.

(13) Ms. Valiasek’s annual base salary was increased from $350,000 to $420,000 effective April 1, 2017.

(14) Includes a discretionary cash bonus paid to Ms. Valiasek in the amount of $45,000 in recognition of

exceptional individual performance.

(15) Includes $4,310 for Section 401(k) plan employer matching contribution.

(16) Dr. Cherry resigned from the Company effective June 7, 2019.

(17) Includes certain cash bonus payments in an aggregate amount of $91,004 under our 2018 cash bonus
plan for the third quarter and annual period approved by the LDCC in its discretion, notwithstanding
the Company’s failure to meet the funding threshold for such periods, as well as a discretionary cash
retention bonus paid to Dr. Cherry in the amount of $50,000. See “Executive Compensation —
Compensation Discussion and Analysis — 2018 Compensation — Cash Bonuses” above for more
information.

(18) Includes $5,500 for Section 401(k) plan employer matching contribution and $1,020 reimbursement for

commuting expenses.

(19) Dr. Cherry’s annual base salary was increased from $358,750 to $375,000 effective April 1, 2017.

(20) Includes $5,400 for Section 401(k) plan employer matching contribution, $1,080 as a stipend for

waiving medical benefits and $1,020 reimbursement for commuting expenses.

(21) Includes $5,300 for Section 401(k) plan employer matching contribution, $1,440 as a stipend for

waiving medical benefits and $1,020 reimbursement for commuting expenses.

(22) Includes certain cash bonus payments in an aggregate amount of $194,140 under our 2018 cash bonus
plan for the third quarter and annual period approved by the LDCC in its discretion, notwithstanding
the Company’s
such periods. See “Executive
Compensation — Compensation Discussion and Analysis — 2018 Compensation — Cash Bonuses”
above for more information.

funding threshold for

to meet

failure

the

(23) Includes $997 as a stipend for waiving medical benefits and $1,440 for taxes associated with long term

disability insurance premiums.

(24) Mr. Alvarez joined us on October 16, 2017. The amount shown in the “Salary” column for 2017

represents a partial year’s salary based on his October 16, 2017 start date.

(25) Includes $240 as a stipend for waiving medical benefits and $156 for taxes associated with long term

disability insurance premiums.

(26) Includes certain cash bonus payments in an aggregate amount of $65,437 under our 2018 cash bonus
plan for the third quarter and annual period approved by the LDCC in its discretion, notwithstanding
such periods. See “Executive
the Company’s
Compensation — Compensation Discussion and Analysis — 2018 Compensation — Cash Bonuses”
above for more information.

funding threshold for

to meet

failure

the

(27) Includes $5,500 for Section 401(k) plan employer matching contribution.

(28) Ms. Kelsey joined us on August 7, 2017. The amount shown in the “Salary” column for 2017 represents

a partial year’s salary based on her August 7, 2017 start date.

(29) Includes $178,976 for relocation stipend in connection with Ms. Kelsey’s relocation to our
headquarters in Emeryville, California, $55,961 reimbursement for temporary housing and rental car
expenses and $2,633 for Section 401(k) plan employer matching contribution.

Grants of Plan-Based Awards in 2018

The following table sets forth information regarding grants of compensation in the form of plan-based

awards made during 2018 to our named executive officers.

Name

Grant
Date(1)

Approval
Date of
Grant(1)

Estimated Possible Payouts Under
Non-Equity Incentive Plan Awards

Threshold
($)(2)

Target
($)(2)

Maximum
($)(2)

All Other
Stock
Awards:
Number of
Shares of
Stock or
Units
(#) (3)

All Other
Option
Awards:
Number of
Securities
Underlying
Options
(#)(4)

Exercise or
Base Price
of Option
Awards
($/Sh)(5)

—

John Melo . . . . . . .

—

220,500 375,000 1,192,500

—

John Melo . . . . . . . 5/29/2018 5/22/2018

—

— 700,000(7)

—

— 3,250,000(8)

Kathleen Valiasek . .

—

114,660 194,250

611,100

—

Kathleen Valiasek . . 5/29/2018 5/22/2018

—

— 200,000(9)

Joel Cherry . . . . . . .
Joel Cherry(11) . . . . . 5/29/2018 5/22/2018
Joel Cherry(11) . . . . . 5/29/2018 5/22/2018

—

68,906 117,188

372,656

— 212,500(9)

—

Eduardo Alvarez . . .

—

147,000 250,000

795,000

Eduardo Alvarez . . . 5/29/2018 5/22/2018

—

— 250,000(12)

Nicole Kelsey . . . . .

—

58,065

98,750

314,025

—

—
100,000(10)

—

—
37,500(10)

—

Nicole Kelsey . . . . . 5/29/2018 5/22/2018

—

— 100,000(9)

—

—
50,000(10)

—

Grant
Date
Fair Value
of Stock
and Option
Awards
($)(6)

—

3,556,000

5,122,500

—

1,016,000

370,650

—

1,079,500

138,994

—

1,270,000

—

508,000

185,325

(1) Our Board has adopted a policy regarding the grant date of equity awards under which the grant date
of equity awards generally would be, for awards to ongoing employees, the first business day of the
week following the week in which the award was approved by the LDCC or, for new hire awards, the
first business day of the week following the later of the week in which the award is approved by the
LDCC or the week in which the new hire commences his or her employment. Each of the awards listed
in the table above was approved by the LDCC in April or May 2018, subject to the approval by our
stockholders of such awards and/or certain amendments to the 2010 EIP to, among other things,
increase the annual per-participant award limit thereunder, which approvals were obtained at our 2018
annual meeting of stockholders held on May 22, 2018. In accordance with our policy regarding equity
award grant dates, the awards were granted on May 29, 2018, the first business day of the week
following the week in which such awards were approved.

(2)

In February 2018, the LDCC approved a non-equity incentive plan upon which the eligibility amounts
reported under “Estimated Possible Payouts Under Non-Equity Incentive Plan Awards” were based.
The terms of the plan and actual amounts paid out under the plan are discussed above under
“Executive Compensation - Compensation Discussion and Analysis - 2018 Compensation - Cash
Bonuses” and the amounts paid out under the plan are included in the “Bonus” and “Non-Equity
Incentive Plan Compensation” columns of the “Summary Compensation Table” above. The estimated
possible payouts as of December 31, 2018 shown in this table reflect the potential incentive awards that
could have been paid for the fourth quarter and annual period of 2018 at the threshold, target and
maximum levels for each individual.

(3) Amounts in this column represent RSUs granted under the 2010 EIP.

(4) Amounts in this column represent stock options granted under the 2010 EIP. Mr. Alvarez was not

granted any stock options in 2018.

(5) The exercise price per share of the stock options listed in the table above is the closing price of our
common stock on Nasdaq on the Grant Date, which represents the fair value of our common stock on
the same date. RSU awards do not have any exercise price.

(6) Reflects the grant date fair value of each award computed in accordance with FASB ASC Topic 718,
excluding the effect of estimated forfeitures. The assumptions made in the valuation of the awards are
discussed in Note 12, “Stock-based Compensation” of ”Notes to Consolidated Financial Statements”
in our Annual Report on Form 10-K for the fiscal year ended December 31, 2018.

(7) These RSUs have a four-year vesting schedule from a vesting commencement date of July 1, 2018, with
1/4th of the units vesting annually, subject to continued service through each vesting date. Such
restricted stock units are subject to acceleration of vesting upon termination of employment in
connection with a change of control, as further described below under “Potential Payments upon
Termination and upon Termination Following a Change in Control.”

under

(8) These stock options are subject to performance-based vesting conditions and to acceleration of vesting
in connection with a change of control. For more information regarding these stock options, please see
and Analysis — 2018
above
Compensation — Equity Awards — 2018 CEO Equity Awards — CEO Performance Option.” Such
stock options are also subject to acceleration of vesting upon termination of employment in
connection with a change of control, as further described below under “Potential Payments upon
Termination and upon Termination Following a Change in Control.”

“Executive Compensation - Compensation Discussion

(9) These RSUs have a three-year vesting schedule from a vesting commencement date of May 1, 2018,
with 1/3rd of the units vesting annually, subject to continued service through each vesting date. Such
restricted stock units are subject to acceleration of vesting upon termination of employment in
connection a change of control, as further described below under “Potential Payments upon
Termination and upon Termination Following a Change in Control.”

(10) These stock options have a four-year vesting schedule from a vesting commencement date of May 1,
2018, with 1/4th of the shares subject to the stock options vesting on the first anniversary of the vesting
commencement date, and 1/48th of the shares subject to the stock options vesting each month
thereafter until the fourth anniversary of the vesting commencement date, subject to continued service
through each vesting date. Such stock options are subject to acceleration of vesting upon termination
of employment in connection with a change of control, as further described below under “Potential
Payments upon Termination and upon Termination Following a Change in Control.”

(11) Dr. Cherry resigned from the Company effective June 7, 2019. In connection with his termination of
employment, Dr. Cherry agreed to provide certain consulting services to the Company for a period of
one year following the termination of his employment with the Company (which term may be extended
by the mutual agreement of the parties). In exchange for, and as a result of, such services, Dr. Cherry’s
outstanding equity awards, including his 2018 plan-based equity awards, will continue to remain
outstanding and vest in accordance with, and subject to, the applicable equity plan and the relevant
award agreements during the term of his consulting agreement with the Company.

(12) These RSUs, which were granted to Mr. Alvarez pursuant to the terms of his employment offer letter
with the Company entered into in October 2017, vest in full on October 1, 2019, subject to continued
service through such date. Such RSUs are subject to acceleration of vesting upon termination of
employment, as further described below under “Potential Payments upon Termination and upon
Termination Following a Change in Control.”

Narrative Disclosure to Summary Compensation and Grants of Plan-Based Awards Tables

The material terms of our named executive officers’ annual compensation, including base salaries, cash
bonuses, our equity award granting practices and severance benefits and explanations of decisions for cash
and equity compensation during 2018 are described above under “Executive Compensation —
Compensation Discussion and Analysis.” As noted below under “Agreements with Executive Officers,”

except for certain terms contained in their employment offer letters, equity award agreements and
participation agreements entered into in connection with our Executive Severance Plan, none of our named
executive officers has entered into a written employment agreement with us.

Outstanding Equity Awards as of December 31, 2018

The following table sets forth information regarding outstanding equity awards held by our named

executive officers as of December 31, 2018.

Option Awards

Stock Awards

Number of
Shares or
Units of
Stock That
Have Not
Vested
(#)

Market
Value of
Shares or
Units of
Stock That
Have Not
Vested
($)(33)

740,554(9)(10)(19)(20)(29)

2,473,450

210,532(9)(20)(23)(30)

703,177

Name

John Melo . . . . . . . . . . . .

Kathleen Valiasek . . . . . . . .

Joel Cherry(34)

. . . . . . . . . .

Number of
Securities
Underlying
Unexercised
Options
(#)
Exercisable

Number of
Securities
Underlying
Unexercised
Options
(#)
Unexercisable

Option
Exercise
Price
($/Sh)

306.15

402.60

57.90

43.05

—

52.65

—
3,542(3)(17)
29.40
1,375(3)(18)(28) 24.45
10,035(3)(19)
12,084(3)(20)

3.16

8.85

Option
Expiration
Date

4/20/2020

4/15/2021

4/9/2022

6/3/2023

5/5/2024

6/8/2025

11/9/2025

5/16/2026

6/12/2027

19,866(1)(12)
5,600(2)(13)
6,666(2)(14)
24,066(3)(15)
20,000(3)(16)
24,791(3)(17)
4,625(3)(18)(28)
18,298(3)(19)
7,916(3)(20)

—

3,250,000(21)

5.08

5/29/2028

9,722(4)(22)
791(3)(20)

—

6,944(4)(22)
1,209(3)(20)
100,000(3)(23)

10.35

1/17/2027

4.80

5.08

5/15/2027

5/29/2028

10,904(5)(6)(24)
1,333(5)(6)(25)
1,666(2)(13)
1,666(2)(14)
11,266(3)(15)
6,133(3)(16)
6,416(3)(17)
5,652(3)(18)
8,611(3)(19)
4,195(3)(20)

—

—
917(3)(17)
1,681(3)(18)
4,722(3)(19)
6,405(3)(20)
37,500(3)(23)

64.65

139.80

402.60

57.90

43.05

52.65

29.40

24.45

8.85

4.80

5.08

9/14/2019

1/7/2020

4/15/2021

4/9/2022

6/3/2023

5/5/2024

6/8/2025

11/9/2025

5/16/2026

5/15/2027

5/29/2028

Eduardo Alvarez

. . . . . . . .

11,250(7)(26)

18,750(7)(26)

2.89

10/23/2027

Nicole Kelsey . . . . . . . . . .

5,000(8)(27)

—

4,000(8)(27)
50,000(3)(23)

2.49

5.08

8/14/2027

5/29/2028

233,432(9)(19)(20)(23)

8/22/4034

285,000(11)(31)

951,900

114,000(9)(23)(32)

380,760

(1) These stock options vest as to 1/60th of the shares subject to the stock options each month from the
vesting commencement date, which is a date fixed by the Board or LDCC when granting equity
awards, until the fifth anniversary of the vesting commencement date, subject to continued service
through each vesting date.

(2) These stock options vest as to 1/48th of the shares subject to the stock options each month from the
vesting commencement date until the fourth anniversary of the vesting commencement date, subject to
continued service through each vesting date.

(3) These stock options vest as to 1/4th of the shares subject to the stock options on the first anniversary of
the vesting commencement date, and as to an additional 1/48th of the shares subject to the stock
options each month thereafter until the fourth anniversary of the vesting commencement date, subject
to continued service through each vesting date.

(4) These stock options vest as to 1/5th of the shares subject to the stock options on the six-month
anniversary of the vesting commencement date, as to an additional 1/5th of the shares subject to the
stock options vesting on the first anniversary of the vesting commencement date, and as to an
additional 1/60th of the shares subject to the stock options each month thereafter until the fourth
anniversary of the vesting commencement date, subject to continued service through each vesting date.

(5) These stock options were granted under the 2005 Stock Option/Stock Issuance Plan to certain of our

named executive officers and were immediately exercisable, regardless of vesting schedule.

(6) These stock options vest as to 1/5th of the shares subject to the stock options on the first anniversary of
the vesting commencement date, and as to an additional 1/60th of the shares subject to the stock
options each month thereafter until the fifth anniversary of the vesting commencement date, subject to
continued service through each vesting date.

(7) These stock options vest as to 1/4th of the shares subject to the stock options on the first anniversary of
the vesting commencement date, and as to an additional 1/16th of the shares subject to the stock
options each month thereafter until the second anniversary of the vesting commencement date, subject
to continued service through each vesting date.

(8) These stock options vest as to 50% of the shares subject to the stock options on the first anniversary of
the vesting commencement date, and as to an additional 1/72nd of the shares subject to the stock
options each month thereafter until the fourth anniversary of the vesting commencement date, subject
to continued service through each vesting date.

(9) These RSUs vest as to 1/3rd of the units annually from the vesting commencement date until the third
anniversary of the vesting commencement date, subject to continued service through each vesting date.

(10) These RSUs vest as to 1/4th of the units annually from the vesting commencement date until the fourth
anniversary of the vesting commencement date, subject to continued service through each vesting date.

(11) These RSUs fully vest on October 1, 2019, subject to continued service through such date.

(12) The vesting commencement date of this award was April 20, 2010.

(13) The vesting commencement date of this award was January 1, 2011.

(14) The vesting commencement date of this award was April 1, 2012.

(15) The vesting commencement date of this award was April 1, 2013.

(16) The vesting commencement date of this award is April 1, 2014.

(17) The vesting commencement date of this award is June 8, 2015. This award is subject to acceleration of
vesting upon termination of employment in connection with a change of control, as further described
below under “Potential Payments upon Termination and upon Termination Following a Change in
Control.”

(18) The vesting commencement date of this award is November 1, 2015. This award is subject to
acceleration of vesting upon termination of employment in connection with a change of control, as
further described below under “Potential Payments upon Termination and upon Termination
Following a Change in Control.”

(19) The vesting commencement date of this award is May 1, 2016. This award is subject to acceleration of
vesting upon termination of employment in connection with a change of control, as further described
below under “Potential Payments upon Termination and upon Termination Following a Change in
Control.”

(20) The vesting commencement date of this award is May 1, 2017. This award is subject to acceleration of
vesting upon termination of employment in connection with a change of control, as further described
below under “Potential Payments upon Termination and upon Termination Following a Change in
Control.”

under

(21) These stock options are subject to performance-based vesting conditions and to acceleration of vesting
in connection with a change of control. For more information regarding these stock options, please see
above
and Analysis — 2018
Compensation — Equity Awards — 2018 CEO Equity Awards — CEO Performance Option.” Such
stock options are also subject to acceleration of vesting upon termination of employment in
connection with a change of control, as further described below under “Potential Payments upon
Termination and upon Termination Following a Change in Control.”

“Executive Compensation — Compensation Discussion

(22) The vesting commencement date of this award is January 4, 2017. This award is subject to acceleration
of vesting upon termination of employment in connection with a change of control, as further
described below under “Potential Payments upon Termination and upon Termination Following a
Change in Control.”

(23) The vesting commencement date of this award is May 1, 2018. This award is subject to acceleration of
vesting upon termination of employment in connection with a change of control, as further described
below under “Potential Payments upon Termination and upon Termination Following a Change in
Control.”

(24) The vesting commencement date of this award was November 3, 2008.

(25) The vesting commencement date of this award was October 27, 2009.

(26) The vesting commencement date of

this award is October 16, 2017. This award is subject to
acceleration of vesting upon termination of employment, as further described below under “Potential
Payments upon Termination and upon Termination Following a Change in Control.”

(27) The vesting commencement date of this award is August 7, 2017. This award is subject to acceleration
of vesting upon termination of employment in connection with a change of control, as further
described below under “Potential Payments upon Termination and upon Termination Following a
Change in Control.”

(28) A portion of this award, when aggregated with other equity awards granted to Mr. Melo in 2015,
inadvertently exceeded the annual per-participant award limit contained in the 2010 EIP (the
“Plan Limit”) and accordingly was void. On November 9, 2015, Mr. Melo was granted an award of
30,000 stock options and 20,000 RSUs, of which 24,000 stock options and 16,000 RSUs exceeded the
Plan Limit. In June 2017, the LDCC voided the portion of the awards that exceeded the Plan Limit,
which included 9,500 vested stock options, 14,500 unvested stock options and 10,666 RSUs. In
addition, in June 2017 Mr. Melo returned 3,330 of the 4,162 shares of common stock that he received
upon the vesting of one third of the original RSUs subject to the award on November 1, 2016 to the
Company, representing the portion of such shares that exceeded the Plan Limit and were void, with the
remaining 2,004 shares that exceeded the Plan Limit having been withheld by the Company upon
vesting to satisfy Mr. Melo’s tax withholding obligation. In recognition of the value lost on the voiding
of these awards, in June 2017 the Company paid a cash bonus of $140,000 to Mr. Melo.

(29) The vesting commencement date of this award is July 1, 2018. This award is subject to acceleration of
vesting upon termination of employment in connection with a change of control, as further described
below under “Potential Payments upon Termination and upon Termination Following a Change in
Control.”

(30) The vesting commencement date of this award is January 1, 2017. This award is subject to acceleration
of vesting upon termination of employment in connection with a change of control, as further
described below under “Potential Payments upon Termination and upon Termination Following a
Change in Control.”

(31) The vesting commencement date of this award is October 1, 2017. This award is subject to acceleration
of vesting upon termination of employment, as further described below under “Potential Payments
upon Termination and upon Termination Following a Change in Control.”

(32) The vesting commencement date of this award is August 1, 2017. This award is subject to acceleration
of vesting upon termination of employment in connection with a change of control, as further
described below under “Potential Payments upon Termination and upon Termination Following a
Change in Control.”

(33) Calculated by multiplying the number of units that had not vested as of December 31, 2018 by $3.34,
the closing price of our common stock on the Nasdaq Global Select Market on December 31, 2018.

(34) Dr. Cherry resigned from the Company effective June 7, 2019. In connection with his termination of
employment, Dr. Cherry agreed to provide certain consulting services to the Company for a period of
one year following the termination of his employment with the Company (which term may be extended
by the mutual agreement of the parties). In exchange for, and as a result of, such services, Dr. Cherry’s
outstanding equity awards will continue to remain outstanding and vest in accordance with, and
subject to, the applicable equity plan and the relevant award agreements during the term of his
consulting agreement with the Company.

Option Exercises and Stock Vested During 2018

The following table sets forth information regarding the exercise of options and vesting of RSUs held

by our named executive officers during 2018.

Option Awards

Stock Awards

Name

Number of
Shares
Acquired on
Exercise
(#)

Value
Realized on
Exercise
($)

Number of
Shares
Acquired on
Vesting
(#)

John Melo . . . . . . . . . . . . . . . . . . . . . . . . . . .
Kathleen Valiasek . . . . . . . . . . . . . . . . . . . . . .
Joel Cherry . . . . . . . . . . . . . . . . . . . . . . . . . . .
Eduardo Alvarez . . . . . . . . . . . . . . . . . . . . . . .
Nicole Kelsey . . . . . . . . . . . . . . . . . . . . . . . . .

—
—
—
—
—

35,778
5,267
16,783
35,000
7,000

Value
Realized on
Vesting
($)(1)

226,804
25,406
110,437
262,150
48,720

(1) Value realized on vesting is calculated by multiplying the number of units vesting by the closing price
of our common stock on Nasdaq on the date of vesting (or most recent closing price in the event the
date of vesting falls on a non-trading day).

Pension Benefits

None of our named executive officers participates in, or has an account balance in, a qualified or

non-qualified defined benefit plan sponsored by us.

Non-Qualified Deferred Compensation

None of our named executive officers participates in, or has an account balance in, a traditional

non-qualified deferred compensation plan or any other deferred compensation plan maintained by us.

Potential Payments upon Termination and upon Termination Following a Change in Control

for successive additional one-year periods unless we provide six months’ notice of non-renewal prior to the
end of the applicable term. In May 2016, May 2017 and February 2018, the LDCC reviewed the terms of
the Severance Plan and elected to allow it to automatically renew upon the expiration of its initial term in
November 2016 and renewal terms in November 2017 and November 2018, respectively. The LDCC
adopted the Severance Plan to provide a consistent and updated severance framework for our executive
officers that aligns with peer practices. All of our named executive officers, and all senior level employees of
Amyris that are eligible to participate in the Severance Plan (or, collectively, the “participants”), have
entered into participation agreements to participate in the Severance Plan. Generally, the benefits under the
Severance Plan supersede and replace any rights the participants have in connection with any change of
control or severance benefits contained in such participants’ employment offer letters, equity award
agreements or any other agreement that specifically relates to accelerated vesting of equity awards;
provided, that (i) our CEO is entitled to the rights and benefits provided for in the CEO Performance
Option in connection with a change of control of Amyris, as described above and (ii) in the event of any
conflict between the terms of the CEO Performance Option and Mr. Melo’s participation agreement or the
Severance Plan relating to accelerated vesting of equity awards, the terms of the CEO Performance Option
would govern and control.

Upon the execution of a participation agreement, the participants are eligible for the following benefits

under the Severance Plan.

Upon termination by us of a participant’s employment other than for “cause” (as defined below) or the
the participant, or upon resignation by the participant of such participant’s
(collectively referred to as an “Involuntary

death or disability of
employment
Termination”), the participant becomes eligible for the following severance benefits:

for “good reason” (as defined below)

•

12 months of base salary continuation (18 months for our CEO)

12 months of health benefits continuation (18 months for our CEO)

Upon an Involuntary Termination of a participant at any time within the period beginning
three months before and ending 12 months after a change of control (as defined below) of the Company,
the participant becomes eligible for the following severance benefits:

•

18 months of base salary continuation (24 months for our CEO)

18 months of health benefits continuation (including for our CEO)

Automatic acceleration of vesting and exercisability of all outstanding equity awards then held by
the participant

In addition, as noted in the table below, Mr. Alvarez’s participation agreement provides that in the
event he undergoes an Involuntary Termination (whether or not in connection with a change of control),
the vesting and exercisability of certain of his equity awards will accelerate.

In each case, the benefits are contingent upon the participant complying with various requirements,
including non-solicitation and confidentiality obligations
to us, and on execution, delivery and
non-revocation by the participant of a standard release of claims in favor of the Company within 60 days
of the participant’s separation from service (as defined in Section 409A of the Code). The benefits are
subject to forfeiture if, among other things, the participant breaches any of his or her obligations under the
Severance Plan and related agreements. The benefits are also subject to adjustment and deferral based on
applicable tax rules relating to change-in-control payments and deferred compensation.

Under the Severance Plan, “cause” generally encompasses the participant’s: (i) gross negligence or
intentional misconduct; (ii) failure or inability to satisfactorily perform any assigned duties; (iii) commission
of any act of fraud or misappropriation of property or material dishonesty; (iv) conviction of a felony or a
crime involving moral turpitude; (v) unauthorized use or disclosure of the confidential information or trade
secrets of Amyris or any of our affiliates that use causes material harm to Amyris; (vi) material breach of
contractual obligations or policies; (vii) failure to cooperate in good faith with investigations; or (viii)
failure to comply with confidentiality or intellectual property agreements. Prior to any determination that

“cause” under the Severance Plan has occurred, we are generally required to provide notice to the
participant specifying the event or actions giving rise to such determination and a 10-day cure period
(30 days in the case of failure or inability to satisfactorily perform any assigned duties).

Under the Severance Plan, “good reason” generally means: (i) a material reduction of the participant’s
role at Amyris; (ii) certain reductions of base salary; (iii) a workplace relocation of more than 50 miles; or
(iv) our failure to obtain the assumption of the Severance Plan by a successor. In order for a participant to
assert good reason for his or her resignation, he or she must provide us written notice within 90 days of the
occurrence of the condition and allow us 30 days to cure the condition. Additionally, if we fail to cure the
condition within the cure period, the participant must terminate employment with us within 30 days of the
end of the cure period.

Under the Severance Plan, a “change of control” will generally be deemed to occur if

(i) Amyris
completes a merger or consolidation after which Amyris’s stockholders before the merger or consolidation
do not own at least a majority of the outstanding voting securities of the acquiring or surviving entity after
such merger or consolidation, (ii) Amyris sells all or substantially all of its assets, (iii) any person or entity
acquires more than 50% of Amyris’s outstanding voting securities or (iv) a majority of Amyris’s directors
cease to be directors over any one-year period.

To the extent any severance benefits to a named executive officer constitute deferred compensation
subject to Section 409A of the Code and such officer is deemed a “specified employee” under Section 409A,
we will defer payment of such benefits to the extent necessary to avoid adverse tax treatment.

Dr. Cherry was not eligible for and did not receive any benefits under the Plan in connection with his

separation from the Company in June 2019.

The following table summarizes the potential amounts payable to each of our named executive officers
under the Severance Plan upon an Involuntary Termination (i) other than in connection with a change of
control of the Company and (ii) in connection with a change of control of the Company, assuming in each
case that such Involuntary Termination occurred on December 31, 2018.

Involuntary Termination Not in
Connection with a Change of Control

Involuntary Termination
in Connection with a Change of Control

Name

Base
Salary
($)

John Melo . . . . . . . . . . . . . . . . . . . . . . . . 900,000
Kathleen Valiasek . . . . . . . . . . . . . . . . . . 420,000
Joel Cherry(3)
. . . . . . . . . . . . . . . . . . . . . 375,000
Eduardo Alvarez(4)
. . . . . . . . . . . . . . . . . 400,000
Nicole Kelsey . . . . . . . . . . . . . . . . . . . . . 395,000

Value of
Accelerated
Options or
Shares
($)(1)

Continuing
Health
Benefits
($)

Value of
Accelerated
Options or
Shares
($)(2)

Base
Salary
($)

— 1,200,000
— 630,000
— 562,500
600,000
— 592,500

35,262
24,660
24,660

2,475,625
703,177
779,663
— 960,338
384,160

20,600

— 960,338

Continuing
Health
Benefits
($)

35,262
16,440
16,440

13,733

(1) Other than with respect to certain equity awards granted to Mr. Alvarez, as noted below, accelerated
vesting is only applicable in the event of an Involuntary Termination in connection with a change of
control.

(2) With respect to outstanding options as of December 31, 2018, calculated by multiplying the number of
shares underlying unvested stock options that would vest as a result of an Involuntary Termination in
connection with a change of control by the excess of $3.34, the closing price of our common stock on
Nasdaq on December 31, 2018, over the exercise price of the stock options. Unvested stock options
with exercise prices higher than $3.34 are excluded from the calculation. With respect to outstanding
RSUs as of December 31, 2018, calculated by multiplying the number of outstanding unvested RSUs
that would vest as a result of an Involuntary Termination in connection with a change of control by
$3.34, the closing price of our common stock on Nasdaq on December 31, 2018.

(3) Dr. Cherry resigned from the Company effective June 7, 2019. Dr. Cherry was not eligible for and did

not receive any benefits under the Plan in connection with his separation from the Company.

(4) Mr. Alvarez’s participation agreement provides that in the event that prior to full vesting of
Mr. Alvarez’s new hire equity awards, including his 2018 RSU award set forth in the “Grants of
Plan-Based Awards in 2018” table above (collectively, the “Alvarez New Hire Awards”), Mr. Alvarez’s
employment with the Company terminates in circumstances entitling him to severance benefits under
the Severance Plan, whether or not in connection with a change of control, then upon such
termination the vesting and exercisability of each Alvarez New Hire Award shall be automatically
accelerated in full.

Pay Ratio Disclosure

In August 2015, pursuant to a mandate of the Dodd-Frank Wall Street Reform and Consumer
Protection Act, the Securities and Exchange Commission adopted a rule requiring annual disclosure of the
ratio of the median of the annual total compensation of all employees of the Company, other than its
principal executive officer, to the total annual compensation of the Company’s principal executive officer.
The Company’s principal executive officer is Mr. Melo, our CEO.

For 2018:

•

the annual total compensation of our median employee was $121,378; and

the annual total compensation of Mr. Melo, as reported in the “Summary Compensation Table”
above, was $9,638,012.

Thus, for 2018, the ratio of our CEO’s annual total compensation to our median employee’s annual
total compensation was approximately 79 to 1. This ratio is a reasonable estimate calculated in a manner
consistent with Item 402(u) of Regulation S-K.

In accordance with the rule, for purposes of determining the ratio of our CEO’s annual total
compensation to our median employee’s annual total compensation for 2018, we are using the same median
employee identified in the proxy statement for our 2018 annual meeting of stockholders because there has
been no change in our employee population or our employee compensation arrangements that resulted in a
significant change of the pay distribution to our employee population, or would significantly impact the
pay ratio disclosure. In determining the median of the annual total compensation of all employees of the
Company (other than Mr. Melo), we prepared a list of all employees as of December 31, 2017. We then
calculated the annual cash compensation (base salary and actual and target bonus) of our employees as of
that date for the 12-month period from January 1, 2017 through December 31, 2017. We did not include any
contractors or other non-employee workers in our employee population. Salaries and wages were
annualized for permanent employees who were not employed for the full year of 2017. We used exchange
rates in effect as of December 31, 2017 to convert the base salaries and other compensation amounts of our
non-U.S. employees to U.S. dollars. We did not make any cost-of-living adjustments.

Using this approach, we selected the individual at the median of our employee population. We then
calculated total compensation for this individual using the same methodology we use for our named
executive officers as set forth in the “Summary Compensation Table” above.

Agreements with Executive Officers

We do not have formal employment agreements with any of our named executive officers. The initial
compensation of each named executive officer was set forth in an employment offer or promotion letter
that we executed with such executive officer at the time his or her employment with us commenced (or at
the time of her or his promotion, as the case may be). Each employment offer letter provides that the
named executive officer’s employment is “at will.”

As a condition to their employment, our named executive officers entered into non-competition,
non-solicitation and proprietary information and inventions assignment agreements. Under these
agreements, each named executive officer has agreed (i) not to solicit our employees during her or his
employment and for a period of 12 months after the termination of his or her employment, (ii) not to
compete with us or assist any other person to compete with us during her or his employment, and (iii) to
protect our confidential and proprietary information and to assign to us intellectual property developed
during the course of his or her employment.

See above under “Executive Compensation — Potential Payments upon Termination and upon
Termination Following a Change in Control” for a description of potential payments to our named
executive officers upon termination of employment, including in connection with a change of control of the
Company.

Limitation of Liability and Indemnification

Our Certificate of Incorporation limits the personal liability of directors for breach of fiduciary duty
to the maximum extent permitted by the Delaware General Corporation Law (“DGCL”), and provides that
no director will have personal liability to us or to our stockholders for monetary damages for breach of
fiduciary duty or other duty as a director. However, these provisions do not eliminate or limit the liability of
any of our directors for:

•

any breach of the director’s duty of loyalty to us or our stockholders;

acts or omissions not in good faith or which involve intentional misconduct or a knowing
violation of law;

voting or assenting to unlawful payments of dividends, stock repurchases or other distributions;
or

any transaction from which the director derived an improper personal benefit.

Any amendment to or repeal of these provisions will not eliminate or reduce the effect of these
provisions in respect of any act, omission or claim that occurred or arose prior to such amendment or
repeal. If the DGCL is amended to provide for further limitations on the personal liability of directors of
corporations, then the personal liability of our directors will be further limited to the greatest extent
permitted by the DGCL.

In addition, our Bylaws provide that we must indemnify our directors and officers to the fullest extent
permitted by the DGCL, and we must advance expenses, including attorneys’ fees, to our directors and
officers, in connection with legal proceedings related to their status or service, subject to very limited
exceptions.

We maintain an insurance policy that covers certain liabilities of our directors and officers arising out

of claims based on acts or omissions in their capacities as directors or officers.

Certain of our non-employee directors may, through their relationships with their employers, be

insured and/or indemnified against certain liabilities incurred in their capacity as members of the Board.

We have entered into indemnification agreements with each of our directors and executive officers that
may be broader
than the specific indemnification provisions contained in the DGCL. These
indemnification agreements require us, among other things, to indemnify our directors and executive
officers against liabilities that may arise by reason of their status or service. These indemnification
agreements also require us to advance all expenses incurred by the directors and executive officers in
investigating or defending against any such action, suit or proceeding. We believe that these agreements are
necessary to attract and retain qualified individuals to serve as directors and executive officers.

As previously disclosed in our filings with the Securities and Exchange Commission, Amyris and our
Chief Executive Officer, John Melo, and former CFO (and current Chief Business Officer), Kathleen
Valiasek, are named parties to a securities class action complaint filed in April 2019. The complaint seeks
unspecified damages on behalf of a purported class that would comprise all persons and entities that
purchased or otherwise acquired our securities between March 15, 2018 and March 19, 2019. The
complaint alleges securities law violations based on statements and omissions made by Amyris during such
period. Subsequent to the filing of the securities class action complaint, two separate purported shareholder
derivative complaints were filed based on similar allegations to those made in the securities class action
complaint and name Amyris as a nominal defendant and name a number of Amyris’s current and former
officers and directors as additional defendants. The lawsuits seek to recover, on the Company’s behalf,
unspecified damages purportedly sustained by the Company in connection with allegedly misleading
statements and/or omissions made in connection with the Company’s securities filings, as well as a series of
changes to the Company’s corporate governance policies, restitution to the Company from the individual

defendants, and an award of attorneys’ fees. These cases are in the initial pleadings stage. In the event that
liability is found or a financial settlement is reached with respect to such legal proceedings, Mr. Melo,
Ms. Valiasek or our other current and former officers or directors named in the complaints could seek
indemnification from Amyris. We are not presently aware of any other pending litigation or proceeding
involving any person who is or was one of our directors, officers, employees or other agents or is or was
serving at our request as a director, officer, employee or agent of another corporation, partnership, joint
venture, trust or other enterprise, for which indemnification is sought, and we are not aware of any
threatened litigation that may result in claims for indemnification.

Insofar as indemnification for liabilities arising under the Securities Act may be permitted to directors,
officers or persons controlling our company pursuant to the foregoing provisions, policies and agreements,
we have been informed that,
the Securities and Exchange Commission, such
indemnification is against public policy as expressed in the Securities Act and is, therefore, unenforceable.

in the opinion of

DIRECTOR COMPENSATION

Mr. Melo did not receive any compensation in connection with his service as a director due to his
status as an employee of the company. The compensation that we pay to Mr. Melo is discussed in the
“Executive Compensation” section of this Proxy Statement.

Director Compensation for 2018

During the fiscal year ended December 31, 2018, our non-employee directors who served during 2018

received the compensation set forth below.

Name

John Doerr . . . . . . . . . . . . . . . . . . . . . . . . . . .
Geoffrey Duyk(3)
. . . . . . . . . . . . . . . . . . . . . .
Philip Eykerman(4)
. . . . . . . . . . . . . . . . . . . . .
Christoph Goppelsroeder(5)
. . . . . . . . . . . . . . .
Frank Kung(6) . . . . . . . . . . . . . . . . . . . . . . . . .
Steven Mills(7)(8)
. . . . . . . . . . . . . . . . . . . . . . .
Carole Piwnica . . . . . . . . . . . . . . . . . . . . . . . .
Fernando de Castro Reinach(9) . . . . . . . . . . . . .
HH Sheikh Abdullah bin Khalifa Al Thani(10)
. .
Christophe Vuillez(11)
. . . . . . . . . . . . . . . . . . .
R. Neil Williams . . . . . . . . . . . . . . . . . . . . . . .
Patrick Yang . . . . . . . . . . . . . . . . . . . . . . . . . .

Fees Earned or
Paid in Cash
($)(1)

49,000
13,166
40,000
40,000

40,000
20,510
54,500
27,751
40,000
40,000
70,000
45,000

Stock
Awards
($)(2)(12)

15,771
—
15,771
—

15,771
15,363
15,771
—
15,771
—
15,771
15,771

Option
Awards
($) (2)(12)

17,579
—
17,579
—

17,579
17,109
17,579
—
17,579
—
17,579
17,579

All Other
Director
Compensation
($)

—
—
—
—

—
—
—
—
—
—
—
—

Total
($)(13)

82,351
13,166
73,351
40,000

73,351
52,982
87,851
27,751
82,351
40,000
103,351
78,351

(1) Reflects board, committee chair and committee member retainer fees earned during 2018.

(2) The amounts in the “Stock Awards” and “Option Awards” columns reflect the aggregate grant date
fair value of such awards computed in accordance with FASB ASC Topic 718. The assumptions made
in the valuation of the awards are discussed in Note 12, “Stock-based Compensation” of ”Notes to
Consolidated Financial Statements” in our Annual Report on Form 10-K for the fiscal year ended
December 31, 2018. These amounts do not correspond to the actual value that may be recognized by
our non-employee directors.

(3)

In July 2017, Dr. Duyk, notified us that, effective July 1, 2017, he had elected to decline all cash and
equity compensation accruing, payable or issuable to him under our non-employee director
compensation program until such time as he revoked such election in a signed writing delivered to an
officer of the company. On September 21, 2018, Dr. Duyk revoked such election effective as of such
date.

(4) All cash compensation earned by Mr. Eykerman during 2018 was paid directly to DSM, which
designated Mr. Eykerman to serve on our Board, and he did not receive any cash benefit from such
payments.

(5) All cash compensation earned by Mr. Goppelsroeder during 2018 was paid directly to DSM, which
designated Mr. Goppelsroeder to serve on our Board, and he did not receive any cash benefit from
such payments. In addition, Mr. Goppelsroeder has to date declined each equity award granted to him
pursuant to our non-employee director compensation program, without prejudice to future awards.

(6) All cash compensation earned by Dr. Kung during 2018 was paid directly to Vivo, which designated
Dr. Kung to serve on our Board, and Dr. Kung did not receive any cash benefit from such payments.

Pursuant to an agreement between Dr. Kung and Vivo, Dr. Kung has agreed, subject to certain
conditions and exceptions, to remit the equity compensation he receives under our non-employee
director compensation program to Vivo if and when such equity compensation becomes vested and/or
exercised.

(7) Mr. Mills was appointed to our Board and the Audit Committee on August 1, 2018 and the LDCC on
November 6, 2018, and the fees earned by him in 2018 represent retainer fees earned for the portions of
2018 that he served on our Board, the Audit Committee and the LDCC, respectively.

(8) Upon joining our Board in August 2018, Mr. Mills received an initial award under the 2010 EIP of an
option to purchase 3,466 shares of our common stock and 2,266 RSUs. This award was contemplated
by our non-employee director compensation program (described in “Narrative to Director
Compensation Tables” below). The stock option and RSU awards vest in full on August 1, 2019. The
grant date fair value for these awards, as calculated under FASB ASC Topic 718, is as shown:

Name

Number of
Shares
of Stock
or Units
(#)

Number of
Securities
Underlying
Options
(#)

Date of
Grant

Steven Mills . . . . . . . . . . . . . . . .
Steven Mills . . . . . . . . . . . . . . . .

8/6/2018
8/6/2018

—
2,266

3,466
—

Exercise
Price Per
Share
($)

6.78

Stock
Awards
($)(2)

Option
Awards
($)(2)

— 15,363

— 17,109
—

(9) Dr. Reinach resigned from our Board and the Audit Committee effective August 1, 2018, and the fees
earned by him in 2018 represent retainer fees earned for the portion of 2018 that he served on our
Board, the Audit Committee, respectively. Upon resignation from the Board, Dr. Reinach entered into
a consulting agreement with Amyris to provide certain consulting and advisory services to the
company in exchange for an award of 203,804 RSUs, as described in more detail below under
“Transactions with Related Persons — Reinach Consulting Agreement.” As a result of Dr. Reinach’s
entry into a consulting agreement with, and continued provision of
to, Amyris,
notwithstanding his resignation from the Board, Dr. Reinach’s outstanding equity awards will continue
to remain outstanding and vest in accordance with, and subject to, the 2010 EIP and the relevant
award agreements.

services

(10) HH Sheikh Abdullah bin Khalifa Al Thani resigned from our Board effective May 14, 2019, at which
time all of his outstanding equity awards ceased vesting: all of his vested options remained exercisable
for a period of three months after May 14, 2019, and all of his unvested options and RSUs were
forfeited.

(11) All cash compensation earned by Mr. Vuillez during 2018 was paid directly to Total, which designated
Mr. Vuillez to serve on our Board, and he did not receive any cash benefit from such payments. In
addition, Mr. Vuillez has to date declined each equity award granted to him pursuant to our
non-employee director compensation program, without prejudice to future awards. Mr. Vuillez
resigned from our Board effective May 20, 2019.

(12) In August 2018, each of our non-employee directors other than Dr. Duyk, Mr. Goppelsroeder and
Mr. Vuillez (and excluding Dr. Reinach, who resigned from our Board in August 2018, and Mr. Mills,
who joined our Board in August 2018) received an annual award under the 2010 EIP of an option to
purchase 3,466 shares of our common stock and 2,266 RSUs. These awards were contemplated by our
non-employee director compensation program (described in “Narrative to Director Compensation
Tables” below). These option and RSU awards vested in full on August 1, 2019 (subject to continued
service through such date). The grant date fair value of these awards, as calculated under FASB ASC
Topic 718, is as shown:

Name
John Doerr . . . . . . . . . . . . . . . .
John Doerr . . . . . . . . . . . . . . . .
Philip Eykerman . . . . . . . . . . . . .
Philip Eykerman . . . . . . . . . . . . .
Frank Kung(6)
. . . . . . . . . . . . . .
Frank Kung(6)
. . . . . . . . . . . . . .
Carole Piwnica . . . . . . . . . . . . . .
Carole Piwnica . . . . . . . . . . . . . .
HH Sheikh Abdullah bin Khalifa

Number of
Shares
of Stock
or Units
(#)

—
2,266
—
2,266
—
2,266
—
2,266

Number of
Securities
Underlying
Options
(#)
3,466
—
3,466
—
3,466
—
3,466
—

Date of
Grant
8/1/2018
8/1/2018
8/1/2018
8/1/2018
8/1/2018
8/1/2018
8/1/2018
8/1/2018

Exercise
Price Per
Share
($)
6.96

Stock
Awards
($)(2)

Option
Awards
($)(2)

— 15,771

6.96

— 15,771

— 17,579
—
— 17,579
—
— 17,579
—
— 17,579
—

Al Thani(10)

. . . . . . . . . . . . . .

8/1/2018

—

3,466

6.96

— 17,579

HH Sheikh Abdullah bin Khalifa

Al Thani(10)

. . . . . . . . . . . . . .
R. Neil Williams . . . . . . . . . . . . .
R. Neil Williams . . . . . . . . . . . . .
Patrick Yang . . . . . . . . . . . . . . .
Patrick Yang . . . . . . . . . . . . . . .

8/1/2018
8/1/2018
8/1/2018
8/1/2018
8/1/2018

2,266
—
2,266
—
2,266

—
3,466
—
3,466
—

— 15,771

6.96

— 15,771

—
— 17,579
—
— 17,579
—

(13) As of December 31, 2018, the non-employee directors who served during 2018 held the following

outstanding equity awards:

Name
John Doerr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Geoffrey Duyk(3)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Philip Eykerman . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Christoph Goppelsroeder(5) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Frank Kung(6)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Steven Mills(8)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Carole Piwnica . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Fernando de Castro Reinach(9) . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
HH Sheikh Abdullah bin Khalifa Al Thani(10)
. . . . . . . . . . . . . . . . . .
Christophe Vuillez(11)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
R. Neil Williams . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Patrick Yang . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Outstanding
Options
(Shares)
10,265
4,666
8,199
—
6,466
3,466
10,265
6,799
9,865
—
9,465
17,065(14)

Outstanding
Stock Awards
(Units)
2,266
—
3,599
—
3,599
2,266
2,266
203,804
2,266
—
2,266
2,266

(14) Includes an option to purchase 8,000 shares of our common stock, which Dr. Yang received for

consulting work provided to us in 2013 – 2014 prior to his appointment to our Board.

Narrative to Director Compensation Tables

Under our current non-employee director compensation program,

in each case subject to final

approval by our Board with respect to equity awards:

•

Each non-employee director receives an annual cash retainer of $40,000 and an annual equity
award consisting of an option to purchase 3,466 shares of our common stock and 2,266 RSUs,
vesting in full after one year (in each case subject to continued service through the applicable
vesting date). Any new Board members will receive a pro-rated annual equity award upon joining
our Board, which award will vest in full on the one-year anniversary of the grant of the most
recent annual Board equity awards.

The non-executive Board chair, if any, receives an additional annual award of 7,300 RSUs. The
award becomes fully vested after one year (subject to continued service through the applicable
vesting date).

•

The chair of the Audit Committee receives an additional annual cash retainer of $30,000.

The chair of the LDCC receives an additional annual cash retainer of $10,000.

The chair of the Nominating and Governance Committee receives an additional annual cash
retainer of $9,000.

Audit Committee, LDCC and Nominating and Governance Committee members other than the
chair receive an additional annual cash retainer of $7,500, $5,000 and $4,500, respectively.

In general, all of the retainers described above are paid quarterly in arrears. In cases where a
non-employee director serves for part of the year in a capacity entitling him or her to a retainer payment,
the retainer is prorated to reflect his or her period of service in that capacity. Non-employee directors are
also eligible for reimbursement of their expenses incurred in attending Board and committee meetings.

COMPENSATION COMMITTEE INTERLOCKS AND INSIDER PARTICIPATION

The members of the LDCC during 2018 were Steven Mills, Carole Piwnica and Patrick Yang. None of
these directors was an officer or employee of Amyris or any of our subsidiaries during 2018, nor are any of
these directors former officers of Amyris or any of our subsidiaries, except for Steven Mills, who served as
the Chief Financial Officer of Amyris from May 2012 to December 2013. Except as set forth under
“Transactions with Related Persons” below, none of these directors has any relationships with us of the
type that are required to be disclosed under Item 404 of Regulation S-K. None of our executive officers has
served as a member of the board of directors or as a member of the compensation or similar committee of
any entity that has one or more executive officers who have served on our Board or the LDCC during 2018.

The following is a description of each transaction since the beginning of 2018, and each currently

proposed transaction, in which:

TRANSACTIONS WITH RELATED PERSONS

•

we have been or are to be a participant;

the amount involved exceeds the lesser of $120,000 or 1% of the average of our total assets for the
last two completed fiscal years; and

any of our directors, executive officers or holders of more than 5% of any class of our capital
stock at the time of the transactions in issue, or any immediate family member of or person
sharing the household with any of these individuals, had or will have a direct or indirect material
interest.

Transactions with DSM

Value Sharing Agreement Amendments and Assignment

In December 2017, in connection with the sale of our production facility located in Brotas, Brazil (the
“Brotas Facility”) to an affiliate of Koninklijke DSM N.V. (“DSM”), with which we have commercial and
financial relationships and which owns greater than five percent of our outstanding common stock and has
the right to designate two members of our Board of Directors, we entered into a value sharing agreement
(the “Value Sharing Agreement”) with DSM, pursuant to which DSM agreed to make certain royalty
payments to us representing a portion of the profit on the sale of products produced using farnesene
purchased under that certain Renewable Farnesene Supply Agreement, dated as of April 26, 2016 (as
amended, the “Nenter Supply Agreement”), between us and Nenter & Co., Inc. (“Nenter”), realized by
Nenter and paid to DSM in accordance with the Nenter Supply Agreement. In addition, pursuant to the
Value Sharing Agreement, DSM agreed to guarantee certain minimum annual royalty payments for the first
three calendar years of the Value Sharing Agreement, subject to future offsets in the event that the royalty
payments to which we would otherwise have been entitled under the Value Sharing Agreement for
such years fall below certain milestones. Under the Value Sharing Agreement, we are required to use certain
value share payments received by us with respect to the first three calendar years of the Value Sharing
Agreement in excess of the guaranteed minimum annual value share payments for such years, if any, to
repay amounts outstanding under the Credit Agreement, dated as of December 28, 2017, between us and
DSM.

During 2018, we and DSM amended the Value Sharing Agreement to (i) provide for the use of
estimates in calculating quarterly value share payments (subject to true-up), (ii) modify how the guaranteed
minimum annual value share payment for 2018 will be offset against value payments accruing during 2018
and (iii) accelerate the minimum annual value share payment for 2019 from December 31, 2018 to June 30,
2018 in exchange for a fee of $750,000.

On April 16, 2019, the Company assigned to DSM, and DSM assumed, all of the Company’s rights
and obligations under the Value Sharing Agreement, for aggregate consideration to the Company of
$57.0 million, $29.1 million of which was paid to the Company in cash, with the remaining $27.9 million
being used to pay certain existing obligations of the Company to DSM, including certain obligations under
the Supply Agreement Amendment (as described below).

Supply Agreement Amendments

In December 2017, in connection with the sale of the Brotas Facility to DSM, we entered into a Supply
Agreement (the “Supply Agreement”) with DSM, pursuant to which DSM will supply us with certain
products useful in our business that were previously, and are expected to continue to be, manufactured at
the Brotas Facility, at prices and on production and delivery terms and specifications set forth in the Supply
Agreement, which prices are based upon DSM’s manufacturing cost plus an agreed margin. The Supply
Agreement originally was set to expire (i) with respect to non-farnesene related products, on the date that
our planned new manufacturing facility in Brazil is fully operational and meets its production targets, but in
any event no later than December 31, 2021 and (ii) with respect to farnesene-related products, on
December 28, 2037, subject in each case to earlier termination in certain circumstances.

On November 19, 2018, the Company and DSM entered into Amendment No. 1 to the Supply
Agreement (the “Supply Agreement Amendment”), pursuant to which (i) the outside expiration date of the
Supply Agreement with respect to non-farnesene related products was extended to December 31, 2022, with
specified pricing terms added for products manufactured during 2022, (ii) DSM committed to produce
certain non-farnesene related products for us for two months of each calendar year during the term of the
Supply Agreement and (iii) we agreed to (A) pay DSM a cash reservation fee in the total amount of
$17.3 million, payable in installments during 2018 and 2019, (B) issue 1,643,991 shares of our common
stock to DSM (see below under “Securities Purchase Agreement” for more information) and (C) pay DSM
a cash fee of $7.3 million, payable on or before March 29, 2019, plus, if the closing price of our common
stock on the trading day immediately preceding the date of such payment is less than $4.41 per share, an
amount equal to such deficiency multiplied by 1,643,991.

On April 16, 2019, the Company and DSM entered into a second amendment to the Supply
Agreement, as well as amendments to the Performance Agreement and the Quota Purchase Agreement
entered into in connection with the December 2017 sale of the Brotas Facility to DSM, pursuant to which
(i) DSM agreed to reduce certain manufacturing costs and fees paid by the Company related to the
production of farnesene under the Supply Agreement through 2021, as well as remove the priority of
certain customers over the Company with respect to production capacity at the Brotas Facility, (ii) the
Company agreed to provide DSM rights to conduct certain process and downstream recovery
improvements under the Performance Agreement at facilities other than the Brotas Facility in exchange for
DSM providing the Company with a license to such improvements and (iii) the Company released DSM
from its obligation to provide manufacturing and support services under the Quota Purchase Agreement in
connection with the Company’s planned new manufacturing facility, which is no longer planned to be
located at the Brotas, Brazil location.

Securities Purchase Agreement

On November 20, 2018, we issued 1,643,991 shares of our common stock (the “DSM Shares”) to DSM
in a private placement pursuant to a securities purchase agreement, dated November 19, 2018, between us
and DSM (the “DSM SPA”), in consideration of certain agreements of DSM set forth in the DSM Supply
Agreement Amendment. Pursuant to the DSM SPA, we agreed to file a registration statement providing for
the resale by DSM of the DSM Shares and to use commercially reasonable efforts to (i) cause such
registration statement to become effective within 181 days following the date of the DSM SPA and (ii) keep
such registration statement effective until DSM does not own any DSM Shares or the DSM Shares are
eligible for resale under Rule 144 without regard to volume limitations.

Letter Agreement

On November 19, 2018, we entered into a letter agreement (the “Letter Agreement”) with DSM,
pursuant to which, in consideration of the agreements of DSM set forth in the Supply Agreement
Amendment, we agreed (i) to cause the removal of certain existing liens on intellectual property owned by
us and licensed to DSM (the “Subject Intellectual Property”) and (ii) if such liens were not removed prior to
December 15, 2018, to issue to DSM shares of our common stock with a value equal to $5,000,000. As a
result of the entry into an amendment to our senior secured credit facility on December 14, 2019 to remove
the Subject Intellectual Property from the lien granted by us thereunder, we satisfied our obligations under
the Letter Agreement, and therefore we were not required to issue shares of our common stock (or
otherwise make payment) to DSM pursuant to the Letter Agreement.

Brotas Facility Purchase Price Adjustment Letter

On November 19, 2018, we entered into a letter agreement with DSM, pursuant to which we agreed to
make a cash payment to DSM of $1.8 million in respect of an adjustment to the purchase price for certain
assets sold by us to DSM in connection with sale of the Brotas Facility in December 2017 and related
transactions pursuant to the terms of the agreements related to such sale.

Supply Agreement Payment Letter

In November 2018, we entered into a letter agreement with DSM, pursuant to which we agreed to
make a cash payment to DSM of $0.6 million in respect of certain agreements by DSM to allocate
production capacity at the Brotas Facility in 2018 under the Supply Agreement.

Credit Agreement

On September 17, 2019, the Company and DSM entered into a credit agreement (the “2019 DSM
Credit Agreement”) to make available to the Company a secured credit facility in an aggregate principal
amount of $8.0 million, to be issued in separate installments of $3.0 million, $3.0 million and $2.0 million,
respectively, with each installment being subject to certain closing conditions, including the payment of
certain existing obligations of the Company to DSM. On September 17, 2019, the Company borrowed the
first installment of $3.0 million under the 2019 DSM Credit Agreement, all of which proceeds were used to
pay certain existing obligations of the Company to DSM, and issued to DSM a promissory note in the
principal amount of $3.0 million. On September 19, 2019, the Company borrowed the second installment of
$3.0 million under the 2019 DSM Credit Agreement, all of which proceeds were used to pay certain existing
obligations of the Company to DSM, and issued to DSM a promissory note in the principal amount of
$3.0 million. On September 23, 2019, the Company borrowed the final installment of $2.0 million under the
2019 DSM Credit Agreement, $1.5 million of which proceeds were used to pay certain existing obligations
of the Company to DSM, and issued to DSM a promissory note in the principal amount of $2.0 million.
The promissory notes issued under the 2019 DSM Credit Agreement (i) mature on August 7, 2022,
(ii) accrue interest at a rate of 12.5% per annum from and including the applicable date of issuance, which
interest is payable quarterly in arrears on each January 1, April 1, July 1 and October 1, beginning
January 1, 2020, and (iii) are secured by a first-priority lien on certain Company intellectual property
licensed to DSM. The Company may at its option repay the amounts outstanding under the 2019 DSM
Credit Agreement before the maturity date, in whole or in part, at a price equal to 100% of the amount
being repaid plus accrued and unpaid interest on such amount to the date of repayment. In addition, the
Company is required to repay the amounts outstanding under the 2019 DSM Credit Agreement (i) in an
amount equal to the gross cash proceeds, if any, received by the Company upon the exercise by DSM of
certain common stock purchase warrants issued by the Company to DSM in 2017 and (ii) in full upon the
request of DSM at any time following the receipt by the Company of at least $50.0 million of gross cash
proceeds from one or more sales of equity securities of the Company on or prior to June 30, 2020.

Commercial Transactions

In July and September 2017, we entered into three separate collaboration agreements with DSM (the
“DSM Collaboration Agreements”) to jointly develop three new molecules in the Health and Nutrition
field (the “DSM Ingredients”) using our technology, which we would produce and DSM would
commercialize. Pursuant to the DSM Collaboration Agreements, DSM will, subject to certain conditions,
provide funding for the development of the DSM Ingredients and, upon commercialization, the parties
would enter into supply agreements whereby DSM would purchase the applicable DSM Ingredients from us
at prices agreed by the parties. The development activities will be directed by a joint steering committee with
equal representation by DSM and us. In addition, the parties will share product margin from DSM’s sales
of products that incorporate the DSM Ingredients subject to the DSM Collaboration Agreements.

In June 2018, we and DSM amended and restated one of the DSM Collaboration Agreements to more
clearly define the research and development funding responsibility, amounts and criteria under the
agreement. Pursuant to the amended agreement, DSM agreed to fund additional research and development
costs upon the achievement of certain milestones, and would then recoup a portion of such funding
through a reduction in the royalty percentage paid by DSM to us (once products subject to the agreement
have been commercialized) until such amount is recouped by DSM, at which point the royalty percentage
would return to its previous level.

In 2018, we recognized $10.7 million in revenue relating to agreements and transactions with DSM,
including those described above, and held $1.1 million in accounts receivable as well as $8.0 million of
unbilled receivables and $4.3 million of contingent consideration receivable from DSM as of December 31,
2018.

Transactions with Foris

August 2018 Warrant Transaction

On August 17, 2018, we entered into warrant exchange agreements (the “Warrant Exchange
Agreements”) with Foris Ventures, LLC (“Foris”), an entity affiliated with director John Doerr of Kleiner
Perkins Caufield & Byers, a current stockholder, and an owner of greater than five percent of our
outstanding common stock, and affiliates of Vivo Capital LLC (collectively, “Vivo”), an entity affiliated
with director Frank Kung and which owns greater than five percent of our outstanding common stock and
has the right to designate one member of our Board of Directors, pursuant to which Foris and Vivo agrees
to exercise certain of their common stock purchase warrants issued in May 2017 and August 2017,
respectively (the “Prior Cash Warrants”), representing an aggregate of 10,452,504 shares, in full for cash
and (ii) surrender certain other of their common stock purchase warrants issued in May 2017 and
August 2017, respectively (the “Prior Dilution Warrants”), in the case of Foris after exercising such warrant
in full for 2,106,217 shares, to us for cancellation, and in exchange we agreed to issue to Foris and Vivo new
warrants (the “New Warrants”) to purchase an aggregate of 12,097,164 shares of our common stock in a
private placement, with the New Warrants having substantially identical terms as the Prior Cash Warrants,
except that (A) the expiration date of the New Warrants would be 21 months after issuance (in comparison
to the five-year term of
the Prior Cash Warrants), (B) the New Warrants would not contain any
anti-dilution protection (in comparison to the full-ratchet anti-dilution protection provided in Prior Cash
Warrants), other than standard adjustments in the event of any dividends or distributions on our Common
Stock, or any stock split, reverse stock split, recapitalization, reorganization or similar transaction, (C) the
New Warrants would only permit exercise after the six-month anniversary of issuance, and would only
permit “cashless” or “net” exercise after the twelve-month anniversary of issuance to the extent that there is
not an effective registration statement covering the resale of the shares of common stock underlying the
New Warrants and (D) the exercise price of the New Warrants would be $7.52 per share (in comparison to
$4.40 per share for the Prior Cash Warrants), subject to adjustment. In connection with the entry into the
Warrant Exchange Agreements, we entered into amendments to the Prior Cash Warrants and Prior
Dilution Warrants with Foris and Vivo to (i) in the case of Foris, remove a beneficial ownership limitation
from such warrants and (ii) in the case of Vivo, remove a beneficial ownership limitation from such
warrants and reduce the exercise price of Vivo’s Prior Cash Warrants from $6.39 per share to $4.40 per
share (the “Warrant Exchange”).

In connection with the Warrant Exchange, on August 17, 2018, we entered into an underwriting
agreement (the “Underwriting Agreement”) with B. Riley FBR, Inc. (the “Underwriter”), Foris and Vivo
relating to the sale of up to an aggregate of 8,802,270 shares of our common stock by Foris and Vivo,
including the shares issuable to the Foris upon the exercise of its Prior Cash Warrants (the “Secondary
Offering”). The price to the public in the Secondary Offering was $6.25 per share, and the Underwriter
agreed to purchase the shares of common stock from Vivo and Foris to be sold in the Secondary Offering at
a price of $6.22 per share. The Secondary Offering closed on August 21, 2018; we did not receive any
proceeds from the Secondary Offering, but agreed to pay certain offering expenses, as well as a structuring
and advisory fee to the Underwriter equal to 4.5% of the gross proceeds of the Secondary Offering. At the
closing of the Secondary Offering and the concurrent settlement of the Warrant Exchange, we received
proceeds of approximately $43 million.

Loan and Security Agreement

On April 15, 2019, the Company, GACP Finance Co., LLC (“GACP”) and Foris entered into a Loan
Purchase Agreement, pursuant to which Foris agreed to purchase and assume from GACP, and GACP
agreed to sell and assign to Foris, the outstanding loans under the Loan and Security Agreement, dated
June 29, 2018, as amended (the “LSA”), among the Company, certain subsidiaries of the Company and

GACP, and all documents and assets related thereto. In connection with such purchase and assignment, the
Company agreed to repay Foris $2.5 million of the purchase price paid by Foris to GACP (the “Company
LPA Obligation”). The closing of the loan purchase and assignment occurred on April 16, 2019.

On August 14, 2019, the Company and Foris entered into an Amendment No 5 and Waiver to the LSA
(the “LSA Amendment and Waiver”), pursuant to which (i) the maturity date of the loans under the LSA
was extended from July 1, 2021 to July 1, 2022, (ii) the interest rate for the loans under the LSA was
modified from the sum of (A) the greater of (x) the prime rate as reported in the Wall Street Journal or
(y) 4.75% plus (B) 9% to the greater of (A) 12% or (B) the rate of interest payable with respect to any
indebtedness of the Company, (iii) the amortization of the loans under the LSA was delayed until
December 16, 2019, (iv) certain accrued and future interest and agency fee payments under the LSA were
delayed until December 16, 2019, (v) certain covenants under the LSA, including related definitions, were
amended to provide the Company with greater operational and financial flexibility, including, without
limitation, to permit the incurrence of the indebtedness under the Naxyris Loan Facility (as described
below) and the granting of liens with respect thereto, subject to the terms of an intercreditor agreement
between Foris and Naxyris S.A. (“Naxyris”) governing the respective rights of the parties with respect to,
among other things, the assets securing the Naxyris Loan Agreement and the LSA (the “Intercreditor
Agreement”), (vi) certain outstanding unsecured promissory notes issued by the Company to Foris on
April 8, 2019, June 11, 2019, July 10, 2019 and July 26, 2019 (as described below under “Foris Credit
Agreements”), in an aggregate principal amount of $32.5 million, as well as the Company LPA Obligation,
were added to the loans under the LSA, made subject to the LSA and secured by the security interest in the
collateral granted to Foris under the LSA, and such promissory notes and contractual obligation were
cancelled in connection therewith, and (vii) Foris agreed to waive certain existing defaults under the LSA,
including with respect to covenants related to quarterly minimum revenues, minimum liquidity amounts
and a minimum asset coverage ratio. After giving effect to the LSA Amendment and Waiver, there is
$71.0 million aggregate principal amount of loans outstanding under the LSA. In connection with the entry
into the LSA Amendment and Waiver, on August 14, 2019 the Company issued to Foris a warrant to
purchase up to 1,438,829 shares of common stock at an exercise price of $2.87 per share, with an exercise
term of two years from issuance. Pursuant to the terms of the warrant, Foris may not exercise the warrant
to the extent that, after giving effect to such exercise, Foris, together with its affiliates, would beneficially
own in excess of 19.99% of the number of shares of common stock outstanding after giving effect to such
exercise, unless the Company has obtained stockholder approval to exceed such limit in accordance with
Nasdaq rules and regulations, which the Company is seeking at the 2019 annual meeting of stockholders;
see “Proposal 3 — Approval of the issuance of shares of our common stock issuable upon the exercise of
warrants and conversion of preferred stock issued to Foris Ventures, LLC in accordance with Nasdaq
Marketplace Rules 5635(b) and 5635(d)” for more information.

Foris Credit Agreements

On April 8, 2019, the Company and Foris entered into a credit agreement to make available to the
Company an unsecured credit facility in an aggregate principal amount of $8.0 million (the April Foris
Credit Agreement), which the Company borrowed in full on April 8, 2019 and issued to Foris a promissory
note in the principal amount of $8.0 million (the April Foris Note). The April Foris Note has a maturity
date of October 14, 2019. In connection with the entry into the April Foris Credit Agreement and the
issuance of the April Foris Note, which has no stated interest rate, the Company agreed to pay Foris a fee of
$1.0 million, payable on or prior to the maturity date of the April Foris Note (the April Foris Note Fee);
provided, that the April Foris Note Fee would be reduced to $0.5 million if the Company repaid the April
Foris Note in full by July 15, 2019.

On June 11, 2019, the Company and Foris entered into a credit agreement to make available to the
Company an unsecured credit facility in an aggregate principal amount of $8.5 million, which the Company
borrowed in full on June 11, 2019 and issued to Foris a promissory note in the principal amount of
$8.5 million (the June Foris Note). The June Foris Note (i) accrues interest at a rate of 12.5% per annum
from and including June 11, 2019, which interest is payable on the maturity date or the earlier repayment or
other satisfaction of the June Foris Note, and (ii) matures on August 28, 2019; provided, that if certain
warrants held by DSM are exercised, then the maturity date of the June Foris Note will be the business day
immediately following such exercise.

On July 10, 2019, the Company and Foris entered into a credit agreement to make available to the
Company an unsecured credit facility in an aggregate principal amount of $16.0 million (the July Foris
Credit Agreement), of which the Company borrowed $8.0 million on July 10, 2019 and $8.0 million on
July 26, 2019 and issued to Foris promissory notes, each in the principal amount of $8.0 million, on such
dates (the July Foris Notes). The July Foris Notes (i) accrue interest at a rate of 12.5% per annum from and
including the respective date of issuance, which interest is payable on the maturity date or the earlier
repayment or other satisfaction of the applicable July Foris Note, and (ii) mature on December 31, 2019. In
connection with the entry into the July Foris Credit Agreement, the Company and Foris amended the New
Warrant issued to Foris on August 17, 2018 (see above under “August 2018 Warrant Transaction”) to
reduce the exercise price of such warrant from $7.52 per share to $2.87 per share.

The Company may at its option repay the amounts outstanding under the April Foris Note (including
the April Foris Note Fee), the June Foris Note and the July Foris Notes before their respective maturity
dates, in whole or in part, at a price equal to 100% of the amount being repaid plus, in the case of the June
Foris Note and the July Foris Notes, accrued and unpaid interest on such amount to the date of repayment.

On August 14, 2019, the April Foris Note, the June Foris Note and the July Foris Notes were added to
the loans under the LSA, made subject to the LSA and secured by the security interest in the collateral
granted to Foris under the LSA, and such notes were cancelled in connection therewith. See above under
“Loan and Security Agreement” for additional information.

On August 28, 2019, the Company and Foris entered into a credit agreement to make available to the
Company an unsecured credit facility in an aggregate principal amount of $19.0 million (the August Foris
Credit Agreement), which the Company borrowed in full on August 28, 2019 and issued to Foris a
promissory note in the principal amount of $19.0 million (the August Foris Note). The August Foris Note
(i) accrues interest at a rate of 12% per annum from and including August 28, 2019, which interest is
payable quarterly in arrears on each March 31, June 30, September 30 and December 31, beginning
December 31, 2019, and (ii) matures on January 1, 2023. The Company may at its option repay the amounts
outstanding under the August Foris Note before the maturity date, in whole or in part, at a price equal to
100% of the amount being repaid plus accrued and unpaid interest on such amount to the date of
repayment.

In connection with the entry into the August Foris Credit Agreement, on August 14, 2019 the
Company issued to Foris a warrant to purchase up to 4,871,795 shares of common stock at an exercise
price of $3.90 per share, with an exercise term of two years from issuance in a private placement pursuant
to the exemption from registration under Section 4(a)(2) of
the Securities Act and Regulation D
promulgated under the Securities Act. The exercise price of the warrant is subject to standard adjustments
but does not contain any anti-dilution protection, and the warrants only permit “cashless” or “net” exercise
after the six-month anniversary of issuance of the applicable warrant, and only to the extent that there is
not an effective registration statement covering the resale of the shares of common stock underlying the
applicable warrant. In addition, Foris may not exercise the warrant to the extent that, after giving effect to
such exercise, Foris, together with its affiliates, would beneficially own in excess of 19.99% of the number of
shares of common stock outstanding after giving effect to such exercise, unless the Company has obtained
stockholder approval to exceed such limit in accordance with Nasdaq rules and regulations, which the
Company is seeking at the 2019 annual meeting of stockholders; see “Proposal 3 — Approval of the
issuance of shares of our common stock issuable upon the exercise of warrants and conversion of preferred
stock issued to Foris Ventures, LLC in accordance with Nasdaq Marketplace Rules 5635(b) and 5635(d)”
for more information.

Private Placements

On April 16, 2019, the Company sold and issued to Foris 6,732,369 shares of common stock at a price
of $2.87 per share, as well as a warrant to purchase up to 5,424,804 shares of common stock at an exercise
price of $2.87 per share, with an exercise term of two years from issuance, in a private placement pursuant
the Securities Act and Regulation D
to the exemption from registration under Section 4(a)(2) of
promulgated under the Securities Act, for aggregate cash proceeds to the Company of $20.0 million.

On April 26, 2019, the Company sold and issued to Foris 2,832,440 shares of common stock at a price
of $5.12 per share, as well as a warrant to purchase up to 3,983,230 shares of common stock at an exercise

price of $5.12 per share, with an exercise term of two years from issuance, in a private placement pursuant
the Securities Act and Regulation D
to the exemption from registration under Section 4(a)(2) of
promulgated under the Securities Act, for aggregate cash proceeds to the Company of $15.0 million. On
August 28, 2019, in connection with the entry into the August Foris Credit Agreement (as described above
under “Foris Credit Agreements”), the Company and Foris amended the warrant issued to Foris on
April 26, 2019 to reduce the exercise price of such warrant from $5.12 per share to $3.90 per share.

The exercise price of the warrants issued in the foregoing private placements is subject to standard
adjustments but does not contain any anti-dilution protection, and the warrants only permit “cashless” or
“net” exercise after the six-month anniversary of issuance of the applicable warrant, and only to the extent
that there is not an effective registration statement covering the resale of the shares of common stock
underlying the applicable warrant. In addition, in connection with the foregoing private placements, the
Company agreed not to effect any exercise or conversion of any Company security, and Foris agreed not to
exercise or convert any portion of any Company security, to the extent that after giving effect to such
exercise or conversion, Foris, together with its affiliates, would beneficially own in excess of 19.99% of the
number of shares of common stock outstanding immediately after giving effect to such exercise or
conversion, and the warrants contained a similar limitation. The Company intends to seek stockholder
approval for Foris to exceed such limitation in accordance with Nasdaq rules and regulations at the 2019
annual meeting of stockholders; see “Proposal 3 — Approval of the issuance of shares of our common
stock issuable upon the exercise of warrants and conversion of preferred stock issued to Foris Ventures,
LLC in accordance with Nasdaq Marketplace Rules 5635(b) and 5635(d)” for more information.

Convertible Note Exchange

On May 14, 2019, the Company exchanged $5.0 million aggregate principal amount of its 6.50%
Convertible Senior Notes due 2019 held by Foris, including accrued and unpaid interest thereon up to, but
excluding, May 15, 2019, for 1,122,460 shares of common stock and a warrant to purchase up to 352,638
shares of common stock at an exercise price of $4.56 per share, with an exercise term of two years from
issuance, in a private exchange pursuant to the exemption from registration under Section 3(a)(9) of the
Securities Act. On August 28, 2019, in connection with the entry into the August Foris Credit Agreement
(as described above under “Foris Credit Agreements”), the Company and Foris amended the warrant issued
to Foris on May 14, 2019 to reduce the exercise price of such warrant from $4.56 per share to $3.90 per
share. The exercise price of the warrant issued in the foregoing exchange is subject to standard adjustments
but does not contain any anti-dilution protection, and the warrant only permits “cashless” or “net” exercise
after the six-month anniversary of the exercisability of such warrant, and only to the extent that there is not
an effective registration statement covering the resale of the shares of common stock underlying such
warrant. In addition, the exercisability of such warrant is subject to stockholder approval in accordance
with Nasdaq rules and regulations, which the Company is seeking at the 2019 annual meeting of
stockholders; see “Proposal 3 — Approval of the issuance of shares of our common stock issuable upon the
exercise of warrants and conversion of preferred stock issued to Foris Ventures, LLC in accordance with
Nasdaq Marketplace Rules 5635(b) and 5635(d)” for more information.

Transactions with Total

R&D Note Amendments

On March 21, 2016, in connection with the restructuring of the ownership and rights of Total Amyris
BioSolutions B.V. (“TAB”), the joint venture between us and Total Raffinage Chimie (together with its
affiliates, “Total”), with which we have a commercial and financial relationship and which owns greater than
five percent of our outstanding common stock and has the right to designate one member of our Board of
Directors, we issued to Total a 1.5% Senior Unsecured Convertible Note (RS-10) (as amended, the “R&D
Note”) in the principal amount of $3.7 million. The R&D Note was previously amended in February and
May 2017.

On March 30, 2018, we entered into a third amendment to the R&D Note with Total, pursuant to
which (i) the maturity date of the R&D Note was extended from March 31, 2018 to May 31, 2018 and
(ii) accrued and unpaid interest on the amounts outstanding under the R&D Note would be payable on
March 31, 2018 and May 31, 2018.

On May 31, 2018, we entered into a fourth amendment to the R&D Note with Total, pursuant to
which (i) the maturity date of the R&D Note was extended from May 31, 2018 to July 2, 2018 and
(ii) accrued and unpaid interest on the amounts outstanding under the R&D Note would be payable on
May 31, 2018 and July 2, 2018.

Tranche II Note Letter Agreement

In November 2018, Total converted its Tranche II Senior Convertible Note (the “Tranche II Note”),
which was issued by us to Total in January 2014, and which was scheduled to mature on January 15, 2019,
into shares of common stock in accordance with the terms of the Tranche II Note. In connection with such
conversion, we entered into a letter agreement with Total, pursuant to which we agreed to pay Total future
interest on the Tranche II Note being converted up to, but excluding, the maturity date for such note, which
interest was converted by Total into common stock at the conversion price for the Tranche II Notes.

Convertible Note Exchange and Extensions

On May 15, 2019, the Company exchanged $9.7 million aggregate principal amount of its 6.50%
Convertible Senior Notes due 2019 held by Total for a new senior convertible note with an equal principal
amount and with substantially identical terms, except that the new note had a maturity date of June 14,
2019, in a private exchange pursuant to the exemption from registration under Section 3(a)(9) of the
Securities Act. Effective June 14, 2019, the Company and Total agreed to extend the maturity date of the
new note from June 14, 2019 to July 18, 2019. Effective July 18, 2019, the Company and Total agreed to
(i) further extend the maturity date of the new note from July 18, 2019 to August 28, 2019 and (ii) increase
the interest rate on the new note to 10.5% per annum, beginning July 18, 2019. Effective August 28, 2019,
the Company and Total agreed to (i) further extend the maturity date of the new note from August 28, 2019
to October 28, 2019 and (ii) increase the interest rate on the new note to 12% per annum, beginning
August 28, 2019.

Commercial Transactions

In October 2016, we entered into an assistance agreement with the United States Department of
Energy relating to a research grant award under which we, with the assistance of
two specialized
subcontractors, including Total, will work to develop a manufacturing-ready process utilizing wood as the
cellulosic feedstock to produce farnesene. The program that is the subject of the award is being performed
and funded on a milestone basis. Under the award, we and our subcontractors could collectively receive
reimbursement for up to $7.0 million in costs expended by us and our subcontractors over the program’s
three year term if all of the program’s milestones are achieved. In April 2017, we entered into a Master
Subrecipient Agreement with Total
in connection with the grant award (the “Master Subrecipient
Agreement”), pursuant to which Total would perform certain services in connection with the program and
would be reimbursed for such services, up to a maximum amount of approximately $350,000. In
March 2018, we and Total amended the Master Subrecipient Agreement to reflect the extension of the
program through the end of 2018.

In May 2018, we and Total entered into an agreement to terminate, effective April 30, 2018, Total’s
sublease of certain space in our pilot plants, which sublease was scheduled to expire in April 2019, pursuant
to which Total agreed to pay us $62,000 to satisfy its remaining obligations under the sublease and we
agreed to purchase from Total certain laboratory equipment located in the subleased premises for a
purchase price of $0.5 million.

In July 2018, we and Total entered into an agreement to terminate, effective May 31, 2018, the Pilot
Plant Services Agreement, dated April 4, 2014, as amended, between us and Total, pursuant to which we
provided Total with fermentation and downstream separation scale-up services and training to Total
employees and which was scheduled to expire in April 2019. In accordance with the terms of the Pilot Plant
Services Agreement, no payments were due by either party in connection with the termination.

We engage in sales of our products to Total (including TAB) in the ordinary course of our business. In
2018, we made product sales to Total of $0.3 million and held $0.1 million in accounts receivable from Total
as of December 31, 2018.

Transactions with Vivo

See above under “August 2018 Warrant Transaction”.

On April 29, 2019, the Company sold and issued to Vivo 913,529 shares of common stock at a price of
$4.76 per share, as well as warrants to purchase up to an aggregate of 1,212,787 shares of common stock at
an exercise price of $4.76 per share, with an exercise term of two years from issuance, in a private placement
pursuant to the exemption from registration under Section 4(a)(2) of the Securities Act and Regulation D
promulgated under the Securities Act, for aggregate cash proceeds to the Company of $4.5 million. The
exercise price of the warrants issued in the foregoing private placement is subject to standard adjustments
but does not contain any anti-dilution protection, and the warrants only permit “cashless” or “net” exercise
after the six-month anniversary of issuance, and only to the extent that there is not an effective registration
statement covering the resale of the shares of common stock underlying the applicable warrant. In addition,
in connection with the foregoing private placement, the Company agreed not to effect any exercise or
conversion of any Company security, and Vivo agreed not to exercise or convert any portion of any
Company security, to the extent that after giving effect to such exercise or conversion, Vivo, together with
its affiliates, would beneficially own in excess of 19.99% of the number of shares of common stock
outstanding immediately after giving effect to such exercise or conversion, and the warrants contained a
similar limitation.

Reinach Consulting Agreement

In November 2018, we entered into a consulting agreement, effective August 1, 2018, with Fernando
Reinach, a former director who resigned from our Board effective August 1, 2018 (the “Reinach Consulting
Agreement”). Pursuant to the Reinach Consulting Agreement, Dr. Reinach agreed to perform certain
consulting services relating to our operations in Brazil for a period of three (3) years, including serving as a
member of our advisory panel, and was appointed to a one (1)-year term on such panel by our Board of
Directors in November 2018. As compensation for such services, Dr. Reinach was granted an award of
203,804 RSUs under the 2010 EIP, which award vests as to 1/3rd of the units annually from August 1, 2018,
subject to continued service through each vesting date. The Reinach Consulting Agreement expires on
August 1, 2021, subject to the right of either party to earlier terminate the Reinach Consulting Agreement
on ten (10) day’s prior written notice to the other party. In the event the Reinach Consulting Agreement is
terminated by us prior to its expiration date other than for cause, any unvested RSUs will accelerate and
vest in full upon such termination.

Cherry Consulting Agreement

In June 2019, we entered into a consulting agreement with Joel Cherry, our former President, Research
and Development who resigned from the Company effective June 7, 2019 (the “Cherry Consulting
Agreement”). Pursuant to the Cherry Consulting Agreement, Dr. Cherry agreed to perform certain
consulting services for the Company, and as compensation for such services, Dr. Cherry’s outstanding
equity awards (see “Executive Compensation” in this Proxy Statement for more information) will continue
to remain outstanding and vest in accordance with, and subject to, the 2010 EIP and the relevant award
agreements during the term of the Cherry Consulting Agreement. The Cherry Consulting Agreement
expires on June 8, 2019, which term may be extended by mutual agreement of the parties, subject to the
right of either party to earlier terminate the Cherry Consulting Agreement on thirty (30) day’s prior written
notice to the other party or upon a breach of the agreement by the other party.

Officer Loans

In March, April, May and June 2019, Kathleen Valiasek, the Company’s former Chief Financial
Officer and current Chief Business Officer, provided loans to the Company in an aggregate principal
amount of $1.2 million. Such amounts were repaid by the Company no later than twelve days after such
loans were made and interest was accrued on each loan, while outstanding, at a rate of 12% per annum, for
which the total interest accrued was $2,296.

Naxyris Loan and Security Agreement

On August 14, 2019,

the Company’s subsidiaries (the “Subsidiary
Guarantors”) and, as lender, Naxyris, an existing stockholder of the Company and an investment vehicle

the Company, certain of

owned by Naxos Capital Partners SCA Sicar, which is affiliated with NAXOS S.A.R.L. (Switzerland), for
which director Carole Piwnica serves as director, entered into a Loan and Security Agreement (the “Naxyris
Loan Agreement”) to make available to the Company a secured term loan facility in an aggregate principal
amount of up to $10,435,000 (the “Naxyris Loan Facility”), which the Company borrowed in full on
August 14, 2019. Loans under the Naxyris Loan Facility have a maturity date of July 1, 2022 and accrue
interest at a rate per annum equal to the greater of (i) 12% or (ii) the rate of interest payable with respect to
any indebtedness of the Company plus 25 basis points, which interest will be payable monthly in arrears,
provided that all interest accruing from and after August 14, 2019 through December 1, 2019 shall be due
and payable on December 15, 2019.

The obligations of the Company under the Naxyris Loan Facility are (i) guaranteed by the Subsidiary
Guarantors and (ii) secured by a perfected security interest in substantially all of the assets of the Company
and the Subsidiary Guarantors (the “Collateral”), junior in payment priority to the Company’s obligations
under the LSA (see above under “Transactions with Foris — Loan and Security Agreement”), subject to
certain limitations and exceptions, as well as the terms of the Intercreditor Agreement (as defined above).
Mandatory prepayments of the outstanding amounts under the Naxyris Loan Facility will be required
upon the occurrence of certain events, including asset sales, a change in control, and the incurrence of
additional indebtedness, subject to certain exceptions and reinvestment rights. Outstanding amounts under
the Naxyris Loan Facility must also be prepaid to the extent that the borrowing base exceeds the
outstanding principal amount of the loans under the Naxyris Loan Facility. In addition, the Company may
at its option prepay the outstanding principal amount of the loans under the Naxyris Loan Facility in full
before the maturity date. Any prepayment of the loans under the Naxyris Loan Facility prior to the
maturity date, whether pursuant to a mandatory or optional prepayment, is subject to a prepayment charge
equal to one year’s interest at the then-current interest rate for the Naxyris Loan Facility. Upon the
repayment of the loans under the Naxyris loan facility, whether on the maturity date or earlier pursuant to
an optional or mandatory prepayment, the Company will pay Naxyris an end of term fee. In addition,
(i) the Company will be required to pay a fee equal to 6% of any amount the Company fails to pay within
three business days of its due date and (ii) any interest that is not paid when due will be added to principal
and will bear compound interest at the applicable rate. The affirmative and negative covenants in the
Naxyris Loan Agreement relate to, among other items: (i) payment of taxes; (ii) financial reporting;
(iii) maintenance of insurance; and (iv) limitations on indebtedness, liens, mergers, consolidations and
acquisitions, transfers of assets, dividends and other distributions in respect of capital stock, investments,
loans and advances, and corporate changes. The Naxyris Loan Agreement also contains financial
covenants, including covenants related to minimum revenue, liquidity, and asset coverage.

Compensation Arrangements

Stephanie Kung, the daughter of director Frank Kung, is a non-executive employee of Amyris and
received employment compensation in excess of $120,000 in 2018 and we expect that she will receive
employment compensation in excess of $120,000 in 2019.

Indemnification Arrangements

Please see “Executive Compensation — Limitation of Liability and Indemnification” above for

information regarding our indemnification arrangements with our directors and executive officers.

Executive Compensation and Employment Arrangements

Please see “Executive Compensation” above for information regarding our compensation arrangements
with our executive officers, including equity awards and employment agreements with our executive officers.

Registration Rights Agreements

and certain purchasers of our 9.50% Convertible Senior Notes due 2019, (iv) the warrant to purchase
common stock issued by us to Nenter & Co., Inc. on November 16, 2016, (v) the Securities Purchase
Agreement, dated May 8, 2017, by and among us and certain investors, (vi) the Securities Purchase
Agreement, dated May 31, 2017, by and between us and the investor named therein, (vii) the Securities
Purchase Agreement, dated August 2, 2017, by and between us and DSM International B.V., (viii) the
Stockholder Agreement, dated August 3, 2017, by and between us and affiliates of Vivo Capital LLC,
(ix) the Amended and Restated Stockholder Agreement, dated August 7, 2017, by and between us and
DSM International B.V., (x) the DSM SPA, (xi) the Registration Rights Agreement, dated December 10,
2018, by and among us and the investors party thereto, (xii) the Security Purchase Agreement, dated
April 24, 2019, by and between us and ETP BioHealth (I) Fund LP and (xiii) the common stock purchase
warrants issued by us to each of Schottenfeld Opportunities Fund II, L.P., Phase Five Partners, LP and
Koyote Trading, LLC on September 10, 2017.

Related-Party Transactions Policy

Our Related-Party Transactions Policy adopted by our Board of Directors requires that any
transaction with a related party that must be reported under applicable SEC rules, other than certain
compensation related matters, must be reviewed and approved or ratified by the Audit Committee of our
Board of Directors or another independent body of our Board of Directors. Our Related-Party
Transactions Policy contains specific procedures to be followed, and factors to be considered, in connection
with the review of such transactions, but does not contain specific standards for approval of such
transactions.

HOUSEHOLDING OF PROXY MATERIALS

The SEC has adopted rules that permit companies and Intermediaries to satisfy the delivery
requirements for proxy statements and annual reports, including Notices of Internet Availability of Proxy
Materials, with respect to two or more stockholders sharing the same address by delivering a single Notice
of Internet Availability of Proxy Materials (the “Notice”) or other proxy materials addressed to those
stockholders. This process, which is commonly referred to as “householding,” potentially means extra
convenience for stockholders and cost savings for companies.

A number of brokers with account holders who are Amyris stockholders may be “householding” our
proxy materials. A single copy of the Notice or other proxy materials may be delivered to multiple
stockholders sharing an address unless contrary instructions have been received from the affected
stockholders. Once you have received notice from your broker that
they will be “householding”
communications to your address, “householding” will continue until you are notified otherwise or you
submit contrary instructions. If, at any time, you no longer wish to participate in “householding” and would
prefer to receive a separate Notice or other proxy materials, you may: (1) notify your broker; (2) direct your
written request to Amyris Investor Relations at 5885 Hollis Street, Suite 100, Emeryville, California 94608
or to investor@amyris.com; or (3) contact Amyris Investor Relations at (510) 740-7481. Stockholders who
currently receive multiple copies of the Notice or other proxy materials at their addresses and would like to
request “householding” of their communications should contact their brokers or Amyris Investor Relations
at the address or telephone number above. In addition, we will promptly deliver, upon written or oral
request to the address or telephone number above, a separate copy of the Notice or other proxy materials to
a stockholder at a shared address to which a single copy of such documents was delivered.

AVAILABLE INFORMATION

We will provide to any stockholder entitled to vote at our 2019 Annual Meeting of Stockholders, at no
charge, a copy of our Annual Report on Form 10-K for the fiscal year ended December 31, 2018 (the
“Form 10-K”), including the financial statements and the financial statement schedules contained in the
Form 10-K. We make our Annual Reports on Form 10-K, as well as our other SEC filings, available free of
charge through the investor relations section of our website located at http://investors.amyris.com as soon
as reasonably practicable after they are filed with or furnished to the SEC. Information contained on or
accessible through our website or contained on other websites is not deemed to be part of this Proxy
Statement. In addition, you may request a copy of the Form 10-K by sending an e-mail request to Amyris
Investor Relations at investor@amyris.com, calling (510) 740-7481, or writing to Amyris Investor Relations
at 5885 Hollis Street, Suite 100, Emeryville, California 94608.

STOCKHOLDER PROPOSALS TO BE PRESENTED AT NEXT ANNUAL MEETING

Stockholder proposals may be included in our proxy statement for an annual meeting so long as they
are provided to us on a timely basis and satisfy the other conditions set forth in SEC regulations under
Rule 14a-8 regarding the inclusion of stockholder proposals in company-sponsored proxy materials.
Because we expect to hold our 2020 Annual Meeting of Stockholders (the “2020 Annual Meeting”) in
May 2020, for a stockholder proposal to be considered for inclusion in our proxy statement for the 2020
Annual Meeting, we must receive the proposal at our principal executive offices, addressed to the Secretary,
not earlier than the close of business on the 105th day prior to the 2020 Annual Meeting and not later than
the close of business on the later of (x) the 75th day prior to the 2020 Annual Meeting or (y) the 10th day
following the date on which public announcement of the date of the 2020 Annual Meeting is first made.
You are also advised to review our Bylaws, which contain additional requirements about advance notice of
stockholder proposals.

OTHER MATTERS

The Board knows of no other matters that will be presented for consideration at the annual meeting. If
any other matters are properly brought before the meeting, it is the intention of the persons named in the
accompanying proxy to vote on such matters in accordance with their best judgment.

BY ORDER OF THE BOARD OF DIRECTORS,

Emeryville, California
October 10, 2019

Nicole Kelsey
General Counsel and Secretary

UNITED STATES
SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

FORM 10-K

(Mark One)

☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the fiscal year ended December 31, 2018

☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from

Commission File Number: 001-34885

AMYRIS, INC.

(Exact name of registrant as specified in its charter)

Delaware
(State or other jurisdiction of
incorporation or organization)

55-0856151
(I.R.S. Employer
Identification No.)

5885 Hollis Street, Suite 100, Emeryville, California 94608
(Address of principal executive offices and Zip Code)

(510) 450-0761
(Registrant’s telephone number, including area code)

Securities registered pursuant to Section 12(b) of the Act:

Title of each class
Common Stock, $0.0001 par value per share

Trading symbol(s)
AMRS

Name of each exchange on which registered
Nasdaq Global Select Market

Securities registered pursuant to Section 12(g) of the Act: None

Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act. Yes ☐ No ☒

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act. Yes ☐ No ☒

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act
of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to
such filing requirements for the past 90 days. Yes ☐ No ☒

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to
Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to
submit such files). Yes ☐ No ☒

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company,
or an emerging growth company. See definitions of “large accelerated filer”, “accelerated filer”, “smaller reporting company”, and “emerging growth
company” in Rule 12b-2 of the Exchange Act.

Large accelerated filer
Non-accelerated filer

☐
☐

Accelerated filer
Smaller reporting company
Emerging Growth Company

☒
☒
☐

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with

any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes ☐ No ☒

The aggregate market value of the registrant’s common stock held by non-affiliates of the registrant as of June 28, 2019, the last business day of
the registrant’s most recently completed second fiscal quarter, was $226.5 million based upon the closing price of the registrant’s common stock
reported for such date on the Nasdaq Global Select Market.

Number of shares of the registrant’s common stock outstanding as of September 26, 2019: 103,400,207

DOCUMENTS INCORPORATED BY REFERENCE

None.

EXPLANATORY NOTE

This Annual Report on Form 10-K as of and for the year ended December 31, 2018 includes
consolidated financial statements for the years ended December 31, 2017 and 2018 and quarterly financial
data for fiscal years 2017 and 2018. The consolidated financial statements for the year ended December 31,
2017 and the interim periods ended March 31, 2017, June 30, 2017, September 30, 2017, December 31,
2017, March 31, 2018, June 30, 2018 and September 30, 2018 have been restated in this Annual Report on
Form 10-K.

As previously announced on April 5, 2019 and May 14, 2019, the Audit Committee (the Audit
Committee) of the Board of Directors of the Company (the Board) and the Board, respectively, determined
that the Company will restate its interim condensed consolidated financial statements for the quarterly and
year-to-date periods ended March 31, 2018, June 30, 2018 and September 30, 2018 (collectively, the 2018
Non-Reliance Periods) and its audited consolidated financial statements for the year ended December 31,
2017 (the Restated 2017 Financial Statements). The Company also disclosed that investors should no longer
rely upon (i) the Company’s previously released condensed consolidated financial statements for the 2018
Non-Reliance Periods, (ii) the consolidated financial statements for the Restated 2017 Financial Statements,
including management’s assessment of internal control over financial reporting as of December 31, 2017,
(iii) earnings releases for these periods and (iv) other communications relating to the 2018 Non-Reliance
Periods and Restated 2017 Financial Statements.

During the course of the re-audit of the Restated 2017 Financial Statements, in addition to incorrectly
accounting for certain payment obligations under the Ginkgo Partnership Agreement as previously
disclosed, the Company identified other accounting and financial reporting errors related to (i) the
recognition of certain deemed dividends to preferred stock holders, (ii) incorrect accounting treatment for
the derecognition of certain debt and derivative liability instruments, (iii) errors in computing tax expense,
(iv) incorrect revenue recognition for certain non-cash consideration received under a collaboration
agreement, (v) the timing of certain revenue recognition between quarters within 2017, (vi) computation of
earnings (loss) per share, (vii) correction of errors in cash flow statements for non-cash adjustments, and
(viii) computation of loss on extinguishment of certain debt instruments.

Also, during the preparation and audit of the Company’s consolidated financial statements for fiscal
2018 and as previously disclosed, the Company identified material errors impacting the first, second and
third quarters of 2018 related to revenue recognition for a sell-through royalty-based contract, the timing of
recognition for certain expenses between quarters and unrecorded foreign currency transactions gains. The
Company subsequently identified other accounting and financial reporting errors related to (i) the
accounting treatment for the derecognition of certain derivative liability instruments, (ii) the timing of
expense recognition for an element in the series of transactions with Koninklijke DSM N.V. that closed in
November 2018, (iii) computational errors in calculating the gain/loss on the change in the fair value of
certain derivative liabilities, (iv) the accounting treatment of deal costs related to certain equity financing
transactions and (v) the timing and classification of certain expense reimbursement arrangements.

This Annual Report on Form 10-K (Form 10-K) for the year ended December 31, 2018 reflects
changes to the Consolidated Balance Sheet at December 31, 2017 and the Consolidated Statements of
Operations, Comprehensive Loss, Stockholders’ Deficit, and Cash Flows for the year ended December 31,
2017, and the related notes thereto, and provides restated quarterly data for the quarters ended June 30,
2017, September 30, 2017, December 31, 2017, March 31, 2018, June 30, 2018 and September 30, 2018.

AMYRIS, INC.
FORM 10-K
FOR THE YEAR ENDED DECEMBER 31, 2018

TABLE OF CONTENTS

PART I

Item 1.

Business

Item 1A. Risk Factors

Item 1B. Unresolved Staff Comments

Item 2.

Item 3.

Properties

Legal Proceedings

Item 4. Mine Safety Disclosures

PART II

Item 5. Market for Registrant’s Common Equity, Related Stockholder Matters and Issuer

Purchases of Equity Securities
Selected Financial Data

Item 6.
Item 7. Management’s Discussion and Analysis of Financial Condition and Results of

Operations

Item 7A. Quantitative and Qualitative Disclosures About Market Risk
Item 8.
Item 9.

Financial Statements and Supplementary Data
Changes in and Disagreements with Accountants on Accounting and Financial
Disclosure

Item 9A. Controls and Procedures
Item 9B. Other Information

PART III

Item 10. Directors, Executive Officers and Corporate Governance
Item 11. Executive Compensation
Item 12.

Security Ownership of Certain Beneficial Owners and Management and Related
Stockholder Matters

Item 13. Certain Relationships and Related Transactions, and Director Independence
Item 14.

Principal Accounting Fees and Services

Item 15. Exhibits and Financial Statement Schedule

PART IV

47
49

49
58
59

187
187
191

192
199

232
237
241

243

FORWARD-LOOKING STATEMENTS

This Annual Report on Form 10-K contains forward-looking statements within the meaning of the
Private Securities Litigation Reform Act of 1995. All statements contained in this Annual Report on
Form 10-K other than statements of historical fact, including any projections of financing needs, revenue,
expenses, earnings or losses from operations, or other financial items; any statements of the plans, strategies
and objectives of management for future operations; any statements concerning product research,
development and commercialization plans and timelines; any statements regarding expected production
capacities, volumes and costs; any statements regarding anticipated benefits of our products and
expectations for commercial relationships; any other statements of expectation or belief; and any statements
of assumptions underlying any of the foregoing, are forward-looking statements. The words “believe,”
“may,” “will,” “estimate,” “continue,” “anticipate,” “intend,” “expect,” and similar expressions are intended
to identify forward-looking statements, but are not the exclusive means of identifying such statements. We
have based these forward-looking statements largely on our current expectations and projections about
future events and trends that we believe may affect our financial condition, results of operations, business
strategy, short-term and long-term business operations and objectives, and financial needs. These
forward-looking statements are subject to a number of risks, uncertainties and assumptions, including those
described in Part I, Item 1A, “Risk Factors” in this Annual Report on Form 10-K. Moreover, we operate in
a very competitive and rapidly changing environment. New risks emerge from time to time. It is not possible
for our management to predict all risks, nor can we assess the impact of all factors on our business or the
extent to which any factor, or combination of factors, may cause actual results to differ materially from
those contained in any forward-looking statements we may make. In light of these risks, uncertainties and
assumptions, the future events and trends discussed in this Annual Report on Form 10-K may not occur,
and actual results could differ materially and adversely from those anticipated or implied in the
forward-looking statements contained herein.

We undertake no obligation to revise or publicly release the results of any revision to these
forward-looking statements, except as required by law. Given these risks and uncertainties, readers are
cautioned not to place undue reliance on such forward-looking statements.

Unless expressly indicated or the context requires otherwise, the terms “Amyris,” the “Company,” “we,”
“us,” and “our” in this Annual Report on Form 10-K refer to Amyris, Inc., a Delaware corporation, and,
where appropriate, its consolidated entities.

ITEM 1. BUSINESS

Overview

PART I

We are a leading industrial biotechnology company that applies its technology platform to engineer,
manufacture and sell high performance, natural, sustainably-sourced products into the Health & Wellness,
Clean Beauty, and Flavor & Fragrance markets. Our proven technology platform enables us to rapidly
engineer microbes and use them as catalysts to metabolize renewable, plant-sourced sugars into large
volume, high-value ingredients. Our biotechnology platform and industrial fermentation process replace
existing complex and expensive manufacturing processes. We have successfully used our technology to
develop and produce eight distinct molecules at commercial volumes, leading to more than 15 commercial
ingredients used by thousands of leading global brands.

We believe that industrial biotechnology represents a third industrial revolution, bringing together
biology and engineering to generate new, more sustainable materials to meet the growing global demand for
bio-based replacements for petroleum-based and traditional animal- or plant-derived ingredients. We
continue to build demand for our current portfolio of products through an extensive sales network provided
by our collaboration partners that represent the leading companies in the world for our target market
sectors. We also have a small group of direct sales and distributors who support our Clean Beauty market.
Via our partnership model, our partners invest in the development of each molecule to bring it from the lab
to commercial scale and use their extensive sales forces to sell our ingredients and formulations to their
customers as part of their core business. We capture long-term revenue both through the production and
sale of the molecule to our partners and through royalty revenues from our partners’ product sales to their
customers.

We were founded in 2003 in the San Francisco Bay area by a group of scientists from the University of
California, Berkeley. Our first major milestone came in 2005 when, through a grant from the Bill & Melinda
Gates Foundation, we developed technology capable of creating microbial strains that produce artemisinic
acid, which is a precursor of artemisinin, an effective anti-malarial drug. In 2008, we granted royalty-free
licenses to allow Sanofi S.A. to produce artemisinic acid using our technology. Building on our success with
artemisinic acid, in 2007 we began applying our technology platform to develop, manufacture and sell
sustainable alternatives to a broad range of markets.

skincare products,

We focused our initial development efforts primarily on the production of Biofene®, our brand of
renewable farnesene, a long-chain, branched hydrocarbon molecule that we manufacture through
fermentation using engineered microbes. Our farnesene derivatives are sold in thousands of products as
nutraceuticals,
ingredients. The
commercialization of farnesene pushed us to create a more cost efficient, faster and accurate development
process in the lab and drive manufacturing costs down. This investment has enabled our technology
platform to rapidly develop microbial strains and commercialize target molecules. In 2014, we began
manufacturing additional molecules for the Flavor & Fragrance industry. In 2015, we began investing to
expand our capabilities to other small molecule chemical classes beyond terpenes, which comprised our
initial research efforts, via our collaboration with the Defense Advanced Research Projects Agency
(DARPA). In 2016 we expanded into the production of proteins.

solvents, polymers, and lubricant

fragrances,

We have invested over $600 million in infrastructure and technology to create microbes that produce
molecules from sugar or other feedstocks at commercial scale. This platform has been used to design, build,
optimize and upscale strains producing eight distinct molecules at commercial volumes, leading to more
than 15 commercial ingredients used by thousands of leading global brands. Our time to market for
molecules has decreased from seven years to potentially less than a year, mainly due to our ability to
leverage the technology platform we have built.

computational tools, strain construction tools, screening and analytics tools, and advanced lab automation
and data integration. Full integration of the platform with our large-scale manufacturing capability enables
us to engineer precisely with the end specification and commercial production requirements guiding our
developments. Our state-of-the-art infrastructure includes industry-leading strain engineering and lab
automation located in Emeryville, California, pilot scale production facilities in Emeryville, California and
Campinas, Brazil, a demonstration-scale facility in Campinas, Brazil and a commercial-scale production
facility in Leland, North Carolina, which is owned and operated by our Aprinnova joint venture to convert
our Biofene into squalane and other final products.

We are able to use a wide variety of feedstocks for production, but have focused on accessing Brazilian

sugarcane for our large-scale production because of its renewability, low cost and relative price stability.

Several years ago, we made the strategic decision to transition our business model from developing and
commercializing molecules in low margin commodity markets to higher margin specialty markets. We began
the transition by commercializing and supplying farnesene-derived squalane as a cosmetic ingredient sold to
formulators and distributors. We then entered into collaboration and supply agreements for the
development and commercialization of molecules within the Flavor & Fragrance and Clean Beauty markets
where we utilize our strain generation technology to develop molecules that meet the customer’s rigorous
specifications.

During this transition, we solidified the business model of partnering with our customers to create
sustainable, high performing,
low-cost molecules that replace an ingredient in their supply chain,
commercially scale and manufacture those molecules, and share in the profits earned by our customers once
our customers sell their products into these specialty markets. These three steps constitute our collaboration
revenues, renewable product revenues, and royalty revenues.

In 2017, we decided to monetize the use of one of our lower margin molecules, farnesene, in certain
fields of use while retaining any associated royalties. We began discussions with our partners and ultimately
made the decision to license farnesene to Koninklijke DSM N.V. (DSM) for use in these fields. We also sold
to DSM our subsidiary Amyris Brasil Ltda. (Amyris Brasil), which owned and operated the purpose-built,
large-scale manufacturing facility in Brotas, Brazil
that manufactures farnesene, a key, biobased
intermediate ingredient in certain of our products, in 2017.

The Brotas facility was built to batch manufacture one commodity product at a time (originally for
high-volume production of biofuels, a business we have exited), which is an inefficient manufacturing
process that is not suited for the high margin specialty markets in which we operate today. The inefficiencies
we experienced at the Brotas facility included idling the facility for two weeks at a time to prepare for the
next product batch manufacture. These inefficiencies caused a significant increase in our cost of goods sold.
We are in the process of constructing a new purpose-built, large-scale production facility in Brazil (see the
Manufacturing section below), which we anticipate will allow for the manufacture of five products
concurrently and over 10 different products annually. As part of the December 2017 sale of the Brotas
facility, we contracted with DSM for the use of the Brotas facility to manufacture products for us to fulfill
our product supply commitments to our customers until our new production facility becomes operational.
In September 2019, we obtained the necessary permits and broke ground on our Specialty Ingredients Plant
(SIP). We expect the facility to be fully operational in Q1 of 2021. This facility will allow us to manufacture
five products at once and to produce both our specialty ingredients portfolio and our new sweetener
product.

As discussed above, on December 28, 2017, we completed the sale of Amyris Brasil, which operated
our Brotas production facility, to DSM and concurrently entered into a series of commercial agreements
and a credit agreement with DSM. At closing, we received $33.0 million in contractual cash consideration
for the capital stock of Amyris Brasil, which was subject to certain post-closing working capital adjustments
and reimbursements from DSM contingent on DSM’s utilization of certain Brazilian tax benefits it
acquired with its purchase of Amyris Brasil. We used $12.6 million of the cash proceeds received to repay
certain indebtedness of Amyris Brasil. The total fair value of the contractual consideration received in
connection with the sales agreement for Amyris Brasil was $56.9 million and resulted in a pretax gain of
$5.7 million from continuing operations, recognized in fiscal 2017.

Concurrent with the sale of Amyris Brasil, we entered into a series of commercial agreements with
DSM including (i) a license agreement to DSM of our farnesene product for DSM to use in the Vitamin E
and Lubricants specialty markets; (ii) a royalty agreement, pursuant to which DSM agreed to pay us
specified royalties representing a portion of the profit on the sale of Vitamin E produced from farnesene
sold under the supply agreement with Nenter & Co., Inc. (“Nenter”) assigned to DSM; (iii) a performance
agreement to perform research and development to optimize farnesene for production and sale of farnesene
products; and (iv) a transition services agreement in which we provided finance, legal, logistics, and human
resource services to support the Brotas facility under DSM ownership for a six-month period with a DSM
option to extend for six additional months. At closing, DSM paid to us a nonrefundable license fee of
$27.5 million and a nonrefundable minimum royalty revenue payment of $15.0 million. DSM also agreed to
pay the Company nonrefundable minimum royalty amounts in 2018 and 2019. The future nonrefundable
minimum annual royalty payments were determined to be fixed and determinable with a fair value of
$17.8 million and were included as part of the total arrangement consideration subject to allocation of this
overall multiple-element divestiture transaction. In November 2018 and April 2019, we amended the supply
agreement with DSM and entered into various other agreements with DSM. See Note 10, “Revenue
Recognition”, Note 11, “Related Party Transactions” and Note 16, “Subsequent Events” in Part II, Item 8
of this Annual Report on Form 10-K for a full listing and details of agreements with DSM.

In the second quarter of 2018, we successfully demonstrated our industrial process at full scale to
produce a high-purity, zero calorie sweetener derived from sugarcane. We believe that the molecule we are
producing from sugarcane, Reb M, is one of the leading natural sweeteners. When derived from the Stevia
plant, Reb M is found in very limited quantities along with many impurities that leave an unacceptable taste
in the mouth of the consumer. The Reb M that we produce from sugarcane is more sustainable and lower
cost than other natural sweeteners, and has a specific technical profile that we believe is advantaged in taste
and total process economics for blends and formulations. In December 2018, we received notification from
the U.S. Food and Drug Administration (the FDA) that we received its “Generally Regarded As Safe”
designation concurrence, and began producing commercial quantities of Reb M at DSM’s Brotas facility
during the fourth quarter of 2018.

In June and December 2018, we and our contract manufacturer, Antibióticos de León (ADL),
executed amendments to our January 2018 production agreement, thereby providing us additional tank
capacity at ADL’s production facility in León, Spain. These amendments provide additional, cost-effective
manufacturing capability to meet higher than expected product demand from our partners. The amended
agreement includes a commitment to running a certain number of batches at ADL’s production facility
from the period September 1, 2018 through December 31, 2019 for up to four of our products.

On June 29, 2018, we closed a $36 million term loan with Great American Capital Partners, LLC
(GACP), a subsidiary of B. Riley Capital Management, LLC, an SEC Registered Investment Advisor and
wholly-owned subsidiary of B. Riley Financial, Inc. The term loan matures on July 1, 2021, subject to
certain early maturity conditions. The net proceeds from the term loan were used to pay off the Company’s
senior secured loan facility with Stegodon Corporation and the related party convertible promissory note
issued to Total Raffinage Chimie (as assignee of Total Energies Nouvelles Activités USA) (Total) in
March 2016. The term loan also includes an additional $35 million accordion credit facility that provides us
with another option for financing construction of our planned production facility in Brazil, if necessary.
See Note 5, “Debt” and Note 16, “Subsequent Events” in Part II, Item 8 of this Annual Report on Form
10-K for more information.

In the second quarter of 2018, we executed an agreement for a significant project consortium in
Europe with the Universidade Católica Portuguesa (UCP) Porto Campus and AICEP Portugal Global
(AICEP). UCP is a university system, including the leading biotech school in Portugal, and operates 15
research centers. AICEP is an independent public entity of the Government of Portugal, focused in
encouraging foreign companies to invest in Portugal. In conjunction with this agreement, we opened a
subsidiary in Porto, Portugal. The primary purpose of this subsidiary is to conduct a research and
development project together with Escola Superior de Biotecnologia o Universidade Católica Portuguese.
This subsidiary will be the second R&D center of Amyris and will be responsible for certain areas of
research, namely valorization of fermentation residues and wastes and the advancement of the Company’s
Artificial Intelligence (AI) and Informatics platform. The overall multi-year project is valued up to

approximately $50 million including investment funding and incentives allotted across the parties involved.
We have sole responsibility for commercialization and majority ownership of all intellectual property (IP)
generated. We believe this is the largest biotechnology grant ever awarded in Portugal and one of the largest
ever approved by the AICEP for commercial applications.

In the third quarter of 2018, we entered into a supply and distribution agreement for our new,
sugarcane-derived, zero calorie sweetener with ASR Group, the world’s largest cane sugar refiner. Also in
the third quarter of 2018, we entered into a license and collaboration agreement with a subsidiary of Yifan
Pharmaceutical Co., Ltd., which is one of the leading Chinese pharmaceutical companies. Such license and
collaboration agreement was expanded in November 2018.

On December 10, 2018, we closed the offering and sale of an aggregate of $60 million of convertible
notes to two investors in a private placement. The notes mature on December 10, 2021. See Note 5, “Debt”
and Note 16, “Subsequent Events” in Part II, Item 8 of this Annual Report on Form 10-K for more
information.

On May 2, 2019, we consummated a $300 million research, collaboration and license agreement (the
Cannabinoid Agreement) with LAVVAN, Inc., a newly formed investment-backed company (Lavvan), for
the development, manufacture and commercialization of cannabinoids. Under the agreement, the Company
will perform research and development activities and Lavvan will be responsible for the commercialization
of the cannabinoids developed under the agreement. The Cannabinoid Agreement is being principally
funded on a milestone basis, with the Company also entitled to receive certain supplementary research and
development funding from Lavvan. The Company could receive aggregate funding of up to $300 million
over the term of the Cannabinoid Agreement if all of the milestones are achieved. Additionally, the
agreement provides for royalties to the Company on Lavvan’s gross profit margin once products are
commercialized; these payments will be due for the next 20 years. Consummation of the transactions
contemplated by the Cannabinoid Agreement included the formation of a special purpose entity to hold
certain intellectual property created during the collaboration (the Cannabinoid Collaboration IP), the
the Cannabinoid
licensing of certain Company intellectual property to Lavvan,
Collaboration IP to the Company and Lavvan, and the granting by the Company to Lavvan of a lien on
our background intellectual property being licensed to Lavvan under the Cannabinoid Agreement, which
would be subordinated to the lien on such intellectual property under the GACP Term Loan Facility (see
Note 5, “Debt”).

the licensing of

On May 10, 2019, the Company and Raizen Energia S.A. (Raizen) entered into an agreement relating
to the formation and operation of a joint venture relating to the production, sale and commercialization of
alternative sweetener products. In connection with the formation of the joint venture, among other things,
(i) the joint venture will construct a manufacturing facility on land owned by Raizen and leased to the joint
venture (the Sweetener Plant), (ii) the Company will grant to the joint venture an exclusive, royalty-free,
worldwide, license to certain technology owned by the Company relevant to the joint venture’s business, and
(iii) the Company and Raizen will enter into a shareholders agreement setting forth the rights and
obligations of the parties with respect to, and the management of, the joint venture. The formation of the
joint venture is subject to certain conditions, including certain regulatory approvals and the achievement of
certain technological and economic milestones relating to the Company’s existing production of
its
alternative sweetener product. If such conditions are not satisfied by December 31, 2019, the joint venture
will automatically terminate. In addition, notwithstanding the satisfaction of the closing conditions, Raizen
may elect not to consummate the formation and operation of the joint venture, in which event, the
Company will retain the right to construct and operate the Sweetener Plant.

Technology

We have developed innovative microbial engineering and screening technologies that allow us to
transform the way microbes metabolize sugars. Specifically, we engineer microbes, such as yeast, and use
them as catalysts to convert sugar, through fermentation, into high-value molecules. In 2015, we were
awarded an investment by DARPA to expand the capabilities of our technology platform beyond
terpenoids. The investment has resulted in us developing an integrated platform with artificial intelligence
that will speed up the development and commercialization of small molecules across 15 different chemical
classes. We have also developed our technology to be able to produce large molecules, such as proteins.

We devote substantial resources to our research and development efforts. As of December 31, 2018,
our research and development organization included 199 employees, 109 of whom held Ph.D.s. We have
invested more than $600 million to date in our research and development capabilities that has resulted in an
almost 6x improvement in speed to market and 24x improvement in cost of manufacturing. These
achievements are due to the leading strain engineering and upscaling and commercialization capabilities we
have developed from our investment.

Strain Engineering
Companies and researchers around the world are continuously learning how the complex biological
processes in organisms work. Because there is so much that is still unknown, the best method for
development of commercially viable strains is to test as many hypotheses as accurately and quickly as
possible to accelerate the learning curve.

We have developed a high-throughput strain engineering system that is currently capable of producing
and screening more than 100,000 yeast strains per month, which enables us to achieve an approximately
90% lower cost per strain than we achieved in 2009. We generated more than 360,000 unique strains in
2018, surpassing 6.3 million unique strains created since our inception, with each strain testing for improved
production of the target molecules. In addition, through our lab-scale and pilot-plant fermentation
operations, and our proprietary analytical tools, we are now able to predict, with high reliability, the
performance of candidate strains at industrial scale.

Upscaling and Commercialization
The riskiest part of commercializing biotechnology is often the scale up and manufacturing due to the
perceived unpredictability of biotechnology at different scales. We have built scale-up and manufacturing
capabilities as our advantage by heavily investing in prediction models and analytics to quickly ascertain
how a strain’s behavior at one scale will translate in another scale. We’ve successfully scaled up and
manufacture eight distinct molecules at commercial volumes to date, leading to more than 15 commercial
ingredients used by thousands of leading global brands. The results of our advantage are accelerated speed
to market, lower overall development costs, and a significantly lower risk profile for any project we
undertake.

A strain must be improved to increase the level of efficiency of production, and tested for performance
in larger-volume facilities, before it is implemented at commercial-scale manufacturing facilities. Our unique
infrastructure to support this scale-up process includes lab-scale fermenters (0.5 to 2 liter), operating pilot
plants in our facilities in Emeryville, California and Campinas, Brazil (300 liters), two 5,000-liter fermenters
in our Campinas demonstration facility and five years’ experience owning and operating the 1,200,000-liter
production facility in Brotas, Brazil that we sold in late 2017. Each of these stages mimic the conditions
found in larger scale fermentation so that our findings may translate predictably from lab scale to pilot and
ultimately to commercial scale. Our infrastructure is so accurate that we can go straight from lab scale to
commercial scale for our fermentations. Typically, the only reason we ever invest in the pilot scale step is to
produce enough product to accurately test our downstream processing since our fermentation process is
already robust.

The complexities that can arise at industrial scale manufacturing are significant and it takes an
experienced team to not only address issues as they arise, but to also have the foresight to prevent issues
from arising. With five years of experience operating the production facility in Brotas, Brazil that we
designed (prior to selling the facility in late 2017), we have been able to develop a world-class manufacturing
team. This team has successfully brought on line a production facility and scaled up and manufactured
eight molecules at commercial scale that are currently used in thousands of consumer goods products
around the world. Our effort also expands into continued strain and process improvements to ensure our
manufacturing is robust and the most cost advantaged.

Product Markets and Partnerships

There are three market areas that are our primary focus and key to our growth: Health & Wellness,
Clean Beauty and Flavor & Fragrance. Each of these markets embodies our core competencies of
sustainably providing clean ingredients in markets where we can be the most impactful, not only from a
growth and revenue standpoint, but also for healthier living.

We believe that our leadership in biotechnology is demonstrated by collaboration partners, who come
fermentation expertise. Together we seek to reduce
to us to access our platform and industrial
environmental impact, enhance performance, reduce supply and price volatility, and improve profit margins.
Our partners include Flavor & Fragrance companies such as Firmenich S.A. (Firmenich) and Givaudan
International, SA (Givaudan), and nutraceutical companies such as DSM. A portion of our work has also
been funded by the U.S. government, including the Department of Energy (DOE) and DARPA, to develop
technologies and processes capable of improving the ability to utilize biotechnology for the production of a
broader range of molecules.

Health & Wellness

Our Health & Wellness focus includes alternative sweeteners, nutraceuticals, such as vitamins, and food
ingredients. As consumers continue to demand higher nutritional performance, cleaner labels and
convenience from their food, the demand for specific ingredients that are often difficult and expensive to
procure will continue to grow. Animal farming is also being impacted by the growing demand for protein
and the need to change farming practices, such as reducing antibiotic use. Our technology can be employed
to provide affordable access to these desired ingredients for both human and animal health. To date,
product revenue in this area has been from a derivative made from our Biofene® product by our partner. In
late 2018, we began to produce at commercial scale an alternative, non-nutritive sweetener.

During 2015, we announced the signings of our first ingredient supply agreement and collaboration
agreement for the global nutraceuticals market. Under the supply agreement, we sourced Biofene to our
partner, which was then further processed into a nutraceutical product. In 2016, we made the first
large-scale shipments of Biofene to our partner, who successfully produced and sold a nutraceutical product
to its customers. In 2017 and 2018, we expanded our collaborations in nutraceuticals to four vitamins and a
human nutrition ingredient.

Flavor & Fragrance Markets

Our technology enables us to cost-effectively produce natural oils and aroma chemicals that are
commonly used in the Flavor & Fragrance market. Many of the natural ingredients used in the Flavor &
Fragrance market are expensive because there is limited supply and the synthetic alternatives require
complex chemical conversions. We offer Flavor & Fragrance companies a natural route to procure these
high-value ingredients without sacrificing cost or quality. To date, we have successfully brought four
Flavor & Fragrance ingredients to market with our collaboration partners. We also have several other
ingredients under development.

In late 2013, we commenced commercial production of our first Flavor & Fragrance ingredient for a
range of applications, from perfumes to laundry detergent, which is marketed by a collaboration partner
which is a global Flavor & Fragrance leader. In 2014, we completed our first production campaign of this
ingredient and shipped it to this collaboration partner. In late 2015, we commenced production and initial
sales of our second Flavor & Fragrance ingredient to the same collaboration partner. During 2018, we
shipped five compounds destined for the Flavor & Fragrance market (including compounds converted by
our partners to Flavor & Fragrance ingredients) to our partners.

We are currently working to develop and commercialize a variety of Flavor & Fragrance ingredients

that are either direct fermentation products or derivatives of fermentation products.

Clean Beauty

Our Clean Beauty focus includes skincare and cosmetic ingredients we develop and commercialize with
our partners and our branded Biossance and Neossance product lines. We have several cosmetic ingredients
currently under development. Our Biossance and Neossance products are discussed further in the
Amyris-branded Product Markets section below.

Amyris-branded Product Markets

Through basic chemical finishing steps, we are able to convert our farnesene into squalane, which is
used today as a premium emollient in Clean Skincare products. We believe that our squalane offers
performance attributes equal or superior to those of squalane derived from conventional sources. The

ingredient traditionally has been manufactured from olive oil or extracted from deep-sea shark liver oil,
which requires that the shark be killed in order to harvest its liver oil. The relatively high price and unstable
supply of squalane in the past meant that its use was generally limited to luxury products or small
quantities in mass-market product formulations. With our ability to produce a reliable supply of low-cost
squalane that eliminates the need to harvest shark liver oil, we offer this ingredient at a price that we believe
will drive increasing adoption by formulators. In addition to squalane, we offer a second, lower-cost
emollient, hemisqualane, for the cosmetics market. In December 2016, we and Nikko Chemicals Co., Ltd.
(Nikko) formed a joint venture, in which we hold a 50% interest, for our business-to-business sales of
Neossance squalane and hemisqualane. See below under “Joint Venture” for more information regarding
our Aprinnova joint venture. The joint venture currently has supply agreements with several regional
distributors, including those with locations in Japan, South Korea, Europe, Brazil and North America, and,
in some cases, directly with cosmetics formulators, which we transferred to the joint venture during the
formation process.

Our consumer skincare products, sold under our Biossance brand, feature our Biofene-derived
squalane. Under our Biossance brand, we market and sell our products directly to retailers and consumers.
Biossance was initially sold solely through our ecommerce branded website and in 2016, we expanded the
product line to include an expansive line of high-performance skincare products and opened up sales
through Home Shopping Network (HSN). In October 2016, we announced our Biossance product line
would begin to be carried at Sephora in 2017. In February 2017, we launched a full squalane-based
consumer cosmetic line at participating Sephora stores and Sephora online. All of the products are based
on our commitment to No Compromise®. Since the launch of Biossance, sales have grown, and with
Sephora’s partnership, we are looking to expand to more stores.

Manufacturing

Until December 2017, we owned and operated a purpose-built, large-scale production facility located
in Brotas, Brazil. In December 2017, we sold the facility to a unit of DSM and entered into a supply
agreement with DSM for us to purchase output from the facility. See Note 13, “Divestiture” and Note 11,
“Related Party Transactions” in Part II, Item 8 of this Annual Report on Form 10-K for additional
information regarding our December 2017 transaction with DSM.

In September 2019, we obtained the necessary permits and broke ground on our Specialty Ingredients
Plant (SIP). We expect the facility to be fully operational in Q1 of 2021. This facility will allow us to
manufacture five products at once and to produce both our specialty ingredients portfolio and our new
sweetener product. During construction, we are manufacturing our products at
four contract
manufacturing sites in Brazil, the U.S. and Spain. In addition, in May 2019 we entered into an agreement
with Raizen Energia S.A. (Raizen) for the formation and operation of a joint venture relating to the
production, sale and commercialization of alternative sweetener products whereby the parties would
construct a manufacturing facility exclusively for sweetener molecules on land owned by Raizen and leased
to the joint venture; see Note 16, “Subsequent Events” in Part II, Item 8 of this Annual Report on
Form 10-K for more details.

For many of our products, we perform additional distillation or chemical finishing steps to convert
initial target molecules into other finished products, such as renewable squalane. We have agreements with
several facilities in the U.S. and Brazil to perform these downstream steps for such products. We may enter
into additional agreements with other facilities for finishing services and to access flexible production
capacity and an array of other services as we develop additional products. In December 2016, we purchased
a manufacturing facility in Leland, North Carolina, which had been previously operated by Glycotech Inc.
(Glycotech) to convert our Biofene into squalane and other final products. We subsequently contributed
that facility to our Aprinnova joint venture. See below under “Joint Venture” for more information
regarding our Aprinnova joint venture.

Joint Venture

Aprinnova, LLC

In December 2016, we entered into joint venture agreements with Nikko related to the formation of a
joint venture to focus on the worldwide commercialization of our Neossance cosmetic ingredients business.

In December 2016, we formed the joint venture under the name Neossance, LLC, and later changed the
name to Aprinnova, LLC (the Aprinnova JV), which is jointly owned by us and Nikko. Pursuant to the
joint venture agreements, we contributed certain assets to the Aprinnova JV, including certain intellectual
property and other commercial assets relating to our Neossance cosmetic ingredients business, as well as the
production facility in Leland, North Carolina and related assets purchased by us from Glycotech in
December 2016. We also agreed to provide the Aprinnova JV with licenses to certain intellectual property
necessary to make and sell products associated with the Neossance business. At the closing of the formation
of the joint venture, Nikko purchased a 50% interest in the Aprinnova JV in exchange for an initial payment
to Amyris of $10.0 million and payment to Amyris of any profits distributed in cash to Nikko from the
Aprinnova JV during the three year period following December 12, 2016, up to a maximum of
$10.0 million. In addition, as part of the formation of the Aprinnova JV, we and Nikko agreed to make
certain working capital loans to the Aprinnova JV and we further agreed to execute a supply agreement to
supply farnesene to the Aprinnova JV, to purchase all of our requirements for the Aprinnova JV products
from the Aprinnova JV, to transfer all of our customers for the Aprinnova JV products to the Aprinnova
JV, to guarantee a maximum production cost for certain Aprinnova JV products, and to bear any cost of
production above such guaranteed costs.

Product Distribution and Sales

We distribute and sell our products directly to distributors or collaboration partners, or through joint
ventures, depending on the market. For most of our products, we sell directly to our collaboration partners,
except for our consumer care products, which we sell to distributors and formulators (other than our
Biossance brand, which we sell directly to retailers and consumers). Generally, our collaboration agreements
include commercial terms, and sales are contingent upon achievement of
technical and commercial
milestones.

For the year ended December 31, 2018, revenue from 10%-or-more customers and from all other

customers was as follows:

(In thousands)

Firmenich . . . . . . . . . . . . . . . . . . . . . . . . . . . .
DSM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
DARPA . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Givaudan . . . . . . . . . . . . . . . . . . . . . . . . . . . .
All other customers . . . . . . . . . . . . . . . . . . . . .

Renewable
Products

$ 3,727
18
—
4,078
25,775

Licenses
and
Royalties

$1,700
5,958
—
—
—

Grants and
Collaborations

Total
Revenue

% of Total
Revenue

$ 5,717
4,735
8,436
4,358
(898)

$11,144
10,711
8,436
8,436
24,877

$63,604

17.5%
16.8%
13.3%
13.3%
39.1%

100.0%

Total revenue . . . . . . . . . . . . . . . . . . . . . . . .

$33,598

$7,658

$22,348

Intellectual Property

Our success depends in large part upon our ability to obtain and maintain proprietary protection for
our products and technologies, and to operate without infringing on the proprietary rights of others. We
seek to avoid the latter by monitoring patents and publications in our product areas and technologies to be
aware of developments that may affect our business, and to the extent we identify such developments,
evaluate and take appropriate courses of action. With respect to the former, our policy is to protect our
proprietary position by, among other methods, filing for patent applications on inventions that are
important to the development and conduct of our business with the U.S. Patent and Trademark Office (the
USPTO), and its foreign counterparts.

As of December 31, 2018, we had 512 issued U.S. and foreign patents and 313 pending U.S. and
foreign patent applications that are owned or co-owned by or licensed to us. We also use other forms of
protection (such as trademark, copyright, and trade secret) to protect our intellectual property, particularly
where we do not believe patent protection is appropriate or obtainable. We aim to take advantage of all of
the intellectual property rights that are available to us and believe that this comprehensive approach
provides us with a strong proprietary position.

Patents extend for varying periods according to the date of patent filing or grant and the legal term of
patents in various countries where patent protection is obtained. The actual protection afforded by patents,
which can vary from country to country, depends on the type of patent, the scope of its coverage and the
availability of legal remedies in the country. See “Risk Factors — Risks Related to Our Business — Our
proprietary rights may not adequately protect our technologies and product candidates.”

We also protect our proprietary information by requiring our employees, consultants, contractors and
other advisers to execute nondisclosure and assignment of invention agreements upon commencement of
their respective employment or engagement. Agreements with our employees also prevent them from
bringing the proprietary rights of third parties to us. In addition, we also require confidentiality or material
transfer agreements from third parties that receive our confidential data or materials.

Trademarks

Amyris, the Amyris logo, Biofene, Biossance and No Compromise are trademarks or registered
trademarks of Amyris, Inc. This report also contains trademarks and trade names of other businesses that
are the property of their respective holders.

Competition

We expect that our renewable products will compete with products produced from traditional sources
as well as from alternative production methods that established enterprises and new companies are seeking
to develop and commercialize.

Health & Wellness

Many active ingredients in the nutraceutical market are made via chemical synthesis by suppliers that
have a deep chemistry knowhow and production facilities, including ingredient suppliers. We may compete
directly with these companies with respect to specific ingredients or attempt to provide customers with more
cost effective or higher performing alternatives. For food ingredients, we compete with companies that
produce products from plant- and animal-derived sources as well as with companies that are also
developing biotechnology production solutions to produce specific molecules.

Flavor & Fragrance

The main competition in the Flavor & Fragrance and cosmetic actives markets is from products
derived from plant and animal sources as well as chemical synthesis. The products derived from plant and
animal sources are typically produced at a higher cost, lower purity and create a greater impact on the
environment compared to our products. Products derived from chemical synthesis are often produced at a
low cost but have ramifications on sustainability as well as non-natural sourcing. There are also companies
that are working to develop products using similar technology to us.

Clean Beauty

We develop and sell active cosmetic ingredients and consumer products in the Clean Beauty market,
creating a competitive landscape that includes ingredient suppliers as well as consumer goods companies,
such as Procter & Gamble and Estee Lauder. Most skincare ingredients are derived from plant and animal
sources or created using chemical synthesis. Plant- and animal-sourced ingredients are typically higher in
cost, lower in purity and have a greater impact on the environment versus our products. Products derived
from chemical synthesis are often produced at a low cost but have ramifications on sustainability as well as
non-natural sourcing. There are also companies that are working to develop products using similar
technology to us.

Competitive Factors

We believe the primary competitive factors in our target markets are:

•

product price;

product performance and other measures of quality;

•

infrastructure compatibility of products;

sustainability; and

dependability of supply.

We believe that, for our products to succeed in the market, we must demonstrate that our products are
comparable or better alternatives to existing products and to any alternative products that are being
developed for the same markets based on some combination of product cost, availability, performance, and
consumer preference characteristics.

Regulatory Matters

Environmental Regulations

involve the use, generation, handling,

Our development and production processes

storage,
transportation and disposal of hazardous chemicals and radioactive and biological materials. We are subject
to a variety of federal, state, local and international laws, regulations and permit requirements governing the
use, generation, manufacture, transportation, storage, handling and disposal of these materials in the
United States, Brazil and other countries where we operate or may operate or sell our products in the
future. These laws, regulations and permits can require expensive fees, pollution control equipment or
operational changes to limit actual or potential impact of our technology on the environment and violation
of these laws could result in significant fines, civil sanctions, permit revocation or costs from environmental
remediation. We believe we are currently in substantial compliance with applicable environmental
regulations and permitting. However, future developments including the commencement of or changes in
the processes relating to commercial manufacturing of one or more of our products, more stringent
environmental regulation, policies and enforcement, the implementation of new laws and regulations or the
discovery of unknown environmental conditions may require expenditures that could have a material
adverse effect on our business, results of operations or financial condition. See “Risk Factors — Risks
Relating to Our Business — We may incur significant costs to comply with environmental laws and regulations,
and failure to comply with these laws and regulations could expose us to significant liabilities.”

GMM Regulations

The use of genetically-modified microorganisms (GMMs), such as our yeast strains, is subject to laws
and regulations in many countries. In the United States, the Environmental Protection Agency (EPA)
regulates the commercial use of GMMs as well as potential products produced from the GMMs. Various
states within the United States could choose to regulate products made with GMMs as well. While the
strain of genetically modified yeast that we use, S. cerevisiae, is eligible for exemption from EPA review
because it is generally recognized as safe, we must satisfy certain criteria to achieve this exemption,
including but not limited to, use of compliant containment structures and safety procedures. In Brazil,
GMMs are regulated by the National Biosafety Technical Commission (CTNBio) under its Biosafety Law
No. 11.105-2005. We have obtained commercial approvals from CTNBio to use our GMMs in a contained
environment in our Brazil facilities for research and development purposes, in manufacturing and at
contract manufacturing facilities in Brazil.

We expect to encounter GMM regulations in most if not all of the countries in which we may seek to
make our products; however, the scope and nature of these regulations will likely vary from country to
country. If we cannot meet the applicable requirements in countries in which we intend to produce our
products using our yeast strains, then our business will be adversely affected. See “Risk Factors — Risks
Related to Our Business — Our use of genetically-modified feedstocks and yeast strains to produce our
products subjects us to risks of regulatory limitations and rejection of our products.”

Chemical Regulations

Our renewable products may be subject to government regulations in our target markets. In the United
States, the EPA administers the requirements of the Toxic Substances Control Act (TSCA), which regulates
the commercial registration, distribution and use of many chemicals. Before an entity can manufacture or
distribute significant volumes of a chemical, it needs to determine whether that chemical is listed in the

TSCA inventory. If the substance is listed, then manufacture or distribution can commence immediately. If
not, then in most cases a “Chemical Abstracts Service” number registration and pre-manufacture notice
must be filed with the EPA, which has 90 days to review the filing. A similar requirement exists in Europe
under the Registration, Evaluation, Authorization and Restriction of Chemical Substances (REACH)
regulation. See “Risk Factors — Risks Related to Our Business — We may not be able to obtain regulatory
approval for the sale of our renewable products.” In 2013, the EPA registered farnesane as a new chemical
substance under the TSCA, which enables us to manufacture and sell farnesane without restriction in the
United States.

Other Regulations

Certain of our current or proposed products in the Health & Wellness, Clean Beauty, and Flavor &
Fragrance markets,
including alternative sweeteners, nutraceuticals, Flavor & Fragrance ingredients,
skincare ingredients, cosmetic actives, and our proposed cannabinoid products, may be subject to regulation
by the FDA, as well as similar agencies of states and foreign jurisdictions where these products are
manufactured, sold or proposed to be sold. Pursuant to the Federal Food, Drug, and Cosmetic Act (the
FDCA), the FDA regulates the processing, formulation, safety, manufacture, packaging, labeling and
distribution of food ingredients, vitamins, and cosmetics. Generally, in order to be marketed and sold in the
United States, a relevant product must be generally recognized as safe, approved and not adulterated or
misbranded under the FDCA and relevant regulations issued thereunder. The FDA has broad authority to
enforce the provisions of the FDCA applicable to food ingredients, vitamins and cosmetics, including
powers to issue a public warning letter to a company, to publicize information about illegal products, to
request a recall of illegal products from the market, and to request the United States Department of Justice
to initiate a seizure action, an injunction action, or a criminal prosecution in the U. S. courts. Failure to
obtain requisite approval from, or comply with the laws and regulations of, the FDA or similar agencies of
states and applicable foreign jurisdictions could prevent us from fully commercializing certain of our
products. See “Risk Factors — Risks Related to Our Business — We may not be able to obtain regulatory
approval for the sale of our renewable products.” Our proposed cannabinoid products may also be subject to
regulation under various federal, state and foreign-controlled substance laws and regulations. See “Risk
Factors — Our cannabinoid initiative is uncertain and may not yield commercial results and is subject to
significant regulatory risks.”

In addition, our end-user products such as our Biossance brand skincare products are subject to the
regulations of the United States Federal Trade Commission (FTC) and similar agencies of states and
foreign jurisdictions where these products are sold or proposed to be sold regarding the advertising of such
products. In recent years, the FTC has instituted numerous enforcement actions against companies for
failure to have adequate substantiation for claims made in advertising or for the use of false or misleading
advertising claims. The FTC has broad authority to enforce its laws and regulations applicable to cosmetics,
including the ability to institute enforcement actions which often result in consent decrees, injunctions, and
the payment of civil penalties by the companies involved. Failure to comply with the laws and regulations of
the FTC or similar agencies of states and applicable foreign jurisdictions could impair our ability to market
our end-user products.

Employees

As of December 31, 2018, we had 503 full-time employees, of whom 410 were in the United States and
93 were in Brazil. Except for labor union representation for Brazil-based employees based on labor code
requirements in Brazil, none of our employees is represented by a labor union or is covered by a collective
bargaining agreement. We have never experienced any employment-related work stoppages, and we consider
relations with our employees to be good.

Corporate Information

We were originally incorporated in California in 2003 under the name Amyris Biotechnologies, Inc.
and then reincorporated in Delaware in 2010 and changed our name to Amyris, Inc. Our principal executive
offices are located at 5885 Hollis Street, Suite 100, Emeryville, California 94608, and our telephone number
is (510) 450-0761. Our common stock is listed on The Nasdaq Global Select Market under the symbol
“AMRS”.

Available Information

Our website address is www.amyris.com. Our Annual Reports on Form 10-K, Quarterly Reports on
Form 10-Q, Current Reports on Form 8-K, and other reports filed pursuant to Sections 13(a) and 15(d) of
the Securities Exchange Act of 1934 (the Exchange Act), as well as amendments thereto, are filed with the
U.S. Securities and Exchange Commission (the SEC) and are available free of charge on our website at
investors.amyris.com promptly after such reports are available on the SEC’s website. We may use our
investors.amyris.com website as a means of disclosing material non-public information and complying with
our disclosure obligations under Regulation FD.

The SEC maintains an Internet site that contains reports, proxy and information statements, and other

information regarding issuers that file electronically with the SEC at www.sec.gov.

The information contained in or accessible through our website or contained on other websites is not
incorporated into this filing. Further, any references to URLs contained in this report are intended to be
inactive textual references only.

ITEM 1A. RISK FACTORS

Investing in our common stock involves a high degree of risk. You should carefully consider the risks and
uncertainties described below, together with all of the other information set forth in this Annual Report on
Form 10-K, including the consolidated financial statements and related notes, which could materially affect our
business, financial condition or future results. If any of the following risks actually occurs, our business,
financial condition, results of operations and future prospects could be materially and adversely harmed. The
trading price of our common stock could decline due to any of these risks, and, as a result, you may lose all or
part of your investment.

Risks Related to Our Business

The restatement of our previously issued financial statements has been time-consuming and expensive and
could expose us to additional risks that could materially adversely affect our financial position, results of
operations and cash flows.

On April 5, 2019, our Audit Committee, after consultation with management and KPMG LLP
(KPMG), our former independent registered public accounting firm, determined that we would restate our
interim condensed consolidated financial statements for the quarterly and year-to-date periods ended
March 31, 2018, June 30, 2018 and September 30, 2018, included in our Quarterly Reports on Form 10-Q
for the fiscal quarters ended March 31, 2018, June 30, 2018 and September 30, 2018, respectively. In
addition, on May 14, 2019, our Board of Directors, upon the recommendation of the Audit Committee
after consultation with senior management and KPMG, determined that we would restate our audited
consolidated financial statements for the year ended December 31, 2017. During the preparation and audit
of our consolidated financial statements for the fiscal year ended December 31, 2018 included in this
Annual Report on Form 10-K, we concluded that material errors were made as described in Note 2,
“Restatement of Consolidated Financial Statements” to the Consolidated Financial Statements herein. The
consolidated financial statements and related information included in our previously filed Annual Report
on Form 10-K for the year ended December 31, 2017 and Quarterly Reports on Form 10-Q for the periods
ended March 31, 2018, June 30, 2018 and September 30, 2018 and all earnings press releases and similar
communications issued by us for such periods should not be relied upon and are superseded in their entirety
by this Annual Report on Form 10-K.

Accordingly, this Annual Report on Form 10-K as of and for the year ended December 31, 2018
includes: (1) changes to our consolidated financial statements to reflect the restatement of our audited
consolidated financial statements for the year ended December 31, 2017 and our unaudited interim
condensed consolidated financial statements for the quarterly and year-to-date periods ended March 31,
2018, June 30, 2018 and September 30, 2018; (2) changes as to reflect the restatement of our unaudited
quarterly and year-to-date periods ended March 31, 2017, June 30, 2017 and September 30, 2017 for
additional errors identified during the re-audit of our consolidated financial statements for the year ended
December 31, 2017; (3) expanded risk factor disclosures within this Part I, Item 1A; and (4) additional
disclosures and conclusions regarding our disclosure controls and procedures and internal control over
financial reporting in Part II, Item 9A.

As a result of the restatement and associated non-reliance on previously issued financial information,
we have become subject to a number of additional expenses and risks, including unanticipated expenses for
accounting and legal fees in connection with or related to the restatement. Likewise, the attention of our
management team has been diverted by these efforts. In addition, we could also be subject to additional
shareholder, governmental, regulatory or other actions or demands in connection with the restatement or
other matters. Any such proceedings will, regardless of the outcome, consume a significant amount of
management’s time and attention and may result in additional legal, accounting, insurance and other
expenses. If we do not prevail in any such proceeding, we could be required to pay damages or settlement
costs. In addition, the restatement and related matters could impair our reputation or could cause our
customers, shareholders, or other counterparties to lose confidence in us. Any of these occurrences could
have a material adverse effect on our business, results of operations, financial condition and stock price.

We have identified material weaknesses in our internal control over financial reporting which, if not corrected,
could affect the reliability of our consolidated financial statements and have other adverse consequences.

Our management is responsible for establishing and maintaining adequate internal control over
financial reporting, as defined in Rule 13a-15(f) under the Exchange Act. Section 404 of
the
Sarbanes-Oxley Act of 2002 (Section 404) and related SEC rules require management to assess the
effectiveness of our internal control over financial reporting. Based on the assessment as of December 31,
2018, our management believes that our internal control over financial reporting was not effective at that
date due to material weaknesses we identified. A material weakness is a deficiency, or combination of
control deficiencies, in internal control over financial reporting, such that there is a reasonable possibility
that a material misstatement of our annual or interim financial statements will not be prevented or detected
on a timely basis.

Based on management’s assessment, we have identified the following material weaknesses:

•

Our control environment is not effective because we lack a sufficient number of trained resources
with assigned responsibility and accountability over the application of generally accepted
accounting principles and financial reporting and related internal controls over complex,
significant non-routine transactions and routine transactions;

• We did not have an effective risk assessment process to identify and analyze necessary changes in
business operations resulting from complex significant non-routine transactions and completeness
and adequacy of required disclosures;

• We did not have an effective internal and external information and communication process to
ensure that relevant and reliable information was communicated timely across the organization, to
enable financial personnel to effectively carry out their financial reporting and internal control
roles and responsibilities; and

•

The Company did not design, implement and operate effective monitoring activities over complex,
significant non-routine transactions and the accounting for income taxes to ascertain whether the
processes and internal controls were present and functioning.

As a consequence of

information and
communication and monitoring activities components, we did not design,
implement, and maintain
effective control activities at the transaction level over all significant accounts to mitigate the risk of
material misstatement in financial reporting, specifically:

the ineffective control environment, risk assessment,

• We did not retain the required documentation to demonstrate the consistent and timely operation
of the controls at a sufficient level of precision to prevent and detect potential misstatements; and

• We did not design and operate effective controls over account reconciliations, review and approval
of manual journal entries, complex, significant non-routine transactions related to licenses and
royalty revenue recognition, derivative liabilities, currency translation adjustments and the
completeness and accuracy and timely preparation of
financial statement presentation and
disclosures, including earnings per share.

The control deficiencies contributed to the restatement of our audited consolidated financial
statements for the year ended December 31, 2017 and resulted in material errors to our interim condensed
consolidated financial statements for the quarterly and year-to-date periods ended March 31, 2017, June 30,
2017, September 30, 2017, March 31, 2018, June 30, 2018 and September 30, 2018, as described above, and
material and immaterial misstatements to the preliminary consolidated financial statements as of and for
the year ended December 31, 2018. Material misstatements were corrected prior to the issuance of the
consolidated financial statements as of and for the year ended December 31, 2018. However, the control
deficiencies resulted in the restatement discussed above and create a reasonable possibility that a further
material misstatement of our annual or interim consolidated financial statements would not be prevented or
detected on a timely basis. Furthermore, the control deficiencies contributed to a delay in the timely filing of
our periodic reports. Therefore, we concluded that these control deficiencies are material weaknesses and
our internal control over financial reporting is not effective as of December 31, 2018.

See Part II, Item 9A “Controls and Procedures” of this Annual Report on Form 10-K for additional
information. If not remediated, the material weaknesses could result in further material misstatements to
our annual or interim consolidated financial statements that would not be prevented or detected on a timely
basis, or in delayed filing of required periodic reports. Our management has developed, and begun to
implement, a plan to remediate the material weaknesses. We cannot, however, assure you that we will be able
to implement the plan, or to remediate the material weaknesses in a timely manner. Furthermore, during the
course of re-design of existing processes and controls, implementation of additional processes and controls
and testing of the operating effectiveness of such re-designed and additional processes and controls, we may
identify additional control deficiencies that could give rise to other material weaknesses, in addition to the
currently identified material weaknesses. We expect the remediation plan to extend over multiple financial
reporting periods in 2019 and 2020. If our remedial measures are insufficient to address the material
weakness, or if additional material weaknesses or significant deficiencies in our internal controls are
discovered or occur in the future, we may be unable to report our financial results accurately or on a timely
basis, which could cause our reported financial results to be materially misstated and result in the loss of
investor confidence and adversely affect the market price of our common stock and our ability to access the
capital markets, and we could be subject to sanctions or investigations by the Nasdaq Stock Market
(Nasdaq), the SEC or other regulatory authorities.

If we fail to maintain an effective system of internal controls, we may not be able to report our financial results
accurately or in a timely manner or prevent fraud; in that case, our stockholders could lose confidence in our
financial reporting, which would harm our business and could negatively impact the price of our stock.

Effective internal controls are necessary for us to provide reliable financial reports and help us to
prevent fraud. In addition, Section 404 of the Sarbanes-Oxley Act of 2002 (Section 404) requires us and
our independent registered public accounting firm to evaluate and report on our internal control over
financial reporting. The process of implementing our internal controls and complying with Section 404 is
expensive and time consuming, and requires significant continuous attention of management. We cannot be
certain that these measures will ensure that we maintain adequate controls over our financial processes and
reporting in the future. In addition, to the extent we create joint ventures or have any variable interest
entities and the financial statements of such entities are not prepared by us, we will not have direct control
over their financial statement preparation. As a result, we will, for our financial reporting, depend on what
these entities report to us, which could result in us adding monitoring and audit processes to those
operations and increase the difficulty of implementing and maintaining adequate internal control over our
financial processes and reporting in the future, which could lead to delays in our external reporting. In
particular, this may occur in instances in which where we are establishing such entities with commercial
partners that do not have sophisticated financial accounting processes in place, or where we are entering
into new relationships at a rapid pace, straining our integration capacity. Additionally, if we do not receive
the information from the joint venture or variable interest entity on a timely basis, it could cause delays in
our external reporting. Even if we conclude in the future, and our independent registered public accounting
firm concurs, that our internal control over financial reporting provides reasonable assurance regarding the
reliability of financial reporting and the preparation of financial statements for external purposes in
accordance with generally accepted accounting principles, because of its inherent limitations, internal
control over financial reporting may not prevent or detect fraud or misstatements. Failure to implement
required new or improved controls, or difficulties encountered in their implementation, could harm our
results of operations or cause us to fail to meet our reporting obligations, which could reduce the market’s
confidence in our financial statements and harm our stock price. In addition, failure to comply with
Section 404 could subject us to a variety of administrative sanctions, including SEC action, the suspension
or delisting of our common stock from the stock exchange on which it is listed, and the inability of
registered broker-dealers to make a market in the Company’s common stock, which could further reduce
our stock price and could harm our business.

We have incurred losses to date, anticipate continuing to incur losses in the future, and may never achieve or
sustain profitability.

We have incurred significant operating losses since our inception, and we expect to continue to incur
losses and negative cash flows from operations for at least the next 12 months following the issuance of this
Annual Report on Form 10-K. As of December 31, 2018, we had negative working capital of $119.5 million
and an accumulated deficit of $1.5 billion.

As of December 31, 2018, our debt (including related party debt), net of deferred discount and
issuance costs of $17.1 million and a fair value adjustment of $2.1 million, totaled $209.7 million, of which
$147.7 million is classified as current. Our debt agreements contain various covenants, including certain
restrictions on our business that could cause us to be at risk of contractual defaults, such as restrictions on
additional indebtedness, material adverse effect and cross default clauses. A failure to comply with the
covenants and other provisions of our debt instruments, including any failure to make a payment when
required, would generally result in events of default under such instruments, which could permit
acceleration of a substantial portion of such indebtedness. If such indebtedness is accelerated, it would
generally also constitute an event of default under our other outstanding indebtedness, permitting
acceleration of a substantial portion of such other outstanding indebtedness. We have in the past, including
in July 2019, had certain of our debt instruments accelerated for failure to make a payment when due. While
we have been able to cure these defaults to date to avoid additional cross-acceleration, we may not be able to
cure such a default promptly in the future. See Note 16, “Subsequent Events” in Part II, Item 8 of this
Annual Report on Form 10-K for additional information.

Our cash and cash equivalents of $45.4 million as of December 31, 2018 will not be sufficient to fund
expected future negative cash flows from operations and cash debt service obligations through
September 30, 2020. These factors raise substantial doubt about our ability to continue as a going concern
within one year after the date that these financial statements are issued. The financial statements do not
include any adjustments that might result from the outcome of this uncertainty. Our ability to continue as a
going concern will depend, in large part, on our ability to achieve positive cash flows from operations
during the 12 months from the date of this filing, and refinance or extend other existing debt maturities
occurring later in 2019, all of which is uncertain and outside our control. Further, our operating plan for
2019 contemplates a significant reduction in our net operating cash outflows as compared to the year ended
December 31, 2018, resulting from (i) revenue growth from sales of existing and new products with positive
gross margins, (ii) reduced production costs as a result of manufacturing and technical developments, and
(iii) cash inflows from collaborations and grants. If we are unable to complete these actions, we expect to be
unable to meet our operating cash flow needs and our obligations under our existing debt facilities. This
could result in an acceleration of our obligation to repay all amounts outstanding under those facilities, and
the Company may be forced to obtain additional equity or debt financing, which may not occur timely or
on reasonable terms, if at all, and/or liquidate our assets. In such a scenario, the value received for assets in
liquidation or dissolution could be significantly lower than the value reflected in these financial statements.

Our consolidated financial statements do not include any adjustments that might result from the
outcome of this uncertainty, which could have a material adverse effect on our financial condition and
cause investors to suffer the loss of all or a substantial portion of their investment.

We will require significant cash inflows from the sales of renewable products, licenses and royalties, and grants
and collaborations and, if needed, financings to fund our anticipated operations and to service our debt
obligations and may not be able to obtain such funding on favorable terms, if at all.

Our planned working capital needs and operating and capital expenditures for 2019, and our ability to
service our outstanding debt obligations, are dependent on significant inflows of cash from grants and
collaborations, licenses and royalties, and product sales and, if needed, additional financing arrangements.
We will continue to need to fund our research and development and related activities and to provide
working capital to fund production, procurement, storage, distribution and other aspects of our business.
Some of our anticipated funding sources, such as research and development collaborations, are subject to
the risks that we may not be able to meet milestones, or that collaborations may end prematurely for
the project or a
reasons that may be outside of our control (including technical

infeasibility of

collaborator’s right to terminate without cause). The inability to generate sufficient cash flow, as described
above, could have an adverse effect on our ability to continue with our business plans and our status as a
going concern.

If we are unable to raise additional funding, or if other expected sources of funding are delayed or not
received, our ability to continue as a going concern would be jeopardized and we would take the following
actions:

•

Shift focus to existing products and customers with significantly reduced investment in new
product and commercial development efforts;

Reduce expenditures for third party contractors, including consultants, professional advisors and
other vendors;

Reduce or delay uncommitted capital expenditures,
related the
construction and commissioning of the new production facility in Brazil, nonessential facilities
and lab equipment, and information technology projects; and

including expenditures

Closely monitor our working capital position with customers and suppliers, as well as suspend
operations at pilot plants and demonstration facilities.

Implementing this plan could have a negative impact on our ability to continue our business as

currently contemplated, including, without limitation, delays or failures in our ability to:

•

Achieve planned production levels;

Develop and commercialize products within planned timelines or at planned scales; and

Continue other core activities.

Furthermore, any inability to scale-back operations as necessary, and any unexpected liquidity needs,
could create pressure to implement more severe measures. Such measures could have an adverse effect on
our ability to meet contractual requirements and increase the severity of the consequences described above.

Our existing financing arrangements provide our secured lenders with liens on substantially all of our assets,
including our intellectual property, and contain financial covenants and other restrictions on our actions, which
may cause significant risks to our stockholders and may impact our ability to pursue certain transactions and
operate our business.

As of December 31, 2018, our debt totaled $209.7 million, net of discount and issuance costs of
$17.1 million and a fair value adjustment of $2.1 million, of which $147.7 million is classified as current.
Our cash balance is substantially less than the principal amount of our outstanding debt, and we will be
required to generate cash from operations or raise additional working capital through future financings or
sales of assets to enable us to repay this indebtedness as it becomes due. There can be no assurance that we
will be able to do so.

In addition, we have granted liens on substantially all of our assets, including our intellectual property,
as collateral in connection with certain financing arrangements with a current aggregate principal amount
outstanding of $81.5 million, and have agreed to significant covenants in connection with such transactions
(see Note 5, “Debt” and Note 16, “Subsequent Events” in Part II, Item 8 of this Annual Report on
Form 10-K), including covenants that materially limit our ability to take certain actions, including our
ability to pay dividends, make certain investments and other payments, incur additional indebtedness,
undertake certain mergers and consolidations, and encumber and dispose of assets, and customary events
of default, including failure to pay amounts due, breaches of covenants and warranties, material adverse
effect events, certain cross defaults and judgements, and insolvency. For example, the loan and security
agreements relating to our secured term loan credit facilities that closed in June 2018 and August 2019
prevent us from incurring additional indebtedness, making investments, encumbering our assets, engaging in
certain corporate transactions, such as mergers and consolidations, and transferring or otherwise disposing
of assets, subject in each case to certain exceptions, and also require us to maintain certain liquidity and
asset coverage levels and meet certain revenue requirements. A failure to comply with the covenants and
other provisions of our debt instruments, including any failure to make a payment when required, would

generally result in events of default under such instruments, which could permit acceleration of such
indebtedness and could result in a material adverse effect on us. If such indebtedness is accelerated, it would
generally also constitute an event of default under our other outstanding indebtedness, permitting
acceleration of a substantial portion of our indebtedness. Any required repayment of our indebtedness as a
result of acceleration or otherwise would lower our current cash on hand such that we would not have those
funds available for use in our business or for payment of other outstanding indebtedness.

If we are at any time unable to generate sufficient cash flow from operations to service our
indebtedness when payment is due, we may be required to attempt to renegotiate the terms of the
instruments relating to the indebtedness, seek to refinance all or a portion of the indebtedness or obtain
additional financing. There can be no assurance that we would be able to successfully renegotiate such
terms, that any such refinancing would be possible or that any additional financing could be obtained on
terms that are favorable or acceptable to us, if at all. Any debt financing that is available could cause us to
incur substantial costs and subject us to covenants that significantly restrict our ability to conduct our
business. If we seek to complete additional equity financings, the interests of existing equity holders may be
diluted. If we are unable to make payment on our secured debt instruments when due, the lenders under
such instruments may foreclose on and sell the assets securing such indebtedness to satisfy our payment
obligations, which could prevent us from accessing those assets for our business and conducting our
business as planned, which could materially harm our financial condition and results of operations.

In addition, certain of our outstanding securities contain anti-dilution adjustment provisions that may
be triggered by future issuances of equity or equity-linked instruments in financing transactions. If such
adjustment provisions are triggered, the conversion or exercise price of such securities will decrease and/or
the number of shares issuable upon conversion or exercise of such securities will increase. In such event,
existing stockholders will be further diluted and the effective issuance price of such equity or equity-linked
instruments will be reduced, which may harm our ability to engage in future financing transactions to fund
our business.

Our substantial leverage may place us at a competitive disadvantage in our industry.

We continue to have substantial debt outstanding and we may incur additional indebtedness from time
to time to finance working capital, product development efforts, strategic acquisitions, investments and
partnerships, or capital expenditures, or for other general corporate purposes, subject to the restrictions
contained in our debt agreements. Our significant indebtedness and debt service requirements could
adversely affect our ability to operate our business and may limit our ability to take advantage of potential
business opportunities. For example, our high level of indebtedness presents the following risks:

•

we will be required to use a substantial portion of our cash flow from operations to pay principal
and interest on our indebtedness, thereby reducing the availability of our cash flow to fund
working capital, capital expenditures, product development efforts, acquisitions, investments and
strategic alliances and for other general corporate requirements;

our substantial
leverage increases our vulnerability to economic downturns and adverse
competitive and industry conditions and could place us at a competitive disadvantage compared
to those of our competitors that are less leveraged;

our debt service obligations could limit our flexibility in planning for, or reacting to, changes in
our business and our industry and could limit our ability to pursue other business opportunities,
borrow more money for operations or capital in the future and implement our business strategies;

our level of indebtedness and the covenants in our debt instruments may restrict us from raising
additional financing on satisfactory terms to fund working capital, capital expenditures, product
development efforts, strategic acquisitions,
investments and alliances, and for other general
corporate requirements;

our secured loan agreements restrict our ability to grant additional liens on our assets, which may
make it more difficult to secure additional financing in the future; and

our substantial leverage may make it difficult for us to attract additional financing when needed.

We are currently ineligible to use a registration statement on Form S-3 to register the offer and sale of
securities, which could adversely affect our ability to raise future capital.

As a result of the delayed filing of this Annual Report on Form 10-K, our Quarterly Report on
Form 10-Q for the fiscal quarter ended March 31, 2019 and our Quarterly Report on Form 10-Q for the
fiscal quarter ended June 30, 2019 with the SEC, we will not be eligible to register the offer and sale of our
securities using a registration statement on Form S-3 until one year from the date we regain and maintain
status as a current filer. Should we wish to register the offer and sale of our securities to the public prior to
the time we are eligible to use Form S-3, both our transaction costs and the amount of time required to
complete the transaction could increase, potentially harming our financial condition.

Future revenues are difficult to predict, and our failure to predict revenue accurately may cause our results to
be below our expectations or those of analysts or investors and could result in our stock price declining.

Our revenues are comprised of product revenues, licenses and royalties revenues, and grants and
collaborations revenues. We generate the substantial majority of our product revenues from sales to
collaboration partners and distributors, and only a small portion from direct sales. Our collaboration,
supply and distribution agreements do not usually include any specific purchase obligations. The sales
volume of our products in any given period has been difficult to predict. A significant portion of our
product sales is dependent upon the interest and ability of third-party distributors to create demand for,
and generate sales of, such products to end-users. For example, if such distributors are unsuccessful in
creating pull-through demand for our products with their customers, such distributors may purchase less of
our products from us than we expect. Also, under revenue recognition rules, we are required to estimate
royalties. These estimates could be subject to material adjustment in subsequent periods.

In addition, many of our new and novel products are intended to be a component of other companies’
products; therefore, sales of our products may be contingent on our collaboration partners and/or
customers’ timely and successful development and commercialization of end-use products that incorporate
our products, and price volatility in the markets for such end-use products, which may include commodities,
could adversely affect the demand for our products and the margin we receive for our product sales, which
could harm our financial results. While we maintain certain clawback rights to our technology in the event
our collaboration partners are unable or unwilling to commercialize the products we create for them, we
may be restricted from or unable to market or sell such products or technologies to other potential
collaboration partners, which could hinder the growth of our business. In addition, certain of our
collaboration partners have the right to terminate their agreements with us if we undergo a change of
control or a sale of our business, which could discourage a potential acquirer from making an offer to
acquire us.

Further, we have in the past entered into, and expect in the future to enter into, research and
development collaboration arrangements pursuant to which we receive payments from our collaboration
partners. Some of such collaboration arrangements include advance payments in consideration for grants of
exclusivity or research and development activities to be performed by us. It has in the past been difficult for
us to know with certainty when we will sign a new collaboration arrangement and receive payments
thereunder. In addition, a portion of the advance payments we receive under our collaboration agreements
is typically classified as deferred revenue and recognized over multiple quarters or years. As a result,
achievement of our quarterly and annual financial goals has been difficult to forecast with certainty. Once a
collaboration agreement has been signed, receipt of cash payments and/or recognition of related revenues
may depend on our achievement of research, development, production or cost milestones, which may be
difficult to predict. Our collaboration arrangements may also include future royalty payments upon
commercialization of the products subject to the collaboration arrangements, which is uncertain and
depends in part on the success of the counterparty in commercializing the relevant product. As a result, our
receipt of royalty revenues and the timing thereof is difficult to predict with certainty.

Furthermore, we have begun to market and sell some of our products directly to end-consumers,
initially in the cosmetics market. Because we have limited experience in marketing and selling directly to
consumers, it is difficult to predict how successful our efforts will be and we may not achieve the product
sales we expect to achieve on the timeline we anticipate, if at all. These factors have made it difficult to

predict future revenues and have resulted in our revenues being below our previously announced guidance
or analysts’ estimates. We continue to face these risks in the future, which may cause our stock price to
decline.

Our financial results could vary significantly from quarter to quarter and are difficult to predict.

Our revenues and results of operations could vary significantly from quarter to quarter because of a
variety of factors, many of which are outside of our control. As a result, comparing our results of
operations on a period-to-period basis may not be meaningful. Factors that could cause our quarterly
results of operations to fluctuate include:

•

achievement, or failure, with respect to technology, product development or manufacturing
milestones needed to allow us to enter identified markets on a cost-effective basis or obtain
milestone-related payments from collaboration partners;

delays or greater than anticipated expenses associated with the completion, commissioning,
acquisition or retrofitting of new production facilities, or the time to ramp up and stabilize
production at a new production facility or the transition (including ramp up) to producing new
molecules at existing facilities or with a new contract manufacturer;

impairment of assets based on shifting business priorities and working capital limitations;

disruptions in the production process at any manufacturing facility, including disruptions due to
seasonal or unexpected downtime as a result of feedstock availability, contamination, safety or
other technical difficulties, or scheduled downtime as a result of transitioning equipment to the
production of different molecules;

losses of, or the inability to secure new, major customers, collaboration partners, suppliers or
distributors;

losses associated with producing our products as we ramp to commercial production levels;

failure to recover value added tax (VAT) that we currently reflect as recoverable in our financial
statements (e.g., due to failure to meet conditions for reimbursement of VAT under local law);

the timing, size and mix of product sales to customers;

increases in price or decreases in availability of feedstock;

the unavailability of contract manufacturing capacity altogether or at reasonable cost;

exit costs associated with terminating contract manufacturing relationships;

fluctuations in foreign currency exchange rates;

change in the fair value of derivative instruments;

fluctuations in the price of and demand for sugar, ethanol, petroleum-based and other products
for which our products are alternatives;

seasonal variability in production and sales of our products;

competitive pricing pressures, including decreases in average selling prices of our products;

unanticipated expenses or delays associated with changes in governmental regulations and
environmental, health, labor and safety requirements;

departure of executives or other key management employees resulting in transition and severance
costs;

our ability to use our net operating loss carryforwards to offset future taxable income;

business interruptions such as earthquakes, tsunamis and other natural disasters;

our ability to integrate businesses that we may acquire;

our ability to successfully collaborate with joint venture partners;

•

risks associated with the international aspects of our business; and

changes in general economic, industry and market conditions, both domestically and in our
foreign markets.

Due to the factors described above, among others, the results of any quarterly or annual period may
not meet our expectations or the expectations of our investors and may not be meaningful indications of
our future performance.

A limited number of customers, collaboration partners and distributors account for a significant portion of our
revenues, and the loss of major customers, collaboration partners or distributors could harm our operating
results.

Our revenues have varied significantly from quarter to quarter and are dependent on sales to, and
collaborations with, a limited number of customers, collaboration partners and/or distributors. We cannot
be certain that customers, collaboration partners and/or distributors that have accounted for significant
revenues in past periods, individually or as a group, will continue to generate similar revenues in any future
period. If we fail to renew with, or if we lose, a major customer, collaborator or distributor, or group of
customers, collaboration partners or distributors, our revenues could decline if we are unable to replace the
lost revenues with revenues from other sources. Further, since our business depends in part on such
collaboration agreement, it may be difficult for us to replace any such lost revenues through additional
collaborations in any period, as revenue from such new collaborations will often be recognized over multiple
quarters or years.

If we do not meet technical, development and commercial milestones in our collaboration agreements, our
future revenues and financial results will be adversely impacted.

We have entered into a number of agreements regarding the development of certain of our products
and, in some cases, for ultimate sale of certain products to the customer under the agreement. Most of these
agreements do not affirmatively obligate the other party to purchase specific quantities of any products,
and most contain important conditions that must be satisfied before additional research and development
funding or product purchases would occur. These conditions include research and development milestones
and technical specifications that must be achieved to the satisfaction of our collaboration partners, which
we cannot be certain we will achieve. If we do not achieve these contractual milestones or specifications, our
revenues and financial results will be adversely affected.

We face challenges producing our products at commercial scale or at reduced cost and may not be able to
commercialize our products to the extent necessary to make a profit or sustain and grow our current business.

To commercialize our products, we must be successful in using our yeast strains to produce target
molecules at commercial scale and at a commercially viable cost. If we cannot achieve commercially-viable
production economics for enough products to support our business plan, including through establishing
and maintaining sufficient production scale and volume, we will be unable to achieve a sustainable products
business.

In order to be competitive in the markets we are targeting, our products must have superior qualities or
be competitively priced relative to alternatives available in the market. Our production costs depend on
many factors that could have a negative effect on our ability to offer our planned products at competitive
prices, including, in particular, our ability to establish and maintain sufficient production scale and volume,
and feedstock and contract manufacturing costs.

We face financial risk associated with scaling up production to reduce our production costs. To reduce
per-unit production costs, we must increase production to achieve economies of scale and to be able to sell
our products with positive margins. However, if we do not sell production output in a timely manner or in
sufficient volumes, our investment in production will harm our cash position and generate losses.
Additionally, we may incur added costs in storage and we may face issues related to the decrease in quality
of our stored products, which could adversely affect the value of such products. Since achieving competitive
product prices generally requires increased production volumes and our manufacturing operations and cash
flows from sales are in their early stages, we have had to produce and sell products at a loss in the past, and

may continue to do so as we build our business. If we are unable to achieve adequate revenues from a
combination of product sales and other sources, we may not be able to invest in production and we may not
be able to pursue our business plans. In addition, in order to attract potential collaboration or joint venture
partners, or to meet payment milestones under existing or future collaboration agreements, we have in the
past and may in the future be required to guarantee or meet certain levels of production costs. If we are
unable to reduce our production costs to meet such guarantees or milestones, our net cash flow will be
further reduced.

If we are not able to successfully commence, scale up or sustain operations at existing and planned
manufacturing facilities, our customer relationships, business and results of operations may be adversely
affected.

in 2012.

first purpose-built,

large-scale production facility located in Brotas, Brazil

A substantial component of our planned production capacity in the near and long term depends on
successful operations at our existing and potential large-scale production plants. We commenced operations
In
at our
December 2016, we acquired a production facility in Leland, North Carolina, which facility had been
previously operated by our partner Glycotech Inc. to perform chemical conversion and production of
certain of our end-products, and which facility was subsequently transferred to our newly-formed joint
venture with Nikko, as further described in Note 11, “Related Party Transactions” in Part II, Item 8 of this
Annual Report on Form 10-K. In December 2017, we sold the Brotas facility to DSM and concurrently
entered into a supply agreement with DSM for us to purchase output from the facility, which represents a
significant portion of our expected supply needs (see Note 13, “Divestiture”, Note 10, “Revenue
Recognition” and Note 11, “Related Party Transactions” in Part II, Item 8 of this Annual Report on
Form 10-K for more information). We are building a new purpose-built, large-scale specialty ingredients
plant in Brazil, which we anticipate will allow for the manufacture of five products concurrently and over
10 different products annually. We currently anticipate completing construction of the facility by the end of
2020; however, there can be no assurances that we will be able to complete such facility on our expected
timeline, if at all. In addition, in May 2019 we entered into a joint venture agreement with Raizen for the
production, sale and commercialization of alternative sweetener products, pursuant to which the parties
would construct a manufacturing facility exclusively for alternative sweetener products on land owned by
Raizen and leased to the joint venture; see Note 16, “Subsequent Events” in Part II, Item 8 of this Annual
Report on Form 10-K for more details. The consummation of the transactions contemplated by the joint
venture agreement, including the construction of a manufacturing facility for the production of alternative
sweetener products, is subject to conditions, including certain regulatory approvals and the achievement of
certain technological and economic milestones relating to the production of our alternative sweetener
product, and there can be no assurances that the construction of such facility will occur on our expected
timeline, if at all. Delays or problems in the construction, start-up or operation of such facilities could cause
delays in our ramp-up of production and hamper our ability to reduce our production costs. Delays in
construction can occur due to a variety of factors, including regulatory requirements and our ability to
fund construction and commissioning costs.

Once our large-scale production facilities are built, acquired or retrofitted, we must successfully
commission them, if necessary, and they must perform as we expect. If we encounter significant delays, cost
overruns, engineering issues, contamination problems, equipment or raw material supply constraints,
unexpected equipment maintenance requirements, safety issues, work stoppages or other serious challenges
in bringing these facilities online and operating them at commercial scale, we may be unable to produce our
renewable products in the time frame and at the cost we have planned. It is difficult to predict the effects of
scaling up production of industrial fermentation to commercial scale, as it involves various risks to the
quality and consistency of our molecules. In addition, in order to produce molecules at existing and
potential future plants, we have been and may in the future be required to perform thorough transition
activities, and modify the design of the plant. Any modifications to the production plant could cause
complications in the operations of the plant, which could result in delays or failures in production. If any of
these risks occur, or if we are unable to create or obtain additional manufacturing capacity necessary to
meet existing and potential customer demand, we may need to continue to use, or increase our use of,
contract manufacturing sources, which may not be available on terms acceptable to us, if at all, and
generally entail greater cost to us to produce our products and would therefore reduce our anticipated gross

margins and may also prevent us from accessing certain markets for our products. Further, if our efforts to
increase (or commence, as the case may be) production at these facilities are not successful, our partners
may decide not to work with us to develop additional production facilities, demand more favorable terms or
delay their commitment to invest capital in our production. If we are unable to create and sustain
manufacturing capacity and operations sufficient to satisfy the existing and potential demand of our
customers and partners, our business and results of operations may be adversely affected.

In addition, the production of our products at our planned purpose-built, large-scale production
facilities will require large volumes of feedstock. For our planned large-scale production facilities in Brazil,
we plan to rely primarily on Brazilian sugarcane. While in certain cases we have entered into feedstock
agreements with suppliers, including Raizen, which we expect to supply the sugarcane feedstock necessary
to produce our products at our planned large-scale production facilities in Brazil, that specify the pricing,
quantity and product specifications for our feedstocks, we cannot predict the future availability or price of
these various feedstocks, nor can we be sure that our mill partners, including Raizen, will be able to supply
it in sufficient quantities or in a timely manner. Furthermore, to the extent we are required to rely on sugar
feedstock other than Brazilian sugarcane, the cost of such feedstock may be higher than we expect,
increasing our anticipated production costs. Feedstock crop yields and sugar content depend on weather
conditions, such as rainfall and temperature. Weather conditions have historically caused volatility in the
ethanol and sugar industries by causing crop failures or reduced harvests. Excessive rainfall can adversely
affect the supply of sugarcane and other sugar feedstock available for the production of our products by
reducing the sucrose content and limiting growers’ ability to harvest. Crop disease and pestilence can also
occur from time to time and can adversely affect feedstock growth, potentially rendering useless or unusable
all or a substantial portion of affected harvests. With respect to sugarcane, our initial primary feedstock,
seasonal availability and price, the limited amount of time during which it keeps its sugar content after
harvest, and the fact that sugarcane is not itself a traded commodity, increases these risks and limits our
ability to substitute supply in the event of such an occurrence. If production of sugarcane or any other
feedstock we may use to produce our products is adversely affected by these or other conditions, our
production will be impaired, and our business will be adversely affected.

Our use of contract manufacturers exposes us to risks relating to costs, contractual terms and logistics.

In addition to our existing and planned production facilities discussed above, we must commercially
produce, process and manufacture our products through the use of contract manufacturers, including
DSM, and we anticipate that we will continue to use contract manufacturers for the foreseeable future.
Establishing and operating contract manufacturing facilities requires us to make significant capital
expenditures, which reduces our cash and places such capital at risk. Also, contract manufacturing
agreements may contain terms that commit us to pay for capital expenditures and other costs and amounts
incurred or expected to be earned by the plant operators and owners, which can result in contractual
liability and losses for us even if we terminate a particular contract manufacturing arrangement or decide to
reduce or stop production under such an arrangement. Further, we cannot be sure that contract
manufacturers will be available when we need their services, that they will be willing to dedicate a portion of
their capacity to our projects, or that we will be able to reach acceptable price, delivery and other terms with
them for the provision of their production services.

The locations of contract manufacturers can pose additional cost, logistics and feedstock challenges. If
production capacity is available at a plant that is remote from usable chemical finishing or distribution
facilities, or from customers, we will be required to incur additional expenses in shipping products to other
locations. Such costs could include shipping costs, compliance with export and import controls, tariffs and
additional taxes, among others. In addition, we may be required to use feedstock from a particular region
for a given production facility. The feedstock available in such region may not be the least expensive or most
effective feedstock for production, which could significantly raise our overall production cost or reduce our
product’s quality until we are able to optimize the supply chain.

Loss or termination of contract manufacturing relationships could harm our ability to meet our production
goals.

As discussed above, we rely on contract manufacturers, including DSM, to produce and/or provide
downstream processing of our products, and we anticipate that we will need to use contract manufacturers
for the foreseeable future. If we are unable to secure the services of contract manufacturers when and as
needed, we may lose customer opportunities and the growth of our business may be impaired. If we shift
priorities and adjust anticipated production levels
(or cease production altogether) at contract
manufacturing facilities, such adjustments or cessations could also result in disputes or otherwise harm our
business relationships with contract manufacturers. In addition, reliance on external sources for our other
target molecules could create a risk for us if a single source or a limited number of sources of
manufacturing runs into operational issues, creating risk of loss of sales and profitability. Reducing or
stopping production at one facility while increasing or starting up production at another facility generally
results in significant losses of production efficiency, which can persist for significant periods of time. Also,
in order for production to commence under our contract manufacturing arrangements, we generally must
provide equipment for such operations, and we cannot be assured that such equipment can be ordered or
installed on a timely basis, at acceptable costs, or at all. Further, in order to establish operations at new
contract manufacturing facilities, we need to transfer our yeast strains and production processes from our
labs to commercial plants controlled by third parties, which may pose technical or operational challenges
that delay production or increase our costs.

Our ability to establish substantial commercial sales of our products is subject to many risks, any of which
could prevent or delay revenue growth and adversely impact our customer relationships, business and results of
operations.

There can be no assurance that our products will be approved or accepted by customers, including
customers of our branded products, or that we will be able to sell our products profitably at prices and with
features sufficient to establish demand. The potential customers for our products generally have well
developed manufacturing processes and arrangements with suppliers of the chemical components of their
products and may have a resistance to changing these processes and components. These potential customers
frequently impose lengthy and complex product qualification procedures on their suppliers, influenced by
consumer preference, manufacturing considerations such as process changes and capital and other costs
associated with transitioning to alternative components, supplier operating history, established business
relationships and agreements, regulatory issues, product liability and other factors, many of which are
unknown to, or not well understood by, us. Satisfying these processes may take many months. Similarly,
customers of our branded products may have a resistance to accept our alternative compositions for such
products. Additionally, we may be subject to product safety testing and may be required to meet certain
regulatory and/or product safety standards. Meeting these standards can be a time consuming and
expensive process, and we may invest substantial time and resources into such qualification efforts without
ultimately securing approval. If we are unable to convince these potential customers, the consumers who
purchase end-products containing our products and the customers of our direct to consumer products that
our products are comparable to the chemicals that they currently use or that the use of our products is
otherwise to their benefit, we will not be successful in entering these markets and our business will be
adversely affected. Moreover, in order to successfully market our direct to consumer products, we must
continue to build our sales, marketing, managerial, compliance, and related capabilities or make
arrangements with third parties to perform these services. If we are unable to establish adequate sales,
marketing, and distribution capabilities, whether independently or with third parties, we may not be able to
appropriately commercialize such products.

The price and availability of sugarcane and other feedstocks can be volatile as a result of changes in industry
policy and may increase the cost of production of our products.

In Brazil, Conselho dos Produtores de Cana-de-Açúcar, Açúcar e Etanol do Estado de São Paulo
(Council of Sugarcane, Sugar and Ethanol Producers in the State of São Paulo, or “Consecana”), an
industry association of producers of sugarcane, sugar and ethanol, sets market terms and prices for general
supply, lease and partnership agreements for sugarcane. If Consecana makes changes to such terms and
prices, it could result in higher sugarcane prices and/or a significant decrease in the volume of sugarcane

available for the production of our products. In addition, if the availability of sugarcane juice or syrup or
other feedstocks is restricted or limited due to weather conditions, land conditions or any other reason, we
may not be able to manufacture our products in a timely or cost-effective manner, or at all, which would
have a material adverse effect on our business.

We expect to face competition for our products from existing suppliers, including from price declines in
petroleum and petroleum-based products, and if we cannot compete effectively against these companies,
products or prices, we may not be successful in bringing our products to market, demand for some of our
renewable products may decline, or we may be unable to further grow our business.

We expect that our renewable products will compete with both the traditional products that are
currently being used in our target markets and with the alternatives to these existing products that
established enterprises and new companies are seeking to produce. In the markets that we have entered, and
in other markets that we may seek to enter in the future, we will compete primarily with the established
providers of ingredients currently used in products in these markets. Producers of these incumbent products
include global health and nutrition companies, large international chemical companies and companies
specializing in specific products, such as flavor or fragrance ingredients, squalane or essential oils. We may
also compete in one or more of these markets with products that are offered as alternatives to the
traditional products being offered in these markets.

With the emergence of many new companies seeking to produce products from renewable sources, we
may face increasing competition from such companies. As they emerge, some of these companies may be
able to establish production capacity and commercial partnerships to compete with us. If we are unable to
establish production and sales channels that allow us to offer comparable products at attractive prices, we
may not be able to compete effectively with these companies.

We believe the primary competitive factors in our target markets are:

•

product price;

product performance and other measures of quality;

sustainability; and

dependability of supply.

The global health and nutrition companies, large international chemical companies and companies
specializing in specific products with whom we compete are much larger than us, have, in many cases, well
developed distribution systems and networks for their products, have valuable historical relationships with
the potential customers we are seeking to serve and have much more extensive sales and marketing
programs in place to promote their products. In order to be successful, we must convince customers that
our products are at least as effective as the traditional products they are seeking to replace and we must
provide our products on a cost basis that does not greatly exceed these traditional products and other
available alternatives. Some of our competitors may use their influence to impede the development and
acceptance of renewable products of the type that we are seeking to produce.

While most of our products do not compete with, and do not serve as alternatives to, petroleum-based
products, we anticipate that some of our renewable products will be marketed as alternatives to
corresponding petroleum-based products. We believe that for our renewable products to succeed in the
market, we must demonstrate that our products are comparable or better alternatives to existing products
and to any alternative products that are being developed for the same markets based on some combination
of product cost, availability, performance, and consumer preference characteristics.

We are subject to risks related to our reliance on collaboration arrangements to fund development and
commercialization of our products, and our financial results may be adversely impacted if we fail to meet
technical, development or commercial milestones in such agreements.

For most product markets we are seeking to enter, we have collaboration partners to fund the research
and development, commercialization and production efforts required for the target products. Typically, we
provide limited exclusive rights and revenue sharing with respect to the production and sale of particular
products in specific markets in exchange for such up-front funding. These exclusivity, revenue-sharing and

other similar terms limit our ability to commercialize our products and technology, and may impact the size
of our business or our profitability in ways that we do not currently envision. In addition, most of these
agreements do not affirmatively obligate the other party to purchase specific quantities of any products,
and most contain important conditions that must be satisfied before additional research and development
funding or product purchases would occur. These conditions include research and development programs
and milestones, and technical specifications that must be achieved to the satisfaction of our collaboration
partners. We may focus our efforts and resources on potential discovery efforts, product targets or
candidates that require substantial technical, financial and human resources which we cannot be certain we
will achieve.

In addition, we may encounter numerous uncertainties and difficulties in developing, manufacturing
and commercializing any new products subject to these collaboration arrangements that may delay or
prevent us from realizing their expected benefits or enhancing our business, including uncertainties on the
feasibility of taking new molecules to commercial scale. Any failure to successfully develop, produce and
commercialize products under our existing and future collaboration arrangements could have a material
adverse effect on our business, financial conditions, earnings and prospects.

Revenues from these types of relationships are a key part of our cash plan for 2019 and beyond. If we
fail to collect expected collaboration revenues, or to identify and add sufficient additional collaborations to
fund our planned operations, we may be unable to fund our operations or pursue development and
commercialization of our planned products. To achieve our collaboration revenue targets from year to year,
we may be obliged to enter into agreements that contain less favorable terms. Historically, the process of
negotiating and finalizing collaboration arrangements with our partners has at times been lengthy and
unpredictable. Furthermore, as part of our current and future collaboration arrangements, we may be
required to make significant capital investments at our existing or planned production facilities in order to
develop, produce and commercialize molecules or other products. Any failure or difficulties in maintaining
existing collaboration arrangements or establishing new collaboration arrangements, or building up or
retooling our operations to meet the demands of our collaboration partners could have a significant
negative impact on our business, including our ability to achieve commercial viability for our products, lead
to the inability to meet our contractual obligations and could cause us to allocate or divert capital,
personnel and other resources from our organization which could adversely affect our business and
reputation.

Our collaboration arrangements may restrict or prevent our future business activity in certain markets or
industries, which could harm our ability to grow our business.

As part of our collaboration arrangements in the ordinary course of business, we may grant to our
partners exclusive rights with respect to the development, production and/or commercialization of
particular products or types of products in specific markets in exchange for up-front funding and/or
downstream royalty arrangements. These rights may inhibit potential collaboration or strategic partners or
potential customers from entering into negotiations with us about further business opportunities, and we
may be restricted or prevented from engaging with other partners or customers in those markets, which may
limit our ability to grow our business or influence our strategic focus, and may lead to an inefficient
allocation of capital resources.

In the past, we have had to grant concessions to existing partners in exchange for such partners
waiving or modifying their exclusive rights with respect to a particular product, type of product or market
so that we could engage with a third party with respect to such product, product type or market. There can
be no assurance that existing partners will be willing to grant waivers of or modify their exclusive rights in
the future on favorable terms, if at all. If we are unable to engage other potential partners with respect to
particular products, product types or markets for which we have previously granted exclusive rights, our
ability to grow our business would be harmed and our results of operations may be adversely affected.

Third parties may misappropriate our yeast strains.

Third parties, including collaboration partners, contract manufacturers, other contractors and shipping
agents, often have custody or control of our yeast strains. If our yeast strains were stolen, misappropriated
or reverse engineered, they could be used by other parties who may be able to reproduce the yeast strains
for their own commercial gain. If this were to occur, it would be difficult for us to challenge and prevent this

type of use, especially in countries where we have limited intellectual property protection or that do not have
robust intellectual property law regimes.

Certain rights we have granted to Total S.A., DSM and other existing stockholders, including in relation to our
future securities offerings, could substantially impact our company.

In connection with certain investments of Total S.A. (Total) in our company, our Certificate of
Incorporation includes a provision that excludes Total from prohibitions on business combinations between
us and an “interested stockholder.” This provision could have the effect of discouraging potential acquirers
from making offers to acquire us, and give Total more access to Amyris than other stockholders if Total
decides to pursue an acquisition.

In addition, each of Total, DSM, Vivo Capital LLC and Naxyris S.A. has the right to designate one or

more directors to serve on our Board of Directors pursuant to agreements between us and such investors.

In May 2017, we entered into an agreement with DSM, which was amended and restated in
August 2017, pursuant to which we agreed (i) that for as long as there is a DSM-designated director serving
on our Board of Directors, we will not engage in certain commercial or financial transactions or
arrangements without the consent of such director, and (ii) to provide DSM with certain exclusive
negotiating rights in connection with certain future commercial projects and arrangements. These
provisions could discourage other potential partners from approaching us with business opportunities, and
could restrict, delay or prevent us from pursuing or engaging in such opportunities, which could adversely
affect our business.

Additionally, in connection with their investments in Amyris, we granted certain investors, including
DSM, a right of first investment if we propose to sell securities in certain financing transactions. With these
rights, such investors may subscribe for a portion of any such new financing and require us to comply with
certain notice periods, which could discourage other investors from participating in, or cause delays in our
ability to close, such a financing.

Our relationship with DSM exposes us to financial and commercial risks.

In May 2017, DSM made an investment in our company and, in connection therewith, we entered into
a stockholder agreement with DSM (subsequently amended) which provides DSM with certain rights,
including the right to designate two members of our board of directors as well as exclusive negotiating
rights in connection with certain future commercial projects and arrangements. Subsequently, in July and
September 2017, we entered into collaboration agreements (and related license agreements) with DSM to
jointly develop three new molecules in the Health and Nutrition field using the Company’s technology,
which the Company would produce and DSM would commercialize. In December 2017, we completed the
sale of our Brotas, Brazil production facility to DSM and, in connection therewith, entered into several
commercial agreements with DSM, including a supply agreement to procure a substantial portion of our
product supply requirements, and borrowed $25 million from DSM. For more information regarding these
and other transactions and arrangements with DSM, please see Note 5, “Debt,” Note 7, “Stockholders’
Deficit,” Note 10, “Revenue Recognition”, Note 11, “Related Party Transactions,” Note 13, “Divestiture”
and Note 16, “Subsequent Events” in Part II, Item 8 of this Annual Report on Form 10-K.

There can be no assurance that our partnership with DSM will be successful, and the partnership may
prevent us from pursuing other business opportunities in the future. If the partnership is unsuccessful, our
ability to continue with our business plans could be adversely affected. In addition, negative developments
in one aspect of our relationship with DSM could negatively affect other aspects of our relationship with
DSM. In such event, our financial condition and business operations could be adversely affected.

In addition, DSM, due to the presence of its representatives on our board of directors, equity
ownership in our company, and commercial relationships with us, may be able to control or significantly
influence our management, operations and affairs, as well as matters requiring stockholder approval,
including the election of directors and the approval of significant corporate transactions, such as mergers,
consolidations or the sale of all or substantially all of our assets. Due to its various relationships with the
Company, DSM may have interests different than, and may not act in the best interests of, our other

stockholders. Consequently, our relationship with DSM may have the effect of delaying or preventing a
change of control, or a change in our management or board of directors, or discouraging a potential
acquirer from making a tender offer or otherwise attempting to obtain control of our company, even if such
actions would benefit our other stockholders.

A significant portion of our operations are centered in Brazil, and our business will be adversely affected if we
do not operate effectively in that country.

For the foreseeable future, we will be subject to risks associated with the concentration of essential
product sourcing and operations in Brazil. The Brazilian government has changed in the past, and may
change in the future, monetary, taxation, credit, tariff, labor and other policies to influence the course of
Brazil’s economy. For example, the government’s actions to control inflation have involved interest rate
adjustments. We have no control over, and cannot predict what policies or actions the Brazilian government
may take in the future. Our business, financial performance and prospects may be adversely affected by,
among others, the following factors:

•

delays or failures in securing licenses, permits or other governmental approvals necessary to build
and operate facilities and use our yeast strains to produce products;

rapid consolidation in the sugar and ethanol industries in Brazil, which could result in a decrease
in competition;

political, economic, diplomatic or social instability in or affecting Brazil;

changing interest rates;

tax burden and policies;

effects of changes in currency exchange rates;

any changes in currency exchange policy that lead to the imposition of exchange controls or
restrictions on remittances abroad;

inflation;

land reform or nationalization movements;

changes in labor related policies;

export or import restrictions that limit our ability to move our products out of Brazil or interfere
with the import of essential materials into Brazil;

changes in, or interpretations of foreign regulations that may adversely affect our ability to sell
our products or repatriate profits to the United States;

tariffs, trade protection measures and other regulatory requirements;

compliance with United States and foreign laws that regulate the conduct of business abroad;

compliance with privacy, anti-corruption and anti-bribery laws, including certain anti-corruption
and privacy laws recently enacted in Brazil;

an inability, or reduced ability, to protect our intellectual property in Brazil including any effect of
compulsory licensing imposed by government action; and

difficulties and costs of staffing and managing foreign operations.

We cannot predict whether the current or future Brazilian government will implement changes to
existing policies on taxation, exchange controls, monetary strategy, labor relations, social security and the
like, nor can we estimate the impact of any such changes on the Brazilian economy or our operations.

Brazil’s economy has recently experienced quarters of slow or negative gross domestic product growth
and has, through 2018, experienced high inflation and a growing fiscal deficit of its federal government
accounts. Although recent data has shown signs of an economic recovery in Brazil, there is no assurance
the
that such recovery will continue. In addition, major corruption scandals involving members of

executive, state-controlled enterprises and large private sector companies have been disclosed and are the
subject of ongoing investigation by federal authorities. The final outcome of these investigations and their
impact on the Brazilian economy is not yet known and cannot be predicted with certainty.

We are subject to the risks of doing business globally.

We maintain operations in foreign jurisdictions other than Brazil, and may in the future expand, or
seek to expand, our operations to additional foreign jurisdictions. For example, in 2018 we announced plans
to increase our commercial activities in China. Operating in China exposes us to political, legal and
economic risks. In particular, the political, legal and economic climate in China, both nationally and
regionally, is fluid and unpredictable. Our ability to operate in China may be adversely affected by changes
in U.S. and Chinese laws and regulations such as those related to taxation, import and export tariffs,
environmental regulations, land use rights, intellectual property, currency controls, network security and
other matters. In addition, we may not obtain or retain the requisite permits to operate in China, and costs
or operational limitations may be imposed in connection with obtaining and complying with such permits.
In addition, Chinese trade regulations are in a state of flux, and we may become subject to other forms of
taxation, tariffs and duties in China. Furthermore, our counterparties in China may use or disclose our
confidential information or intellectual property to competitors or third parties, which could result in the
illegal distribution and sale of counterfeit versions of our products. If any of these events occur, our
business, financial condition and results of operations could be materially and adversely affected.

In addition, a significant percentage of the production, downstream processing and sales of our
products occurs outside the United States or with vendors, suppliers or customers located outside the
United States. If tariffs or other restrictions are placed by the United States on foreign imports from Brazil
or other countries where we operate or seek to operate, or any related counter-measures are taken, our
business, financial condition and results of operations may be harmed. In 2018, President Trump imposed
tariffs on steel and aluminum imports and additional tariffs on goods imported from certain specified
countries, including China, and has indicated potential future tariffs on a range of goods from certain
countries. In response, certain countries, including China, have imposed retaliatory tariffs on U.S. goods
imported into such countries. If further tariffs are imposed on a broader range of imports, or if further
retaliatory trade measures are taken by other countries in response to additional tariffs, our operating
performance could be harmed. Tariffs may increase our cost of goods, which could result in lower gross
margin on certain of our products. If we raise prices to account for any such increase in costs of goods, the
competitiveness of the affected products could potentially be reduced. In either case, increased tariffs on
imports from Brazil or other countries where we operate or seek to operate could materially and adversely
affect our business, financial condition and results of operations. Furthermore, in retaliation for any tariffs
imposed by the United States, other countries may implement tariffs on a wide range of American
products, which could increase the cost of our products for non-U.S. customers located in such countries.
Any increase in the cost of our products for non-U.S. customers, which represent a substantial portion of
our sales, could result in a decrease in demand for our products by such customers. Trade restrictions
implemented by the United States or other countries could materially and adversely affect our business,
financial condition and results of operations.

Many, if not all of the above-mentioned risks also apply to our operations in other foreign jurisdictions
where we operate or seek to operate. If any of these risks were to occur, our operations and business would
be adversely affected.

We are subject to new U.S. foreign investment regulations which may impose additional burdens on or may
limit certain investors’ ability to purchase our common stock, potentially making our common stock less
attractive to investors.

In October 2018, the U.S. Department of Treasury announced a pilot program to implement part of
the Foreign Investment Risk Review Modernization Act (FIRRMA), effective November 10, 2018. The
pilot program expands the jurisdiction of the Committee on Foreign Investment in the United States
(CFIUS), to include certain direct or indirect foreign investments in a defined category of U.S. companies,
including companies involved in critical infrastructure and critical technologies. Among other things,
FIRRMA empowers CFIUS to require certain mandatory filings in connection with certain foreign

investments in U.S. companies and permits CFIUS to charge filing fees related to such filings. Such filings
are subject to review by CFIUS, which will have the authority to recommend that the President block or
impose conditions on certain foreign investments in companies subject to CFIUS’s oversight. Any such
restrictions on the ability of foreign investors to invest in our company could limit our ability to engage in
strategic transactions that may benefit our stockholders, including a change of control, and may prevent
our stockholders from receiving a premium for their shares of our common stock in connection with a
change of control, and could also affect the price that some investors are willing to pay for our common
stock.

Ethical, legal and social concerns about products using genetically modified microorganisms could limit or
prevent the use of our products and technologies and could harm our business.

Our technologies and products involve the use of genetically modified microorganisms (GMMs).
Public perception about the safety of, and ethical, legal or social concerns over, genetically engineered
products, including GMMs, could affect public acceptance of our products. If we are not able to overcome
any such concerns relating to our products, our technologies may not be accepted by our customers or
end-users. In addition, the use of GMMs has in the past received negative publicity, which could lead to
greater regulation or restrictions on imports of our products. If our technologies and products are not
accepted by our customers or their end-users due to negative publicity or lack of public acceptance, our
business could be significantly harmed.

Our use of genetically-modified feedstocks and yeast strains to produce our products subjects us to risks of
regulatory limitations and rejection of our products.

The use of GMMs, such as our yeast strains, is subject to laws and regulations in many countries, some
of which are new and some of which are still evolving. In the United States, the Environmental Protection
Agency (EPA), regulates the commercial use of GMMs as well as potential products produced from
GMMs. Various states or local governments within the United States could choose to regulate products
made with GMMs as well. While the strain of genetically modified yeast that we currently use for the
development and commercial production of our target molecules, S. cerevisiae, is eligible for exemption
from EPA review because it is generally recognized as safe, we must satisfy certain criteria to achieve this
exemption, including but not limited to use of compliant containment structures and safety procedures, and
we cannot be sure that we will meet such criteria in a timely manner, or at all. If exemption of S. cerevisiae
is not obtained, our business may be substantially harmed. In addition to S. cerevisiae, we may seek to use
different GMMs in the future that will require EPA approval. If approval of different GMMs is not
secured, our ability to grow our business could be adversely affected.

In Brazil, GMMs are regulated by the National Biosafety Technical Commission (CTNBio). We have
obtained approvals from CTNBio to use GMMs in a contained environment in our Brazil facilities for
research and development purposes as well as at contract manufacturing facilities in Brazil for industrial
scale production of target products. In addition, we have obtained initial commercial approvals from
CTNBio for five of our yeast strains, with two of these strains being approved for feed purposes. As we
continue to develop new yeast strains and deploy our technology at new production facilities in Brazil, we
will be required to obtain further approvals from CTNBio in order to use these strains in industrial scale
commercial production in Brazil. We may not be able to obtain such approvals on a timely basis, or at all,
and if we do not, our ability to produce our products in Brazil could be impaired, which would adversely
affect our results of operations and financial condition.

In addition to our production operations in the United States and Brazil, we have been party to
contract manufacturing agreements with parties in other production locations around the world, including
Europe. The use of GMM technology is regulated in the European Union, which has established various
directives for member states regarding regulation of the use of such technology, including notification
processes for contained use of such technology. We expect to encounter GMM regulations in most, if not
all, of the countries in which we may seek to establish production capabilities and/or conduct sales to
customers or end-use consumers, and the scope and nature of these regulations will likely be different from
country to country. If we cannot meet the applicable regulatory requirements in the countries in which we
produce or sell, or intend to produce or sell, products using our yeast strains, or if it takes longer than

anticipated to obtain the necessary regulatory approvals, our business could be adversely affected.
Furthermore, there are various governmental, non-governmental and quasi-governmental organizations
that review and certify products with respect to the determination of whether products can be classified as
“natural” or other similar classifications. While the certification from such governmental organizations, and
verification from non-governmental and quasi-governmental organizations are generally not mandatory,
some of our current or prospective customers, collaboration partners or distributors may require that we
meet the standards set by such organizations as a condition precedent to purchasing or distributing our
products. We cannot be certain that we will be able to satisfy the standards of such organizations, and any
delay or failure to do so could harm our ability to sell or distribute some or all of our products to certain
customers and prospective customers, which could have a negative impact on our business.

We may not be able to obtain regulatory approval for the sale of our renewable products.

Our renewable chemical products may be subject to government regulation in our target markets. In
the United States, the EPA administers the Toxic Substances Control Act (the TSCA), which regulates the
commercial registration, distribution, and use of many chemicals. Before an entity can manufacture or
distribute a new chemical subject to the TSCA, it must file a Pre-Manufacture Notice, or PMN, to add the
chemical to a product. The EPA has 180 days to review the filing but may request additional data, which
could significantly extend the timeline for approval. As a result, we may not receive EPA approval to list
future molecules on the TSCA registry as expeditiously as we would like, resulting in delays or significant
increases in testing requirements. A similar program exists in the European Union, called REACH. Under
this program, chemicals imported or manufactured in the European Union in certain quantities must be
registered with the European Chemicals Agency, and this process could cause delays or entail significant
costs. To the extent that other countries in which we are producing or selling (or seeking to produce or sell)
our products, such as Brazil and various countries in Asia, rely on TSCA or REACH (or similar laws and
programs) for chemical registration or regulation in their jurisdictions, delays with the United States or
European authorities, or any relevant authorities in such other countries, may delay entry into these
markets as well. In addition, some of our Biofene-derived products are sold for the cosmetics market, and
some countries may impose additional regulatory requirements or permits for such uses, which could
impair, delay or prevent sales of our products in those markets. Also, certain of our current or proposed
products in the Flavor & Fragrance, Clean Beauty and Health & Wellness markets, including alternative
sweeteners, nutraceuticals, Flavor & Fragrance ingredients, skincare ingredients and cosmetic actives, may
be subject to the approval of and regulation by the FDA, the European Food Safety Authority, as well as
similar agencies of states and foreign jurisdictions where these products are sold or proposed to be sold.

We expect to encounter regulations in most, if not all, of the countries in which we may seek to
produce, import or sell our products (and our customers may encounter similar regulations in selling
end-use products to consumers), and we cannot assure you that we (or our customers) will be able to obtain
necessary approvals in a timely manner or at all. If our products do not meet applicable regulatory
requirements in a particular country, then we (or our customers) may not be able to commercialize our
products in such country and our business will be adversely affected. In addition, any enforcement action
taken by regulators against us or our products could cause us to suffer adverse publicity, which could harm
our reputation and our relationship with our customers and vendors.

In addition, many of our products are intended to be a component of our collaboration partners and/
or customers’ (or their customers’) end-use products. Such end-use products may be subject to various
regulations, including regulations promulgated by the EPA, the FDA, or the European Food Safety
Authority. If our company or our collaboration partners and customers (or their customers) are not
successful in obtaining any required regulatory approval for their end-use products that incorporate our
products, or fail to comply with any applicable regulations for such end-use products, whether due to our
products or otherwise, demand for our products may decline and our revenues will be adversely affected.

Changes in government regulations, including subsidies and economic incentives, could have a material adverse
effect on our business.

The markets where we sell our products are heavily influenced by foreign, federal, state and local
government regulations and policies. Changes to existing or adoption of new domestic or foreign federal,
state and local legislative initiatives that impact the production, distribution or sale of products may harm

our business. The uncertainty regarding future standards and policies may also affect our ability to develop
our products or to license our technologies to third parties and to sell products to our end customers. Any
inability to address these requirements and any regulatory or policy changes could have a material adverse
effect on our business, financial condition and results of operations.

Furthermore, the production of our products will depend on the availability of feedstock, especially
sugarcane. Agricultural production and trade flows are subject to government policies and regulations.
Governmental policies affecting the agricultural industry, such as taxes, tariffs, duties, subsidies, incentives
and import and export restrictions on agricultural commodities and commodity products can influence the
planting of certain crops, the location and size of crop production, whether unprocessed or processed
commodity products are traded, the volume and types of imports and exports, and the availability and
competitiveness of feedstocks as raw materials. Future government policies may adversely affect the supply
of feedstocks, restrict our ability to use sugarcane or other feedstocks to produce our products, or
encourage the use of
feedstocks more advantageous to our competitors, which would put us at a
commercial disadvantage and could negatively impact our future revenues and results of operations.

Our cannabinoid initiative is uncertain and may not yield commercial results and is subject to significant
regulatory risks.

In 2019, we announced a new collaboration arrangement aimed at developing, producing and
commercializing fermentation-derived cannabinoids. While we believe there are substantial business
opportunities for us in this field, there can be no assurance that our activities will be successful, or that any
research and development and product testing efforts will result in commercially saleable products, or that
the market will accept or respond positively to our products.

In addition, the market for cannabinoids is heavily regulated. Cannabinoids may be viewed as
qualifying as controlled substances under the federal Controlled Substances Act of 1970 (CSA), and may be
subject to a high degree of regulation including, among other things, certain registration,
licensing,
insurance and other requirements
manufacturing, security, record keeping, reporting,
administered by the U.S. Drug Enforcement Administration (DEA) and/or the FDA.

import, export,

Individual states and countries have also established controlled substance laws and regulations, which
may differ from U.S. federal law. We or our partner may be required to obtain separate state or country
registrations, permits or licenses in order to be able to develop produce, sell, store and transport
cannabinoids.

Complying with laws and regulations relating to cannabinoids is evolving, complex and expensive, and
may divert management’s attention and resources from other aspects of our business. Failure to maintain
compliance with such laws and regulations may result in regulatory action that could have a material
adverse effect on our business, results of operations and financial condition. The DEA, FDA or state
agencies may seek civil penalties, refuse to renew necessary registrations, or initiate proceedings to revoke
those registrations. In certain circumstances, violations could lead to criminal proceedings.

We may incur significant costs to comply with environmental laws and regulations, and failure to comply with
these laws and regulations could expose us to significant liabilities.

We use intermediate substances, hazardous chemicals and radioactive and biological materials in our
business, and such materials are subject to a variety of federal, state and local laws and regulations
governing the use, generation, manufacture, storage, handling and disposal of these materials in the United
States, European Union and Brazil. Although we have implemented safety procedures for handling and
disposing of these materials and related waste products in an effort to comply with these laws and
regulations, we cannot be sure that our safety measures and those of our contractors will prevent accidental
injury or contamination from the use, storage, handling or disposal of hazardous materials. In the event of
contamination or injury, we could be held liable for any resulting damages, and any liability could exceed
our insurance coverage. There can be no assurance that violations of environmental, health and safety laws
will not occur in the future as a result of human error, accident, equipment failure or other causes.
Compliance with applicable environmental laws and regulations may be expensive, and the failure to
comply with past, present, or future laws could result in the imposition of fines, third party property

damage, product liability and personal injury claims, investigation and remediation costs, the suspension of
production, or a cessation of operations, and our liability may exceed our total assets. Liability under
environmental laws can be joint and several, without regard to comparative fault, and may be punitive in
nature. Furthermore, environmental
imposing greater
compliance costs and increasing risks and penalties associated with violations, which could impair our
research, development or production efforts and otherwise harm our business.

laws could become more stringent over time,

Our proprietary rights may not adequately protect our technologies and product candidates.

Our commercial success will depend substantially on our ability to obtain patents and maintain
adequate legal protection for our technologies and product candidates in the United States and other
countries. As of September 23, 2019, we had 621 issued United States and foreign patents and 243 pending
United States and foreign patent applications that were owned or co-owned by or licensed to us. We will be
able to protect our proprietary rights from unauthorized use by third parties only to the extent that our
proprietary technologies and future products are covered by valid and enforceable patents or are effectively
maintained as trade secrets.

We apply for patents covering both our technologies and product candidates, as we deem appropriate.
However, filing, prosecuting, maintaining and defending patents on product candidates in all countries
throughout the world would be prohibitively expensive, and our intellectual property rights in some
countries outside the United States are less extensive than those in the United States. We may also fail to
apply for patents on important technologies or product candidates in a timely fashion, or at all. Our existing
and future patents may not be sufficiently broad to prevent others from practicing our technologies or from
designing products around our patents or otherwise developing competing products or technologies. In
addition, the patent positions of companies like ours are highly uncertain and involve complex legal and
factual questions for which important legal principles remain unresolved. No consistent policy regarding
the breadth of patent claims has emerged to date in the United States and the landscape is expected to
become even more uncertain in view of recent rule changes by the United States Patent Office, or USPTO.
Additional uncertainty may result from legal decisions by the United States Federal Circuit and Supreme
Court as they determine legal
issues concerning the scope and construction of patent claims and
inconsistent interpretation of patent laws or from legislation enacted by the U.S. Congress. The patent
situation outside of the United States is even less predictable. As a result, the validity and enforceability of
patents cannot be predicted with certainty. Moreover, we cannot be certain whether:

•

we (or our licensors) were the first to make the inventions covered by each of our issued patents
and pending patent applications;

we (or our licensors) were the first to file patent applications for these inventions;

others will independently develop similar or alternative technologies or duplicate any of our
technologies;

any of our or our licensors’ patents will be valid or enforceable;

any patents issued to us (or our licensors) will provide us with any competitive advantages, or will
be challenged by third parties;

we will be able to identify when others are infringing our (or our licensed) valid patent claims;

we will develop additional proprietary products or technologies that are patentable; or

the patents of others will have an adverse effect on our business.

We do not know whether any of our pending patent applications or those pending patent applications
that we license will result in the issuance of any patents. Even if patents are issued, they may not be
sufficient to protect our technology or product candidates. The patents we own or license and those that
may be issued in the future may be challenged, invalidated, rendered unenforceable, or circumvented, and
the rights granted under any issued patents may not provide us with proprietary protection or competitive
advantages. Moreover, third parties could practice our inventions in territories where we do not have patent
protection or in territories where they could obtain a compulsory license to our technology where patented.

Such third parties may then try to import products made using our inventions into the United States or
other territories. Accordingly, we cannot ensure that any of our pending patent applications will result in
issued patents, or even if issued, predict the breadth, validity and enforceability of the claims upheld in our
and other companies’ patents.

Many companies have encountered significant problems in protecting and defending intellectual
property rights in foreign jurisdictions. The legal systems of certain countries do not favor the enforcement
of patents or other intellectual property rights, which could hinder us from preventing the infringement of
our patents or other intellectual property rights. Proceedings to enforce our patent rights in the United
States or foreign jurisdictions could result in substantial costs and divert our efforts and attention from
other aspects of our business, could put our patents at risk of being invalidated or interpreted narrowly and
our patent applications at risk of not issuing and could provoke third parties to assert patent infringement
or other claims against us. We may not prevail in any lawsuits that we initiate and the damages or other
remedies awarded, if any, may not be commercially meaningful. Accordingly, our efforts to enforce our
intellectual property rights around the world may be inadequate to obtain a significant commercial
advantage from the intellectual property that we develop or license from third parties.

Moreover, we have granted certain of our lenders liens on substantially all of our assets, including our
intellectual property, as collateral. If we default on our payment obligations under these secured loans, such
lenders have the right to foreclose upon and control the disposition of our assets, including our intellectual
property assets, to satisfy our payment obligations under such instruments. If such default occurs, and our
intellectual property assets are sold or licensed, our business could be materially adversely affected.

Unauthorized parties may attempt to copy or otherwise obtain and use our products or technology.
Monitoring unauthorized use of our intellectual property is difficult, and we cannot be certain that the
steps we have taken will prevent unauthorized use of our technology, particularly in certain foreign
countries where the local laws may not protect our proprietary rights as fully as in the United States or may
provide, today or in the future, for compulsory licenses. Moreover, in some cases our ability to determine if
our intellectual property is being unlawfully used by a competitor may be limited. If competitors are able to
use our technology, our ability to compete effectively could be harmed. Moreover, others may
independently develop and obtain patents for technologies that are similar to, or superior to, our
technologies. If that happens, we may need to license these technologies, and we may not be able to obtain
licenses on reasonable terms, if at all, which could cause harm to our business.

We rely in part on trade secrets to protect our technology, and our failure to obtain or maintain trade secret
protection could adversely affect our competitive business position.

We rely on trade secrets to protect some of our technology, particularly where we do not believe patent
protection is appropriate or obtainable. However, trade secrets are difficult to maintain and protect. Our
strategy for contract manufacturing and scale-up of commercial production requires us to share
confidential
information with our international business partners and other parties. Our product
development collaborations with third parties, including with Givaudan, Firmenich, DSM and Yifan,
require us to share certain confidential information. While we use reasonable efforts to protect our trade
secrets, our or our business partners’ employees, consultants, contractors or scientific and other advisors
may unintentionally or willfully disclose our proprietary information to competitors. Enforcement of claims
that a third party has illegally obtained and is using trade secrets is expensive, time consuming and
uncertain. In addition, foreign courts are sometimes less willing than United States courts to protect trade
secrets. If our competitors lawfully obtain or independently develop equivalent knowledge, methods and
know-how, we would not be able to assert our trade secrets against them.

We require new employees and consultants to execute proprietary information and inventions
agreements upon the commencement of an employment or consulting arrangement with us. We
additionally require contractors, advisors, corporate collaboration partners, outside scientific collaboration
partners and other third parties that may receive trade secret information to execute such agreements. These
agreements generally require that all confidential information developed by the individual or made known
to the individual by us during the course of the individual’s relationship with us be kept confidential and
not be disclosed to third parties. These agreements also generally provide that inventions conceived by the
individual in the course of rendering services to us shall be our exclusive property. Nevertheless, our

proprietary information may be disclosed, or these agreements may be unenforceable or difficult to enforce.
If any of our trade secrets were to be lawfully obtained or independently developed by a competitor, we
would have no right to prevent such third party, or those to whom they communicate such technology or
information, from using that technology or information to compete with us. Additionally, trade secret law
in Brazil differs from that in the United States, which requires us to take a different approach to protecting
our trade secrets in Brazil. Some of these approaches to trade secret protection may be novel and untested
under Brazilian law and we cannot guarantee that we would prevail if our trade secrets are contested in
Brazil. If any of the above risks materializes, our failure to obtain or maintain trade secret protection could
adversely affect our competitive business position.

If we or one of our collaboration partners is sued for infringing intellectual property rights or other proprietary
rights of third parties, litigation could be costly and time consuming and could prevent us from developing or
commercializing our future products.

Our commercial success depends on our and our collaboration partners ability to operate without
infringing the patents and proprietary rights of other parties and without breaching any agreements we
have entered into with regard to our technologies and product candidates. We cannot determine with
certainty whether patents or patent applications of other parties may materially affect our ability to conduct
our business. Our industry spans several sectors,
including biotechnology, renewable fuels, renewable
specialty chemicals and other renewable compounds, and is characterized by the existence of a significant
number of patents and disputes regarding patent and other intellectual property rights. Because patent
applications remain unpublished and confidential for eighteen months and can take several years to issue,
there may currently be pending applications, unknown to us, that may result in issued patents that cover our
technologies or product candidates. There may be a significant number of patents and patent applications
relating to aspects of our technologies filed by, and issued to, third parties. The existence of third-party
patent applications and patents could significantly reduce the coverage of patents owned by or licensed to
us and our collaboration partners and limit our ability to obtain meaningful patent protection. If we wish
to make, use, sell, offer to sell, or import the technology or compound claimed in issued and unexpired
patents owned by others, we may need to obtain a license from the owner, develop or obtain alternative
technologies, enter into litigation to challenge the validity of the patents or incur the risk of litigation in the
event that the owner asserts that we infringe its patents. If patents containing competitive or conflicting
claims are issued to third parties and these claims are ultimately determined to be valid, we and our
collaboration partners may be enjoined from pursing research, development, or commercialization of
products, or be required to obtain licenses to these patents, or to develop or obtain alternative technologies.

If a third party asserts that we infringe upon its patents or other proprietary rights, we could face a

number of issues that could seriously harm our competitive position, including:

•

infringement and other intellectual property claims, which could be costly and time consuming to
litigate, whether or not the claims have merit, and which could prevent or delay getting our
products to market and divert management attention from our business;

substantial damages for past infringement, which we may have to pay if a court determines that
our product candidates or technologies infringe a third party’s patent or other proprietary rights;

a court prohibiting us from selling or licensing our technologies or future products unless the
holder licenses the patent or other proprietary rights to us, which it is not required to do;

the International Trade Commission (ITC) prohibiting us from importing our products into the
United States; and

if a license is available from a third party, such third party may require us to pay substantial
royalties or grant cross licenses to our patents or proprietary rights.

The industries in which we operate, and the biotechnology industry in particular, are characterized by
frequent and extensive litigation and patent agency procedures regarding patents and other intellectual
property rights. Many biotechnology companies have employed intellectual property litigation as a way to
gain a competitive advantage. If any of our competitors have filed patent applications or obtained patents
that claim inventions also claimed by us, we may have to participate in interference proceedings declared by

the relevant patent regulatory agency to determine priority of invention and, thus, the right to the patents
for these inventions in the United States. In addition, third parties may be able to challenge the validity of
one or more of our patents using available post-grant procedures including oppositions and inter partes
reviews (IPR). These proceedings could result in substantial cost to us even if the outcome is favorable.
Even if successful, an interference or post-grant proceeding may result in loss of certain claims. Our
involvement in litigation, interferences, opposition proceedings or other intellectual property proceedings
inside and outside of the United States, to defend our intellectual property rights, or as a result of alleged
infringement of the rights of others, may divert management time from focusing on business operations and
could cause us to spend significant resources, all of which could harm our business and results of
operations.

Many of our employees were previously employed at universities, biotechnology, specialty chemical or
oil companies, including our competitors or potential competitors. We may be subject to claims that these
employees or we have inadvertently or otherwise used or disclosed trade secrets or other proprietary
information of their former employers. Litigation may be necessary to defend against these claims. If we fail
in defending such claims, in addition to paying monetary damages, we may lose valuable intellectual
property rights or personnel and be enjoined from certain activities. A loss of key research personnel or
their work product could hamper or prevent our ability to commercialize our product candidates, which
could severely harm our business. Even if we are successful in defending against these claims, litigation
could result in substantial costs and demand on management resources.

We may need to commence litigation to enforce our intellectual property rights, which would divert resources
and management’s time and attention and the results of which would be uncertain.

Enforcement of claims that a third party is using our proprietary rights without permission is
expensive, time consuming and uncertain. Significant litigation would result in substantial costs, even if the
eventual outcome is favorable to us and would divert management’s attention from our business objectives.
In addition, an adverse outcome in litigation could result in a substantial loss of our proprietary rights and
we may lose our ability to exclude others from practicing our technology or producing our product
candidates.

The laws of some foreign countries do not protect intellectual property rights to the same extent as do
the laws of the United States. Many companies have encountered significant problems in protecting and
defending intellectual property rights in certain foreign jurisdictions. The legal systems of certain countries,
particularly certain developing countries, do not favor the enforcement of patents and other intellectual
property protection, particularly those relating to biotechnology and/or bioindustrial technologies. This
could make it difficult for us to stop the infringement of our patents or misappropriation of our other
intellectual property rights. Proceedings to enforce our patent rights in foreign jurisdictions could result in
substantial costs and divert our efforts and attention from other aspects of our business. Moreover, our
efforts to protect our intellectual property rights in such countries may be inadequate.

We do not have exclusive rights to intellectual property we develop under U.S. federally funded research grants
and contracts, including with DARPA and DOE, and we could ultimately share or lose the rights we do have
under certain circumstances.

Some of our intellectual property rights have been or may be developed in the course of research
funded by the U.S. government, including under our agreements with DARPA and DOE. As a result, the
U.S. government may have certain rights to intellectual property embodied in our current or future products
pursuant to the Bayh-Dole Act of 1980. Government rights in certain inventions developed under a
government-funded program include a non-exclusive, non-transferable, irrevocable worldwide license to use
inventions for any governmental purpose. In addition, the U.S. government has the right to require us, or an
assignee or exclusive licensee to such inventions, to grant licenses to any of these inventions to a third party
if
(i) adequate steps have not been taken to commercialize the invention;
(ii) government action is necessary to meet public health or safety needs; (iii) government action is necessary
to meet requirements for public use under federal regulations; or (iv) the right to use or sell such inventions
is exclusively licensed to an entity within the U.S. and substantially manufactured outside the U.S. without
the U.S. government’s prior approval. Additionally, we may be restricted from granting exclusive licenses for

they determine that:

the right to use or sell our inventions created pursuant to such agreements unless the licensee agrees to
the invention in the U.S.). The U.S.
additional restrictions (e.g., manufacturing substantially all of
government also has the right to take title to these inventions if we fail to disclose the invention to the
government and fail to file an application to register the intellectual property within specified time limits. In
addition, the U.S. government may acquire title in any country in which a patent application is not filed
within specified time limits. Additionally, certain inventions are subject to transfer restrictions during the
term of these agreements and for a period thereafter, including sales of products or components, transfers
to foreign subsidiaries for the purpose of the relevant agreements, and transfers to certain foreign third
parties. If any of our intellectual property becomes subject to any of the rights or remedies available to the
U.S. government or third parties pursuant to the Bayh-Dole Act of 1980, this could impair the value of our
intellectual property and could adversely affect our business.

Loss of, or inability to secure government contract revenues could impair our business.

We have contracts or subcontracts with certain governmental agencies or their contractors, including
DARPA. Generally, these agreements, as they may be amended or modified from time to time, have fixed
terms and may be terminated, modified or be subject to recovery of payments by the government agency
under certain conditions (such as failure to comply with detailed reporting and governance processes or
failure to achieve milestones). Under these agreements, we are also subject to audits, which can result in
corrective action plans and penalties up to and including termination. If these governmental agencies
terminate these agreements with us,
it could reduce our revenues which could harm our business.
Additionally, we anticipate securing additional government contracts as part of our business plan for 2019
and beyond. If we are unable to secure such government contracts, it could harm our business.

Our products subject us to product-safety risks, and we may be sued for product liability.

The design, development, production and sale of our products involve an inherent risk of product
liability claims and the associated adverse publicity. Our products could be used by a wide variety of
consumers with varying levels of sophistication. Although safety is a priority for us, we are not always in
control of the final uses and formulations of the products we supply or their use as ingredients. Our
products could have detrimental impacts or adverse impacts we cannot anticipate. Despite our efforts,
negative publicity about Amyris, including product safety or similar concerns, whether real or perceived,
could occur, and our products could face withdrawal, recall or other quality issues. In addition, we may be
named directly in product liability suits relating to our products, even for defects resulting from errors of
our commercial partners, contract manufacturers, chemical finishers, customers or end users of our
products. These claims could be brought by various parties, including customers who are purchasing
products directly from us or other users who purchase products from our customers. We could also be
named as co-parties in product liability suits that are brought against the contract manufacturers with
whom we partner to produce our products. Insurance coverage is expensive, may be difficult to obtain and
may not be available in the future on acceptable terms. We cannot be certain that our contract
manufacturers or the sugar and ethanol producers who partner with us to produce our products will have
adequate insurance coverage to cover against potential claims. Any insurance we do maintain may not
provide adequate coverage against potential losses, and if claims or losses exceed our liability insurance
coverage, our business would be adversely impacted. In addition, insurance coverage may become more
expensive, which would harm our results of operations.

We may become subject to lawsuits or indemnity claims in the ordinary course of business, which could
materially and adversely affect our business and results of operations.

From time to time, we may in the ordinary course of business be named as a defendant in lawsuits,
indemnity claims and other legal proceedings. These actions may seek, among other things, compensation
for alleged personal injury, employment discrimination, breach of contract, property damage and other
losses or injunctive or declaratory relief. In the event that such actions, claims or proceedings are ultimately
resolved unfavorably to us at amounts exceeding our accrued liability, or at material amounts, the outcome
could materially and adversely affect our reputation, business and results of operations. In addition,
payments of significant amounts, even if reserved, could adversely affect our liquidity position. For more

information regarding our current legal proceedings, please refer to the section entitled “Legal Proceedings”
in Part I, Item 3 of this Annual Report on Form 10-K.

We may not be able to fully enforce covenants not to compete with and not to solicit our employees, and
therefore we may be unable to prevent our competitors from benefiting from the expertise of such employees.

Our proprietary information and inventions agreements with our employees contain non-compete and
non-solicitation provisions. These provisions prohibit our employees from competing directly with our
business or proposed business or working for our competitors during their term of employment, and from
directly or indirectly soliciting our employees or consultants to leave our company for any purpose. Under
applicable U.S. and Brazilian law, we may be unable to enforce these provisions. If we cannot enforce these
provisions with our employees, we may be unable to prevent our competitors from benefiting from the
expertise of such employees. Even if these provisions are enforceable, they may not adequately protect our
interests. The defection of one or more of our employees to a competitor could materially adversely affect
our business, results of operations and ability to capitalize on our proprietary information.

Loss of key personnel, including key management personnel, and/or failure to attract and retain additional
personnel could delay our product development programs and harm our research and development efforts and
our ability to meet our business objectives.

Our business involves complex, global operations across a variety of markets and requires a
management team and employee workforce that is knowledgeable in the many areas in which we operate.
As we continue to build our business, we will need to hire and retain qualified research and development,
management and other personnel to succeed. The process of hiring, training and successfully integrating
qualified personnel into our operations in the United States, Brazil and other countries in which we may
seek to operate, can be a lengthy and expensive one. The market for qualified personnel is very competitive
because of
the limited number of people available who have the necessary technical skills and
understanding of our technology and products. Our failure to hire and retain qualified personnel could
impair our ability to meet our research and development and business objectives and adversely affect our
results of operations and financial condition.

The loss of any key member of our management or key technical and operational employees, or the
failure to attract or retain such employees, could prevent us from developing and commercializing our
products for our target markets and executing our business strategy. In addition, we may not be able to
attract or retain qualified employees in the future due to the intense competition for qualified personnel
among biotechnology and other technology-based businesses. Furthermore, any reductions to our
workforce as part of potential cost-saving measures, such as those discussed above with respect to our 2019
operating plan, may make it more difficult for us to attract and retain key employees. If we do not maintain
the necessary personnel to accomplish our business objectives, we may experience staffing constraints that
will adversely affect our ability to meet the demands of our collaboration partners and customers in a
timely fashion or to support our internal research and development programs and operations. In particular,
our product and process development programs depend on our ability to attract and retain highly skilled
technical and operational personnel. Competition for such personnel from numerous companies and
academic and other research institutions may limit our ability to do so on acceptable terms. All of our U.S.
employees are “at-will” employees, which means that either the employee or we may terminate their
employment at any time.

Our operations rely on sophisticated information technology and equipment systems, a disruption of which
could harm our operations.

We rely on various information technology and equipment systems, some of which are dependent on
services provided by third parties, to manage our technology platform and operations. These systems
provide critical data and services for internal and external users, including research and development
activities, procurement and inventory management, transaction processing, financial, commercial and
legal and tax
operational data, partner and joint venture activities, human resources management,
compliance and other processes necessary to operate and manage our business. These systems are complex
and are frequently updated as technology improves, and include software and hardware that is licensed,
leased or purchased from third parties. If our information technology and equipment systems experience

breaches or other failures or disruptions, our systems and the information contained therein could be
compromised. While we have implemented security measures and disaster recovery plans designed to
mitigate the effects of any failures or disruption of these systems, such measures may not adequately
prevent adverse events such as breaches or failures from occurring or mitigate their severity if they do
occur. If our information technology or equipment systems are breached, damaged or fail to function
properly due to internal errors or defects, implementation or integration issues, catastrophic events or power
outages, we may experience a material disruption in our ability to manage our business operations. Failure
or disruption of these systems could have an adverse effect on our operating results and financial condition.

Increased information systems security threats and more sophisticated and targeted computer invasions could
pose a risk to our technology platform and operations.

Increased information systems security threats, cyber- or phishing-attacks and more sophisticated,
targeted computer invasions pose a risk to the security of our systems and networks, and the
confidentiality, availability, and integrity of our data, operations, and communications. Cyber-attacks
against our technology platform and infrastructure could result in exposure of confidential information, the
modification of critical data, and/or the failure of critical operations. Likewise, improper or inadvertent
employee behavior, including data privacy breaches by employees and others with permitted access to our
systems may pose a risk that sensitive data may be exposed to unauthorized persons or to the public. While
we attempt to mitigate these risks by employing a number of measures, including security measures,
employee training, incident response procedures, comprehensive monitoring of our networks and systems,
and maintenance of backup and protective systems, if these measures prove inadequate, we could be
adversely affected by, among other things,
intellectual property, proprietary and
information, data integrity, and communications or customer data, having our business
confidential
operations interrupted and increased costs to prevent, respond to, or mitigate these cyber security threats.

loss or damage of

Growth may place significant demands on our management and our infrastructure.

We have experienced, and expect to continue to experience, expansion of our business as we continue
to make efforts to develop and bring our products to market. We have grown from 18 employees at the end
of 2005 to 503 full-time employees at December 31, 2018. Our growth and diversified operations have
placed, and may continue to place, significant demands on our management and our operational and
financial infrastructure. In particular, continued growth could strain our ability to:

•

manage multiple research and development programs;

operate multiple manufacturing facilities around the world;

develop and improve our operational, financial and management controls;

enhance our reporting systems and procedures;

recruit, train and retain highly skilled personnel;

develop and maintain our relationships with existing and potential business partners;

maintain our quality standards; and

maintain customer satisfaction.

Managing our growth will require significant expenditures and allocation of valuable management
resources. If we fail to achieve the necessary level of efficiency in our organization as it grows, our business,
results of operations and financial condition would be adversely impacted.

Our international operations expose us to the risk of fluctuation in currency exchange rates and rates of
foreign inflation, which could adversely affect our results of operations.

We currently incur significant costs and expenses in Brazilian real and may in the future incur
additional expenses in foreign currencies and derive a portion of our revenues in the local currencies of
customers throughout the world. As a result, our revenues and results of operations are subject to foreign
exchange fluctuations, which we may not be able to manage successfully. During the past few decades, the

Brazilian currency in particular has faced frequent and substantial exchange rate fluctuations in relation to
foreign currencies mostly because of political and economic conditions. There can be no assurance that the
Brazilian real will not significantly appreciate or depreciate against the United States dollar in the future.
We also bear the risk that the rate of inflation in the foreign countries where we incur costs and expenses or
the decline in value of the United States dollar compared to those foreign currencies will increase our costs
as expressed in United States dollars. For example, future measures by the Central Bank of Brazil to control
inflation, including interest rate adjustments, intervention in the foreign exchange market and actions to fix
the value of the real, may weaken the United States dollar in Brazil. Whether in Brazil or elsewhere, we may
not be able to adjust the prices of our products to offset the effects of inflation or foreign currency
appreciation on our cost structure, which could increase our costs and reduce our net operating margins. If
we do not successfully manage these risks through hedging or other mechanisms, our revenues and results
of operations could be adversely affected.

Our U.S. GAAP operating results could fluctuate substantially due to the accounting for embedded derivatives
in our convertible debt and equity instruments, and debt that we measure at fair value.

Features in several of our outstanding convertible debt and equity instruments are accounted for under
Accounting Standards Codification 815, Derivatives and Hedging (ASC 815), as embedded derivatives.
ASC 815 requires companies to bifurcate conversion options from their host instruments and account for
them as free standing derivative financial instruments according to certain criteria. The current fair value of
the derivative is remeasured to fair value at each balance sheet date, with a resulting non-cash gain or loss
related to the change in the fair value of the derivative being charged to earnings (loss) in the statement of
operations. We have determined that we must bifurcate and account for certain features of our convertible
debt and equity instruments as embedded derivatives in accordance with ASC 815. We have recorded these
embedded derivative liabilities as non-current liabilities on our consolidated balance sheet with a
corresponding discount at the date of issuance that is netted against the principal amount of the applicable
instrument. The derivative liabilities are remeasured to fair value at each balance sheet date, with a resulting
non-cash gain or loss related to the change in the fair value of the derivative liabilities being recorded in
other income or expenses. There is no current observable market for this type of derivative and, as such, we
determine the fair value of the embedded derivatives using the binomial lattice model. The valuation model
uses the stock price, conversion price, maturity date, risk-free interest rate, estimated stock volatility and
estimated credit spread. Changes in the inputs for these valuation models may have a significant impact on
the estimated fair value of the embedded derivative liabilities. For example, an increase in our stock price
would result in an increase in the estimated fair value of the embedded derivative liabilities, if in this
example, each of the other elements of the valuation model remained substantially unchanged from the last
measurement date. The embedded derivative liabilities may have, on a U.S. GAAP basis, a substantial effect
on our balance sheet from quarter to quarter and it is difficult to predict the effect on our future U.S.
GAAP financial results, since valuation of these embedded derivative liabilities are based on factors largely
outside of our control and may have a negative impact on our statement of operations and balance sheet.
The effects of these embedded derivatives may cause our U.S. GAAP operating results to be below
expectations, which may cause our stock price to decline. See Note 4, “Fair Value Measurement” in Part II,
Item 8 of this Annual Report on Form 10-K for more information regarding the valuation of embedded
derivatives in certain of our outstanding debt and equity instruments.

In addition, we account for one of our outstanding debt instruments at fair value. That instrument is
remeasured to fair value at each balance sheet date, with a resulting non-cash gain or loss related to the
change in fair value recorded in other income or expense.

Our ability to use our net operating loss carryforwards to offset future taxable income may be subject to
certain limitations.

In general, under Section 382 of the Internal Revenue Code (the Code), a corporation that undergoes
an “ownership change”, as defined in the Code, is subject to limitations on its ability to utilize its
pre-ownership change net operating loss carryforwards (NOLs) to offset future taxable income. During the
three years ended December 31, 2017, changes in our share ownership resulted in a significant reduction in
our NOLs pursuant to Section 382 of the Code. Future changes in our stock ownership, some of which are
outside of our control, could result in an ownership change under Section 382 of the Code; if that occurs,

our ability to utilize NOLs could be further limited. Furthermore, our ability to utilize NOLs of companies
that we may acquire in the future may be subject to limitations under Section 382 of the Code. For these
reasons, we may not be able to utilize a material portion of our reported NOLs as of December 31, 2018,
even if we attain profitability, which could adversely affect our results of operations.

Our headquarters and other facilities are located in active earthquake and tsunami or in active hurricane zones,
and an earthquake, hurricane or other type of natural disaster affecting us or our suppliers could cause
resource shortages, disrupt our business and harm our results of operations.

We conduct our primary research and development operations in the San Francisco Bay Area in an
active earthquake and tsunami zone, and certain of our suppliers conduct their operations in the same
region or in other locations that are susceptible to natural disasters. In addition, California and some of the
locations where certain of our suppliers are located have experienced shortages of water, electric power and
natural gas from time to time. The occurrence of a hurricane or associated flooding in the Wilmington,
North Carolina area could cause damage to our facility located in Leland or result in localized extended
outages of utilities or transportation systems. The occurrence of a natural disaster, such as an earthquake,
hurricane, drought or flood, or localized extended outages of critical utilities or transportation systems, or
any critical resource shortages, affecting us or our suppliers could cause a significant interruption in our
business, damage or destroy our facilities, production equipment or inventory or those of our suppliers and
cause us to incur significant costs or result in limitations on the availability of our raw materials, any of
which could harm our business, financial condition and results of operations. The insurance we maintain
against fires, earthquakes and other natural disasters may not be adequate to cover our losses in any
particular case. Our facilities undergo annual loss control audits and both our Emeryville and Leland
facilities have emergency actions plans outlining emergency response practices for these and other
emergency scenarios. Training on emergency response is provided to all employees at hire and annually
thereafter as a refresh.

Our stock price may be volatile.

The market price of our common stock has been, and we expect it to continue to be, subject to
significant volatility, and it has declined significantly from our initial public offering price. As of
December 31, 2018, the reported closing price of our common stock on Nasdaq was $3.34 per share.
Market prices for securities of early stage companies have historically been particularly volatile. Such
fluctuations could be in response to, among other things, the factors described in this “Risk Factors”
section, or other factors, some of which are beyond our control, such as:

•

fluctuations in our financial results or outlook or those of companies perceived to be similar to us;

changes in estimates of our financial results or recommendations by securities analysts;

changes in market valuations of similar companies;

changes in the prices of commodities associated with our business such as sugar and petroleum or
changes in the prices of commodities that some of our products may replace, such as oil and other
petroleum sourced products;

changes in our capital structure, such as future issuances of securities or the incurrence of debt;

announcements by us or our competitors of significant contracts, acquisitions or strategic
partnerships;

regulatory developments in the United States, Brazil, and/or other foreign countries;

litigation involving us, our general industry or both;

additions or departures of key personnel;

investors’ general perception of us; and

changes in general economic, industry and market conditions.

Furthermore, stock markets have experienced price and volume fluctuations that have affected, and
continue to affect, the market prices of equity securities of many companies. These fluctuations often have
been unrelated or disproportionate to the operating performance of those companies. These broad market
fluctuations, as well as general economic, political and market conditions, such as recessions, interest rate
changes and international currency fluctuations, may negatively affect the market price of our common
stock.

In the past, many companies that have experienced volatility and sustained declines in the market price
of their stock have become subject to securities class action and derivative action litigation. We were
involved in two such lawsuits which were dismissed in 2014, were involved in five such lawsuits that were
dismissed in September 2017, July 2018 and September 2018, respectively, are currently involved in two such
lawsuits, as described in more detail below under “Legal Proceedings,” and we may be the target of this type
of litigation in the future. Securities litigation against us could result in substantial costs and divert our
management’s attention from other business concerns, which could seriously harm our business.

If our common stock is delisted from Nasdaq, our business, financial condition, results of operations and stock
price could be adversely affected, and the liquidity of our stock and our ability to obtain financing could be
impaired.

On April 3, 2019, we received a letter from Nasdaq notifying us that we were not in compliance with
the requirement of Nasdaq Listing Rule 5250(c)(1) for continued listing on Nasdaq as a result of our failure
to timely file this Annual Report on Form 10-K. In accordance with the notice, we were required to submit
to Nasdaq a plan to regain compliance with Nasdaq’s requirements for continued listing within 60 calendar
days of the date of the notice, or by June 3, 2019. On May 14 and August 16, 2019, we received further
letters from Nasdaq notifying us that we were not in compliance with the requirement of Nasdaq Listing
Rule 5250(c)(1) for continued listing on Nasdaq as a result of our failure to timely file our Quarterly Report
on Form 10-Q for the fiscal quarter ended March 31, 2019 and Quarterly Report on Form 10-Q for the
fiscal quarter ended June 30, 2019, respectively, as well as our continued delinquency in filing this Annual
Report on Form 10-K. On June 3, 2019, we submitted to Nasdaq a plan to regain compliance with
Nasdaq’s requirements for continued listing. On June 12, 2019, Nasdaq granted us an exception until
August 15, 2019 to regain compliance with Nasdaq’s requirements for continued listing and on July 25,
2019, Nasdaq extended the exception to September 30, 2019. There can be no assurance, however, that we
will regain compliance with Nasdaq’s rules for continued listing by such deadline, or at all, or that, if we
regain compliance, we will maintain compliance with Nasdaq’s rules for continued listing, including the
requirements that we timely file our periodic reports with the SEC and maintain a stock price of at least
$1.00 per share, or that our common stock will remain listed on Nasdaq.

Any delisting of our common stock from Nasdaq could adversely affect our ability to attract new
investors, decrease the liquidity of our outstanding shares of common stock, reduce our flexibility to raise
additional capital, reduce the price at which our common stock trades, and increase the transaction costs
inherent in trading such shares with overall negative effects for our stockholders. In addition, the delisting
of our common stock could deter broker-dealers from making a market in or otherwise seeking or
generating interest in our common stock, and might deter certain institutions and persons from investing in
our securities at all. Furthermore, the delisting of our common stock from Nasdaq would constitute a
including agreements governing our outstanding
breach under certain of our financing agreements,
convertible indebtedness, which could result in an acceleration of such indebtedness. If such indebtedness is
accelerated, it would generally also constitute an event of default under our other outstanding indebtedness,
permitting acceleration of such other outstanding indebtedness as well. For these reasons and others, the
delisting of our common stock from Nasdaq could materially adversely affect our business, financial
condition and results of operations.

The concentration of our capital stock ownership with insiders will limit the ability of other stockholders to
influence corporate matters and presents risks related to the operations of our significant stockholders.

As of August 30, 2019, significant stockholders held an aggregate total of 45.5% of the Company’s
total common shares outstanding, as follows: Foris Ventures, LLC (Foris) (17.0%), DSM (12.6%), Total
(9.6%), and Vivo Capital LLC (Vivo) (6.3%). Furthermore, each of these parties holds convertible preferred

stock, convertible promissory notes and/or warrants, pursuant to which they may acquire additional shares
of our common stock and thereby increase their ownership interest in our company. Additionally, each of
DSM, Total and Vivo have the right to designate one or more directors to serve on our Board of Directors
pursuant to agreements between us and such stockholders, and Foris is indirectly owned by John Doerr, one
of our current directors. This significant concentration of share ownership may adversely affect the trading
price of our common stock because investors often perceive disadvantages in owning stock in companies
with stockholders with significant interests. Also, these stockholders, acting together, may be able to control
or significantly influence our management and affairs and matters requiring stockholder approval,
including the election of directors and the approval of significant corporate transactions, such as mergers,
consolidations or the sale of all or substantially all of our assets, and may not act in the best interests of our
other stockholders. Consequently, this concentration of ownership may have the effect of delaying or
preventing a change of control, or a change in our management or Board of Directors, or discouraging a
potential acquirer from making a tender offer or otherwise attempting to obtain control of our company,
even if such actions would benefit our other stockholders.

In addition, certain of our significant stockholders are also our commercial partners and have various
rights in connection with their security ownership in us. These stockholders may have interests that are
different from those of our other stockholders, including with respect to our company’s commercial
transactions. While we have a related-party transactions policy that requires certain approvals of any
transaction between our company and a significant stockholder or its affiliates, there can be no assurance
that our significant stockholders will act in the best interests of our other stockholders, which could harm
our results of operations and cause our stock price to decline.

The market price of our common stock could be negatively affected by future sales of our common stock.

If our existing stockholders, particularly our largest stockholders, our directors, their affiliates, or our
executive officers, sell a substantial number of shares of our common stock in the public market, the market
price of our common stock could decrease significantly. The perception in the public market that these
stockholders might sell our common stock could also depress the market price of our common stock and
could impair our future ability to obtain capital, especially through an offering of equity securities.

We have in place, or have agreed to file, registration statements for the resale of certain shares of our
common stock held by, or issuable to, certain of our largest stockholders. All of our common stock sold
pursuant to an offering covered by such registration statements will be freely transferable. In addition,
shares of our common stock issued or issuable under our equity incentive plans have been registered on
Form S-8 registration statements and may be freely sold in the public market upon issuance, except for
shares held by affiliates who have certain restrictions on their ability to sell.

If securities or industry analysts do not publish or cease publishing research or reports about us, our business or
our market, or if they change their recommendations regarding our stock adversely, our stock price and trading
volume could decline.

The trading market for our common stock will be influenced by the research and reports that industry
or securities analysts may publish about us, our business, our market or our competitors. If any of the
analysts who cover us change their recommendation regarding our stock adversely, or provide more
favorable relative recommendations about our competitors, our stock price would likely decline. If any
analyst who may cover us were to cease coverage of our company or fail to regularly publish reports on us,
we could lose visibility in the financial markets, which in turn could cause our stock price or trading volume
to decline.

We do not expect to declare any dividends in the foreseeable future.

We do not anticipate declaring any cash dividends to holders of our common stock in the foreseeable
future. In addition, certain of our equipment leases and credit facilities currently restrict our ability to pay
dividends. Consequently, investors may need to rely on sales of their shares of our common stock after
price appreciation, which may never occur, as the only way to realize any future gains on their investment.
Investors seeking cash dividends should not purchase our common stock.

Anti-takeover provisions contained in our Certificate of Incorporation and Bylaws, as well as provisions of
Delaware law, could impair a takeover attempt.

Our Certificate of Incorporation and Bylaws contain provisions that could delay or prevent a change
in control of our company. These provisions could also make it more difficult for stockholders to nominate
directors and take other corporate actions. These provisions include:

•

a staggered Board of Directors;

authorizing the Board of Directors to issue, without stockholder approval, preferred stock with
rights senior to those of our common stock;

authorizing the Board of Directors to amend our Bylaws, to increase the number of directors and
to fill board vacancies until the end of the term of the applicable class of directors;

prohibiting stockholder action by written consent;

limiting the liability of, and providing indemnification to, our directors and officers;

eliminating the ability of our stockholders to call special meetings; and

requiring advance notification of stockholder nominations and proposals.

Section 203 of the Delaware General Corporation Law prohibits, subject to some exceptions, “business
combinations” between a Delaware corporation and an “interested stockholder,” which is generally defined
as a stockholder who becomes a beneficial owner of 15% or more of a Delaware corporation’s voting stock,
for a three-year period following the date that the stockholder became an interested stockholder. We have
agreed to opt out of Section 203 through our Certificate of Incorporation, but our Certificate of
Incorporation contains substantially similar protections to our company and stockholders as those afforded
under Section 203, except that we have agreed with Total that it and its affiliates will not be deemed to be
“interested stockholders” under such protections.

These and other provisions in our Certificate of Incorporation and our Bylaws could discourage
potential takeover attempts, reduce the price that investors are willing to pay in the future for shares of our
common stock and result in the market price of our common stock being lower than it would be without
these provisions.

ITEM 1B. UNRESOLVED STAFF COMMENTS

Not applicable.

ITEM 2. PROPERTIES

The following is a summary of our principal facilities as of December 31, 2018. We lease our principal
office and research and development facilities located in Emeryville, California. We hold a 50% ownership
interest in a manufacturing facility and related land located in Leland, North Carolina and lease a pilot
plant and demonstration facility and related office and laboratory space located in Campinas, Brazil. Our
lease agreements expire at various dates through the year 2031.

Location

U.S.

Approximate
Square Feet

Operations

Emeryville, California

136,000

Executive offices; research and development,
administrative and pilot plant

Leland, North Carolina

19,400

Manufacturing (joint venture with Nikko)

BRAZIL

Campinas, Brazil

44,000

Pilot plant, research and development and administrative

We have a dormant lease of approximately 500,000 square feet of land in Pradópolis, Brazil, on which
we previously began construction of a manufacturing facility with our joint venture partner São Martinho,
which was approximately 50% complete when we halted construction in 2013. We have no future plans for
this site. See Note 3, “Balance Sheet Details” for additional information.

We believe that our current facilities are suitable and adequate to meet our needs and that suitable
additional space will be available to accommodate the foreseeable expansion of our operations. Based on
our anticipated volume requirements for 2019 and beyond, we will likely need to identify and secure access
to additional production capacity in 2019 and beyond, which we plan to obtain by constructing new
facilities and by increasing our use of contract manufacturers, including our collaboration partner, DSM.
We are currently making plans to secure such additional capacity.

ITEM 3. LEGAL PROCEEDINGS

On April 3, 2019, a securities class action complaint was filed against Amyris and our CEO, John G.
Melo, and former CFO (and current Chief Business Officer), Kathleen Valiasek, in the U.S. District Court
for the Northern District of California. The complaint seeks unspecified damages on behalf of a purported
class that would comprise all persons and entities that purchased or otherwise acquired our securities
between March 15, 2018 and March 19, 2019. The complaint alleges securities law violations based on
statements and omissions made by the Company during such period. Subsequent to the filing of the
securities class action complaint described above, on June 21, 2019, a purported shareholder derivative
complaint was filed in the U.S. District Court for the Northern District of California (Bonner v. Doerr,
et al., Case No. 4:19-cv-03621) based on similar allegations to those made in the securities class action
complaint described above. The derivative complaint names Amyris, Inc. as a nominal defendant and names
a number of the Company’s current and former officers and directors as additional defendants. The lawsuit
seeks to recover, on the Company’s behalf, unspecified damages purportedly sustained by the Company in
connection with allegedly misleading statements and/or omissions made in connection with the Company’s
securities filings. The derivative complaint also seeks a series of changes to the Company’s corporate
governance policies, restitution to the Company from the individual defendants, and an award of attorneys’
fees. These cases are in the initial pleadings stage. We believe the complaints lack merit, and intend to
defend ourselves vigorously. Given the early stage of these proceedings, it is not yet possible to reliably
determine any potential liability that could result from these matters.

We may be involved, from time to time, in legal proceedings and claims arising in the ordinary course
of our business. Such matters are subject to many uncertainties and there can be no assurance that legal
proceedings arising in the ordinary course of business or otherwise will not have a material adverse effect on
our business, results of operations, financial position or cash flows. For additional information, see “Other
Matters” in Note 9, “Commitments and Contingencies” in Part II, Item 8 of this Annual Report on
Form 10-K.

ITEM 4. MINE SAFETY DISCLOSURES

Not applicable.

PART II

ITEM 5. MARKET FOR REGISTRANT’S COMMON EQUITY AND RELATED STOCKHOLDER

MATTERS

Market Information for Common Stock

Our common stock is traded on the Nasdaq Global Select Market under the symbol AMRS.

At September 26, 2019, there were 70 holders of record (not including beneficial holders of stock held

in street names) of our common stock.

Dividend Policy

We have never declared or paid any cash dividend on our common stock. We intend to retain any

future earnings and do not expect to pay cash dividends in the foreseeable future.

Recent Sales of Unregistered Equity Securities and Use of Proceeds

For information regarding unregistered sales of our equity securities for prior periods within the
two years ended December 31, 2018, see the financial statements included in Part II, Item 8 of this Annual
Report on Form 10-K previously filed with the SEC.

On November 20, 2018, we issued 1,643,991 shares of common stock (the DSM Shares) to DSM
pursuant to a securities purchase agreement, dated November 19, 2018, between us and DSM,
in
consideration of certain agreements of DSM set forth in the Supply Agreement Amendment (see Note 7,
“Stockholders’ Deficit” and Note 10, “Revenue Recognition” in Part II, Item 8 of this Annual Report on
Form 10-K for more information regarding the issuance of the DSM Shares and the Supply Agreement
Amendment).

On December 10, 2018, we issued $60 million in aggregate principal amount of senior convertible notes
(the December 2018 Notes), with an initial conversion price of $6.32 per share, pursuant to a securities
purchase agreement, dated December 6, 2018, among us and the investors named therein. See Note 5,
“Debt” in Part II, Item 8 of this Annual Report on Form 10-K for more information regarding the
December 2018 Notes, including the conversion terms thereof.

No underwriters or agents were involved in the issuance of the DSM Shares. Oppenheimer & Co. Inc.
acted as placement agent and B. Riley FBR, Inc. acted as our advisor in connection with the issuance of the
December 2018 Notes, and we paid an aggregate of $3.8 million in fees to such agent and advisor in
connection with the offering and sale of the December 2018 Notes. The DSM Shares and December 2018
Notes were issued in separate private placements pursuant to the exemption from registration under
Section 4(a)(2) of
the Securities Act of 1933, as amended (the Securities Act), and Regulation D
promulgated under the Securities Act (Regulation D), without general solicitation, made only to and with
“accredited investors” as defined in Regulation D. DSM is an existing stockholder and is affiliated with
members of our Board of Directors. The holders acquired the DSM Shares and December 2018 Notes for
investment purposes only and without intent to resell, were able to fend for themselves in these transactions,
and are accredited investors as defined in Rule 501 of Regulation D promulgated under Section 3(b) of the
Securities Act, and appropriate restrictions were set forth in the securities purchase agreements and
securities relating to the transactions. These holders had adequate access, through their relationships with
us, to information about us.

See Note 16, “Subsequent Events” in Part II, Item 8 of this Annual Report on Form 10-K for

information regarding unregistered sales of our equity securities subsequent to December 31, 2018.

Securities Authorized for Issuance under Equity Compensation Plans

Number of
securities to
be
issued upon
exercise of
outstanding
options,
warrants
and rights

Weighted-
average
exercise
price of
outstanding
options,
warrants
and rights

Number of
securities to
be
issued upon
vesting
of
outstanding
restricted
stock
units

Number of
securities
remaining
available for
future
issuance
under
equity
compensation
plans(1)(2)

Plan category

Equity compensation plans approved by security

holders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

5,390,270

$11.55

5,294,803

2,559,213

Equity compensation plans not approved by security

holders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

—

Total . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

5,390,270

$11.55

5,294,803

2,559,213

(1)

Includes 2,359,750 shares reserved for future issuance under our 2010 Equity Incentive Plan and
382,824 shares reserved for future issuance under our 2010 Employee Stock Purchase Plan. No shares
are reserved for future issuance under our 2005 Stock Option/Stock Issuance Plan other than shares
issuable upon exercise of equity awards outstanding under such plan.

The number of shares available for grant and issuance under our 2010 Equity Incentive Plan is
increased on January 1 of each year during the term of the plan by an amount equal to the lesser
of (1) five percent (5%) of our shares outstanding on the immediately preceding December 31 and (2) a
number of shares as may be determined by our Board of Directors or the Leadership Development and
Compensation Committee in their discretion. In addition, shares will again be available for grant and
issuance under our 2010 Equity Incentive Plan that are:

•

subject to an award granted under our 2010 Equity Incentive Plan and that are subsequently
forfeited or repurchased by us at the original issue price;

surrendered pursuant to an exchange program; or

subject to an award granted under our 2010 Equity Incentive Plan that otherwise terminates
without shares being issued.

The number of shares reserved for issuance under our 2010 Employee Stock Purchase Plan is increased
on January 1 of each year during the term of the plan by an amount equal to the lesser of (1) one percent
(1%) of our shares outstanding on the immediately preceding December 31 and (2) a number of shares as
may be determined by our Board of Directors or the Leadership Development and Compensation
Committee of the Board in their discretion, provided that the aggregate number of shares issued over the
term of our 2010 Employee Stock Purchase Plan shall not exceed 1,666,666 shares.

For more information regarding our 2010 Equity Incentive Plan and 2010 Employee Stock Purchase

Plan, see Note 12, “Stock-based Compensation” in Part II, Item 8 of this Annual Report on Form 10-K.

Stock Performance Graph

Not required — Smaller Reporting Company scaled disclosure accommodation.

ITEM 6. SELECTED FINANCIAL DATA

Not required — Smaller Reporting Company scaled disclosure accommodation.

ITEM 7. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND

RESULTS OF OPERATIONS

Restatement of 2017 Financial Information

The accompanying Management’s Discussion and Analysis of Financial Condition and Results of
Operations gives effect to the restatement adjustments made to the previously reported Consolidated
Financial Statements for the year ended December 31, 2017. For additional information and a detailed
discussion of the restatement, see the Explanatory Note to this Annual Report on Form 10-K and Note 2,
“Restatement of Consolidated Financial Statements” to our consolidated financial statements included in
Part II, Item 8 of this Annual Report on Form 10-K.

Overview

As a leading industrial biotechnology company, we apply our technology platform to engineer,
manufacture and sell high performance, natural, sustainably-sourced products into the Health & Wellness,
Clean Beauty, and Flavor & Fragrance markets. Our proven technology platform enables us to rapidly
engineer microbes and use them as catalysts to metabolize renewable, plant-sourced sugars into large
volume, high-value ingredients. Our biotechnology platform and industrial fermentation process replace
existing complex and expensive manufacturing processes. We have successfully used our technology to
develop and produce eight distinct molecules at commercial volumes, leading to more than 15 commercial
ingredients used by thousands of leading global brands.

We believe that industrial synthetic biology represents a third industrial revolution, bringing together
biology and engineering to generate new, more sustainable materials to meet the growing global demand for
bio-based replacements for petroleum-based and traditional animal- or plant-derived ingredients. We
continue to build demand for our current portfolio of products through an extensive sales network provided
by our collaboration partners that represent leading companies for our target market sectors. We also have a
small group of direct sales and distributors who support our Clean Beauty market. Via our partnership
model, our partners invest in the development of each molecule to bring it from the lab to commercial scale
and use their extensive sales force to sell our ingredients and formulations to their customers as part of their
core business. We capture long-term revenue both through the production and sale of the molecule to our
partners and through royalty revenues from our partners’ product sales to their customers.

We were founded in 2003 in the San Francisco Bay area by a group of scientists from the University of
California, Berkeley. Our first major milestone came in 2005 when, through a grant from the Bill & Melinda
Gates Foundation, we developed technology capable of creating microbial strains that produce artemisinic
acid, which is a precursor of artemisinin, an effective anti-malarial drug. In 2008, we granted royalty-free
licenses to allow Sanofi-Aventis to produce artemisinic acid using our technology. Building on our success
with artemisinic acid, in 2007 we began applying our technology platform to develop, manufacture and sell
sustainable alternatives to a broad range of markets.

skincare products,

We focused our initial development efforts primarily on the production of Biofene®, our brand of
renewable farnesene, a long-chain, branched hydrocarbon molecule that we manufacture through
fermentation using engineered microbes. Our farnesene derivatives are sold in hundreds of products as
nutraceuticals,
ingredients. The
commercialization of farnesene pushed us to create a more cost efficient, faster and accurate development
process in the lab and drive manufacturing costs down. This investment has enabled our technology
platform to rapidly develop microbial strains and commercialize target molecules. In 2014, we began
manufacturing additional molecules for the Flavor & Fragrance industry; in 2015 we began investing to
expand our capabilities to other small molecule chemical classes beyond terpenes via our collaboration with
the Defense Advanced Research Projects Agency (DARPA); and in 2016 we expanded into proteins.

solvents, polymers, and lubricant

fragrances,

We have invested over $600 million in infrastructure and technology to create microbes that produce
molecules from sugar or other feedstocks at commercial scale. This platform has been used to design, build,
optimize and upscale strains producing eight distinct molecules at commercial volumes, leading to more
than 15 commercial ingredients used by thousands of leading global brands. Our time to market for
molecules has decreased from seven years to less than a year for our most recent molecule, mainly due to
our ability to leverage the technology platform we have built.

Our technology platform has been in active use since 2007 and has been integrated with our
commercial production since 2011, creating an organism development process that we believe makes us an
industry leader in the successful scale-up and commercialization of biotech-produced ingredients. The key
performance characteristics of our platform that we believe differentiate us include our proprietary
computational tools, strain construction tools, screening and analytics tools, and advanced lab automation
and data integration. Having this fully integrated with our large scale manufacturing process and capability
enables us to always engineer with the end specification and requirements guiding our technology. Our
state-of-the-art infrastructure includes industry-leading strain engineering and lab automation located in
Emeryville, California, pilot scale production facilities in Emeryville, California and Campinas, Brazil, a
demonstration-scale facility in Campinas, Brazil and a commercial-scale production facility in Leland,
North Carolina, which is owned and operated by our Aprinnova joint venture to convert our Biofene into
squalane and other final products.

We are able to use a wide variety of feedstocks for production, but have focused on accessing Brazilian
sugarcane for our large-scale production because of its renewability, low cost and relative price stability. We
have also successfully used other feedstocks such as sugar beets, corn dextrose, sweet sorghum and cellulosic
sugars at various manufacturing facilities.

Several years ago, we made the strategic decision to transition our business model from collaborating
and commercializing molecules in low margin commodity markets to higher margin specialty markets. We
began the transition by first commercializing and supplying farnesene-derived squalane as a cosmetic
ingredient sold to formulators and distributors. We also entered into collaboration and supply agreements
for the development and commercialization of molecules within the Flavor & Fragrance and Clean Beauty
markets where we utilize our strain generation technology to develop molecules that meet the customer’s
rigorous specifications.

During this transition, we solidified the business model of partnering with our customers to create
sustainable, high performing,
low-cost molecules that replace an ingredient in their supply chain,
commercially scale and manufacture those molecules, and share in the profits earned by our customers once
our customer sells its product into these specialty markets. These three steps constitute our collaboration
revenues, renewable product revenues, and royalty revenues.

During 2017, we completed several development agreements with DSM and others for new products
such as Vitamin A, a human nutrition molecule and others, and in late 2018 we began commercial
production and shipment of a new sweetener product developed from the Reb M molecule, which is a
superior sweetener and sugar replacement. Our goal is to bring two to three new molecules per year to
commercial production in the future.

In 2017, we decided to monetize the use of one of our lower margin molecules, farnesene, in the
Vitamin E and Lubricants specialty markets while retaining any associated royalties, and licensed farnesene
to Koninklijke DSM N.V. (DSM) for use in these fields. Also in 2017, we sold to DSM our subsidiary
Amyris Brasil Ltda. (Amyris Brasil), which operated our purpose-built, large-scale manufacturing facility
located in Brotas, Brazil.

The Brotas facility was built to batch manufacture one commodity product at a time (originally for
high-volume production of biofuels, a business Amyris has exited), which is an inefficient manufacturing
process that is not suited for the high margin specialty markets in which we operate today. We currently
manufacture nine specialty products and expect to increase the number of specialty products we
manufacture by two to three products a year. The inefficiencies we experienced included having to idle the
facility for two weeks at a time to prepare for the next product batch manufacture. These inefficiencies
caused our cost of goods sold to be significantly higher. We are building a new purpose-built, large-scale
specialty ingredients plant in Brazil, which we anticipate will allow for the manufacture of five products
concurrently and over 10 different products annually. As part of the December 2017 sale of Brotas, we
contracted with DSM for the use of Brotas to manufacture products for us to fulfill our product supply
commitments to our customers until our new production facility becomes operational, which we expect to
occur in 2021. We have expanded the new facility’s design to produce both our specialty ingredients
portfolio and our new sweetener product.

Concurrent with the sale of Amyris Brasil, we entered into a series of commercial agreements with
DSM including (i) a license agreement to DSM of our farnesene product for DSM to use in the Vitamin E
and lubricant specialty markets; (ii) a royalty agreement, pursuant to which DSM agreed to pay us specified
royalties representing a portion of the profit on the sale of Vitamin E produced from farnesene sold under
the supply agreement with Nenter & Co., Inc. (“Nenter”) assigned to DSM; (iii) a performance agreement
to perform research and development to optimize farnesene for production and sale of farnesene products;
and (iv) a transition services agreement where we provide finance, legal, logistics, and human resource
services to support the Brotas facility under DSM ownership for a six-month period with a DSM option to
extend for six additional months. At closing, DSM paid to us a nonrefundable license fee of $27.5 million
and a nonrefundable minimum royalty revenue payment of $15.0 million. In June 2018, DSM paid us a
nonrefundable minimum royalty revenue payment of $9.3 million and will also pay us a nonrefundable
minimum royalty amount in 2019. The future nonrefundable minimum annual royalty payments were
determined to be fixed and determinable at December 31, 2017 with a fair value of $17.8 million and were
this overall
included as part of
multiple-element divestiture transaction. In November 2018 and April 2019, we amended the supply
agreement with DSM to secure capacity at the Brotas facility for Reb M production through 2022. Under
the amended supply agreement, we paid DSM $1.7 million in cash and $7.3 million in common stock as of
December 31, 2018 and will pay an additional $21.0 million in cash installments over the next 12 months for
a total of $30.0 million to secure the manufacturing capacity. We also entered into other agreements with
DSM in November 2018 that resulted in our (i) evaluating the series of fourth quarter transactions
including the amended supply agreement and other transactions with DSM in 2018 as a combined
arrangement, and then (ii) determining and allocating the fair value to each element transferred. See
Note 10, “Revenue Recognition”, Note 11, “Related Party Transactions” and Note 16, “Subsequent
Events” in Part II, Item 8 of this Annual Report on Form 10-K for information regarding the accounting
treatment of this combined arrangement and for a full listing of our agreements with DSM.

the total arrangement consideration subject

to allocation of

Sales and Revenue

We recognize revenue from product sales, license fees and royalties, and grants and collaborations.

We have research and development collaboration arrangements for which we receive payments from
our collaboration partners, which include DARPA, DSM, Firmenich SA (Firmenich), Givaudan
International SA (Givaudan), and others. Some of our collaboration arrangements provide for advance
payments to us in consideration for grants of exclusivity or research efforts that we will perform. In 2017 we
signed collaboration agreements for an infant nutrition ingredient, and in 2018 we signed a collaboration
agreement for two vitamins that we expect will contribute to our collaboration revenue and ultimately
product sales. Our collaboration agreements, which may require us to achieve milestones prior to receiving
payments, are expected to contribute revenues from product sales and royalties if and when they are
commercialized. See Note 10, “Revenue Recognition” in Part II, Item 8 of this Annual Report on
Form 10-K for additional information.

All of our non-government partnerships include commercial terms for the supply of molecules we
successfully upscale and produce at commercial volumes. The first molecule to generate revenue for us
outside of farnesene was a fragrance molecule launched in 2015. Since the launch, the product has
continued to grow in sales year over year. In 2016, we launched our second fragrance molecule and in 2017,
we launched our third fragrance molecule as well as our first cosmetic active ingredient. Our partners for
these molecules are indicating continued strong growth due to their cost advantaged position, high purity
and sustainable production method. We are continuing to identify new opportunities to apply our
technology and deliver sustainable access to key molecules. As a result, we have a pipeline that we believe
can deliver two to three new molecules each year over the coming years with a flavor ingredient, a cosmetic
active ingredient and a fragrance molecule. In 2019, we are commercially producing and shipping our
Reb M product that is a sweetener and sugar replacement for food and beverages.

As part of the DSM acquisition in 2017 of our farnesene for Vitamin E business, we would receive a
royalty payment on certain sales by Nenter & Co., Inc. of Vitamin E utilizing farnesene produced and sold
by DSM from our technology. In addition, DSM would be obligated to pay us minimum royalties totaling
$18.1 million for 2019 and 2020, of which we received $9.3 million as a discounted accelerated payment
(from an original payment amount of $10.0 million) during 2018. In April 2019, we assigned the right to
receive such royalty payments to DSM; see Note 16, “Subsequent Events” in Part II, Item 8 of this 2018
Form 10-K for additional information.

We have several other collaboration molecules in our development pipeline with partners including
DSM, Givaudan and Firmenich that we expect will contribute revenues from product sales and royalties if
and when they are commercialized.

Critical Accounting Policies and Estimates

Management’s discussion and analysis of results of operations and financial condition are based on
our consolidated financial statements, which have been prepared in accordance with accounting principles
generally accepted in the U.S. (U.S. GAAP). We believe that the critical accounting policies described in this
section are those that significantly impact our financial condition and results of operations and require the
most difficult, subjective or complex judgements, often as a result of the need to make estimates about the
effects of matters that are inherently uncertain. Because of this uncertainty, actual results may vary from
these estimates.

Our most critical accounting estimates include:

•

Recognition of revenue including arrangements with multiple performance obligations;

Valuation and allocation of fair value to various elements of complex related party transactions;

The valuation of freestanding and embedded derivatives, which impacts gains or losses on such
derivatives, the carrying value of debt, preferred stock, interest expense and deemed dividends;
and

The valuation of debt for which we have elected fair value accounting.

For a more detailed discussion of our critical accounting estimates and policies, see Note 1, “Basis of

Presentation and Summary of Significant Accounting Policies” in Part II, Item 8 of this 2018 Form 10-K.

Results of Operations

Revenue

Years Ended December 31,
(In thousands)

Revenue:

2018

2017

(As Restated)

Renewable products . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$33,598

$ 42,370

Licenses and royalties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

7,658

Grants and collaborations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

22,348

48,703

36,598

Total revenue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$63,604

$127,671

2018 vs
2017
% Change

(21)%

(84)%

(39)%

(50)%

2018 Compared to 2017: Total revenue decreased by 50% to $63.6 million in 2018. Renewable products
revenue decreased by 21% to $33.6 million in 2018, primarily due to (i) no product revenue from Nenter in
2018 as compared to $12.1 million in 2017, as the result of our late-2017 assignment of a farnesene supply
agreement to DSM, and (ii) a $5.9 million decrease in product revenue from Firmenich, partly offset by
increases of $5.1 million and $5.0 million in Clean Beauty and Health & Wellness products, respectively.
Licenses and royalties revenue decreased by 84% to $7.7 million in 2018, primarily due to $58.0 million of
one-time license revenue in 2017 upon the license of farnesene for use in certain fields to DSM that did not
recur in 2018, and a $13.1 million revenue offset in 2017 in connection with a Ginkgo partnership
agreement, partly offset by an additional $7.4 million of new Vitamin E-related royalty revenue in 2018
from DSM. Grants and collaborations revenue decreased by 39% to $22.3 million in 2018, primarily due to
no collaboration revenue from Manufacture Francaise de Pnematiques Michelin (Michelin) and Braskem
S.A. (Braskem) in 2018 as compared to $6.2 million in 2017, and a $3.9 million decrease in collaboration
revenue from DARPA as the project approaches completion. Our revenues are dependent on the timing and
nature of arrangements entered into with our customers, which may include multiple performance
obligations for which revenue accounting requires significant judgement and estimates. Based on the nature
of our customer arrangements, our revenues may vary significantly from one period to the next.

Cost and Operating Expenses

Years Ended December 31,
(In thousands)

2018 vs
2017
% Change

2018

2017

(As Restated)

Cost of products sold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$ 36,698

$ 62,307

(41)%

Research and development
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Sales, general and administrative . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Impairment of other assets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

68,722
90,902
3,865

57,562
63,853
—

Total cost and operating expenses . . . . . . . . . . . . . . . . . . . . . . . . . .

$200,187

$183,722

19%
42%
nm

nm = not meaningful

Cost of Products Sold

Cost of products sold includes the costs of raw materials, labor and overhead, amounts paid to
contract manufacturers, inventory write-downs resulting from applying lower of cost or net realizable value
inventory adjustments, and costs related to production scale-up. Because of our product mix, our cost of
products sold does not change proportionately with changes in renewable product revenue.

2018 Compared to 2017: Cost of products sold decreased by 41% to $36.7 million in 2018, primarily
due to a 21% proportional decrease in renewable products revenue and the late-2017 sale of our production
facility in Brotas, Brazil to DSM, which improved our manufacturing cost efficiency.

Research and Development Expenses

2018 Compared to 2017: Research and development expenses increased by 19% to $68.7 million in
2018, primarily due to an 18% headcount increase in research and development to accelerate development
of new products, and a $3.8 million increase in spending on laboratory equipment rentals to automate
testing and expand laboratory capacity.

Sales, General and Administrative Expenses

2018 Compared to 2017: Sales, general and administrative expenses increased by 42% to $90.9 million
in 2018, primarily due to increases in outside services, wages and benefits and non-cash stock-based
compensation. The increase in outside services was due to audit fees, costs to implement new accounting
standards and related internal controls, and sales and marketing expenses to support Biossance growth. The
increase in wages and benefits was due to headcount growth, primarily in Biossance. The $2.9 million
increase in stock-based compensation was due to new grants to existing employees and a 28% headcount
increase.

Impairment of Other Assets

2018 Compared to 2017: In 2018, we impaired $3.9 million of contingent consideration that had been
recorded in 2017 in connection with the December 2017 sale of Amyris Brasil. In 2017, there were no
impairments.

Other Income (Expense), Net

Years Ended December 31,
(In thousands)

2018

2017

(As Restated)

2018 vs 2017
% Change

(Loss) gain on divestiture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Interest expense . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Loss from change in fair value of derivative instruments . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . .
Gain from change in fair value of debt
Loss upon extinguishment of debt
. . . . . . . . . . . . . . . . . . . . . . . . . .
Other income (expense), net . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$ (1,778) $ 5,732
(37,081)
(48,852)
—
(11,897)
(956)

(42,703)
(30,880)
2,082
(17,424)
(2,949)

Total other expense, net . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$(93,652) $(93,054)

(131)%
15%
(37)%
nm
46%
208%

nm = not meaningful

2018 Compared to 2017: Total other expense, net was $93.7 million in 2018, compared to $93.1 million
in 2017. The $0.6 million increase was primarily comprised of a $5.5 million increase in loss upon
extinguishment of debt, an $18.0 million decrease in loss from change in fair value of derivative
instruments, a $5.6 million increase in interest expense, and a $1.8 million loss in 2018 related to working
capital sales price adjustments in connection with the 2017 divestiture of our Brotas, Brazil manufacturing
facility, as compared to a $5.7 million gain in 2017. See Note 13, “Divestiture” in Part II, Item 8 of this
Annual Report on Form 10-K for more information. Also, see Note 1, “Basis of Presentation and Summary
of Significant Accounting Policies — Fair Value Measures” in Part II, Item 8 of this Annual Report on
Form 10-K for a discussion regarding how our closing stock price at the end of the period or immediately
prior to the extinguishment of an embedded derivative or debt or warrant instrument can impact the gain/
loss measurement or change in fair value of our derivative liabilities in any given period.

Income Taxes

For 2018, we recorded $0 income tax expense as a result of recording a full valuation allowance against
our net deferred tax assets due to our history of losses and the unlikelihood of timely recovery of these tax
assets. For 2017, we recorded $6.9 million of income tax expense primarily related to an unrecognized tax
benefit. In addition, there were some current foreign taxes. However, a full valuation allowance has been
recorded against all other net deferred tax assets.

See Note 14, “Income Taxes” in Part II, Item 8 of this Annual Report on Form 10-K for additional

information.

Liquidity and Capital Resources

Years Ended December 31,
(In thousands)

Net cash (used in) provided by:

2018

2017

(As Restated)

Operating activities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$(109,366)

$(101,179)

Investing activities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Financing activities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$ (12,472)
$ 107,957

$ 51,708
$ 77,864

Liquidity. We have incurred significant operating losses since our inception, and we expect to continue
to incur losses and negative cash flows from operations through at least the next 12 months following the
issuance of this Annual Report on Form 10-K. As of December 31, 2018, we had negative working capital
of $119.5 million, an accumulated deficit of $1.5 billion, and cash and cash equivalents of $45.4 million.

As of December 31, 2018, our debt (including amounts owed to related parties), net of $17.1 million of
discount and a fair value adjustment of $2.1 million, totaled $209.7 million, of which $147.7 million is
classified as current. Our debt agreements contain various covenants, including certain restrictions on our
business that could cause us to be at risk of defaults, such as restrictions on additional indebtedness,
material adverse effect and cross default clauses. A failure to comply with the covenants and other
provisions of our debt instruments, including any failure to make a payment when required, would generally
result in events of default under such instruments, which could permit acceleration of a substantial portion
of such indebtedness. If such indebtedness is accelerated, it would generally also constitute an event of
default under our other outstanding indebtedness, which could permit acceleration of a substantial portion
of such other outstanding indebtedness. At December 31, 2018, we failed to meet certain covenants in
connection with the GACP Term Loan Facility (see Note 5, “Debt” in Part II, Item 8 of this Annual Report
on Form 10-K), including those associated with minimum revenue and minimum liquidity requirements. In
April 2019, (i) GACP provided a waiver to us for breaches of all covenant violations under the GACP loan
and security agreement (LSA) occurring prior to, as of and after December 31, 2018 through April 8, 2019,
and (ii) GACP sold and assigned the loans under the LSA and all documents and assets related thereto to
Foris Ventures, LLC (Foris). Subsequently, Foris provided a waiver to us for breaches of certain covenants
under the LSA through June 30, 2020 and amended the financial covenants to provide more favorable
compliance terms and conditions.

See Note 5, “Debt” and Note 16, “Subsequent Events” in Part II, Item 8 of this Annual Report on

Form 10-K for additional information.

During the year ended December 31, 2018, we executed the following transactions in order to improve

our liquidity:

•

In April 2018, warrant holders exercised warrants to purchase an aggregate of 3.6 million shares
of common stock at an exercise price of $4.40 per share, resulting in net proceeds of $14.4 million;

In June and July 2018, we issued new debt for net proceeds of $34.4 million, and repaid
$31.0 million of debt that was coming due;

•

In August 2018, warrant-holders exercised warrants to purchase an aggregate of 12.6 million
shares of common stock at an exercise price of $4.40 per share, resulting in net proceeds of
$43.0 million; and

In December 2018, we issued new debt for net proceeds of $56.2 million.

See Note 5, “Debt” and Note 7, “Stockholders’ Deficit” in Part II, Item 8 of this Annual Report on

Form 10-K for more information regarding these transactions.

On September 16, 2019, the Company failed to pay an aggregate of $63.6 million of outstanding
principal and accrued interest on the Second Exchange Note when due. The failure resulted in an event of
default under the Second Exchange Note and also triggered cross-defaults under other debt instruments of
the Company which permitted the holders of such indebtedness to accelerate the amounts owing under
such instruments. The Company subsequently received waivers from substantially all holders of such other
debt instruments to waive the right to accelerate. As a result, the indebtedness with respect to which the
Company has obtained such waivers continues to be classified as long-term on the Company’s balance
sheet. The indebtedness reflected by the Second Exchange Note continues to be classified as a current
liability on the Company’s balance sheet. In addition, as a result of the payment default, the conversion
price of the Second Exchange Note is subject to adjustment in accordance with the terms of the Second
Exchange Note.

The Company does not currently have sufficient funds to repay the amounts outstanding under the
Second Exchange Note. To date, negotiations with the holder of the Second Exchange Note have not been
successful, and there can be no assurance that a favorable outcome for the Company will be reached. The
Company has executed a term sheet with an existing investor for a term loan, the proceeds of which would
be used to repay a portion of the Second Exchange Note. However, there can be no assurance that the
Company will be able to obtain such financing on its expected timeline, or on acceptable terms, if at all.
Even if the Company does obtain such financing, it will not have sufficient funds to repay the Second
Exchange Note in full without obtaining additional financing, which the Company is attempting to source.
The financial statements do not include any adjustments that might result from the outcome of this
uncertainty.

Our consolidated financial statements as of and for the year ended December 31, 2018 have been
prepared on the basis that we will continue as a going concern, which contemplates the realization of assets
and satisfaction of liabilities in the normal course of business. Due to the factors described above, there is
substantial doubt about our ability to continue as a going concern within one year after the date that the
financial statements included in this Annual Report on Form 10-K are issued. Our ability to continue as a
going concern will depend, in large part, on our ability to achieve positive cash flows from operations
during the 12 months from the date of this filing, and refinance or extend other existing debt maturities
occurring later in 2019, which is uncertain. The financial statements do not include any adjustments that
might result from the outcome of this uncertainty, which could have a material adverse effect on our
financial condition. In addition, if we are unable to continue as a going concern, we may be unable to meet
our obligations under our existing debt facilities, which could result in an acceleration of our obligation to
repay all amounts outstanding under those facilities, and we may be forced to liquidate our assets. In such a
scenario, the values we receive for our assets in liquidation or dissolution could be significantly lower than
the values reflected in our financial statements.

Our operating plan for 2019 contemplates a significant reduction in our net cash outflows, resulting
from (i) revenue growth from sales of existing and new products with positive gross margins, (ii) reduced
production costs as a result of manufacturing and technical developments, and (iii) cash inflows from
collaborations and grants. These factors are expected to improve our liquidity.

If we are unable to generate sufficient cash contributions from product sales, payments from existing
and new collaboration partners, and draw sufficient funds from certain financing commitments due to
contractual restrictions and covenants, we will need to obtain additional funding from equity or other debt
financings, which may not occur timely or on reasonable terms, if at all, and agree to burdensome
covenants, grant further security interests in our assets, enter into collaboration and licensing arrangements
that require us to relinquish commercial rights, or grant licenses on terms that are not favorable.

If we do not achieve our planned operating results, our ability to continue as a going concern would be

jeopardized and we may need to take the following actions to support our liquidity needs in 2019:

•

Shift focus to existing products and customers with significantly reduced investment in new
product and commercial development efforts;

Reduce expenditures for third party contractors, including consultants, professional advisors and
other vendors;

including expenditures

Closely monitor our working capital position with customers and suppliers, as well as suspend
operations at pilot plants and demonstration facilities.

Implementing this plan could have a negative impact on our ability to continue our business as

currently contemplated, including, without limitation, delays or failures in our ability to:

•

Achieve planned production levels;

Develop and commercialize products within planned timelines or at planned scales; and

Continue other core activities.

We expect to fund operations for the foreseeable future with cash currently on hand, cash inflows from
collaborations, grants, product sales, licenses and royalties and equity and debt financings, to the extent
necessary. Some of our research and development collaborations are subject to risk that we may not meet
milestones. Future equity and debt financings, if needed, are subject to the risk that we may not be able to
secure financing in a timely manner or on reasonable terms, if at all. Our planned working capital and
capital expenditure needs for 2019 are dependent on significant inflows of cash from renewable product
sales, new collaborations, and licenses and royalties from existing collaboration partners.

For details, see the following Notes in Part II, Item 8 of this Annual Report on Form 10-K:

•

Note 5, “Debt”

Note 6, “Mezzanine Equity”

Note 7, “Stockholders’ Deficit”

Cash Flows during the Years Ended December 31, 2018 and 2017

Cash Flows from Operating Activities

Our primary uses of cash from operating activities are for personnel costs and costs related to the

production and sales of our products, offset by cash received from sales to customers.

For the year ended December 31, 2018, net cash used in operating activities was $109.4 million, which
was primarily comprised of our $230.2 million net loss, partly offset by $96.3 million of non-cash charges
and a $24.6 million decrease in working capital. Non-cash charges consisted primarily of a $30.9 million
loss from change in fair value of derivative liabilities, $16.6 million of debt discount amortization, a
$17.4 million loss upon extinguishment of debt, and $9.2 million of stock-based compensation. The
decrease in working capital was primarily comprised of a $20.1 million increase in accounts payable and
other accrued liabilities, partly offset by a $6.4 million increase in prepaid expenses and other assets and a
$4.4 million increase in inventories.

For the year ended December 31, 2017, net cash used in operating activities was $101.2 million, which
was comprised of our $156.0 million net loss and a $24.1 million increase in working capital, partly offset
by $72.6 million of non-cash charges. Non-cash charges consisted primarily of a $48.9 million loss from
change in fair value of derivative liabilities, $15.2 million of debt discount amortization, $11.4 million of
depreciation and amortization and $6.3 million of stock-based compensation, partly offset by $8.0 million
of noncash consideration received in connection with license revenue, and a $5.7 million gain in connection

with our divestiture of Amyris Brasil. The decrease in working capital was primarily comprised of a
$19.6 million increase in accounts receivable, a $18.7 million increase in prepaid expenses and other assets, a
$7.9 million increase in contract assets and a $7.2 million decrease in contract liabilities, partly offset by a
$19.3 million increase in accounts payable and accrued liabilities.

Cash Flows from Investing Activities

For the year ended December 31, 2018, net cash used in investing activities was $12.5 million and was

comprised of property, plant and equipment purchases.

For the year ended December 31, 2017, net cash provided by investing activities was $51.7 million,
primarily due to $54.8 million of net proceeds from the sale of Amyris Brasil to DSM and other elements of
the December 2017 transactions with DSM that were accounting for as a combined arrangement, partly
offset by $4.4 million of property, plant and equipment purchases.

Cash Flows from Financing Activities

For the year ended December 31, 2018, net cash provided by financing activities was $108.0 million,
primarily comprised of $94.4 million of net proceeds from debt issued and $60.0 million from the exercises
of warrants and sales of common stock, partly offset by $41.7 million of debt principal payments.

For the year ended December 31, 2017, net cash provided by financing activities was $77.9 million,
primarily comprised of $98.2 million of proceeds from the sales of preferred stock and $18.9 million from
debt issued, partly offset by $37.5 million of debt principal payments.

Off-Balance Sheet Arrangements

None.

Contractual Obligations

The following is a summary of our contractual obligations as of December 31, 2018:

Payable by Year Ended December 31,
(In thousands)

Total

2019

2020

2021

2022

2023

Thereafter

Principal payments on debt . . . . . . . . . $229,615 $155,534 $ 3,828 $55,839 $12,252 $ 265
Interest payments on debt(1) . . . . . . . . .
102
Operating leases
3,034
. . . . . . . . . . . . . . . .
Manufacturing capacity reservation

17,061
10,416

33,706
36,007

6,422
7,226

1,165
7,399

8,653
7,932

fee . . . . . . . . . . . . . . . . . . . . . . . .
Partnership payment obligation . . . . . .
Other . . . . . . . . . . . . . . . . . . . . . . . .

21,036
12,700
5,297

21,036
3,969
3,258

—
3,175
2,038

—
3,175
1

—
2,381
—

—
—
—

$1,897
303
—

—
—
—

Total

. . . . . . . . . . . . . . . . . . . . . . $338,361 $211,274 $25,626 $72,663 $23,197 $3,401

$2,200

(1) Does not include any obligations related to make-whole interest or down-round provisions. Fixed and
variable interest rates are described in Note 5, “Debt” in Part II, Item 8 of this Annual Report on
Form 10-K. Future interest payments shown above for variable-rate debt instruments are measured on
the basis of interest rates for such instruments as of December 31, 2018.

ITEM 7A. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

Not required — Smaller Reporting Company scaled disclosure accommodation.

ITEM 8. FINANCIAL STATEMENTS AND SUPPLEMENTARY DATA

AMYRIS, INC.

INDEX TO CONSOLIDATED FINANCIAL STATEMENTS

Reports of Independent Registered Public Accounting Firms

Consolidated Balance Sheets

Consolidated Statements of Operations

Consolidated Statements of Comprehensive Loss

Consolidated Statements of Stockholders’ Deficit and Mezzanine Equity

Consolidated Statements of Cash Flows

Notes to Consolidated Financial Statements

Page

Report of Independent Registered Public Accounting Firm

To the Board of Directors and Stockholders of
Amyris, Inc.

Opinion on the Consolidated Financial Statements

We have audited the accompanying consolidated balance sheet of Amyris, Inc. and subsidiaries (the
Company) as of December 31, 2018, the related consolidated statements of operations, comprehensive loss,
stockholders’ deficit and mezzanine equity, and cash flows for the year then ended, and the related notes
(collectively, the consolidated financial statements). In our opinion, the consolidated financial statements present
fairly, in all material respects, the financial position of the Company as of December 31, 2018, and the results of
their operations and their cash flows for the year then ended, in conformity with U.S. generally accepted
accounting principles.

We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board
(United States) (“PCAOB”), the Company’s internal control over financial reporting as of December 31, 2018,
based on criteria established in Internal Control — Integrated Framework (2013) issued by the Committee of
Sponsoring Organizations of the Treadway Commission (“COSO”) and our report dated September 30, 2019
expressed an adverse opinion thereon.

Going Concern

The accompanying consolidated financial statements have been prepared assuming that the Company will
continue as a going concern. As discussed in Note 1 to the consolidated financial statements, the Company has
suffered recurring losses from operations and has current debt service requirements that raise substantial doubt
about its ability to continue as a going concern. Management’s plans in regard to these matters are also described
in Note 1. The consolidated financial statements do not include any adjustments that might result from the
outcome of this uncertainty.

Changes in Accounting Principles

As discussed in Notes 1 and 10 to the consolidated financial statements, the Company has changed its
accounting method for recognizing revenue from contracts with customers in fiscal year 2018 due to the adoption
of Topic 606, Revenue from Contracts with Customers, and all related amendments.

Basis for Opinion

These consolidated financial statements are the responsibility of

the Company’s management. Our
responsibility is to express an opinion on these consolidated financial statements based on our audit. We are a
public accounting firm registered with the Public Company Accounting Oversight Board (United States)
(PCAOB) and are required to be independent with respect to the Company in accordance with the U.S. federal
securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the
PCAOB.

We conducted our audit in accordance with the standards of the PCAOB. Those standards require that we
plan and perform the audit to obtain reasonable assurance about whether the consolidated financial statements
are free of material misstatement, whether due to error or fraud.

Our audit included performing procedures to assess the risks of material misstatement of the consolidated
financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such
procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the
consolidated financial statements. Our audit also included evaluating the accounting principles used and
significant estimates made by management, as well as evaluating the overall presentation of the consolidated
financial statements. We believe that our audit provides a reasonable basis for our opinion.

/s/ Macias Gini & O’Connell LLP

We have served as the Company’s auditor since 2019.

San Francisco, California
October 1, 2019

Report of Independent Registered Public Accounting Firm

To the Board of Directors and Stockholders
Amyris, Inc.
Emeryville, CA

Opinion on the Consolidated Financial Statements

We have audited the accompanying consolidated balance sheet of Amyris, Inc. as of December 31,
2017, the related consolidated statements of operations, comprehensive loss, stockholders’ deficit and
mezzanine equity, and cash flows for the year then ended and the related notes (collectively referred to as
the “consolidated financial statements”). In our opinion, the consolidated financial statements present
fairly, in all material respects, the financial position of the Company at December 31, 2017 and the results
of its operations and its cash flows for the year ended December 31, 2017, in conformity with accounting
principles generally accepted in the United States of America.

Restatement to Correct 2017 Misstatements

As discussed in Note 2 to the consolidated financial statements, the 2017 financial statements have

been restated to correct several misstatements.

Going Concern Uncertainty

The accompanying consolidated financial statements have been prepared assuming that the Company
will continue as a going concern. As discussed in Note 1 to the consolidated financial statements, the
Company has suffered recurring losses from operations and has a net capital deficiency and these factors,
among others, raise substantial doubt about its ability to continue as a going concern. Management’s plans
in regard to these matters are also described in Note 1. The consolidated financial statements do not include
any adjustments that might result from the outcome of this uncertainty.

Basis for Opinion

These consolidated financial statements are the responsibility of the Company’s management. Our
responsibility is to express an opinion on the Company’s consolidated financial statements based on our
audit. We are a public accounting firm registered with the Public Company Accounting Oversight Board
(United States) (“PCAOB”) and are required to be independent with respect to the Company in accordance
with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange
Commission and the PCAOB.

We conducted our audit in accordance with the standards of the PCAOB. Those standards require that
we plan and perform the audit to obtain reasonable assurance about whether the consolidated financial
statements are free of material misstatement, whether due to error or fraud.

Our audit included performing procedures to assess the risks of material misstatement of
the
consolidated financial statements, whether due to error or fraud, and performing procedures that respond
to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and
disclosures in the consolidated financial statements. Our audit also included evaluating the accounting
principles used and significant estimates made by management, as well as evaluating the overall
presentation of the consolidated financial statements. We believe that our audit provides a reasonable basis
for our opinion.

/s/ BDO USA, LLP
We have served as the Company’s auditor since 2019.
San Jose, California
September 30, 2019

AMYRIS, INC.

CONSOLIDATED BALANCE SHEETS

December 31,
(In thousands, except shares and per share amounts)

Assets
Current assets:

Cash and cash equivalents
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Restricted cash . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Accounts receivable, net of allowance of $642 and $619, respectively . . . . . . . . . . . .
Accounts receivable – related party, net of allowance of $0 and $23, respectively . . . . .
Contract assets Accounts receivable, unbilled – related party . . . . . . . . . . . . . . . . .
Inventories
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Deferred cost of products sold, current – related party . . . . . . . . . . . . . . . . . . . . .
Prepaid expenses and other current assets . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Total current assets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Property, plant and equipment, net . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Accounts receivable, unbilled, noncurrent – related party . . . . . . . . . . . . . . . . . . . . .
Deferred cost of products sold, noncurrent – related party . . . . . . . . . . . . . . . . . . . .
Restricted cash, noncurrent
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Recoverable taxes from Brazilian government entities . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Other assets
Total assets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Liabilities, Mezzanine Equity and Stockholders’ Deficit
Current liabilities:

Accounts payable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Accrued and other current liabilities
Contract liabilities(1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Debt, current portion (includes instrument measured at fair value of $57,918 and $0,

respectively) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Related party debt, current portion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Total current liabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Long-term debt, net of current portion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Related party debt, net of current portion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Derivative liabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Other noncurrent liabilities
Total liabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Commitments and contingencies (Note 9)
Mezzanine equity:

2018

2017

(As Restated,
Note 2)

45,353
741
16,003
1,349
8,021
9,693
489
10,566
92,215
19,756
1,203
2,828
960
3,005
7,958
127,925

26,844
28,979
8,236

124,010
23,667
211,736
43,331
18,689
42,796
23,192
339,744

57,059
2,994
18,953
4,767
9,901
5,408
—
4,919
104,001
13,892
7,940
—
959
1,445
12,559
140,796

15,515
29,202
4,308

36,924
20,019
105,968
60,220
46,541
116,497
23,658
352,884

Contingently redeemable common stock (Note 6) . . . . . . . . . . . . . . . . . . . . . . . .

5,000

Stockholders’ deficit:

Preferred stock – $0.0001 par value, 5,000,000 shares authorized as of December 31,

2018 and 2017, and 14,656 and 22,171 shares issued and outstanding as of
December 31, 2018 and 2017, respectively . . . . . . . . . . . . . . . . . . . . . . . . . .

Common stock – $0.0001 par value, 250,000,000 shares authorized as of December 31,

2018 and 2017, respectively; 76,564,829 and 45,637,433 shares issued and outstanding
as of December 31, 2018 and 2017, respectively . . . . . . . . . . . . . . . . . . . . . . .
Additional paid-in capital . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Accumulated other comprehensive loss . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Accumulated deficit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . .
Noncontrolling interest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Total stockholders’ deficit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Total liabilities, mezzanine equity and stockholders’ deficit . . . . . . . . . . . . . . .

Total Amyris, Inc. stockholders’ deficit

—

8
1,346,996
(43,343)
(1,521,417)
(217,756)
937
(216,819)
127,925

5
1,114,546
(42,156)
(1,290,420)
(218,025)
937
(217,088)
140,796

(1) The balance in contract liabilities at December 31, 2017 represents deferred revenue, current prior to

the Company’s adoption of ASC 606, “Revenue”.

See accompanying notes to consolidated financial statements.
62

AMYRIS, INC.

CONSOLIDATED STATEMENTS OF OPERATIONS

Years Ended December 31,
(In thousands, except shares and per share amounts)

2018

2017

(As Restated,
Note 2)

Revenue

Renewable products (includes related party revenue of $360 and $1,291,

respectively) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

33,598

42,370

Licenses and royalties, net (includes related party revenue of $5,958 and $57,972,

respectively) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Grants and collaborations (includes related party revenue of $4,735 and $1,679,

respectively) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Total revenue (includes related party revenue of $11,053 and $60,942,

respectively) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

7,658

22,348

48,703

36,598

63,604

127,671

Cost and operating expenses

Cost of products sold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Research and development . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Sales, general and administrative . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Impairment of other assets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Total cost and operating expenses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Loss from operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Other income (expense)

(Loss) gain on divestiture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Interest expense . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Loss from change in fair value of derivative instruments . . . . . . . . . . . . . . . . . .
Gain from change in fair value of debt . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Loss upon extinguishment of debt
Other income (expense), net
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Total other expense, net
Loss before income taxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Provision for income taxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Net loss attributable to Amyris, Inc. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Less deemed dividend related to beneficial conversion feature on Series A preferred

stock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Less deemed dividend related to beneficial conversion feature on Series B preferred

stock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Less deemed dividend related to beneficial conversion feature on Series D preferred

stock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Less deemed dividend upon settlement of make-whole provision on Series A preferred
stock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Less deemed dividend upon settlement of make-whole provision on Series B preferred
stock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Less deemed dividend related to the recognition of discounts on Series A preferred . .
Less deemed dividend related to the recognition of discounts on Series B preferred . . .
Less deemed dividend related to proceeds discount upon conversion of Series D

preferred stock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Add: losses allocated to participating securities . . . . . . . . . . . . . . . . . . . . . . . . .
Net loss attributable to Amyris, Inc. common stockholders, basic . . . . . . . . . . . . . .

36,698
68,722
90,902
3,865
200,187
(136,583)

(1,778)
(42,703)
(30,880)
2,082
(17,424)
(2,949)
(93,652)
(230,235)
—
(230,235)

—

—
—
—

62,307
57,562
63,853
—
183,722
(56,051)

5,732
(37,081)
(48,852)
—
(11,897)
(956)
(93,054)
(149,105)
(6,877)
(155,982)

(562)

(634)

(5,757)

(10,505)

(22,632)
(21,578)
(24,366)

(6,852)
13,991
$ (223,096)

—
40,159
$ (201,857)

Weighted-average shares of common stock outstanding used in computing net loss per
share of common stock, basic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

60,405,910

32,253,570

Basic and diluted loss per share . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

(3.69)

(6.26)

See accompanying notes to consolidated financial statements.
63

CONSOLIDATED STATEMENTS OF COMPREHENSIVE LOSS

AMYRIS, INC.

Years Ended December 31,
(In thousands)

Comprehensive loss:

2018

2017

(As Restated,
Note 2)

Net loss . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$(230,235)

$(155,982)

Foreign currency translation adjustment . . . . . . . . . . . . . . . . . . . . . . . . . .

(1,187)

(1,252)

Comprehensive loss attributable to Amyris, Inc.

. . . . . . . . . . . . . . . . . . . . . .

$(231,422)

$(157,234)

See accompanying notes to consolidated financial statements.
64

CONSOLIDATED STATEMENTS OF STOCKHOLDERS’ DEFICIT AND MEZZANINE EQUITY

AMYRIS, INC.

(In thousands, except number of shares)
December 31, 2016 . . . . . . . . . . . . . . .
Issuance of Series A preferred stock for

Preferred Stock
Shares Amount

Common Stock
Shares

— — 18,273,921

Amount
$ 2

Additional
Paid-in
Capital
$ 990,895

Accumulated
Other
Comprehensive
Loss

Accumulated
Deficit

$(40,904) $(1,134,438)

Noncontrolling
Interest
$937

Total
Stockholders’
Deficit
$(183,508)

Mezzanine
Equity –
Common
Stock
$5,000

cash . . . . . . . . . . . . . . . . . . . . . .

22,140 —

— —

562

Issuance of Series B preferred stock upon

conversion of debt, net of issuance costs
of $0 . . . . . . . . . . . . . . . . . . . . .

Issuance of Series B preferred stock for cash,

net of issuance costs of $860 . . . . . . . .
Issuance of Series D preferred stock for cash,
net of issuance costs of $176 . . . . . . . .

Issuance of common stock due to rounding

from reverse stock split

. . . . . . . . . . .
Issuance of common stock for cash . . . . . .
Issuance of common stock upon conversion

40,204 —

55,700 —

12,958 —

— —

— —
6,473 —
— — 2,826,711 —

of preferred stock . . . . . . . . . . . . . . (108,831) — 17,274,017

Issuance of common stock upon conversion

of debt

. . . . . . . . . . . . . . . . . . . .

Issuance of common stock for settlement of

debt principal payments . . . . . . . . . . .

Issuance of common stock for settlement of

debt interest payments . . . . . . . . . . . .

Issuance of common stock upon exercise of

— — 2,257,786 —

— — 1,246,165 —

— —

400,967 —

11,530

16,675

6,197

—
5,527

—

12,687

10,707

3,436

warrants

. . . . . . . . . . . . . . . . . . .

Issuance of common stock upon restricted

stock settlement

. . . . . . . . . . . . . . .

Issuance of common stock upon ESPP

purchase . . . . . . . . . . . . . . . . . . .

Issuance of common stock upon exercise of

stock options . . . . . . . . . . . . . . . . .

Beneficial conversion feature of Series A

preferred stock . . . . . . . . . . . . . . . .

Deemed dividend on beneficial conversion

feature of Series A preferred stock . . . . .

Beneficial conversion feature to related party

of Series B preferred stock . . . . . . . . .

Deemed dividend to related party on

beneficial conversion feature of Series B
preferred stock . . . . . . . . . . . . . . . .

Beneficial conversion feature of Series D

preferred stock . . . . . . . . . . . . . . . .

Deemed dividend on beneficial conversion

feature of Series D preferred stock . . . . .

Deemed dividend on preferred stock

discounts upon conversion of Series A
preferred stock . . . . . . . . . . . . . . . .

Deemed dividend on preferred stock

discounts upon conversion of Series A
preferred stock . . . . . . . . . . . . . . . .

Deemed dividend on preferred stock

discounts upon conversion of Series B
preferred stock . . . . . . . . . . . . . . . .

Deemed dividend on preferred stock

discounts upon conversion of Series B
preferred stock . . . . . . . . . . . . . . . .

Settlement of make-whole provision on

Series A preferred stock . . . . . . . . . . .

Deemed dividend upon settlement of
make-whole provision on Series A
preferred stock . . . . . . . . . . . . . . . .

Settlement of make-whole provision on

Series B preferred stock . . . . . . . . . . .

Deemed dividend upon settlement of
make-whole provision on Series B
preferred stock . . . . . . . . . . . . . . . .
Stock-based compensation . . . . . . . . . . .
Foreign currency translation adjustment
. . .
Net loss (As Restated, Note 2) . . . . . . . . .
. . .
December 31, 2017 (As restated, Note 2)

— — 3,148,097 —

50,449

— —

156,104 —

(385)

— —

47,058 —

134 —

— —

—

562

(562)

634

— —

(634)

— —

5,757

— —

(5,757)

— —

21,578

— —

(21,578)

— —

24,366

— —

(24,366)

— —

10,505

— —

(10,505)

— —

22,632

— —

— —
— —
— —
— —

—

—
—

—

—
—

—

—
—

—

562

11,530

16,675

6,197

—
5,527

12,687

10,707

3,436

50,449

(385)

—

562

(562)

634

(634)

5,757

(5,757)

21,578

(21,578)

24,366

(24,366)

10,505

(10,505)

22,632

—

—
—

—

— —
— —
— —
— —
$ 5

(22,632)
6,265
—
—
$1,114,546

—
—
(1,252)
—

—
—
—
(155,982)
$(42,156) $(1,290,420)

—
—
—
—
$937

(22,632)
6,265
(1,252)
(155,982)
$(217,088)

—
—
—
—
$5,000

22,171 — 45,637,433

See accompanying notes to consolidated financial statements.
65

CONSOLIDATED STATEMENTS OF STOCKHOLDERS’ DEFICIT AND MEZZANINE
EQUITY — (Continued)

AMYRIS, INC.

Preferred Stock
Shares Amount

Common Stock
Shares

Amount

Additional
Paid-in
Capital

Accumulated
Other
Comprehensive
Loss

Accumulated
Deficit

Noncontrolling
Interest

Total
Stockholders’
Deficit

Mezzanine
Equity –
Common
Stock

(In thousands, except number of shares)
Cumulative effect of change in accounting
principle for ASC 606 (see “Significant
Accounting Policies” in Note 1) . . . . . . . .

Issuance of common stock upon exercise of

warrants

. . . . . . . . . . . . . . . . . . . .

Settlement of derivatives liability upon exercise

of warrants . . . . . . . . . . . . . . . . . . .

Issuance of common stock in private

— —

—

— — 20,891,038

62,152

— —

108,670

placement, net of issuance costs of $0 . . . .

— —

205,168 —

1,415

Issuance of common stock in private

placement – related party, net of issuance
costs of $0 . . . . . . . . . . . . . . . . . . .

Issuance of common stock upon conversion of

— — 1,643,991 —

6,050

preferred stock . . . . . . . . . . . . . . . . . (7,515) — 1,548,480 —

—

Deemed dividend on preferred stock discounts

upon conversion of Series D preferred
stock . . . . . . . . . . . . . . . . . . . . . .

Deemed dividend on preferred stock discounts

upon conversion of Series D preferred
stock . . . . . . . . . . . . . . . . . . . . . .

Issuance of common stock upon conversion of

convertible notes . . . . . . . . . . . . . . . .

Issuance of common stock for settlement of

debt interest payments . . . . . . . . . . . . .

Issuance of common stock upon exercise of

stock options . . . . . . . . . . . . . . . . . .

Issuance of common stock upon ESPP

purchase . . . . . . . . . . . . . . . . . . . .

Issuance of common stock and payment of

— —

6,852

— —

(6,852)

— — 5,674,926

42,368

— —

238,898 —

1,800

— —

70,807 —

— —

246,230 —

288

777

—

(762)

—

(762)

62,154

108,670

1,415

6,050

—

6,852

(6,852)

42,369

1,800

288

777

—

minimum employee taxes withheld upon net
share settlement of restricted stock . . . . . .
Stock-based compensation . . . . . . . . . . . .
Foreign currency translation adjustment
. . . .
Net loss
. . . . . . . . . . . . . . . . . . . . . .
December 31, 2018 . . . . . . . . . . . . . . . . 14,656 — 76,564,829

407,858 —
— —
— —
— —
$ 8

— —
— —
— —
— —

(260)
9,190
—
—
$1,346,996

—
—
(1,187)
—

—
—
—
(230,235)
$(43,343) $(1,521,417)

—
—
—
—
$937

(260)
9,190
(1,187)
(230,235)
$(216,819)

—
—
—
—
$5,000

See accompanying notes to consolidated financial statements.
66

AMYRIS, INC.

CONSOLIDATED STATEMENTS OF CASH FLOWS

Years Ended December 31,
(In thousands)

2018

Operating activities
Net loss
Adjustments to reconcile net loss to net cash used in operating activities:

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $(230,235)

Loss from change in fair value of derivative liabilities
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Loss upon conversion or extinguishment of debt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Amortization of debt discount . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Stock-based compensation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Modification of warrants recorded as legal expense
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Depreciation and amortization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Issuance costs on warrant exercises for cash . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Loss on impairment of other assets
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Debt issuance costs expensed due to fair value option . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Loss (gain) on divestiture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Loss on disposal of property, plant and equipment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Gain on foreign currency exchange rates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Gain from change in fair value of debt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Noncash revenue reduction related to issuance of debt obligations under Ginkgo Partnership Agreement
. . . . . . . .
Receipt of noncash consideration in connection with license revenue . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Changes in assets and liabilities:

Accounts receivable
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Contract assets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Inventories
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Deferred cost of products sold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Prepaid expenses and other assets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Accounts payable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Accrued and other liabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Contract liabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Net cash used in operating activities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Investing activities

Purchases of property, plant and equipment
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Proceeds from divestiture, net of cash transferred . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Maturities of short-term investments
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Sale of short-term investments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Purchase of short-term investments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Net cash (used in) provided by investing activities

30,880
17,424
16,602
9,190
6,764
4,921
4,389
3,865
3,810
1,778
941
(2,223)
(2,082)
—
—

7,448
8,056
(4,416)
(3,317)
(6,383)
11,603
8,461
3,158
(109,366)

(12,472)
—
—
—
—
(12,472)

Financing activities

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Proceeds from issuance of debt, net of issuance costs
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Proceeds from exercise of warrants, net of issuance costs
. . . . . . . . . . . . . . . . . . .
Proceeds from issuance of common stock in private placements, net of issuance costs
Proceeds from ESPP purchases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Proceeds from exercises of common stock options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Principal payments on debt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Debt issuance costs incurred in connection with debt instrument accounted at fair value . . . . . . . . . . . . . . . . . .
Principal payments on capital leases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Payment of minimum employee taxes withheld upon net share settlement of restricted stock units
. . . . . . . . . . . .
Proceeds from issuance of convertible preferred stock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Proceeds from issuance of common stock in August 2017 offering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Issuance costs incurred . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Payment of swap termination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Payment on early redemption of debt
Net cash provided by financing activities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Effect of exchange rate changes on cash, cash equivalents and restricted cash . . . . . . . . . . . . . . . . . . . . . . . . . .
Net (decrease) increase in cash, cash equivalents and restricted cash . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Cash, cash equivalents and restricted cash at beginning of year . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Cash, cash equivalents and restricted cash at end of year

94,371
57,767
1,415
777
288
(41,668)
(3,752)
(981)
(260)
—
—
—
—
—
107,957
(77)
(13,958)
61,012
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $ 47,054

Reconciliation of cash, cash equivalents and restricted cash to the consolidated balance sheets
Cash and cash equivalents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $ 45,353
741
Restricted cash, current . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Restricted cash, noncurrent
960
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Total cash, cash equivalents and restricted cash . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $ 47,054

2017
(As Restated,
Note 2)

$(155,982)

48,852
11,897
15,239
6,265
—
11,358
—
—
—
(5,732)
142
(1,230)
—
13,413
(8,046)

(19,647)
(7,940)
(3,126)
—
(18,730)
5,452
13,877
(7,241)
(101,179)

(4,412)
54,827
12,403
676
(11,786)
51,708

18,925
—
—
—
—
(37,500)
—
—
(385)
98,246
5,759
(2,159)
(3,113)
(1,909)
77,864
186
28,579
32,433
$ 61,012

$ 57,059
2,994
959
$ 61,012

See accompanying notes to consolidated financial statements.
67

CONSOLIDATED STATEMENTS OF CASH FLOWS — (Continued)

AMYRIS, INC.

Years Ended December 31,
(In thousands)

2018

Supplemental disclosures of cash flow information:
Cash paid for interest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $ 18,524
Supplemental disclosures of non-cash investing and financing activities:
. . . . . . . . . . . . . . . . . . . . . . . . $108,670
Derecognition of derivative liabilities upon exercise of warrants
Issuance of common stock upon conversion of convertible notes . . . . . . . . . . . . . . . . . . . . . . . . $ 24,970
6,050
Issuance of common stock – related party . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $
3,664
Accrued interest added to debt principal
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $
1,800
Issuance of common stock for settlement of debt principal and interest payments . . . . . . . . . . . . . $
762
Cumulative effect adjustment of ASC 606 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $
495
Financing of insurance premium under note payable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $
Financing of equipment under financing leases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $
271
Proceeds from Issuance of preferred stock attributed to derivative liabilities . . . . . . . . . . . . . . . . . $
Issuance of convertible preferred stock upon conversion of debt . . . . . . . . . . . . . . . . . . . . . . . . $
Settlement of debt principal by a related party . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $
Issuance of note payable in exchange for debt extinguishment with third party . . . . . . . . . . . . . . . $
Issuance of common stock for settlement of debt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $

$ —
$28,702
$ —
$ 2,816
$ 3,436
$ —
$
467
$ —
— $72,725
— $40,204
— $25,000
— $16,954
— $10,708

2017
(As Restated,
Note 2)

$11,539

See accompanying notes to consolidated financial statements.
68

AMYRIS, INC.

Notes to Consolidated Financial Statements

1. Basis of Presentation and Summary of Significant Accounting Policies

Business Description

Amyris, Inc. (Amyris or the Company) is a leading industrial biotechnology company that applies its
technology platform to engineer, manufacture and sell high performance, natural, sustainably-sourced
products into the Health & Wellness, Clean Beauty, and Flavor & Fragrance markets. The Company’s
proven technology platform enables the Company to rapidly engineer microbes and use them as catalysts to
metabolize renewable, plant-sourced sugars into large volume, high-value ingredients. The Company’s
biotechnology platform and industrial fermentation process replace existing complex and expensive
manufacturing processes. The Company has successfully used its technology to develop and produce several
distinct molecules at commercial volumes.

Going Concern

The Company has incurred significant operating losses since its inception and expects to continue to
incur losses and negative cash flows from operations for at least the next 12 months following the issuance
of the financial statements. As of December 31, 2018, the Company had negative working capital of
$119.5 million and an accumulated deficit of $1.5 billion.

As of December 31, 2018, the Company’s debt (including related party debt), net of deferred discount
and issuance costs of $17.1 million and a change in fair value of $2.1 million, totaled $209.7 million, of
which $147.7 million is classified as current. The Company’s debt agreements contain various covenants,
including certain restrictions on the Company’s business that could cause the Company to be at risk of
defaults, such as restrictions on additional indebtedness, material adverse effect and cross default clauses. A
failure to comply with the covenants and other provisions of the Company’s debt instruments, including
any failure to make a payment when required, would generally result in events of default under such
instruments, which could permit acceleration a substantial portion of such indebtedness. If such
indebtedness is accelerated, it would generally also constitute an event of default under the Company’s
other outstanding indebtedness, permitting acceleration of a substantial portion of such other outstanding
indebtedness. At December 31, 2018, the Company failed to meet certain covenants in connection with the
GACP Term Loan Facility (see Note 5, “Debt”), including those associated with minimum revenue and
minimum liquidity requirements. In April 2019, (i) GACP provided a waiver to the Company for breaches
of all covenant violations under the GACP loan and security agreement (LSA) occurring prior to, as of and
after December 31, 2018 through April 8, 2019, and (ii) GACP sold and assigned the loans under the LSA
and all documents and assets related thereto to Foris Ventures, LLC (Foris). Subsequently, Foris provided a
waiver to the Company for breaches of certain covenants under the LSA through June 30, 2020 and
amended the financial covenants under the LSA to provide more favorable compliance terms and
conditions. See Note 16, “Subsequent Events” for additional information.

Cash and cash equivalents of $45.4 million as of December 31, 2018 are not sufficient to fund expected
future negative cash flows from operations and cash debt service obligations through September 30, 2020.
These factors raise substantial doubt about the Company’s ability to continue as a going concern within one
year after the date that these financial statements are issued. The consolidated financial statements do not
include any adjustments that might result from the outcome of this uncertainty. The Company’s ability to
continue as a going concern will depend, in large part, on its ability to achieve positive cash flows from
operations during the 12 months from the date of this filing, and refinance or extend other existing debt
maturities occurring later in 2019, all of which are uncertain and outside the control of the Company.
Further, the Company’s operating plan for 2019 contemplates a significant reduction in its net operating
cash outflows as compared to the year ended December 31, 2018, resulting from (i) revenue growth from
sales of existing and new products with positive gross margins, (ii) reduced production costs as a result of
manufacturing and technical developments, and (iii) an increase in cash inflows from collaborations and
grants. If the Company is unable to complete these actions, it expects to be unable to meet its operating
cash flow needs and its obligations under its existing debt facilities. This could result in an acceleration of

its obligation to repay all amounts outstanding under those facilities, and the Company may be forced to
obtain additional equity or debt financing, which may not occur timely or on reasonable terms, if at all,
and/or liquidate its assets. In such a scenario, the value received for assets in liquidation or dissolution could
be significantly lower than the value reflected in these financial statements. The Company has in the past,
including in July 2019, had certain of its debt instruments accelerated for failure to make a payment when
due. While we have been able to cure these defaults to date to avoid additional cross-acceleration, we may
not be able to cure such a default promptly in the future.

The Company does not currently have sufficient funds to repay the amounts outstanding under the
Second Exchange Note. To date, negotiations with the holder of the Second Exchange Note have not been
successful, and there can be no assurance that a favorable outcome for the Company will be reached. The
Company has executed a term sheet with an existing investor for a term loan, the proceeds of which would
be used to repay a portion of the Second Exchange Note. However, there can be no assurance that the
Company will be able to obtain such financing on its expected timeline, or on acceptable terms, if at all.
Even if the Company does obtain such financing, it will not have sufficient funds to repay the Second
Exchange Note in full without obtaining additional financing, which the Company is attempting to source.
The consolidated financial statements do not include any adjustments that might result from the outcome
of this uncertainty.

Basis of Consolidation

The accompanying consolidated financial statements have been prepared in accordance with the
accounting principles generally accepted in the United States (U.S. GAAP). The consolidated financial
statements include the accounts of Amyris, Inc. and its wholly-owned and partially-owned subsidiaries in
which the Company has a controlling interest after elimination of all significant intercompany accounts and
transactions.

Investments and joint venture arrangements are assessed to determine whether the terms provide
economic or other control over the entity requiring consolidation of the entity. Entities controlled by means
other than a majority voting interest are referred to as variable-interest entities (VIEs) and are consolidated
when Amyris has both the power to direct the activities of the VIE that most significantly impact its
economic performance and the obligation to absorb losses or the right to receive benefits that could
potentially be significant to the entity. For any investment or joint venture in which (i) the Company does
not have a majority ownership interest, (ii) the Company possesses the ability to exert significant influence
and (iii) the entity is not a VIE for which the Company is considered the primary beneficiary, the Company
accounts for the investment or joint venture using the equity method. Following the adoption of
ASU 2016-01 on January 1, 2018 described in more detail below (which was applicable to the Company on
a prospective basis), equity investments in which the Company does not exert significant influence and that
do not have readily determinable fair values are measured at cost, adjusted for changes from observable
market transactions, less impairment (“adjusted cost basis”). The Company evaluates its investments for
impairment by considering a variety of factors, including the earnings capacity of the related investments.
Fair value measurements for the Company’s equity investments are classified within Level 3 of the fair value
hierarchy based on the nature of the fair value inputs. Realized and unrealized gains or losses are recognized
in other income or expense.

Sale of Subsidiary and Entry into Commercial Agreements

On December 28, 2017, the Company completed the sale of all of the capital stock of its subsidiary
Amyris Brasil, a wholly-owned subsidiary, to DSM Produtos Nutricionais Brasil S.A (DSM), a related
party. Amyris Brasil owned and operated the Company’s production facility in Brotas, Brazil. The
transaction resulted in a pretax gain of $5.7 million from continuing operations in 2017, which was further
adjusted by a $1.8 million loss in 2018 related to the final working capital adjustments between the
Company and DSM. The transaction did not result in presenting Amyris Brasil as a discontinued operation
in the consolidated financial statements, as the sale did not represent a strategic shift that will have a major
effect on the Company’s operations and financial results due to the Company’s continuing commercial
presence and reinvestment in a new production facility under construction in Brazil and its continuing
Brazilian operation through Amyris Biotecnologia do Brasil Ltda. (formerly SMA Indústria Química
Ltda.). The Company and DSM also entered into a series of commercial agreements and a credit agreement
concurrently with the sale of Amyris Brasil. See Note 10, “Revenue Recognition”, Note 11, “Related Party
Transactions”, Note 13, “Divestiture” and Note 16, “Subsequent Events” for further information.

Use of Estimates and Judgements

The preparation of financial statements in conformity with U.S. GAAP requires management to make
estimates, judgements and assumptions that affect the reported amounts of assets and liabilities, disclosures
of contingent assets and liabilities at the date of the financial statements, and the reported amounts of
revenues and expenses during the reporting period. Actual results could differ from those estimates, and
such differences may be material to the consolidated financial statements.

Significant Accounting Policies

Cash and Cash Equivalents

The Company considers all highly liquid investments purchased with an original or remaining maturity
of three months or less at the date of purchase to be cash equivalents. Cash and cash equivalents are
maintained with various financial institutions.

Inventories

Inventories, which consist of farnesene-derived products, flavors and fragrances ingredients and clean
beauty products, are stated at the lower of actual cost or net realizable value and are categorized as finished
goods, work in process or raw material inventories. The Company evaluates the recoverability of its
inventories based on assumptions about expected demand and net realizable value. If the Company
determines that the cost of inventories exceeds their estimated net realizable value, the Company records a
write-down equal to the difference between the cost of inventories and the estimated net realizable value. If
actual net realizable values are less favorable than those projected by management, additional inventory
write-downs may be required that could negatively impact the Company’s operating results. If actual net
realizable values are more favorable, the Company may have favorable operating results when products that
have been previously written down are sold in the normal course of business. The Company also evaluates
the terms of its agreements with its suppliers and establishes accruals for estimated losses on adverse
purchase commitments as necessary, applying the same lower of cost or net realizable value approach that is
used to value inventory. Cost is computed on a weighted-average basis.

Property, Plant and Equipment, Net

Property, plant and equipment are recorded at cost. Depreciation and amortization are computed
straight-line based on the estimated useful lives of the related assets, ranging from 3 to 15 years for
machinery, equipment and fixtures, and 15 years for buildings. Leasehold improvements are amortized over
their estimated useful lives or the period of the related lease, whichever is shorter.

The Company expenses costs for maintenance and repairs and capitalizes major replacements, renewals
and betterments. For assets retired or otherwise disposed, both cost and accumulated depreciation are
eliminated from the asset and accumulated depreciation accounts, and gains or losses related to the disposal
are recorded in the statement of operations for the period.

Impairment

Long-lived assets that are held and used by the Company are reviewed for impairment whenever events
or changes in circumstances indicate that the carrying amount of such assets may not be recoverable.
Determination of recoverability of long-lived assets is based on an estimate of the undiscounted future cash
flows resulting from the use of the asset and its eventual disposition. Measurement of an impairment loss
for long-lived assets that management expects to hold and use is based on the difference between the fair
value of the asset and its carrying value. Long-lived assets to be disposed of are reported at the lower of
carrying amount or fair value less costs to sell.

Recoverable Taxes from Brazilian Government Entities

Recoverable taxes from Brazilian government entities represent value-added taxes paid on purchases in
Brazil, which are reclaimable from the Brazilian tax authorities, net of reserves for amounts estimated not
to be recoverable.

Fair Value Measurements

The carrying amounts of certain financial

instruments, such as cash equivalents, short-term
investments, accounts receivable, accounts payable and accrued liabilities, approximate fair value due to
their relatively short maturities.

The Company measures the following financial assets and liabilities at fair value:

•

Freestanding and bifurcated derivatives in connection with certain debt and equity financings; and

6% Convertible Notes Due 2021 (see Note 4, “Fair Value Measurement”, Note 5, “Debt” and
Note 16, “Subsequent Events”), for which the Company has elected fair value accounting

Fair value is based on the exchange price that would be received for an asset or paid to transfer a
liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly
transaction between market participants. Where available, fair value is based on or derived from observable
market prices or other observable inputs. Where observable prices or inputs are not available, valuation
techniques are applied. These valuation techniques involve some level of management estimation and
judgement, the degree of which is dependent on the price transparency for the instruments or market and
the instruments’ complexity.

Changes to the inputs used in these valuation models have a significant impact on the estimated fair
value of the 6% Convertible Notes Due 2021 and the Company’s embedded and freestanding derivatives.
For example, a decrease (increase) in the estimated credit spread for the Company results in an increase
(decrease) in estimated fair value. Conversely, a decrease (increase) in the stock price results in a decrease
(increase) in estimated fair value.

The changes during 2018 and 2017 in the fair values of the bifurcated compound embedded derivatives
are primarily related to the change in price of the Company’s common stock and are reflected in the
consolidated statements of operations as “Gain (loss) from change in fair value of derivative instruments”.

For debt instruments for which the Company has not elected fair value accounting, fair value is based
on the present value of expected future cash flows and assumptions about the then-current market interest
rates as of the reporting period and the creditworthiness of the Company. Most of the Company’s debt is
carried on the consolidated balance sheet on a historical cost basis net of unamortized discounts and
premiums, because the Company has not elected the fair value option of accounting. However, for the 6%
Notes Due 2021, the Company elected fair value accounting, so that balances reported for that debt
instrument represent fair value as of each balance sheet date; see Note 4, “Fair Value Measurement”, for
additional information. Changes in fair value of the 6% Convertible Notes Due 2021 are reflected in the
consolidated statements of operations as “Gain (loss) from change in fair value of debt”.

For all debt instruments, including any for which the Company has elected fair value accounting, the
Company classifies interest that has been accrued during each period as Interest expense on the
consolidated statements of operations.

Derivatives

Embedded derivatives that are required to be bifurcated from the underlying debt instrument
(i.e., host) are accounted for and valued as separate financial instruments. The Company has evaluated the
terms and features of its convertible notes payable and convertible preferred stock and identified compound
embedded derivatives requiring bifurcation and accounting at fair value, using the valuation techniques
mentioned in the Fair Value Measurements section of this Note, because the economic and contractual
characteristics of the embedded derivatives met the criteria for bifurcation and separate accounting due to
the instruments containing conversion options, certain “make-whole interest” provisions, down-round
conversion price adjustment provisions and/or conversion rate adjustments.

Cash warrants and anti-dilution warrants issued in conjunction with the convertible debt and equity

financings are freestanding financial instruments which are also classified as derivative liabilities.

Noncontrolling Interest

Noncontrolling interests represent the portion of net income (loss), net assets and comprehensive
income (loss) that is not allocable to the Company, in situations where the Company consolidates its equity
investment in a joint venture for which there are other owners. The amount of noncontrolling interest is
comprised of the amount of such interests at the date of the Company’s original acquisition of an equity
interest in a joint venture, plus the other shareholders’ share of changes in equity since the date the
Company made an investment in the joint venture.

Concentration of Credit Risk

Financial instruments that potentially subject the Company to a concentration of credit risk consist
primarily of cash and cash equivalents, short-term investments and accounts receivable. The Company
places its cash equivalents and investments (primarily certificates of deposits) with high credit quality
financial institutions and, by policy, limits the amount of credit exposure with any one financial institution.
Deposits held with banks may exceed the amount of insurance provided on such deposits. The Company
has not experienced any losses on its deposits of cash and cash equivalents and short-term investments.

The Company performs ongoing credit evaluation of its customers, does not require collateral, and

maintains allowances for potential credit losses on customer accounts when deemed necessary.

Customers representing 10% or greater of accounts receivable were as follows:

As of December 31,
Customer B . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Customer C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Customer G . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Customer A (related party) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

2017

2018
24% 10%
19% 15%
11% **
**

38%

** Less than 10%

Customers representing 10% or greater of revenue were as follows:

Years Ended December 31,

Customer A (related party)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Customer B . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Customer C . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Customer D . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Customer E . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Customer F . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

2018

17%
18%
13%
13%
**
**

2017
(As Restated,
Note 2)
46%
13%
**
**
11%
**

** Less than 10%

Revenue Recognition

Year ended December 31, 2017

For the year ended December 31, 2017, the Company recognized revenue from the sale of renewable
products, licenses of and royalties from intellectual property, and grants and collaborative research and
development services. Revenue was recognized when all of the following criteria were met: persuasive
evidence of an arrangement existed, delivery has occurred or services have been rendered, the fee was fixed
or determinable, and collectability was reasonably assured. If sales arrangements contained multiple
elements, the Company evaluated whether the components of each arrangement represent separate units of
accounting.

Renewable Product Sales

The Company’s renewable product sales do not include rights of return, except for sales of Biossance
the product does not meet product specifications and such
products. Returns are only accepted if
nonconformity is communicated to the Company within a set number of days of delivery. The Company
offers a two-year standard warranty provision for squalane products,
the products do not meet
Company-established criteria as set forth in the Company’s trade terms. The Company bases its return
reserve on a historical rate of return for the Company’s squalane products. Revenues are recognized, net of
discounts and allowances, once passage of title and risk of loss has occurred and contractually specified
acceptance criteria have been met, provided all other revenue recognition criteria have also been met.

Licenses and Royalties

License fees for intellectual property transferred to other parties, representing non-refundable
payments received at the time of signature of license agreements, are recognized as revenue upon signature
of the license agreements when the Company has no significant future performance obligations and
collectability of the fees is assured. Upfront payments received at the beginning of licensing agreements
with future service obligations are deferred and recognized as revenue on a systematic basis over the period
during which the related services are rendered and all obligations are performed.

Royalties from intellectual property licenses that allow Amyris’s customers to use the Company’s
intellectual property to produce and sell their products in which the Company shares in the profits are
recognized in the period the royalty report is received.

Grants and Collaborative Research and Development Services

Revenues from collaborative research and development services are recognized as the services are
performed consistent with the performance requirements of the contract. In cases where the planned levels
of research and development services fluctuate over the research term, the Company recognizes revenues
using the proportional performance method based upon actual efforts to date relative to the amount of
expected effort to be incurred by us. When up-front payments are received and the planned levels of
research and development services do not fluctuate over the research term, revenues are recorded on a
ratable basis over the arrangement term, up to the amount of cash received. When up-front payments are
received and the planned levels of research and development services fluctuate over the research term,
revenues are recorded using the proportional performance method, up to the amount of cash received.
Where arrangements include milestones that are determined to be substantive and at risk at the inception of
the arrangement, revenues are recognized upon achievement of the milestone and is limited to those
amounts whereby collectability is reasonably assured.

Grants are agreements that generally provide cost reimbursement for certain types of expenditures in
return for research and development activities over a contractually defined period. Revenues from grants
are recognized in the period during which the related costs are incurred, provided that the conditions under
which the grants were provided have been met and only perfunctory obligations are outstanding.

Year ended December 31, 2018

In accordance with a new revenue recognition standard that the Company adopted January 1, 2018,
the Company recognizes revenue from the sale of renewable products, licenses of and royalties from

intellectual property, and grants and collaborative research and development services. Revenue is measured
based on the consideration specified in a contract with a customer, and transaction price is allocated
utilizing stand-alone selling price. Revenue is recognized when, or as, the Company satisfies a performance
obligation by transferring control over a product or service to a customer. The Company generally does not
incur costs to obtain new contracts. The costs to fulfill a contract are expensed as incurred.

The Company accounts for a contract when it has approval and commitment to perform from both
parties, the rights of the parties are identified, payment terms are established, the contract has commercial
substance and collectability of the consideration is probable. Changes to contracts are assessed for whether
they represent a modification or should be accounted for as a new contract. The Company considers the
following indicators, among others, when determining if it is acting as a principal in the transaction and
recording revenue on a gross basis: (i) the Company is primarily responsible for fulfilling the promise to
provide the specified goods or service, (ii) the Company has inventory risk before the specified good or
service has been transferred to a customer or after transfer of control to the customer and (iii) the
Company has discretion in establishing the price for the specified good or service. If a transaction does not
meet the Company’s indicators of being a principal in the transaction, then the Company is acting as an
agent in the transaction and the associated revenues are recognized on a net basis.

The Company’s significant contracts and contractual terms with its customers are presented in

Note 10, “Revenue Recognition”.

The Company recognizes revenue when control has passed to the customer. The following indicators
are evaluated in determining when control has passed to the customer: (i) the Company has a right to
receive payment for the product or service, (ii) the customer has legal title to the product, (iii) the Company
has transferred physical possession of the product to the customer, (iv) the customer has the significant risk
and rewards of ownership of the product and (v) the customer has accepted the product. For most of the
Company’s renewable products customers, supply agreements between the Company and each customer
indicate when transfer of title occurs.

In some cases, the Company may make a payment to a customer. When that occurs, the Company
evaluates whether the payment is for a distinct good or service receivable from the customer. If the fair value
of the goods or services receivable is greater than or equal to the amount paid to the customer, then the
entire payment is treated as a purchase. If, on the other hand, the fair value of goods or services is less than
the amount paid, then the difference is treated as a reduction in transaction price of the Company’s sales to
the customer.

Performance Obligations

A performance obligation is a promise in a contract to transfer a distinct good or service to the
customer. A contract’s transaction price is allocated to each distinct performance obligation and recognized
as revenue when, or as, the performance obligation is satisfied. The Company’s contracts may contain
multiple performance obligations if a promise to transfer the individual goods or services is separately
identifiable from other promises in the contracts and, therefore, is considered distinct. For contracts with
multiple performance obligations,
the Company determines the standalone selling price of each
performance obligation and allocates the total transaction price using the relative selling price basis.

The following is a description of the principal goods and services from which the Company generates

revenue.

Renewable Product Sales

Revenues from renewable product sales are recognized as a distinct performance obligation on a gross
basis as the Company is acting as a principal in these transactions, with the selling price to the customer
recorded net of discounts and allowances. Revenues are recognized at a point in time when control has
passed to the customer, which typically is upon the renewable products leaving the Company’s facilities with
the first transportation carrier. The Company, on occasion, may recognize revenue under a bill and hold
arrangement, whereby the customer requests and agrees to purchase product but requests delivery at a later
date. Under these arrangements, control transfers to the customer when the product is ready for delivery,
which occurs when the product is identified separately as belonging to the customer, the product is ready for

shipment to the customer in its current form, and the Company does not have the ability to direct the
product to a different customer. It is at this point that the Company has the right to receive payment, the
customer obtains legal title, and the customer has the significant risks and rewards of ownership. The
Company’s renewable product sales do not include rights of return, except for Biossance products, for
which the Company estimates sales returns subsequent to sale and reduces revenue accordingly. For
renewable products other than Biossance, returns are accepted only if the product does not meet product
specifications and such nonconformity is communicated to the Company within a set number of days of
delivery. The Company offers a two-year assurance-type warranty to replace squalane products that do not
meet Company-established criteria as set forth in the Company’s trade terms. An estimate of the cost to
replace the squalane products sold is made based on a historical rate of experience and recognized as a
liability and related expense when the renewable product sale is consummated.

Licenses and Royalties

Licensing of Intellectual Property: When the Company’s intellectual property licenses are determined to
be distinct from the other performance obligations identified in the arrangement, revenue is recognized
from non-refundable, up-front fees allocated to the license at a point in time when the license is transferred
to the licensee and the licensee is able to use and benefit from the license. For intellectual property licenses
that are combined with other promises, the Company utilizes judgment to assess the nature of the
combined performance obligation to determine whether the combined performance obligation is satisfied
over time or at a point in time and, if over time, the appropriate method of measuring progress for purposes
of recognizing revenue from non-refundable, up-front-fees. The Company evaluates the measure of progress
each reporting period and, if necessary, adjusts the measure of performance and related revenue recognized.

Royalties from Licensing of Intellectual Property: The Company earns royalties from the licensing of its
intellectual property whereby the licensee uses the intellectual property to produce and sell its products to its
customers and the Company shares in the profits.

When the Company’s intellectual property license is the only performance obligation, or it is the
predominant performance obligation in arrangements with multiple performance obligations, the Company
applies the sales-based royalty exception which requires the Company to estimate the revenue that is
recognized at a point in time when the licensee’s product sales occur. Estimates of sales-based royalty
revenues are made using the most likely outcome method, which is the single amount in a range of possible
amounts, using the best evidence available at the time, derived from the licensee’s historical sales volumes
and sales prices of its products and recent commodity market pricing data and trends. Estimates are
adjusted to actual or as new information becomes available.

When the Company’s intellectual property license is not the predominant performance obligation in
arrangements with multiple performance obligations, the royalty represents variable consideration and is
allocated to the transaction price of the predominant performance obligation which generally is the supply
of renewable products to the Company’s customers. Revenue is estimated and recognized at a point in time
the amount of variable
when the renewable products are delivered to the customer. Estimates of
consideration to include in the transaction price are made using the expected value method, which is the
sum of probability-weighted amounts in a range of possible amounts determined based on the cost to
produce the renewable product plus a reasonable margin for the profit share. The Company only includes
an amount of variable consideration in the transaction price to the extent it is probable that a significant
reversal in the cumulative revenue recognized will not occur when the uncertainty associated with the
variable consideration is subsequently resolved. Also, the transaction price is reduced for estimates of
customer incentive payments payable by the Company for certain customer contracts.

Grants and Collaborative Research and Development Services

Collaborative Research and Development Services: The Company earns revenues from collaboration
agreements with customers to perform research and development services to develop new molecules using
the Company’s technology and to scale production of the molecules for commercialization and use in the
collaborator’s products. The collaboration agreements generally include providing the Company’s
collaboration partners with research and development services and with licenses to the Company’s
intellectual property to use the technology underlying the development of the molecules and to sell its

products that incorporate the technology. The terms of the Company’s collaboration agreements typically
include one or more of the following: advance payments for the research and development services that will
be performed, nonrefundable upfront license payments, milestone payments to be received upon the
achievement of
the milestone events defined in the agreements, and royalty payments upon the
commercialization of the molecules in which the Company shares in the customer’s profits.

Collaboration agreements are evaluated at inception to determine whether the intellectual property
licenses represent distinct performance obligations separate from the research and development services. If
the licenses are determined to be distinct, the non-refundable upfront license fee is recognized as revenue at
a point in time when the license is transferred to the licensee and the licensee is able to use and benefit from
the license while the research and development service fees are recognized over time as the performance
obligations are satisfied. The research and development service fees represent variable consideration.
Estimates of the amount of variable consideration to include in the transaction price are made using the
expected value method, which is the sum of probability-weighted amounts in a range of possible amounts.
The Company only includes an amount of variable consideration in the transaction price to the extent it is
probable that a significant reversal in the cumulative revenue recognized will not occur when the uncertainty
associated with the variable consideration is subsequently resolved. Revenue is recognized over time using
either an input-based measure of labor hours expended or a time-based measure of progress towards the
satisfaction of the performance obligations. The measure of progress is evaluated each reporting period
and, if necessary, adjustments are made to the measure of progress and the related revenue recognized.

if necessary, adjusts its estimate of

Collaboration agreements that include milestone payments are evaluated at inception to determine
whether the milestone events are considered probable of achievement, and estimates are made of the
amount of the milestone payments to include in the transaction price using the most likely amount method
which is the single amount in a range of possible amounts. If it is probable that a significant revenue
reversal will not occur, the estimated milestone payment amount is included in the transaction price. Each
reporting period, the Company re-evaluates the probability of achievement of the milestone events and any
the overall transaction price. Any such
related constraint and,
adjustments are recorded on a cumulative basis, which would affect collaboration revenues in the period of
adjustment. Generally, revenue is recognized using an input-based measure of progress towards the
satisfaction of the performance obligations which can be labor hours expended or time-based in proportion
to the estimated total project effort or total projected time to complete. The measure of progress is evaluated
each reporting period and, if necessary, adjustments are made to the measure of progress and the related
revenue recognized. Certain performance obligations are associated with milestones agreed between the
Company and its customer. Revenue generated from the performance of services in accordance with these
milestones is recognized upon confirmation from the customer that the milestone has been achieved. In
these cases, amounts recognized are constrained to the amount of consideration received upon achievement
of the milestone.

The Company generally invoices its collaboration partners on a monthly or quarterly basis, or upon
the completion of the effort or achievement of a milestone, based on the terms of each agreement. Deferred
revenue arises from amounts received in advance of performing the research and development activities and
is recognized as revenue in future periods as the performance obligations are satisfied.

Grants: The Company earns revenues from grants with government agencies to, among other things,
provide research and development services to develop molecules using the Company’s technology, and
create research and development tools to improve the timeline and predictability for scaling molecules from
proof of concept to market by reducing time and costs. Grants typically consist of research and
development milestone payments to be received upon the achievement of the milestone events defined in
the agreements.

The milestone payments are evaluated at inception to determine whether the milestone events are
considered probable of achievement and estimates are made of the amount of the milestone payments to
include in the transaction price using the most likely amount method which is the single amount in a range
of possible amounts. If it is probable that a significant revenue reversal will not occur, the estimated
milestone payment amount is included in the transaction price. Each reporting period, the Company
re-evaluates the probability of achievement of the milestone events and any related constraint and, if

necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a
cumulative basis, which would affect grant revenues in the period of adjustment. Revenue is recognized over
time using a time-based measure of progress towards the satisfaction of the performance obligations. The
measure of progress is evaluated each reporting period and, if necessary, adjustments are made to the
measure of progress and the related revenue recognized.

Cost of Products Sold

Cost of products sold includes the production costs of renewable products, which include the cost of
raw materials, in-house manufacturing labor and overhead, amounts paid to contract manufacturers,
including amortization of tolling fees, and period costs including inventory write-downs resulting from
applying lower of cost or net realizable value inventory adjustments. Cost of products sold also includes
certain costs related to the scale-up of production. Shipping and handling costs charged to customers are
recorded as revenues. Outbound shipping costs incurred are included in cost of products sold. Such charges
were not material for any of the periods presented.

The Company recognizes deferred cost of products sold as an asset on the balance sheet when a cost is
incurred in connection with a revenue performance obligation that will not be fulfilled until a future period.

Research and Development

Research and development costs are expensed as incurred and include costs associated with research
performed pursuant to collaborative agreements and government grants,
including internal research.
Research and development costs consist of direct and indirect internal costs related to specific projects, as
well as fees paid to others that conduct certain research activities on the Company’s behalf.

Debt Extinguishment

The Company accounts for the income or loss from extinguishment of debt in accordance with
ASC 470, Debt, which indicates that for all extinguishment of debt, the difference between the reacquisition
consideration and the net carrying amount of the debt being extinguished should be recognized as gain or
loss when the debt is extinguished. Losses from debt extinguishment are shown in the consolidated
statements of operations under “Other income (expense)” as “Loss upon extinguishment of debt”.

Stock-based Compensation

The Company accounts for stock-based employee compensation plans under the fair value recognition
and measurement provisions of U.S. GAAP. Those provisions require all stock-based payments to
employees, including grants of stock options and restricted stock units (RSUs), to be measured using the
grant-date fair value of each award. The Company recognizes stock-based compensation expense net of
expected forfeitures over each award’s requisite service period, which is generally the vesting term. Expected
forfeiture rates are estimated based on the Company’s historical experience. Stock-based compensation
plans are described more fully in Note 12, “Stock-based Compensation”.

Income Taxes

The Company is subject to income taxes in the United States and foreign jurisdictions and uses
estimates to determine its provisions for income taxes. The Company uses the asset and liability method of
accounting for income taxes, whereby deferred tax asset or liability account balances are calculated at the
balance sheet date using current tax laws and rates in effect for the year in which the differences are
expected to affect taxable income.

Recognition of deferred tax assets is appropriate when realization of such assets is more likely than
not. The Company recognizes a valuation allowance against its net deferred tax assets unless it is more likely
than not that such deferred tax assets will be realized. This assessment requires judgement as to the
likelihood and amounts of future taxable income by tax jurisdiction.

assessment or challenge by relevant taxing authorities. Assessing an uncertain tax position begins with the
initial determination of the position’s sustainability, and the tax benefit to be recognized is measured at the
largest amount of benefit that is greater than 50 percent likely of being realized upon ultimate settlement.
As of each balance sheet date, unresolved uncertain tax positions must be reassessed, and the Company will
determine whether (i) the factors underlying the sustainability assertion have changed and (ii) the amount
of the recognized tax benefit is still appropriate. The recognition and measurement of tax benefits requires
significant judgement, and such judgements may change as new information becomes available.

Foreign Currency Translation

The assets and liabilities of foreign subsidiaries, where the local currency is the functional currency, are
translated from their respective functional currencies into U.S. dollars at the rates in effect at each balance
sheet date, and revenue and expense amounts are translated at average rates during each period, with
resulting foreign currency translation adjustments recorded in other comprehensive loss, net of tax, in the
consolidated statements of stockholders’ deficit. As of December 31, 2018 and 2017, cumulative translation
adjustment, net of tax, were $43.3 million and $42.2 million, respectively.

Where the U.S. dollar is the functional currency, remeasurement adjustments are recorded in other
income (expense), net in the accompanying consolidated statements of operations. Net losses resulting from
foreign exchange transactions were $1.6 million and $0.4 million for the years ended December 31, 2018
and 2017, respectively and are recorded in other income (expense), net in the consolidated statements of
operations.

New Accounting Standards or Updates Recently Adopted

During the year ended December 31, 2018 the Company adopted the following Accounting Standards

Updates (ASUs):

Revenue Recognition The Company adopted ASC 606, Revenue from Contracts with Customers, with a
date of initial application of January 1, 2018. As a result, the Company has changed its accounting policy
for revenue recognition as detailed above in “Significant Accounting Policies”. The Company applied
ASC 606 using the modified retrospective approach by recognizing the cumulative effect of initially
applying ASC 606 to all contracts not completed as of the date of adoption as an adjustment to the
opening balance of accumulated deficit at January 1, 2018. Therefore, the comparative information has not
been adjusted and continues to be reported under the legacy revenue recognition guidance of ASC 605,
“Revenue Recognition”.

The Company applied ASC 606 using a practical expedient for contracts that were modified before the
application date, which allowed the Company to determine an aggregate effect of all modifications that
occurred before January 1, 2018, when determining the satisfied and unsatisfied performance obligations,
the transaction price, and allocating that transaction price to the performance obligations instead of
retrospectively restating the contracts for such contract modifications.

The cumulative effect of initially applying ASC 606 resulted in an increase to accumulated deficit at
January 1, 2018 of approximately $0.8 million. The most significant change in accounting policy is the
Company is now required to estimate royalty revenues from licenses of the Company’s intellectual property
and recognize estimated royalty revenues at a point in time when the Company sells its renewable products
to its customers (if the sales-based royalty exception does not apply) or when the licensee sells its products
to its customer (if the sales-based royalty exception does apply).

The following table presents the amounts by which revenue is affected in the current reporting period
by the application of ASC 606 as compared with the legacy guidance that was in effect before the
accounting change.

(In thousands)

Year Ended December 31, 2018

As
Reported

Adjustments

Amounts
Without the
Adoption of
ASC 606

Renewable products . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$33,598

$ —

$33,598

Licenses and royalties

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

7,658

Grants and collaborations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

22,348

5,094

(5,786)

12,752

16,562

Total revenue from all customers . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$63,604

$ (692)

$62,912

Financial Instruments In January 2016, the Financial Accounting Standards Board (FASB) issued ASU
2016-01, Financial Instruments — Overall (Subtopic 825-10): Recognition and Measurement of Financial
Assets and Financial Liabilities, which changes the accounting for equity investments, financial liabilities
under the fair value option, and the presentation and disclosure requirements for financial instruments. The
Company adopted ASU 2016-01 on January 1, 2018. Adoption of this ASU did not impact the Company’s
consolidated financial position, results of operations or cash flows.

Classification of Cash Flow Elements In August 2016, the FASB issued ASU 2016-15, Statement of
Cash Flows (Topic 230): Classification of Certain Cash Receipts and Cash Payments, which affects the
classification of certain cash receipts and cash payments on the statement of cash flows. ASU 2016-15
results in a change in cash flow classification of debt prepayment or extinguishment costs. ASU 2016-15
became effective January 1, 2018 on a retrospective basis. Adoption of this ASU did not impact the
Company’s consolidated financial position, results of operations or cash flows.

Income Taxes Related to Intra-entity Asset Transfers In October 2016, FASB issued ASU 2016-16,
Intra-Entity Transfers of Assets Other Than Inventory on simplifying the accounting for income taxes related
to intra-entity asset transfers. The new guidance allows an entity to recognize the tax expense from the sale
of an asset in the seller’s tax jurisdiction when the transfers occurs, even though the pre-tax effects of that
transaction are eliminated in consolidation. ASU 2016-16 became effective January 1, 2018, which the
Company adopted on a modified retrospective basis.

Restricted Cash in Statement of Cash Flows In November 2016, the FASB issued ASU 2016-18,
Statement of Cash Flows (Topic 230): Restricted Cash, which requires that a statement of cash flows
explain the change during the period in the total of cash, cash equivalents, and amounts generally described
as restricted cash or restricted cash equivalents. Therefore, amounts generally described as restricted cash
and restricted cash equivalents should be included with cash and cash equivalents when reconciling the
beginning-of-period and end-of-period total amounts shown on the statement of cash flows. The
accounting standard update became effective January 1, 2018 using a retrospective transition method for
each period presented. Upon adoption, ASU 2016-18 resulted in a change in the presentation of restricted
cash in the statement of cash flows for current and prior periods presented.

Derecognition of Nonfinancial Assets In February 2017, the FASB issued ASU 2017-05, Other
Income — Gains and Losses from the Derecognition of Nonfinancial Assets (Subtopic 610-20): Clarifying the
Scope of Asset Derecognition Guidance and Accounting for Partial Sales of Nonfinancial Assets, which
requires entities to apply certain recognition and measurement principles in ASC 606 when they
derecognize nonfinancial assets, and in substance, nonfinancial assets, and the counterparty is not a
customer. The guidance applies to: (1) contracts to transfer to a noncustomer a nonfinancial asset or group
of nonfinancial assets, or an ownership interest in a consolidated subsidiary that does not meet the
definition of a business and is not a not-for-profit activity; and (2) contributions of nonfinancial assets that
are not a business to a joint venture or other noncontrolled investee. The accounting standard update
became effective January 1, 2018 on a modified retrospective basis. Adoption of this ASU did not impact
the Company’s consolidated financial position, results of operations or cash flows.

Income Taxes In March 2018, FASB issued ASU 2018-05, Amendments to SEC Paragraphs Pursuant to
SEC Staff Accounting Bulletin No. 118 to address the application of GAAP in situations when a registrant

does not have the necessary information available, prepared or analyzed (including computations) in
reasonable detail to complete the accounting for certain income tax effects of the Tax Act. As of
December 31, 2018, the Company’s analysis for the Transition Tax has been filed with its December 31,
2017 tax return and the Company considered its accounting for this area of the Tax Act to be complete as
of such date and did not make any measurement-period adjustments related to it. In addition, the
Company considered its accounting for changes in the U.S. federal rate and deferred tax impact for the rate
change to be complete. The Company also accounted for the tax impact related to other areas of the Tax
Act and believe its analysis to be completed consistent with the guidance in ASU 2018-05. The Company
recognizes that the IRS is continuing to publish and finalize ongoing guidance with respect to the Act which
may modify accounting interpretation for the Tax Act, the Company would look to account for these
impacts in the period of such change is enacted.

Non-employee Stock-based Compensation In June 2018, the FASB issued ASU 2018-07, Improvements
to Nonemployee Share-Based Payment Accounting, which more closely aligns the accounting for employee
and nonemployee stock-based compensation. Under the new standard, companies are no longer required to
value non-employee awards differently from employee awards. The Company adopted this accounting
standard update on January 1, 2018 using a modified retrospective approach. Adoption of this ASU did
not impact the Company’s consolidated financial position, results of operations or cash flows.

Recent Accounting Standards or Updates Not Yet Effective

Leases In February 2016, the FASB issued ASU 2016-02, Leases (Topic 842), as subsequently
updated, with fundamental changes as to how entities account for leases. Lessees will need to recognize a
right-of-use asset and a lease liability for virtually all of their leases (other than leases that meet the
definition of a short-term lease). The liability will be equal to the present value of lease payments. The asset
will be based on the liability, subject to adjustment, such as for initial direct costs. Additional disclosures for
leases will also be required.

The Company is adopting the new standard effective January 1, 2019 using a modified retrospective
method, and will not restate comparative periods. The modified retrospective transition approach requires
lessees and lessors to recognize and measure existing leases at the date of initial application. The new
standard provides a number of optional practical expedients in transition. The Company expects to elect
the “package of practical expedients”, which permits it not to reassess under the new standard prior
conclusions about lease identification, lease classification and initial direct costs.

The adoption of this standard on January 1, 2019 is expected to have the effect of increasing assets and
liabilities on the consolidated balance sheet by $25.7 million, but is not expected to have a material impact
on the consolidated statements of operations or cash flows. The most significant impact relates to (i) the
recognition of new Right of Use (ROU) assets and lease liabilities on the balance sheet for operating leases;
and (ii) providing significant new disclosures about leasing activities. Upon adoption, the Company will
recognize operating lease liabilities of $33.6 million, based on the present value of the remaining minimum
rental payments under current leasing standards for existing operating leases. The Company will also
recognize ROU assets of $29.7 million, which represents the operating lease liability adjusted for accrued
rent.

Financial Instruments with “Down Round” Features In July 2017, the FASB issued ASU 2017-11,
Earnings Per Share (Topic 260); Distinguishing Liabilities from Equity (Topic 480); Derivatives and Hedging
(Topic 815): Accounting for Certain Financial Instruments with Down Round Features. The amendments of
this ASU update the classification analysis of certain equity-linked financial instruments, or embedded
features, with down round features, as well as clarify existing disclosure requirements for equity-classified
instruments. When determining whether certain financial instruments should be classified as liabilities or
equity instruments, a down round feature no longer precludes equity classification when assessing whether
the instrument is indexed to an entity’s own stock. The accounting standard update will be effective
beginning in the first quarter of fiscal year 2019 using a modified retrospective approach. The Company
completed its assessment of the new standard and determined the impact to the consolidated balance sheet
would be material. The Company anticipates recording a $41.0 million reduction to derivative liabilities and
a corresponding $41.0 million increase to equity on January 1, 2019.

Fair Value Measurement In August 2018, the FASB issued ASU 2018-13, Fair Value Measurement
(Topic 820): Disclosure Framework — Changes to the Disclosure Requirements for Fair Value Measurement,
which amends ASC 820, Fair Value Measurement. ASU 2018-13 modifies the disclosure requirements for
fair value measurements by removing, modifying or adding certain disclosures. The accounting standard
update will be effective beginning in the first quarter of fiscal year 2020, with removed and modified
disclosures to be adopted on a retrospective basis, and new disclosures to be adopted on a prospective basis.
The Company is in the initial stages of evaluating the impact of the new standard on its consolidated
financial statements.

Collaborative Revenue Arrangements In November 2018, the FASB issued ASU 2018-18, Clarifying the
Interaction between Topic 808 and Topic 606, that clarifies the interaction between the guidance for certain
collaborative arrangements and Topic 606, the new revenue recognition standard. A collaborative
arrangement is a contractual arrangement under which two or more parties actively participate in a joint
operating activity and are exposed to significant risks and rewards that depend on the activity’s commercial
success. The ASU provides guidance on how to assess whether certain transactions between collaborative
arrangement participants should be accounted for within the revenue recognition standard. The accounting
standard update will be effective beginning in the first quarter of fiscal year 2020 retroactively. The
Company does not believe that the impact of the new standard on its consolidated financial statements will
be material.

Credit Losses In June 2016, the FASB issued ASU 2016-13, Financial Instruments — Credit Losses
(Topic 326), Measurement of Credit Losses on Financial Instruments. ASU 2016-13 requires entities to
measure all expected credit losses for most financial assets held at the reporting date based on an expected
loss model which includes historical experience, current conditions, and reasonable and supportable
forecasts. Entities will now use forward-looking information to better form their credit loss estimates.
ASU 2016-13 also requires enhanced disclosures to help financial statement users better understand
significant estimates and judgments used in estimating credit losses, as well as the credit quality and
underwriting standards of an entity’s portfolio. ASU 2016-13 will become effective for the Company
beginning in the first quarter of fiscal year 2020. The Company does not believe that the impact of the new
standard on its consolidated financial statements will be material.

2. Restatement of Consolidated Financial Statements

Restatement Background

Subsequent to the issuance of the Company’s unaudited condensed consolidated financial statements
as of September 30, 2018 and as previously announced on April 5, 2019 and May 14, 2019, the Audit
Committee (the Audit Committee) of the Board of Directors of the Company (the Board) and the Board,
respectively, concluded that the Company will restate its interim condensed consolidated financial
statements for the quarterly and year-to-date periods ended March 31, 2018, June 30, 2018 and
September 30, 2018 (collectively, the Restated 2018 Non-Reliance Periods) and its audited consolidated
financial statements for the year ended December 31, 2017 (the Restated 2017 Non-Reliance Consolidated
Financial Statements).

Restated 2017 Non-Reliance Consolidated Financial Statements

The error corrections for the year to date audited 2017 consolidated financial statements have been
reflected throughout these consolidated financial statements and accompanying notes. Also, the tables
below show the impact of each adjustment by the individual financial statement line item caption and
provide a brief description of the adjustment.

Consolidated Balance Sheet

The following table presents the Company’s consolidated balance sheet at December 31, 2017 as

previously reported, restatement adjustments and as restated (in thousands):

December 31, 2017

As
Previously
Reported

Corrections Ref.

As
Restated

(In thousands)
Assets
Current assets:

Cash and cash equivalents . . . . . . . . . . . . . . . . . . . . . . . . . $
Restricted cash . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Accounts receivable, net . . . . . . . . . . . . . . . . . . . . . . . . . . .
Accounts receivable – related party, net . . . . . . . . . . . . . . . .
Accounts receivable, unbilled – related party . . . . . . . . . . . .
Inventories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . .
Prepaid expenses and other current assets
. . . . . . . . . . . . . . . . . . . . . . . . . . . .
Property, plant and equipment, net . . . . . . . . . . . . . . . . . . . . .
Contract assets, noncurrent . . . . . . . . . . . . . . . . . . . . . . . . . .
Restricted cash, noncurrent . . . . . . . . . . . . . . . . . . . . . . . . . .
Recoverable taxes from Brazilian government entities . . . . . . . .
Other assets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Total current assets

Total assets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $

Liabilities, Mezzanine Equity and Stockholders’ Deficit
Current liabilities:

57,059 $
2,994
24,281
9,340

—
—
(5,328)
(4,573)
9,901
—

a
a

5,408
5,525
104,607
13,892
7,940
959
1,445
22,640

(606) b
(606)
—
—
—
—
(10,081)
151,483 $(10,687)

Accounts payable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $
Accrued and other current liabilities . . . . . . . . . . . . . . . . . .
Contract liabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Debt, current portion . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Related party debt, current portion . . . . . . . . . . . . . . . . . . .
Total current liabilities . . . . . . . . . . . . . . . . . . . . . . . . . .
Long-term debt, net of current portion . . . . . . . . . . . . . . . . . .
Related party debt, net of current portion . . . . . . . . . . . . . . . .
Derivative liabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Other noncurrent liabilities . . . . . . . . . . . . . . . . . . . . . . . . . .
Total liabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

15,921 $
29,402
4,880
36,924
20,019
107,146
61,893
46,541
119,978
10,632
346,190

(406) d
e
(200)
f
(572)
—
—
(1,178)
(1,673)
—
(3,481) h
13,026
i
6,694

Commitments and contingencies
Mezzanine equity:

57,059
2,994
18,953
4,767
9,901
5,408
4,919
104,001
13,892
7,940
959
1,445
12,559
140,796

15,515
29,202
4,308
36,924
20,019
105,968
60,220
46,541
116,497
23,658
352,884

Contingently redeemable common stock . . . . . . . . . . . . . . .

5,000

—

5,000

Stockholders’ deficit:

Preferred stock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Common stock – $0.0001 par value . . . . . . . . . . . . . . . . . . .
Additional paid-in capital . . . . . . . . . . . . . . . . . . . . . . . . . .
Accumulated other comprehensive loss . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Accumulated deficit
Total Amyris, Inc. stockholders’ deficit . . . . . . . . . . . . . . . . . .
Noncontrolling interest . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Total stockholders’ deficit . . . . . . . . . . . . . . . . . . . . . . . . . . .
Total liabilities, mezzanine equity and stockholders’ deficit

. . . . $

—
—
5
—
1,048,274
66,272
(42,156)
—
(1,206,767)
(83,653) k
(200,644)
(17,381)
937
—
(17,381)
(199,707)
151,483 $(10,687)

—
5
1,114,546
(42,156)
(1,290,420)
(218,025)
937
(217,088)
140,796

Restatement adjustments:

a. Reclassification of related party accounts receivable to a separate line on the balance sheet.

b. Write-off of unrecoverable receivable in connection with facilities subleased to a related party.

c. Correction of error in recording amounts payable under Ginkgo Partnership Agreement as

prepaid royalties instead of reduction in revenue.

d. Adjustment to uninvoiced receipts liability.

e. Adjustment to accrued liability.

f. Revision to accounting for equity received in satisfaction of a customer receivable.

g. Adjustment to issuance-date fair value of a debt instrument.

h. Make-whole derivative liabilities adjustment.

i. Accrual of the Ginkgo Partnership Payments obligation, net of reduction to deferred revenue

liability.

Correction to the accounting for a make-whole equity instrument in connection with May 2017
equity offering.

Sum of adjustments to net loss for the year ended December 31, 2017 as result of corrections.

Consolidated Statement of Operations

The following table presents the Company’s consolidated statements of operations for the year ended
December 31, 2017 as previously reported, restatement adjustments and as restated (in thousands, except
per share amounts):

Year Ended December 31, 2017

Three Months Ended
(In thousands, except shares and per share amounts)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $
Renewable products
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Licenses and royalties
Grants and collaborations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Total revenue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Cost and operating expenses

Cost of products sold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Research and development
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Sales, general and administrative . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Total cost and operating expenses . . . . . . . . . . . . . . . . . . . . . . . . . .
Loss from operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Other income (expense)

(Loss) gain on divestiture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Interest expense . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
(Loss) gain from change in fair value of derivative instruments . . . . . . . . .
Loss upon extinguishment of debt . . . . . . . . . . . . . . . . . . . . . . . . . . .
Other income (expense), net . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Total other expense, net . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Loss before income taxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Provision for income taxes
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . .
Net loss attributable to Amyris, Inc.
Less deemed dividend on capital distribution to related parties . . . . . . . . . . .
Less deemed dividend related to beneficial conversion feature on Series A

preferred stock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Less deemed dividend related to beneficial conversion feature on Series B

preferred stock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

As
Previously
Reported

45,781
57,703
39,960
143,444

62,713
57,027
63,219
182,959
(39,515)

5,732
(34,033)
(1,742)
(1,521)
(955)
(32,519)
(72,034)
(295)
(72,329)
(8,648)

(562)

(634)

Less deemed dividend related to beneficial conversion feature on Series D

preferred stock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

(5,757)

Less deemed dividend upon settlement of make-whole provision on Series A

preferred stock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Less deemed dividend upon settlement of make-whole provision on Series B

preferred stock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Less deemed dividend related to proceeds discount and issuance costs upon

conversion of Series A preferred stock . . . . . . . . . . . . . . . . . . . . . . . .

Less deemed dividend related to proceeds discount and issuance costs upon

conversion of Series B preferred stock . . . . . . . . . . . . . . . . . . . . . . . .
Less cumulative dividends on Series A and Series B preferred stock . . . . . . . .
Add: losses allocated to participating securities
. . . . . . . . . . . . . . . . . . . .
Net loss attributable to Amyris, Inc. common stockholders . . . . . . . . . . . . . $
Bassic and diluted loss per share attributable to common stockholders

—

—
(5,439)
—
(93,369)

Basic and diluted . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $

(2.89)

Weighted-average shares of common stock outstanding used in computing loss

per share of common stock:
Basic and diluted . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

32,253,570

Reclassifications(1) Corrections Ref As Restated
42,370
48,703
36,598
127,671

—
(15,774) ab
1
ac
(15,773)

$(3,411)
6,774
(3,363)
—

—
(72)
72
—
—

—
—
—
—
—
—
—
—
—
—

—

—
—
—
—

(406) ad
ae
607
562
af
763
(16,536)

—
(3,048) ah
(47,110) ai
(10,376) ak
(1)
(60,535)
(77,071)
(6,582) am
(83,653)
8,648

—

62,307
57,562
63,853
183,722
(56,051)

5,732
(37,081)
(48,852)
(11,897)
(956)
(93,054)
(149,105)
(6,877)
(155,982)
—

(562)

(634)

(5,757)

(10,505) ap

(10,505)

(22,632) aq

(22,632)

(21,578) ar

(21,578)

(24,366) as
5,439 aw
au

40,159
$(108,488)

(24,366)
—
40,159
$ (201,857)

(6.26)

32,253,570

(1) Reclassification of revenue and operating expense by type to conform to the Company’s current

presentation.

Restatement adjustments:

aa. Reclassification of revenue by type to conform to the Company’s current presentation.

ab. Ginkgo partnership obligation and promissory note issuance recorded as reduction to revenue and

correction of errors in recording revenue from non-cash consideration.

ac. Reclassification of revenue by type to conform to the Company’s current presentation.

ad. Correction in connection with a sales return, and adjustment to uninvoiced receipts liability.

ae. Write-off of unrecoverable receivable in connection with facilities subleased to a related party, and
reclassification of operating expense by classification to conform to the Company’s current
presentation.

af. Expense incurred in connection with May 2017 equity offering.

ah. Correction to amortization of debt discounts, and interest expense in connection with partnership

payments obligation.

ai. Correction to accounting for make-whole liability in connection with May 2017 Offering.

ak. Loss on extinguishment of related and unrelated party debt.

am. Tax provision to accrue liability for unrecognized tax benefit.

an. Loss on extinguishment of related and unrelated party debt.

ap. Correction to record deemed dividend in connection with discounts and freestanding instruments

related to preferred stock offerings.

aq. Correction to record deemed dividend in connection with discounts and freestanding instruments

related to preferred stock offerings.

ar. Correction to record deemed dividend in connection with discounts and freestanding instruments

related to preferred stock offerings.

as. Correction to record deemed dividend in connection with discounts and freestanding instruments

related to preferred stock offerings.

au. Correction in the computation of loss per share to reflect participating securities.

av. Correction to weighted-average shares outstanding.

aw. Correction in the computation of net loss per share related to make-whole deemed dividends.

Consolidated Statement of Cash Flows

The following table presents the Company’s consolidated statements of cash flows for the year ended
December 31, 2017 as previously reported, restatement adjustments and as restated (in thousands). In this
table, As Restated amounts reflect the impact of corrections to the consolidated balance sheet as of
December 31, 2017 and the statement of operations for the year ended December 31, 2017, as well as the
Company’s adoption of ASU 2016-18, which changes how restricted cash is reported in statements of cash
flows.

(In thousands)

Operating activities

Year Ended December 31, 2017

As
Previously
Reported

Corrections(1) As Restated

Net loss . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $ (72,329)

(83,653) $(155,982)

Adjustments to reconcile net loss to net cash used in operating activities:

Depreciation and amortization . . . . . . . . . . . . . . . . . . . . . . . . . . .

11,358

(Gain) loss on disposal of property, plant and equipment . . . . . . . . .

Stock-based compensation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Amortization of debt discount . . . . . . . . . . . . . . . . . . . . . . . . . . . .
(Gain) loss upon extinguishment of debt . . . . . . . . . . . . . . . . . . . . .
Receipt of equity in connection with collaboration arrangements

revenue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . .
(Gain) loss from change in fair value of derivative liabilities
(Gain) loss on foreign currency exchange rates . . . . . . . . . . . . . . . . .
Noncash revenue reduction related to issuance of debt obligations . . .
Non-cash gain on divestiture . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Receipt of noncash consideration in connection with license

142

6,265
12,490
1,521

(2,661)
1,742
(1,230)
—
(5,732)

—

—
2,749
10,376

2,661
47,110
—
13,413
—

11,358

142

6,265
15,239
11,897

—
48,852
(1,230)
13,413
(5,732)

revenue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

(8,046)

—

(8,046)

Changes in assets and liabilities:

Accounts receivable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Contract assets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Inventories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Prepaid expenses and other assets . . . . . . . . . . . . . . . . . . . . . . . .
Accounts payable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Accrued and other liabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Contract liabilities

(19,647)
(7,940)
(3,126)
(19,336)
5,858
7,295
(7,241)

—
—
—
606
(406)
6,582
—

(19,647)
(7,940)
(3,126)
(18,730)
5,452
13,877
(7,241)

Net cash used in operating activities

. . . . . . . . . . . . . . . . . . . .

(100,617)

(562)

(101,179)

Investing activities

Proceeds from divestiture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Change in short-term investments . . . . . . . . . . . . . . . . . . . . . . . . .
Change in restricted cash . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Purchases of property, plant and equipment . . . . . . . . . . . . . . . . . .

54,827
712
865
(4,412)

Net cash (used in) provided by investing activities . . . . . . . . . . . . .

51,992

—
581
(865)
—

(284)

54,827
1,293
—
(4,412)

51,708

Financing activities

Proceeds from issuance of convertible preferred stock . . . . . . . . . . .

101,124

(2,878)

98,246

Proceeds from exercises of common stock options . . . . . . . . . . . . . .

160

(160)

—

(In thousands)

Year Ended December 31, 2017

As
Previously
Reported

Corrections(1) As Restated

Payment of minimum employee taxes withheld upon net share

settlement of restricted stock units . . . . . . . . . . . . . . . . . . . . . . .

(385)

—

(385)

Proceeds from issuance of common stock in August 2017

offering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Issuance costs incurred . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Change in restricted cash related to contingently redeemable common
stock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Proceeds from issuance of debt, net of issuance costs . . . . . . . . . . . .

Principal payments on debt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

(37,500)

Payment of swap termination . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Payment on early redemption of debt . . . . . . . . . . . . . . . . . . . . . . .

(3,113)

(1,909)

—

5,759

(2,159)

5,759

(2,159)

1,046

18,925

(1,046)

—

18,925

(37,500)

(3,113)

(1,909)

Net cash provided by financing activities . . . . . . . . . . . . . . . . . . .

78,348

(484)

77,864

Effect of exchange rate changes on cash, cash equivalents and restricted
cash . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Net (decrease) increase in cash, cash equivalents and restricted cash . .
Cash, cash equivalents and restricted cash at beginning of year . . . . .

186

29,909
27,150

Cash, cash equivalents and restricted cash at end of year

. . . . . . . . . $ 57,059

—

(1,330)
5,283

3,953

186

28,579
32,433

61,012

Reconciliation of cash, cash equivalents and restricted cash to the

consolidated balance sheets
Cash and cash equivalents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Restricted cash, current . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Restricted cash, noncurrent . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Total cash, cash equivalents and restricted cash . . . . . . . . . . . . . . . .

Supplemental disclosures of cash flow information:
Cash paid for interest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $ 11,539

Supplemental disclosures of non-cash investing and financing activities:
Issuance of common stock upon conversion of debt

. . . . . . . . . . . . . . $ 28,702

Accrued interest added to debt principal

. . . . . . . . . . . . . . . . . . . . . . $

2,816

Issuance of common stock for settlement of debt principal and interest

payments

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $

3,436

Financing of insurance premium under note payable . . . . . . . . . . . . . . $

467

Issuance of convertible preferred stock upon conversion of debt . . . . . . $ 40,204

Settlement of debt principal by a related party . . . . . . . . . . . . . . . . . . $ 25,000

Issuance of note payable in exchange for debt extinguishment with third

party . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $ 16,954

Issuance of common stock for settlement of debt

. . . . . . . . . . . . . . . . $ 10,708

$ 57,059
2,994
959

$ 61,012

— $ 11,539

— $ 28,702

— $

2,816

— $

3,436

— $

467

— $ 40,204

— $ 25,000

— $ 16,954

— $ 10,708

Issuance of preferred stock attributed to derivative liabilities

. . . . . . . . $

— $ 72,725

$ 72,725

3. Balance Sheet Details

Allowance for Doubtful Accounts
Allowance for doubtful accounts activity and balances were as follows:

(In thousands)

Allowance for doubtful accounts:

Balance at

Beginning of Year Provisions

Recoveries
(Write-offs),
Net

Balance at
End of Year

Year Ended December 31, 2018 . . . . . . . . . . . . . . . . . . .

Year Ended December 31, 2017 (as restated, Note 2) . . . .

$642

$501

$ —

$141

$—

$642

Inventories

December 31,
(In thousands)

2018

2017

(As Restated,
Note 2)

Raw materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$3,901

$ 819

Work in process . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Finished goods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

539
5,253

364
4,225

Total inventories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$9,693

$5,408

Prepaid expenses and other current assets

December 31,
(In thousands)

2018

2017

Prepayments, advances and deposits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Recoverable taxes from Brazilian government entities . . . . . . . . . . . . . . . . . . . . .
Other . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$ 5,644
631
4,291

Total prepaid expenses and other current assets . . . . . . . . . . . . . . . . . . . . . . . .

$10,566

(As Restated,
Note 2)

$3,599
87
1,233

$4,919

Property, plant and equipment, net

December 31,
(In thousands)

2018

2017

(As Restated,
Note 2)

Machinery and equipment

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$ 43,713

$ 46,317

Leasehold improvements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Computers and software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Furniture and office equipment, vehicles and land . . . . . . . . . . . . . . . . . . . . . . .
Construction in progress . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Total property, plant and equipment, gross

. . . . . . . . . . . . . . . . . . . . . . . . . .

39,922
9,987
3,016
1,749

98,387

40,036
9,555
3,415
2,838

102,161

Less: accumulated depreciation and amortization . . . . . . . . . . . . . . . . . . . . . . . .

(78,631)

(88,269)

Total property, plant and equipment, net . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$ 19,756

$ 13,892

Property, plant and equipment, net includes $5.0 million and $4.2 million of machinery and equipment
under capital leases as of December 31, 2018 and 2017, respectively. Accumulated amortization of assets
under capital lease totaled $2.3 million and $1.6 million as of December 31, 2018 and 2017, respectively.

Depreciation and amortization expense, including amortization of assets under capital leases, was

$4.9 million and $11.4 million for the years ended December 31, 2018 and 2017, respectively.

Losses on disposal of property, plant and equipment were $0.9 million and $0.1 million for the years
ended December 31, 2018 and 2017, respectively. Such losses or gains were included in “Research and
development” expense in the consolidated statements of operations.

In December 2017, the Company’s sold its Brotas production plant in Brazil to a unit of DSM
Nutritional Products Ltd (together with its affiliates, DSM); see Note 13, “Divestiture” and Note 11,
“Related Party Transactions” for details.

Other assets

December 31,
(In thousands)

2018

2017

(As Restated,
Note 2)

Contingent consideration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$4,286

$ 8,150

Deposits

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Other

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

2,465

1,207

2,462

1,947

Total other assets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$7,958

$12,559

Accrued and other current liabilities

December 31,
(In thousands)

2018

2017

(As Restated,
Note 2)

Payroll and related expenses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Contract termination fees . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Accrued interest
Asset retirement obligation(1)
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Ginkgo partnership payments obligation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Tax-related liabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Professional services
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Other . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$ 9,220
4,092
3,853
3,063
2,155
2,139
1,173
3,284

$ 7,238
—
8,213
3,587
—
5,837
1,694
2,633

Total accrued and other current liabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$28,979

$29,202

(1) The asset retirement obligation represents liabilities incurred but not yet discharged in connection with

our 2013 abandonment of a partially constructed facility in Pradópolis, Brazil.

Other noncurrent liabilities

December 31,
(In thousands)

2018

2017

(As Restated,
Note 2)

Liability for unrecognized tax benefit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$ 6,582

Deferred rent, net of current portion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Ginkgo partnership payments obligation, net of current portion . . . . . . . . . . . . . .

Contract liabilities, net of current portion . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Contract termination fees, net of current portion(1) . . . . . . . . . . . . . . . . . . . . . . .
Capital leases, net of current portion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Other . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

6,440

6,185

1,587
1,530

195

673

7,818

6,444

383
—

217

2,214

Total other noncurrent liabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$23,192

$23,658

(1) Contract liabilities, net of current portion at December 31, 2018 and 2017 includes $1,204 and $383 in

connection with DSM, which is a related party.

In November 2017, the Company entered into a partnership agreement with one of its former
collaboration partners, Ginkgo Bioworks, Inc. and has an obligation to make quarterly payments of
$0.8 million from December 31, 2018 through September 2022. At December 31, 2018, total future
minimum payments under the agreement totaled $12.7 million. The Company recorded this liability at its
discounted present value of $6.1 million and is accreting the $6.6 million discount to interest expense over
the five-year repayment period. Also, in conjunction with the partnership agreement, the Company issued a
$12.0 million promissory note, which is included in long-term debt at a $8.0 million carrying value, net of
unamortized discount. See Note 10, “Revenue Recognition” for information regarding the Ginkgo
Partnership Agreement and the related accounting treatment for the partnership payments.

In September 2019, the Company was notified by DSM that certain contingent consideration payable
to the Company upon the realization of certain NOL tax benefits transferred to DSM with the sale of the
Brotas facility in December 2017 would not be realized due to changes in DSM’s Brazilian legal entity
structure. The Company considered this information in conjunction with the probability and timing of
DSM’s realization of the underlying NOL tax benefits and determined that $3.9 million of the contingent
consideration receivable was not recoverable as of December 31, 2018.

4. Fair Value Measurement

Assets and liabilities are measured and reported at fair value per related accounting standards that
define fair value as the price that would be received to sell an asset or paid to transfer a liability in an
orderly transaction between market participants at the measurement date. The fair value hierarchy
prioritizes the inputs to valuation techniques used to measure fair value. An asset’s or liability’s level is
based on the lowest level of input that is significant to the fair value measurement. Assets and liabilities
carried at fair value are valued and disclosed in one of the following three levels of the valuation hierarchy:

•

Level 1: Quoted market prices in active markets for identical assets or liabilities.

Level 2: Observable market-based inputs or unobservable inputs that are corroborated by market
data.

Level 3: Unobservable inputs that are not corroborated by market data.

Assets and Liabilities Measured and Recorded at Fair Value on a Recurring Basis

As of December 31, 2018 and 2017, the Company’s financial assets and financial liabilities measured at

fair value on a recurring basis were classified within the fair value hierarchy as follows:

December 31,
(In thousands)

Assets

2018

2017 (As Restated, Note 2)

Level 1 Level 2

Level 3

Total

Level 1

Level 2

Level 3

Total

Money market funds . . . . . . . . . .

$— — $

Certificates of deposit . . . . . . . . . — —

— $

—

— $53,199 $ — $

— $ 53,199

—

— 4,153

—

4,153

Total assets measured and

recorded at fair value . . . . . .

$— — $

— $

— $53,199 $4,153 $

— $ 57,352

Liabilities

6% Convertible Notes Due 2021 . .

$— — $ 57,918 $ 57,918 $ — $ — $

— $

—

Embedded derivatives in

connection with the issuance of
debt and equity instruments . . . — —

Freestanding derivative

instruments in connection with
the issuance of equity
instruments . . . . . . . . . . . . . . . — —

Total liabilities measured and

—

723

42,796

—

— 115,774

115,774

recorded at fair value . . . . . .

$— $— $100,714 $100,714 $ — $ — $116,497 $116,497

There were no transfers between the levels during 2018 or 2017.

The Company’s assessment of the significance of a particular input to the fair value measurement in its
entirety requires management to make judgements and consider factors specific to the asset or liability. The
fair values of money market funds and certificates of deposit are based on fair values of identical assets.
The method of determining the fair value of compound embedded derivative liabilities is described
subsequently in this note. Market risk associated with compound embedded derivative liabilities relates to
the potential reduction in fair value and negative impact to future earnings from a decrease in interest rates.

At December 31, 2018 and December 31, 2017, the carrying value of certain financial instruments,
such as cash equivalents, accounts receivable, prepaid expenses and other current assets, accounts payable
and other current accrued liabilities, approximate fair value due to their relatively short maturities and low
market interest rates, if applicable.

Changes in fair value of derivative liabilities are presented as gains or losses in the consolidated
statements of operations in the line captioned “Gain (loss) from change in fair value of derivative
instruments”.

Changes in the fair value of debt that is accounted for at fair value are presented as gains or losses in
the consolidated statements of operations in the line captioned “Gain (loss) from change in fair value of
debt”.

6% Convertible Notes Due 2021

the end of the calendar year. See Note 5, “Debt” and Part II, Item 8, “Subsequent Events” for further
information related to this debt instrument. For the year ended December 31, 2018, the Company recorded
a $2.1 million gain from change in fair value of debt in connection with the 6% Convertible Notes Due
2021, as follows:

In thousands

Fair value at issuance on December 10, 2018 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Change in fair value . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Fair value at December 31, 2018 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$60,000

(2,082)

$57,918

Derivative Instruments

Derivative instruments measured at fair value on a recurring basis as of December 31, 2018 and 2017

are as follows:

December 31,
(In thousands)

2018

2017

(As Restated,
Note 2)

Equity-related derivative liabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Debt-related derivative liabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$41,272
1,524

$108,887
7,610

Total derivative liabilities

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$42,796

$116,497

The following table provides a reconciliation of the beginning and ending liability balances associated
with derivative liabilities — either freestanding or compound embedded — measured at fair value using
significant unobservable inputs (Level 3):

(in thousands)

2018

2017

Balance at January 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Additions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . .
Loss from change in fair value of derivative liabilities
Derecognition to additional paid-in capital upon conversion or

$ 116,497
4,089
30,880

(As Restated,
Note 2)

$ 4,135
133,517
48,852

extinguishment

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

(108,670)

(70,007)

Balance at December 31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$ 42,796

$116,497

The liabilities associated with freestanding and compound embedded derivatives represent the fair
value of the equity conversion options, make-whole provisions, down round conversion price or conversion
rate adjustment provisions and antidilution provisions in some of the Company’s debt, preferred stock,
cash warrants and antidilution warrants; see Note 5, “Debt”, and Note 7, “Stockholders’ Deficit”. There is
no current observable market for these types of derivatives and, as such, the Company determined the fair
value of the freestanding or embedded derivatives using the Monte Carlo or binomial lattice models.

the Company valued the

convertible note excluding the embedded derivatives is defined as the “without”. This method estimates the
fair value of the embedded and freestanding derivatives by looking at the difference in the values between
each convertible note or share of convertible preferred stock with the embedded and freestanding
derivatives and the fair value of such convertible note or share of convertible preferred stock without the
embedded and freestanding derivatives. The lattice model uses the stock price, conversion price, maturity
date, risk-free interest rate, estimated stock volatility and estimated credit spread. The Company marks the
compound embedded derivatives to market due to the conversion price not being indexed to the Company’s
own stock.

The Company used a Monte Carlo simulation valuation model to determine the fair value of the
May 2017 and August 2017 Cash and Dilution Warrants. Monte Carlo simulation combines a random
number generator based on a probability distribution and additional inputs of volatility, time to expiration
to generate a stock price and other uncertainties. The generated stock price at the time of expiration is then
used to calculate the value of the option. The model then calculates results tens of thousands of times, each
time using a different set of random values from the probability functions. The resulting Monte Carlo
simulation valuation is based on the average of all the calculated results.

The market-based assumptions and estimates used in valuing the compound embedded and

freestanding derivative liabilities include amounts in the following ranges/amounts:

December 31,
Risk-free interest rate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Risk-adjusted discount yield . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Stock price volatility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . .
Probability of change in control
Stock price . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Credit spread . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Estimated conversion dates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

2018
2.5% – 3.0%

2017
1.7% – 2.4%

17.2% – 27.3% 18.4% – 28.5%
45.0% – 85.0% 45.0% – 80.0%

0.0%
$3.34

5.0%
$3.75

14.6% – 24.9% 16.6% – 26.7%

2019 – 2025

2018 – 2025

Changes in valuation assumptions can have a significant impact on the valuation of the embedded and
freestanding derivative liabilities and debt that the Company elects to account for at fair value. For example,
all other things being equal, a decrease/increase in the Company’s stock price, probability of change of
control, credit spread, term to maturity/conversion or stock price volatility decreases/increases the valuation
of the liabilities, whereas a decrease/increase in risk adjusted yields or risk-free interest rates increases/
decreases the valuation of the liabilities. Certain of the convertible notes, shares of convertible preferred
stock and warrants also include conversion or exercise price adjustment features and, for example, certain
issuances of common stock by the Company at prices lower than the current conversion or exercise price
result in a reduction of the conversion price of such notes or convertible preferred stock, or a reduction in
the exercise price of, or an increase in the number of shares subject to, such warrants, which increases the
value of the embedded and freestanding derivative liabilities and debt measured at fair value; see Note 5,
“Debt” for details.

The Series A Preferred Stock issued in May 2017 and Series B Preferred Stock issued in May 2017 (see
Note 7, “Stockholder’s Deficit”) included make-whole provisions, which are accounted for as embedded
derivatives through the July 2017 Shareholder Approval date at which time the make-whole provision
became settleable for a fixed number of common stock shares and ceased to be accounted for as a derivative
liability. Cash and antidilution warrants, classified as freestanding financial instruments, were also issued in
conjunction with the May 2017 Offering, August 2017 DSM Offering and August 2017 Vivo Offering and
are classified as derivative liabilities. The total derivative liability recorded for the securities issued in
connection with the May 2017 Offering, August 2017 DSM Offering and August 2017 Vivo Offering was
$113.1 million.

In June 2012, the Company entered into a cross-currency interest rate swap arrangement with Banco
Pine with respect to the repayment of R$22.0 million (approximately U.S. $6.6 million based on the
exchange rate as of December 31, 2017) of the Banco Pine Note. The swap arrangement exchanged the
principal and interest payments under the Banco Pine Note (see Note 4, “Debt”) for alternative principal
and interest payments that are subject to adjustment based on fluctuations in the foreign currency exchange
rate between the U.S. dollar and Brazilian real. The swap had a fixed interest rate of 3.94%. Changes in the
fair value of the swap were recognized in the consolidated statements of operations, in “Gain (loss) from

change in fair value of derivative instruments”. As of December 31, 2017, the balances of the loan and the
associated cross-currency interest rate swap were zero.

Assets and Liabilities Recorded at Carrying Value

Financial Assets and Liabilities

The carrying amounts of certain financial instruments, such as cash equivalents, accounts receivable,
accounts payable and accrued liabilities, approximate fair value due to their relatively short maturities and
low market interest rates, if applicable. Loans payable, credit facilities and convertible notes are recorded at
carrying value (except for the 6% Convertible Notes Due 2021, which are recorded at fair value), which is
representative of fair value at the date of acquisition. For loans payable and credit facilities recorded at
carrying value, the Company estimates fair value using observable market-based inputs (Level 2); for
convertible notes, the Company estimates fair value based on rates currently offered for instruments with
similar maturities and terms (Level 3). The carrying amount (the total amount of net debt presented on the
balance sheet) of the Company’s debt at December 31, 2018, excluding the 6% Convertible Notes that the
Company records at fair value, and at December 31, 2017, was $151.7 million and $165.4 million,
respectively. The fair value of such debt at December 31, 2018 and at December 31, 2017 was $149.3 million
and $156.9 million, respectively, and was determined by (i) discounting expected cash flows using current
market discount rates estimated for certain of the debt instruments and (ii) using third-party fair value
estimates for the remaining debt instruments.

Assets and Liabilities Measured and Recorded at Fair Value on a Non-Recurring Basis

On November 19, 2018, the Company amended its supply agreement with DSM, as discussed in
Note 10, “Revenue Recognition” to secure production capacity at the Brotas facility in exchange for future
cash payments totaling $22.7 million, the issuance of 1,643,991 million shares common stock valued at
$6.1 million on the date of issuance and a further cash payment for the difference between the fair value of
the common stock and $7.3 million on March 29, 2019. In addition, the Company modified certain
warrants held by DSM which resulted in the transfer of $2.9 million of value to DSM and paid $1.8 million
to settle certain obligations to DSM related to the 2017 sale of the Brotas facility. The Company also
entered into other transactions contemporaneously with the amended supply agreement as discussed in
Note 11, “Related Party Transactions” and Note 16, “Subsequent Events”. This series of transactions with
DSM in November 2018 was accounted for as a combined transaction in which the Company determined
and allocated the fair value of the consideration to each element. The fair value of the consideration
transferred to DSM under the combined arrangement totaled $33.3 million and was allocated as follows (in
thousands):

Element

Manufacturing capacity reservation fee . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Legal settlement and consent waiver
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Working capital adjustment

Fair Value
Allocation

$24,395
6,764
2,145

Total fair value of consideration transferred . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

$33,304

The fair value of these elements is based on Level 3 inputs, which considered the lowest level of input
that is significant to the fair value measurement of these elements. To determine the fair value of the
manufacturing capacity reservation fee, the Company used a discounted cash flow model under a cost
savings valuation approach based on a competing manufacturing quote for similar capacity, location and
timing. The Company used a discount rate of 22.5% and a tax rate of 0% to discount the gross cash flows.
The fair value of the legal settlement for failure to obtain consent from DSM prior to executing the
August 2018 Vivo Warrant transaction and was determined by calculating the difference between the fair
values of the warrants held by Vivo prior to and after the August 2018 Vivo Warrant transaction using a
combination of a Monte Carlo simulation and the Black-Scholes-Merton option pricing model. The fair
value of the working capital adjustment was determined to equal the difference between the preliminary
estimate for working capital upon closing the Brotas facility sale and the final working capital amounts
transferred.

5. Debt

December 31,
(In thousands)

2018

Unamortized
Debt
(Discount)
Premium

Change in
Fair Value

Principal

Net

Principal

2017

Unamortized
Debt
(Discount)
Premium

(As Restated,
Note 2)

Net

Convertible notes payable

6% convertible notes due 2021 . . . . . . . . . $ 60,000 $

— $(2,082) $ 57,918 $

— $

—

2015 Rule 144A convertible notes . . . . . . .

2014 Rule 144A convertible notes . . . . . . .

August 2013 financing convertible notes . .

December 2017 convertible notes . . . . . . .

37,887

24,004

4,415

—

(2,413)

(867)

(70)

—

35,474

23,137

4,345

—

37,887

24,004

4,009

5,000

(9,458)

(3,170)

(2,126)

(25)

28,429

20,834

1,883

4,975

126,306

(3,350)

(2,082)

120,874

70,900

(14,779)

56,121

Related party convertible notes payable

2014 Rule 144A convertible notes . . . . . . .
August 2013 financing convertible notes . .
R&D note . . . . . . . . . . . . . . . . . . . . . . .

Loans payable and credit facilities

GACP term loan facility . . . . . . . . . . . . .
Ginkgo note . . . . . . . . . . . . . . . . . . . . . .
Other loans payable . . . . . . . . . . . . . . . . .
Senior secured loan facility . . . . . . . . . . .
Other credit facilities . . . . . . . . . . . . . . . .

Related party loans payable

DSM note . . . . . . . . . . . . . . . . . . . . . . .
February 2016 private placement
. . . . . . .
Other DSM loan . . . . . . . . . . . . . . . . . . .

24,705
—
—

24,705

36,000
12,000
4,910
—
—

52,910

25,000
—
—

25,000

(1,038)
—
—

(1,038)

(1,349)
(4,047)
(1,047)
—
—

(6,443)

(6,311)
—
—

(6,311)

—
—
—

—

—
—
—
—
—

—

—
—
—

—

23,667

24,705
— 21,711
3,700
—

23,667

50,116

34,651
7,953
3,863

—
12,000
6,463
— 28,566
381
—

46,467

47,410

18,689
—
—

18,689

25,000
2,000
393

27,393

(3,784)
897
(18)

(2,905)

—
(4,862)
(1,277)
(253)
—

(6,392)

(8,039)
—
—

(8,039)

20,921
22,608
3,682

47,211

—
7,138
5,186
28,313
381

41,018

16,961
2,000
393

19,354

Total debt

. . . . . . . . . . . . . . . . . . . . . . . $228,921 $(17,142) $(2,082)

209,697 $195,819

$(32,115)

163,704

Less: current portion . . . . . . . . . . . . . . . .

Long-term debt, net of current portion . . .

(147,677)

$ 62,020

(56,943)

$106,761

Future minimum payments under the debt agreements as of December 31, 2018 are as follows:

Years ending December 31
(In thousands)

Loans
Payable and
Credit
Facilities

Related
Party
Convertible
Notes

Related
Party Loans
Payable and
Credit Facilities

Convertible
Notes

Total

2019 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . $ 134,368

$ 10,219

$ 25,508

$ 2,500

$ 172,595

2020 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

2021 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

2022 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

2023 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Thereafter . . . . . . . . . . . . . . . . . . . . . . . . . .

Total future minimum payments . . . . . . . . . . .
Less: amount representing interest(1) . . . . . . . .
Less: future conversion of accrued interest to

—

9,981

— 34,740

— 13,417

—

367

2,200

—

2,500

27,521

—

12,481

62,261

13,417

367

2,200

134,368
(7,368)

70,924
(18,014)

25,508
(803)

32,521
(7,521)

263,321
(33,706)

principal . . . . . . . . . . . . . . . . . . . . . . . . . .

(694)

—

(694)

Present value of minimum debt payments . . . .

126,306

52,910

24,705

25,000

228,921

Less: current portion of debt principal

. . . . . .

(126,306)

(3,829)

(24,705)

—

(154,840)

Noncurrent portion of debt principal

. . . . . . . $

— $ 49,081

— $25,000

$ 74,081

(1) Excluding net debt discount of $17.1 million that will be amortized to interest expense over the term of

the debt.

Convertible Notes Payable

6% Convertible Notes Due 2021

On December 6, 2018, the Company entered into a securities purchase agreement to issue and sell
$60.0 million in aggregate principal amount of senior convertible notes (the 6% Convertible Notes Due
2021) that are convertible into shares of the Company’s common stock. The securities purchase agreement
prohibits the Company, subject to certain exceptions, from (i) disposing of any common stock or securities
convertible into or exchangeable for shares of common stock during the period commencing on
December 6, 2018 and continuing through the later of (A) the date 90 days after December 10, 2018 and
(B) the date 30 days after the Registration Statement (as defined below) is declared effective and
(ii) effecting or entering into an agreement to effect any issuance involving a variable rate transaction for so
long as the 6% Convertible Notes Due 2021 remain outstanding.

The closing of the issuance and sale of the 6% Convertible Notes Due 2021 occurred on December 10,
2018, for net proceeds, after deducting offering expenses payable by the Company and placement agent and
advisory fees, of $56.2 million.

The 6% Convertible Notes Due 2021 are general unsecured obligations of the Company. Unless earlier
converted or redeemed, the 6% Convertible Notes Due 2021 will mature on the third anniversary of
issuance, subject to the rights of the holders to extend the maturity date in certain circumstances. The 6%
Convertible Notes Due 2021 are convertible from time to time, at the election of the holders, into shares of
common stock at an initial conversion price of $6.32 per share. The conversion price is subject to
adjustment in the event of any stock split, reverse stock split, recapitalization, reorganization or similar
transaction. The Company has the option, upon prior notice to the holders, to settle any conversion of the
6% Convertible Notes Due 2021 in cash.

The 6% Convertible Notes Due 2021 are payable in equal monthly installments beginning April 1, 2019
(each, an Installment Date), in either cash at 108% of such installment amount or, at the Company’s option,
subject to the satisfaction of certain equity conditions (the Equity Conditions), in shares of common stock
at a discount to the then-current market price, subject to a price floor (the Installment Conversion Price).
The holders have the right, upon notice to the Company, to defer all or any portion of any installment

amount to a future Installment Date. In addition, if the Company elects to pay any installments in shares of
common stock, the holders of the 6% Convertible Notes Due 2021 have the right to accelerate amounts
outstanding under their 6% Convertible Notes Due 2021 during such month up to an aggregate of three
times the relevant installment amount.

The 6% Convertible Notes Due 2021 bear interest at a rate of 6% per annum, payable quarterly until
the first Installment Date, and then at each Installment Date thereafter. Interest on the 6% Convertible
Notes Due 2021 may be paid in either cash or, at the Company’s option, subject to the satisfaction of the
Equity Conditions, shares of common stock at the Installment Conversion Price. The Company elected to
make the interest payment due January 1, 2019 in cash.

The 6% Convertible Notes Due 2021 contain customary terms and covenants, including (i) a restriction
on the Company’s ability to incur additional indebtedness, (ii) certain events of default, after which the
holders may require the Company to redeem all or any portion of their 6% Convertible Notes Due 2021 in
cash at a price equal to the greater of (A) 125% of the amount being redeemed and (B) the intrinsic value of
the shares of common stock underlying the amount being redeemed, and (iii) certain other events, after
which the holders may convert all or any portion of the 6% Convertible Notes Due 2021 at a discount to the
Installment Conversion Price.

In the event of a Fundamental Transaction (as defined in the 6% Convertible Notes Due 2021), holders
of the 6% Convertible Notes Due 2021 may require the Company to redeem all or any portion of their 6%
Convertible Notes Due 2021 at a price equal to the greater of (i) 125% of the amount being redeemed and
(ii) a premium to the intrinsic value of the shares of Common Stock underlying the amount being
redeemed.

Notwithstanding the foregoing, the holders will not have the right to convert any portion of a 6%
Convertible Note Due 2021, and the Company will not have the option to pay any amount in shares of
common stock, if (a) the holder, together with its affiliates, would beneficially own in excess of 4.99% (or
such other percentage as determined by the holder and notified to the Company in writing, not to exceed
9.99%, provided that any increase of such percentage will not be effective until 61 days after notice thereof)
of the number of shares of common stock outstanding immediately after giving effect to such conversion or
payment, as applicable (the Ownership Limitation), or (b) the aggregate number of shares issued with
respect to the 6% Convertible Notes Due 2021 (and any other transaction aggregated for such purpose)
after giving effect to such conversion or payment, as applicable, would exceed 15,271,047 shares of common
stock (the Exchange Cap), unless the Company has obtained prior stockholder approval to issue shares in
excess of the Exchange Cap. In the event that (i) the Company is prohibited from issuing any shares of
common stock under the 6% Convertible Notes Due 2021 as a result of the Ownership Limitation (other
than in connection with a conversion of 6% Convertible Notes Due 2021), such shares shall be held in
abeyance (and the related principal amount of the 6% Convertible Notes Due 2021 reinstated) until the
holder shall notify the Company and elect to receive such shares without exceeding the Ownership
Limitation, and (ii) the Company is prohibited from issuing any shares of common stock under the 6%
Convertible Notes Due 2021 as a result of the Exchange Cap, the Company will pay cash in lieu of any
shares that would otherwise be deliverable in excess of the Exchange Cap.

In connection with the offering of the 6% Convertible Notes Due 2021, the Company entered into a
registration rights agreement, dated December 10, 2018, with the purchasers of the 6% Convertible Notes
Due 2021, pursuant to which the Company agreed to file a registration statement (the Registration
Statement) with the Securities and Exchange Commission (the SEC) registering the resale of all of the
shares of common stock issuable pursuant to the terms of the 6% Convertible Notes Due 2021 (the
Registrable Securities) under the Securities Act of 1933, as amended (the Securities Act), within 30 days
following December 10, 2018, and to have the Registration Statement declared effective by the SEC by the
date that is 60 days after December 10, 2018. In the event that the Registration Statement is not filed or
declared effective within the foregoing time frames, or if thereafter, subject to certain exceptions, the
Registration Statement is not effective for any reason or the prospectus contained therein is not available for
use by the holders, Company shall pay to each holder an amount in cash equal to 2% of such holder’s
original principal amount of Notes on the date of such failure and thereafter on every 30 day anniversary
thereof until such failure is cured or no longer prevents the holders from freely disposing of their
Registrable Securities. The Company filed the Registration Statement on January 8, 2019, and it went
effective on February 7, 2019.

The Company has elected to account for the 6% Convertible Notes Due 2021 at fair value pursuant to
U.S. GAAP, as of the issuance date. Management believes that the fair value option better reflects the
underlying economics of
the 6% Convertible Notes Due 2021, which contain multiple embedded
derivatives. Under the fair value election, changes in fair value will be reported in the consolidated
statements of operations as “Gain (loss) from change in fair value of debt” in each reporting period
subsequent to the issuance of the 6% Convertible Notes Due 2021. For the year ended December 31, 2018,
the Company recorded a gain of $2.1 million, which is shown as Change in Fair Value in the table at the
beginning of this Note 4. See Note 4, “Fair Value Measurement” for information about the assumptions
that the Company used to measure the fair value of the 6% Convertible Notes Due 2021.

In May, June and July 2019, the Company exchanged the 6% Convertible Notes Due 2021 for new
senior convertible notes and warrants to purchase common stock. See Note 16, “Subsequent Events” for
additional information.

2015 Rule 144A Convertible Notes

In October 2015, the Company sold $57.6 million aggregate principal amount of 9.50% convertible
senior notes due 2019 (the 2015 Rule 144A Convertible Notes) to certain qualified institutional buyers in a
private placement. Net proceeds from the offering were $54.4 million after payment of offering expenses
and placement agent fees, which together are treated as a debt discount and are being amortized over the
remaining loan term using the effective interest method. The Company used $18.3 million of the net
proceeds to repurchase $22.9 million aggregate principal amount of outstanding 2014 Rule 144A
Convertible Notes as discussed below. The 2015 Rule 144A Convertible Notes bear interest at a rate of
9.50% per year, payable semiannually in arrears on April 15 and October 15 of each year. Interest on the
2015 Rule 144A Convertible Notes is payable, at the Company’s option, entirely in cash or entirely in
common stock valued at 92.5% of a market-based price. The Company elected to make the April 15, 2016
and 2017 and October 15, 2018 interest payments in shares of common stock and the October 15, 2016 and
2017 and April 15, 2018 interest payments in cash. The 2015 Rule 144A Convertible Notes matured on
April 15, 2019. See Note 16, “Subsequent Events”.

The 2015 Rule 144A Convertible Notes are convertible into shares of the Company’s common stock at
a conversion rate of 61.7246 shares per $1,000 principal amount of 2015 Rule 144A Convertible Notes
(which conversion rate is subject to adjustment in certain circumstances), representing an effective
conversion price of approximately $16.20 per share as of December 31, 2018. If converted prior to
maturity, noteholders are entitled to receive a payment (the Early Conversion Payment) equal to the present
value of the remaining scheduled payments of interest on the 2015 Rule 144A Convertible Notes being
converted through April 15, 2019, computed using a discount rate of 0.75%. The Company may make the
Early Conversion Payment, at its election, either in cash or, subject to certain conditions, in common stock
valued at 92.5% of a market-based price. Through December 31, 2018, the Company has elected to make
each Early Conversion Payment in shares of common stock.

In January 2017, the Company issued an additional $19.1 million in aggregate principal amount of
2015 Rule 144A Convertible Notes (the Additional 2015 Rule 144A Convertible Notes) in exchange for the
cancellation of $15.3 million in aggregate principal amount of other outstanding convertible promissory
notes of the Company, with the same terms as the 2015 Rule 144A Convertible Notes; provided, that the
aggregate number of shares issued with respect to the Additional 2015 Rule 144A Convertible Notes (and
any other transaction aggregated for such purpose) cannot exceed 3,652,935 shares of common stock
without prior stockholder approval. The exchange was accounted for as an extinguishment of debt,
resulting in a $0.1 million gain in the year ended December 31, 2017.

In May 2017, the Company exchanged $3.7 million in aggregate principal amount of 2015 Rule 144A
Convertible Notes for shares of its Series B 17.38% Convertible Preferred Stock and warrants to purchase
common stock, as described in more detail in Note 7, “Stockholders’ Deficit”. The exchange was accounted
for as an extinguishment of debt, resulting in a $2.0 million loss in the year ended December 31, 2017.

On April 16, 2019, the Company repaid the 2015 Rule 144A Convertible Notes in full in cash. See

Note 16, “Subsequent Events”.

2014 Rule 144A Convertible Notes

In May 2014, the Company sold $75.0 million in aggregate principal amount of 6.50% Convertible
Senior Notes due 2019 (the 2014 Rule 144A Convertible Notes) to qualified institutional buyers in a private
placement. The net proceeds from the offering were $72.0 million after payment of initial purchaser
discounts and offering expenses, which together are treated as a debt discount and are being amortized over
the remaining loan term. The Company used $9.7 million of the net proceeds to repay convertible notes
previously issued to an affiliate of Total S.A. (together with its affiliates, Total), representing the amount of
2014 Rule 144A Convertible Notes purchased by Total. Certain of the Company’s affiliated entities
(including Total) purchased $24.7 million in aggregate principal amount of 2014 Rule 144A Convertible
Notes. The 2014 Rule 144A Convertible Notes bear interest at an annual rate of 6.5%, payable semiannually
in arrears on May 15 and November 15 of each year in cash. The 2014 Rule 144A Convertible Notes
mature on May 15, 2019, unless earlier converted or repurchased.

The 2014 Rule 144A Convertible Notes are convertible into shares of the Company’s common stock at
a conversion rate of 17.8073 shares per $1,000 principal amount of 2014 Rule 144A Convertible Notes
(which conversion rate is subject to adjustment in certain circumstances), representing an effective
conversion price of approximately $56.16 per share as of December 31, 2018.

In May 2017, the Company exchanged $3.4 million in aggregate principal amount of 2014 Rule 144A
Convertible Notes for shares of its Series B 17.38% Convertible Preferred Stock and warrants to purchase
common stock, as described in more detail in Note 7, “Stockholders’ Deficit”. The exchange was accounted
for as an extinguishment, resulting in a $1.8 million loss for the year ended December 31, 2017.

In May 2019, the Company exchanged a portion of

the 2014 Rule 144A Convertible Notes,
representing $38.2 million aggregate principal amount of 2014 Rule 144A Convertible Notes, for shares of
common stock, warrants to purchase common stock and a new senior convertible note (see Note 16,
“Subsequent Events” for additional information) and repaid the remaining portion of the 2014 Rule 144A
Convertible Notes in cash at maturity.

August 2013 Financing Convertible Notes

In August 2013, the Company entered into a Securities Purchase Agreement (the August 2013 SPA)
with Total and Temasek to sell up to $73.0 million in convertible notes in private placements (the
August 2013 Financing or the Tranche Notes). The August 2013 SPA provided for the August 2013
Financing to be divided into two tranches, each with differing closing conditions. The Tranche I Notes were
due sixty months from the date of issuance (October 16, 2018). Interest accrued on the Tranche I Notes at
5% per six months, compounded semiannually, and was payable in kind by adding to the principal or in
cash. Through maturity, the Company elected to pay interest on the Tranche I Notes in kind. The Tranche I
Notes totaling $15.2 million of principal and accrued interest matured and were repaid in full by conversion
into shares of common stock on October 16, 2018 pursuant to the Maturity Treatment Agreement terms
(see “Related Party Convertible Notes Payable — August 2013 Financing Convertible Notes” below). Upon
conversion of the Tranche I Notes, the Company recognized a $10.9 million loss upon extinguishment of
debt in 2018. See the “Maturity Treatment Agreement” section below for details of the impact of that
agreement on the Tranche Notes.

The Tranche II Notes are due sixty months from the date of issuance (January 15, 2019). Interest
accrues on the Tranche II Notes at 10% per annum, compounded annually, and is payable in kind by adding
to the principal or in cash. Through December 31, 2018, the Company has elected to repay interest on the
Tranche II Notes in kind. On November 8, 2018, the Company repaid in full the Tranche II Notes held by
Total totaling $9.8 million of principal and accrued interest by conversion into shares of common stock
pursuant to the Maturity Treatment Agreement terms (see “Related Party Convertible Notes Payable —
August 2013 Financing Convertible Notes” below). Upon conversion of the Tranche II Notes held by Total,
the Company recognized a $6.5 million loss upon extinguishment of debt.

100

to adjustment

in certain circumstances,

conversion price is subject
including certain price-based
anti-dilution adjustments). The August 2013 SPA and the Tranche Notes contain customary terms,
covenants and restrictions, including a limit on the Company’s debt, subject to certain exceptions and
waivers, of the greater of $200 million or 50% of its consolidated total assets and the Company’s secured
debt of the greater of $125 million or 30% of its consolidated total assets. The August 2013 SPA also
requires the Company to obtain the consent of the holders of a majority of these notes before completing
any change of control transaction or purchasing assets in one transaction or in a series of related
transactions in an amount greater than $20.0 million,
in each case while any Tranche Notes are
outstanding. In addition, the Tranche Notes contain certain events of default after which the Tranche
Notes may become due and payable immediately.

On January 14, 2019, Wolverine agreed to waive payment of the Tranche II Note held by Wolverine at
maturity until July 15, 2019 in exchange for a cash waiver fee, payable on or prior to July 15, 2019, of
$0.6 million. On July 2, 2019, the Company and Wolverine entered into an exchange agreement whereby the
parties agreed to extinguish the Tranche II Note held by Wolverine in exchange for 1,767,632 shares of
common stock and a warrant to purchase 1,080,000 shares of common stock. See Note 16, “Subsequent
Events” for additional information.

Maturity Treatment Agreement
In July 2015, the Company entered into an Exchange Agreement (the 2015 Exchange Agreement) with
Total and Temasek pursuant to which Temasek exchanged $71.0 million in principal amount of outstanding
Tranche Notes and Total exchanged $70.0 million in principal amount of outstanding convertible notes for
shares of the Company’s common stock at a price of $34.50 per share (2015 Exchange). At the closing of
the 2015 Exchange, the Company, Total and Temasek also entered into a Maturity Treatment Agreement
dated July 29, 2015, pursuant to which Total and Temasek agreed to convert any Tranche Notes or 2014
144A Notes held by them that were not canceled in the 2015 Exchange (Remaining Notes) into shares of
the Company’s common stock in accordance with the terms of such Remaining Notes at or prior to
maturity, provided that certain events of default had not occurred with respect to the applicable Remaining
Notes. In May 2017, the Company entered into separate letter agreements with each of Total and Temasek,
pursuant to which the Company agreed that the Remaining Notes consisting of 2014 144A Notes held by
Total ($9.7 million in principal amount as of December 31, 2017) and Temasek ($10.0 million in principal
amount as of December 31, 2017) would no longer be subject to mandatory conversion at or prior to the
maturity of such Remaining Notes. Accordingly, the Company will be required to pay any portion of such
Remaining Notes that remain outstanding at maturity in cash in accordance with the terms of such
Remaining Notes. As of December 31, 2017, after giving effect to such letter agreements, Temasek did not
hold any Remaining Notes and Total held $21.8 million in principal amount of Remaining Notes
(consisting of Tranche Notes), which Remaining Notes were converted to common stock in October and
November 2018 pursuant to the terms of the Maturity Treatment Agreement (see below under “Related
Party Convertible Notes Payable — August 2013 Financing Convertible Notes” for more information). The
2015 Exchange Agreement contains customary terms, covenants and restrictions, including a limit on the
Company’s debt of the greater of $200 million or 50% of its consolidated total assets and the Company’s
secured debt of the greater of $125 million or 30% of its consolidated total assets, subject to certain
exceptions.

December 2017 Convertible Note
In December 2017, the Company issued and sold a convertible note under an April 2017 securities
purchase agreement in the principal amount of $5.0 million with a maturity date of June 1, 2018, for
proceeds to the Company of $5.0 million. The Company identified certain embedded feature that required
bifurcation, but the fair value of these derivative features was $0, due primarily to the short-term maturity
of the note and a significant out of the money conversion price at issuance and through the maturity date.
The Company elected to pay each installment in cash, and the note was repaid in full in May 2018.

Related Party Convertible Notes Payable

August 2013 Financing Convertible Notes
Certain of the August 2013 Financing Convertible Notes were held by related parties; see Note 11,

“Related Party Transactions” for details.

101

On October 16, 2018, the Tranche I Notes held by Total totaling $15.2 million of principal and accrued
interest reached maturity and were converted into 3,448,821 shares of common stock. Upon conversion of
the Tranche I Notes, the Company recognized a $10.9 million loss upon extinguishment of debt.

On November 8, 2018, Total converted its Tranche II Notes totaling $9.8 million of principal and
accrued interest, which were scheduled to mature on January 15, 2019, into shares of common stock. In
connection with such conversion, the Company agreed to pay Total future interest on the Tranche II Notes
being converted up to, but excluding, the maturity date for such notes, which interest was converted by
Total into common stock at the conversion price for the Tranche II Notes. As a result of such conversion,
the Tranche II Notes held by Total converted into 2,226,105 shares of common stock. Upon conversion of
the Tranche II Notes held by Total, the Company recognized a $6.5 million loss upon extinguishment of
debt.

2014 Rule 144A Convertible Notes

Certain of the 2014 Rule 144A Convertible Notes are held by related parties. See Note 11, “Related

Party Transactions” for details.

R&D Note

In March 2016, as a result of the restructuring of the Company’s fuels joint venture with Total, Total
Amyris BioSolutions B.V., the Company issued to Total an unsecured convertible note (the R&D Note) in
the principal amount of $3.7 million, representing the remaining portion of the $105.0 million convertible
note facility between the Company and Total initially established in 2012. In March and May 2018, the
Company and Total amended the R&D Note to extend the maturity to May 31, 2018 and July 2, 2018,
respectively, with accrued and unpaid interest payable on March 31, 2018, May 31, 2018 and July 2, 2018.
On July 2, 2018, the Company repaid the R&D Note in full.

Loans Payable and Credit Facilities

GACP Term Loan Facility

On June 29, 2018, the Company, certain of the Company’s subsidiaries and GACP Finance Co., LLC
(GACP) entered into a Loan and Security Agreement (the LSA) to borrow a $36.0 million secured term
loan (the GACP Term Loan Facility). The LSA also provides for an incremental secured term loan facility
in an aggregate principal amount of up to $35.0 million (the Incremental GACP Term Loan Facility and,
together with the GACP Term Loan Facility, the GACP Term Loan Facilities), subject to certain conditions
and approvals, to fund the construction of a custom-built manufacturing facility in Brazil. The majority of
the net proceeds from the GACP Term Loan Facility were used to repay all amounts outstanding under the
Senior Secured Loan Facility between the Company and Stegodon described below. The remaining net
proceeds were used on July 2, 2018 to repay amounts outstanding under the R&D Note at maturity, as
described above.

Loans under the GACP Term Loan Facilities have a maturity date of July 1, 2021; provided, that if the
Company has not (i) met certain financial conditions on or prior to January 7, 2019 or (ii) refinanced the
2015 Rule 144A Convertible Notes and 2014 Rule 144A Convertible Notes with indebtedness that has a
maturity date which is later than July 1, 2021 or converted such notes into equity prior to January 12, 2019,
then the maturity date will be January 12, 2019. See Note 16, “Subsequent Events” for additional
information about the waiver of this provision. The GACP Term Loan Facilities will amortize beginning on
July 1, 2019 in quarterly installments equal to 2.5% of the original loan amounts, with the remaining
principal balance payable on the maturity date. Loans under the GACP Term Loan Facilities initially
accrued interest at a rate per annum equal to the sum of (i) the greater of (A) the U.S. prime rate as
reported in the Wall Street Journal and (B) 4.0%, plus (ii) 6.25%, payable monthly. The GACP Term Loan
Facilities are guaranteed by the subsidiaries of the Company party to the LSA and collateralized by
first-priority liens on substantially all the Company’s and such subsidiaries’ assets, including intellectual
property, subject to certain exceptions. The LSA includes customary terms, covenants and restrictions,
including mandatory prepayments upon the occurrence of certain events, including asset sales, casualty

102

events, incurrence of additional indebtedness and borrowing base deficiencies, subject to certain exceptions
and reinvestment rights. The LSA contains certain financial covenants that include quarterly minimum
revenues, minimum liquidity amounts and a minimum asset coverage ratio.

The Company paid origination fees at closing equal to 4%, or $1.4 million, of the funded amount of
the GACP Term Loan Facility and other closing costs totaling $0.2 million, plus an agency fee of $25,000
per quarter during the term of the GACP Term Loan Facilities. The $1.6 million of issuance costs will be
amortized using the effective interest method over the expected 3-year loan term.

In November 2018, the Company and GACP amended the LSA to reduce the minimum revenue
requirement for the two fiscal quarters ending December 31, 2018 in exchange for an increase in optional
prepayment fees, an increase in the minimum liquidity amount and an increase in the base interest rate per
annum, from the sum of (i) the greater of (A) the prime rate as reported in the Wall Street Journal or
(B) 4.0% plus (ii) 6.25% to the sum of (i) the greater of (A) the prime rate as reported in the Wall Street
Journal or (B) 4.0% plus (ii) 8.25%. In December 2018, the Company and GACP further amended the LSA
to exclude certain intellectual property licensed to DSM from the loan collateral (see Note 10, “Revenue
Recognition” for more information) in exchange for a further increase in the base interest rate per annum,
from the sum of (i) the greater of (A) the prime rate as reported in the Wall Street Journal or (B) 4.0% plus
(ii) 8.25% to the sum of (i) the greater of (A) the prime rate as reported in the Wall Street Journal or
(B) 4.75% plus (ii) 9.00%.

In April 2019, (i) GACP provided a waiver to the Company for breaches of all covenant violations
under the GACP loan and security agreement (LSA) occurring prior to, as of and after December 31, 2018
through April 8, 2019, and (ii) GACP sold and assigned the loans under the LSA and all documents and
assets related thereto to Foris Ventures, LLC (Foris). Subsequently, Foris provided a waiver to the Company
for breaches of certain covenants under the LSA through June 30, 2020 and amended the financial
covenants under the LSA to provide more favorable compliance terms and conditions. See Note 16,
“Subsequent Events” for additional information.

Senior Secured Loan Facility

In March 2014, the Company entered into a Loan and Security Agreement (the LSA) with Hercules
Technology Growth Capital, Inc. to make available to the Company a secured loan facility (the Senior
Secured Loan Facility) in an initial aggregate principal amount of up to $25.0 million. The LSA was
subsequently amended in June 2014, March 2015 and November 2015 to (i) extend additional credit
facilities to the Company in an aggregate amount of up to $31.0 million, of which $16.0 million was drawn
by the Company, (ii) extend the maturity date of the loans, and (iii) remove, add and/or modify certain
covenants and agreements under the LSA.

In June 2016, Hercules transferred and assigned its rights and obligations under the Senior Secured

Loan Facility to Stegodon Corporation (Stegodon), an affiliate of Ginkgo Bioworks, Inc. (Ginkgo).

In March and May 2018, the Company and Stegodon amended the LSA to extend the date for a
$5.5 million principal payment to May 31, 2018 and July 2, 2018, respectively. Under the amendments, the
interest rate from April 1, 2018 through the date of such $5.5 million principal payment would be the
previously agreed interest rate plus 5.0%.

On June 29, 2018, the Company repaid the Senior Secured Loan Facility in full.

Ginkgo Note

In November 2017, the Company issued an unsecured promissory note in the principal amount of
$12.0 million to Ginkgo (the November 2017 Ginkgo Note) in connection with the termination of the
Ginkgo Collaboration Agreement and the execution of a new partnership agreement (the Ginkgo
Partnership Agreement), which is described in Note 10, “Revenue Recognition”. The November 2017
Ginkgo Note bears interest at 10.5% per annum, payable monthly, and has a maturity date of October 19,
2022. The November 2017 Ginkgo Note may be prepaid in full without penalty or premium at any time,
provided that certain payments have been made under the Company’s partnership agreement with Ginkgo.
The November 2017 Ginkgo Note also contains customary terms, covenants and restrictions, including

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certain events of default after which the note may become due and payable immediately. The Company
recorded the $7.0 million present value of the November 2017 Ginkgo Note as a note payable liability, and
the remaining $5.0 million was recorded as a debt discount which is being accreted to interest expense over
the loan term using the effective interest method. Also, the Company concluded that while no cash was
received from Ginkgo under the November 2017 Ginkgo Note, the transaction represents consideration
payable to a former customer and the present value of the note payable obligation should be recorded as a
reduction of cumulative revenue recognized to date from Ginkgo in the period the November 2017 Ginkgo
Note was executed. As a result, the Company recorded a $7.0 million reduction of license revenues as of
December 31, 2017. See Note 10, “Revenue Recognition” for additional information.

Other Loans Payable

Nikko Note: In December 2016, in connection with the Company’s formation of its cosmetics joint
venture (the Aprinnova JV) with Nikko Chemicals Co., Ltd. (Nikko) made a loan to the Company in the
principal amount of $3.9 million and the Company issued a promissory note (the Nikko Note) to Nikko in
an equal principal amount. The proceeds of the Nikko Note were used to satisfy the Company’s remaining
liabilities related to the Company’s purchase of a manufacturing facility in Leland, North Carolina and
related assets in December 2016, including liabilities under a promissory note in the principal amount of
$3.5 million issued in connection therewith. The Nikko Note (i) bears interest at 5% per year, (ii) has a term
of 13 years, (iii) is payable in equal monthly installments of principal and interest beginning on January 1,
2017 and (iv) is secured by a first-priority lien on 10% of the Aprinnova JV interests owned by the
Company. In addition, (i) the Company repaid $400,000 of the Nikko Note in equal monthly installments
of $100,000 as required on January 1, 2017, February 1, 2017, March 1, 2017 and April 1, 2017 and (ii) the
Company is required to repay the Nikko Note with any profits distributed to the Company by the
Aprinnova JV, beginning with the distributions for the fourth fiscal year of the Aprinnova JV, until the
Nikko Note is fully repaid. The Nikko Note may be prepaid in full or in part at any time without penalty or
premium. The Nikko Note contains customary terms and provisions, including certain events of default
after which the Nikko Note may become due and payable immediately.

Aprinnova Working Capital Loans: In February 2017,

in connection with the formation of the
Aprinnova JV in December 2016, Nikko made a working capital loan to the Aprinnova JV in the principal
amount of $1.5 million and received a promissory note from the Aprinnova JV in an equal amount (the
First Aprinnova Note). The First Aprinnova Note was repayable in $375,000 installments plus accrued
interest on May 1, 2017, August 1, 2017, November 1, 2017 and February 1, 2018. The First Aprinnova
Note was fully repaid in January 2018. In August 2017, Nikko made a second working capital loan to the
Aprinnova JV in the principal amount of $1.5 million and received a promissory note from the Aprinnova
JV in an equal amount (the Second Aprinnova Note). The Second Aprinnova Note is payable in full on
August 1, 2019, with interest payable quarterly. Both notes bear interest at 2.75% per annum. Effective
July 31, 2019, the Company and Nikko agreed to extend the term of the Second Aprinnova Note to
August 1, 2020. See Note 16, “Subsequent Events”.

Related Party Loans Payable

DSM Note

In December 2017, the Company and DSM entered into a credit agreement (the DSM Credit
Agreement) to make available to the Company an unsecured credit facility of $25.0 million. On
December 28, 2017, the Company borrowed $25.0 million under the DSM Credit Agreement, representing
the entire amount available thereunder, and issued a promissory note to DSM in an equal principal amount
(the DSM Note). The Company used the proceeds of the amounts borrowed under the DSM Credit
Agreement to repay all outstanding principal under a promissory note in the principal amount of
$25 million issued to Guanfu Holding Co., Ltd. in December 2016 (the Guanfu Note). Given multiple
elements in the arrangements with DSM, the Company fair valued the DSM Note to determine the
arrangement consideration that should be allocated to the DSM Note. The fair value of the DSM Note was
discounted using a Company specific weighted average cost of capital rate that resulted in a debt discount
of $8.0 million. The debt discount is being amortized over the loan term using the effective interest method.

104

The DSM Note (i) is an unsecured obligation of the Company, (ii) matures on December 31, 2021 and
(iii) accrues interest from and including December 28, 2017 at 10% per annum, payable quarterly. The DSM
Note may be prepaid in full or in part at any time without penalty or premium. In addition, the Company is
required to use certain payments received by the Company from DSM under the Value Sharing Agreement
(see Note 10, “Revenue Recognition”) to repay amounts outstanding under the DSM Credit Agreement.
The DSM Credit Agreement and the DSM Note contain customary terms, covenants and restrictions,
including certain events of default after which the DSM Note may become due and payable immediately.

February 2016 Private Placement

In February 2016, the Company issued and sold $20.0 million in aggregate principal amount of
promissory notes (the February 2016 Notes), as well as warrants to purchase an aggregate of 190,477 shares
of the Company’s common stock, exercisable at a price of $0.15 per share as of December 31, 2018 (the
February 2016 Warrants), resulting in aggregate proceeds to the Company of $20.0 million, in a private
placement to certain existing stockholders of the Company that are affiliated with members of the
Company’s Board of Directors (the Board): Foris Ventures, LLC (Foris, an entity affiliated with director
John Doerr of Kleiner Perkins Caufield & Byers, a current stockholder, and an owner of greater than
five percent of the Company’s outstanding common stock), which purchased $16.0 million aggregate
principal amount of the February 2016 Notes and warrants to purchase 152,381 shares of the Company’s
common stock; Naxyris S.A. (Naxyris, an investment vehicle owned by Naxos Capital Partners SCA Sicar;
director Carole Piwnica is Director of NAXOS UK, which is affiliated with Naxos Capital Partners SCA
Sicar, and was designated as a director of the Company by Naxyris), which purchased $2.0 million
aggregate principal amount of the February 2016 Notes and warrants to purchase 19,048 shares of the
Company’s common stock; and Biolding Investment SA (Biolding, a fund affiliated with director
HH Sheikh Abdullah bin Khalifa Al Thani, who was designated as a director of the Company by Biolding),
which purchased $2.0 million aggregate principal amount of the February 2016 Notes and warrants to
purchase 19,048 shares of the Company’s common stock.

The February 2016 Notes bore interest at 13.50% per annum and had an initial maturity date of
May 15, 2017. In May 2017, the February 2016 Notes purchased by Foris and Naxyris were exchanged for
shares of the Company’s Series B 17.38% Convertible Preferred Stock and warrants to purchase common
stock; see Note 7, “Stockholders’ Deficit”.

In May 2017, the Company and Biolding amended the February 2016 Note issued to Biolding (the
Biolding Note) to extend the maturity of the Biolding Note to November 15, 2017, and on November 13,
2017, the Company and Biolding further amended the Biolding Note to extend the maturity to
December 31, 2017. The Company paid the Biolding Note in full on January 2, 2018.

The February 2016 Warrants each have five-year terms. The February 2016 Warrants purchased by
Naxyris were fully exercised in the year ended December 31, 2017, and a gain of $0.1 million was recorded
in earnings. As of December 31, 2018, none of the 171,429 February 2016 Warrants purchased by Foris or
Biolding have been exercised.

For information regarding related party loans payable subsequent to December 31, 2018, see Note 16,

“Subsequent Events”.

Letters of Credit

In June 2012, the Company entered into a letter of credit agreement for $1.0 million under which it
provided a letter of credit to the landlord for its headquarters in Emeryville, California in order to cover the
security deposit on the lease. This letter of credit is secured by a certificate of deposit. Accordingly, the
Company has $1.0 million of restricted cash, noncurrent in connection with this arrangement as of
December 31, 2018 and 2017.

6. Mezzanine Equity

105

Company agreed to sell and issue 292,398 shares of its common stock to the Gates Foundation in a private
placement at a purchase price per share of $17.10, the average of the daily closing price per share of the
Company’s common stock on the Nasdaq Stock Market for the twenty consecutive trading days ending on
April 7, 2016, for aggregate proceeds to the Company of approximately $5.0 million (the Gates Foundation
Investment). The Securities Purchase Agreement includes customary representations, warranties and
covenants of the parties.

In connection with the entry into the Securities Purchase Agreement, on April 8, 2016, the Company
and the Gates Foundation entered into a Charitable Purposes Letter Agreement, pursuant to which the
Company agreed to expend an aggregate amount not less than the amount of the Gates Foundation
Investment to develop a yeast strain that produces artemisinic acid and/or amorphadiene at a low cost and
to supply such artemisinic acid and amorphadiene to companies qualified to convert artemisinic acid and
amorphadiene to artemisinin for inclusion in artemisinin combination therapies used to treat malaria
commencing in 2017. The Company is currently conducting the project. If the Company defaults in its
obligation to use the proceeds from the Gates Foundation Investment as set forth above or defaults under
certain other commitments in the Charitable Purposes Letter Agreement, the Gates Foundation will have
the right to request that the Company redeem, or facilitate the purchase by a third party of, the Gates
Foundation Investment shares then held by the Gates Foundation at a price per share equal to the greater of
(i) the closing price of the Company’s common stock on the trading day prior to the redemption or
purchase, as applicable, or (ii) an amount equal to $17.10 plus a compounded annual return of 10%. As of
December 31, 2018, the Company’s remaining research and development obligation under this arrangement
was $0.7 million.

7. Stockholders’ Deficit

Warrants

The Company issues warrants in certain debt and equity transactions in order to facilitate raising
equity capital or reduce borrowing costs. In connection with various debt and equity transactions (see
Note 5, “Debt” and below), the Company has issued warrants exercisable for shares of common stock. The
May 2017 and August 2017 cash and dilution warrants, and the July 2015 related party debt exchange
warrants are accounted for as derivative liabilities. See the Temasek Funding Warrant and Series A and B
sections below for more information. The following table summarizes warrant activity for the year ended
December 31, 2018:

Transaction

August 2018 warrant exercise

agreements . . . . . . . . . . . . . . . . . . . .
May 2017 cash and dilution warrants . . .
August 2017 cash and dilution

warrants

. . . . . . . . . . . . . . . . . . . . .

April 2018 warrant exercise agreements . .
July 2015 related party debt exchange . . .
February 2016 related party private

placement

. . . . . . . . . . . . . . . . . . . .

July 2015 private placement . . . . . . . . . .
Other . . . . . . . . . . . . . . . . . . . . . . . . .

Number
Outstanding as of
December 31, 2017

Additional
Warrants Issued

Exercises

Number
Outstanding as of
December 31, 2018

—
18,042,568

12,097,164

—
— (11,749,770)

12,097,164
6,292,798

9,543,234

—
2,082,010

171,429

81,197
1,406

1,713,565

3,616,174
471,204

(7,288,683)

—
(1,889,986)

3,968,116

3,616,174
663,228

—

—
—

—

—
—

171,429

81,197
1,406

29,921,844

17,898,107

(20,928,439)

26,891,512

For information regarding warrants issued subsequent

to December 31, 2018, see Note 16,

“Subsequent Events”.

106

Shares Issuable under Convertible Notes

In connection with various debt transactions (see Note 5, “Debt”), the Company issued certain
convertible notes that are convertible into shares of common stock as follows as of December 31, 2018, at
any time at the election of each debtholder:

Debt Instrument

6% convertible notes due 2021 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

2015 Rule 144A convertible notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

August 2013 financing convertible notes . . . . . . . . . . . . . . . . . . . . . . . . . . . .

2014 Rule 144A convertible notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Number of Shares into Which
Debt Instrument Is Convertible
as of December 31, 2018

9,493,672

2,338,560

1,003,554

867,376

13,703,162

2018 Warrant Exercises and New Warrant Issuances

April 2018 Warrant Transactions

On April 12, 2018, in accordance with the terms of the Warrant Exercise Agreement, certain holders of
the May 2017 Warrants (see below under “May 2017 Offerings”) exercised their May 2017 Cash Warrants
in full to purchase an aggregate of 3,616,174 shares of common stock for net proceeds to the Company of
$14.5 million and surrendered their May 2017 Dilution Warrants for cancellation. Upon exercise of the
May 2017 Cash Warrants and surrender of such May 2017 Dilution Warrants, certain derivative liabilities
representing certain anti-dilution rights contained in the May 2017 Warrants were effectively settled. Under
the terms of the Warrant Exercise Agreements, the exercise of such May 2017 Cash Warrants and surrender
of such May 2017 Dilution Warrants was required on the date of the Warrant Exercise Agreement in order
for the Company to issue new warrants to these same holders to purchase an aggregate of 3,616,174 shares
of common stock, exercisable at a price of $7.00 per share. The new warrants were fully exercisable upon
issuance, with an expiration date of July 12, 2019. The new warrants do not provide the holders with
anti-dilution protection and only permit “cashless” exercise after the six-month anniversary of issuance,
and only to the extent that there is not an effective registration statement covering the resale of the shares of
common stock underlying the new warrants; on September 26, 2018, the Company filed such a registration
statement, which was declared effective on October 11, 2018. The new warrants were evaluated for liability
classification, and while meeting the definition of a derivative, the freestanding instruments met the
indexation and equity classification criteria to be accounted for as equity.

August 2018 Warrant Transactions

In August 2018 in accordance with the terms of the Warrant Exercise Agreements, Foris Ventures,
LLC (Foris) and entities affiliated with Vivo Capital LLC (Vivo), related parties and holders of the
May 2017 Warrants and August 2017 Warrants (see below under “August 2017 Vivo Offering”),
respectively, exercised their Cash Warrants and, in the case of Foris, Dilution Warrants in full and in
accordance with the terms of the Warrant Exercise Agreements, to purchase an aggregate of approximately
12.6 million shares of common stock for $43.0 million in proceeds to the Company, and Vivo subsequently
surrendered their Dilution Warrants for cancellation. In connection with the entry by the Company and
Vivo into Warrant Exercise Agreement, the Company and Vivo amended the August 2017 Vivo Cash
Warrants to (i) reduce the exercise price of such warrants from $6.39 per share to $4.40 per share and
(ii) remove the August 2017 Vivo Offering Beneficial Ownership Limitation from such warrants. Upon
exercise and surrender of such Cash Warrants and Dilution Warrants, certain derivative liabilities
representing certain anti-dilution rights contained in the May 2017 Warrants and August 2017 Warrants
were effectively settled. Under the terms of the Warrants Exercise Agreement, the exercise of the Cash
Warrants and Dilution Warrants and subsequent surrender of the Vivo Dilution Warrants was required on
the date of the Warrants Exercise Agreement in order for the Company to issue a series of new warrants to
these same holders to purchase an aggregate of 12.1 million shares of common stock, exercisable at $7.52
per share. The new warrants are exercisable any time after the six-month anniversary of issuance and for

107

15 months thereafter, with an expiration date in May 2020. The new warrants do not provide the holders
with anti-dilution protection and only permit “cashless” exercise after the twelve-month anniversary of
issuance, and only to the extent that there is not an effective registration statement covering the resale of the
shares of common stock underlying the new warrants. The new warrants were evaluated for liability
classification, and while meeting the definition of a derivative, the freestanding instruments met the
indexation and equity classification criteria to be accounted for as equity.

Temasek Funding Warrant — Related Party

Following amendments to certain common stock purchase warrants in August 2018 (see below under
“May 2017 Offerings” and “August 2017 Vivo Offering”), and a corresponding adjustment to the
conversion price of the August 2013 financing convertible notes from $5.2977 per share to $4.40 per share
(see Note 5, “Debt”), the Temasek Funding Warrant became exercisable for an additional 471,204 shares of
common stock in accordance with its terms. On October 19, 2018, Temasek exercised the Temasek Funding
Warrant with respect to 1,889,986 shares of common stock underlying the Temasek Funding Warrant by
means of a cashless exercise, resulting in the issuance of 1,852,585 shares of common stock to Temasek. As
of December 31, 2018, there were 471,204 shares underlying the Temasek Funding Warrant. As a result of
this exercise, the derivative liability related to the Temasek Funding Warrant decreased by $14.0 million.

November 2018 DSM Securities Purchase Agreement — Related Party

On November 20, 2018, the Company issued 1,643,991 shares of common stock (the DSM Shares) at
$3.68 per share to DSM in a private placement pursuant to a securities purchase agreement, dated
in consideration of certain
November 19, 2018, between the Company and DSM (the DSM SPA),
agreements of DSM set forth in the Supply Agreement Amendment described in Note 10, “Revenue
Recognition”. The Company also agreed to pay DSM the difference between the DSM SPA purchase price
of $4.41 and the closing share price of the Company’s common stock on March 28, 2019, multiplied by
1,643,991. At inception, the Company recorded a $1.2 million derivative liability for the difference between
$4.41 and the Company’s closing stock price on November 20, 2018. At December 31, 2018 fair value based
on the Company’s closing stock price was $1.8 million, resulting in a $0.6 million loss on change in fair
value for the year ended December 31, 2018. At March 28, 2019, the Company’s stock price was $2.10, and
the Company owed DSM $3.8 million in connection with this agreement. Pursuant to the DSM SPA, the
Company agreed to file a registration statement providing for the resale by DSM of the DSM Shares and to
use commercially reasonable efforts to (i) cause such registration statement to become effective within
181 days following the date of the DSM SPA and (ii) keep such registration statement effective until DSM
does not own any DSM Shares or the DSM Shares are eligible for resale under Rule 144 without regard to
information about the
volume limitations. See Note 11, “Related Party Transactions” for additional
accounting for this transaction and other November 2018 transactions with DSM. In April 2019, in
connection with the assignment by the Company of its rights under the Value Sharing Agreement (see
Note 10, “Revenue Recognition”), the Company satisfied its obligation under the Supply Agreement
Amendment relating to the difference between $4.41 and the price of the Company’s common stock on
March 28, 2019. See Note 16, “Subsequent Events” for additional information.

At Market Issuance Sales Agreement

On March 8, 2016, the Company entered into an At Market Issuance Sales Agreement (ATM Sales
Agreement) with FBR Capital Markets & Co. and MLV & Co. LLC (Agents) under which the Company
would be able to issue and sell shares of its common stock having an aggregate offering price of up to
$50.0 million (ATM Shares) from time to time through the Agents, acting as its sales agents, under the
Company’s Registration Statement on Form S-3 (File No. 333-203216), effective April 15, 2015. Sales of the
ATM Shares through the Agents would be made by any method that is deemed an “at the market offering”
as defined in Rule 415 under the Securities Act of 1933, as amended, including by means of ordinary
brokers’ transactions at market prices, in block transactions, or as otherwise agreed by the Company and
the Agents. The Company agreed to pay the applicable Agent a commission rate of up to 3.0% of the gross
proceeds from the sale of any ATM Shares sold through such Agent under the ATM Sales Agreement. The
ATM Sales Agreement included no commitment by other parties to purchase ATM Shares the Company
offers for sale.

108

During the year ended December 31, 2018, the Company issued and sold 205,168 shares of common
stock under the ATM Sales Agreement, at an average price of $6.90 per share, resulting in total net
proceeds to the Company of $1.4 million. During the year ended December 31, 2017, the Company did not
sell any shares of common stock under the ATM Sales Agreement. The ATM Sales Agreement expired on
April 15, 2018, and as a result, zero remained available for issuance under the ATM Sales Agreement as of
December 31, 2018.

May 2017 Offerings

In May 2017, the Company issued and sold an aggregate of 22,140 shares of Series A 17.38%
Convertible Preferred Stock (Series A Preferred Stock), 70,904 shares of Series B 17.38% Convertible
Preferred Stock (Series B Preferred Stock), and warrants to purchase an aggregate of 7,384,190 shares of
common stock at an initial exercise price of $7.80 per share, warrants to purchase an aggregate of 7,384,190
shares of common stock at an initial exercise price of $9.30 per share, and warrants to purchase a number
of shares of common stock sufficient to provide full-ratchet anti-dilution protection with respect to the
effective price paid for the common stock underlying the Series A Preferred Stock and Series B Preferred
Stock (collectively, the May 2017 Warrants) in separate offerings, certain of which were registered under the
Securities Act or others of which were private placements (collectively, the May 2017 Offerings).

The net proceeds to the Company from the May 2017 Offerings were $50.7 million after payment of
offering expenses and placement agent fees. The Series A Preferred Stock and May 2017 Warrants relating
thereto were sold to the purchasers thereof in exchange for aggregate cash consideration of $22.1 million,
and the Series B Preferred Stock and May 2017 Warrants relating thereto were sold to the purchasers
thereof in exchange for (i) aggregate cash consideration of $30.7 million and (ii) the cancellation of
$40.2 million of outstanding indebtedness (including accrued interest thereon) owed by the Company to
certain purchasers, of which $33.1 million was from related parties, as further described below.

Series A and B Preferred Stock

Series A Preferred Stock

Each share of Series A Preferred Stock has a stated value of $1,000 and is convertible at any time, at
the option of the holder, into common stock at a conversion price of $17.25 per share (Preferred Stock
Conversion Rate). The Preferred Stock Conversion Rate is subject to adjustment in the event of any
dividends or distributions of common stock, or any stock split, reverse stock split, recapitalization,
reorganization or similar transaction. If not previously converted at the option of the holder, each share of
Series A Preferred Stock automatically converted on October 9, 2017, the 90th day following the date that
the July 2017 Stockholder Approval (as defined below) was obtained and effected, subject to the May 2017
Offerings Beneficial Ownership Limitation (as defined below).

Dividends, at a rate per year equal to 17.38% of the stated value of the Series A Preferred Stock, will
be payable semiannually from the issuance of the Series A Preferred Stock until the tenth anniversary of the
date of issuance, on each October 15 and April 15, beginning October 15, 2017, on a cumulative basis, at
the Company’s option, in cash, out of any funds legally available for the payment of dividends, or, subject
to the satisfaction of certain conditions, in Common Stock at the Preferred Stock Conversion Rate, or a
combination thereof. Upon the conversion of the Series A Preferred Stock prior to the tenth anniversary of
the date of issuance, the holders of the Series Preferred A Stock shall be entitled to a payment equal to
$1,738 per $1,000 of stated value of the Series A Preferred Stock, less the amount of all prior semiannual
dividends paid on such converted Series A Preferred Stock prior to the relevant conversion date
(Make-Whole Payment), at the Company’s option, in cash, out of any funds legally available for the
payment of dividends, or, subject to the satisfaction of certain conditions, in common stock at the Preferred
Stock Conversion Rate, or a combination thereof. If the Company elects to pay any dividend in the form of
cash, it shall provide each holder with notice of such election not later than the first day of the month of
prior to the applicable dividend payment date.

Unless and until converted into common stock in accordance with its terms, the Series A Preferred
Stock has no voting rights, other than as required by law or with respect to matters specifically affecting the
Series A Preferred Stock.

109

Upon any liquidation, dissolution or winding-up of the Company, the holders of the Series A
Preferred Stock shall be entitled to receive out of the assets of the Company the same amount that a holder
of Common Stock would receive if the Series A Preferred Stock were fully converted to common stock
immediately prior to such liquidation, dissolution or winding-up (without regard to whether such Series A
Preferred Stock is convertible at such time), which amount shall be paid pari passu with all holders of
Common Stock.

The conversion of the Series A Preferred Stock is subject to a beneficial ownership limitation of 4.99%
(or such other percentage not to exceed 9.99%, provided that any increase will not be effective until 61 days
after notice thereof by the holder) of the number of shares of common stock outstanding immediately after
giving effect to the issuance of shares of common stock issuable upon conversion of such Series A Preferred
Stock (May 2017 Offerings Beneficial Ownership Limitation). In addition, prior to obtaining the July 2017
Stockholder Approval (as defined below), the aggregate number of shares issued with respect to the
Series A Preferred Stock (and any other transaction aggregated for such purpose) could not exceed
3,792,778 shares of common stock (May 2017 Exchange Cap).

The Series A Preferred Stock is classified as permanent equity, as the Company controls all actions or
events required to settle the optional and mandatory conversion feature in shares. The Make-Whole
Payment was determined to be an embedded derivative requiring bifurcation and separate recognition as a
derivative liability recognized at its fair value as of the issuance date with subsequent changes in fair value
recorded in earnings until the earlier of (i) July 7, 2017 when the Make-Whole shares became fixed and
certain, (ii) the Series A Preferred Stock is converted into common stock, (iii) the Make-Whole Payment is
voluntarily converted, or (iv) the Make-Whole Payment is paid through declared dividends or cash. A
derivative liability was recognized at fair value on the date of issuance for the Make-Whole Payment in the
amount of $11.0 million. The value of the remaining Make-Whole derivative liability at July 7, 2017 was
extinguished to equity. All Make-Whole Payment conversions into common stock before and after July 7,
2017, were accounted for as a deemed dividend in the period converted. A derivative liability was also
recognized at fair value on the date of issuance for the May 2017 Warrants issued to the Series A holders
(discussed more fully below) in the amount of $10.6 million. The Series A Preferred Stock also contained a
beneficial conversion feature which was recognized up to the amount of $0.6 million of proceeds allocated
to the preferred stock. Net proceeds allocated to the Series A Preferred Stock were $0.6 million.

As of December 31, 2017, all 22,140 shares of Series A Preferred Stock had been converted into
common stock (with the Make-Whole Payment in each case being made in the form of common stock) and
zero shares of Series A Preferred Stock were outstanding. Upon conversion of the Series A Preferred
Shares, the Company recognized a deemed dividend for the unamortized discount related to the allocation
of proceeds to the May 2017 Warrants derivatives totaling $21.6 million, and deemed dividends upon
settlement of the Series A Make-Whole Payment totaling $10.5 million, all as a reduction to Additional
Paid-in Capital and an increase to net loss attributable to Amyris, Inc. common stockholders.

Series B Preferred Stock

The Series B Preferred Stock has substantially identical terms to the Series A Preferred Stock, except
that (i) the conversion of the Series B Preferred Stock was subject to the July 2017 Stockholder Approval
and (ii) the May 2017 Offerings Beneficial Ownership Limitation does not apply to DSM. The Series B
Preferred Stock was classified as permanent equity at issuance due to the lack of a cash redemption feature
and because the holder’s only recourse to affect conversion was to require the Company to continually seek
shareholder approval, thus effectively giving the Company control over the actions or events necessary to
settle an optional or mandatory conversion feature in shares. As described in more detail below under
“July 2017 Stockholder Approval,” in July 2017 the Company’s stockholders approved removing a
restriction preventing the Series B Preferred Stock issued in the May 2017 Offerings from being convertible
into common stock.

The investors that purchased shares of the Series B Preferred Stock included related parties affiliated
the Board: Foris exchanged an aggregate principal amount of $27.0 million of
with members of
indebtedness, plus accrued interest thereon, for 30,729 shares of Series B Preferred Stock and May 2017
Warrants to purchase 4,877,386 shares of Common Stock and Naxyris exchanged an aggregate principal
amount of $2.0 million of indebtedness, plus accrued interest thereon, for 2,333 shares of Series B Preferred

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Stock and May 2017 Warrants to purchase 370,404 shares of common stock. The fair value of the Series B
Preferred Stock, the embedded Make-Whole payment and the related warrants exceeded the carrying value
of the related party debt and accrued interest exchanged by $8.6 million which was recorded as a loss upon
extinguishment of debt as the Company determined that the related parties were acting in their interests as
debt holders.

The investors that purchased shares of the Series B Preferred Stock also included non-related party
holders of the Company’s 2014 Rule 144A Convertible Notes and 2015 Rule 144A Convertible Notes.
These investors exchanged all or a portion of their holding of such indebtedness, including accrued interest
thereon, representing an aggregate of $3.4 million of 2014 Rule 144A Convertible Notes and $3.7 million of
2015 Rule 144A Convertible Notes, for Series B Preferred Stock and May 2017 Warrants in the May 2017
Offerings. The fair value of the Series B Preferred Stock, the embedded Make-Whole payment and the
related warrants exceeded the carrying value of the debt and accrued interest exchanged by $1.9 million,
which was recognized as a loss on extinguishment of debt in other income (expense).

Issuance costs of $1.2 million were netted against the proceeds. Additional

issuance costs of
$0.2 million were expensed as debt extinguishment costs for debt that was exchanged in the May 2017
Offerings.

Upon the closing of the May 2017 Offerings, all such exchanged indebtedness was canceled and the
agreements relating thereto, including any note purchase agreements or unsecured or secured promissory
notes (including any security interest relating thereto), were terminated, except to the extent such investors
or other investors retain a portion of such indebtedness.

A derivative liability was recognized at fair value on the date of issuance for the May 2017 DSM
Series B Make-Whole Payment in the amount of $12.4 million. A derivative liability was also recognized at
fair value on the date of issuance for the May 2017 Warrants issued to DSM (discussed more fully below) in
the amount of $11.9 million. Upon conversion of the DSM Series B Preferred Shares, the Company
recognized a deemed dividend for the unamortized discounts related to the allocation of proceeds to the
May 2017 DSM Make-Whole Payment and May 2017 Warrants derivatives totaling $24.4 million, and a
deemed dividend upon settlement of all May 2017 Series B Make-Whole Payments totaling $22.6 million,
all as a reduction to Additional Paid in Capital and an increase to net loss attributable to Amyris, Inc.
common stockholders. The Series B Preferred Stock issued to DSM in the May 2017 Offerings also
contained a contingent beneficial conversion feature that was recognized in the three months ending
September 30, 2017 upon the July 2017 Stockholder Approval, which eliminated the contingency. As a
result, $0.6 million was recorded as a reduction to Additional Paid in Capital and was considered a deemed
dividend, increasing net loss attributable to Amyris, Inc. common stockholders.

As of December 31, 2018, 89,528 shares of Series B Preferred Stock (including the Series B Preferred
Stock issued in the August 2017 DSM Offering) have been converted into common stock (with the
Make-Whole Payment in each case being made in the form of common stock) and 6,376 shares of Series B
Preferred Stock were outstanding. At December 31, 2017, 9,213 shares of Series B Preferred Stock were
outstanding.

May 2017 Warrants

The Company issued to each investor in the May 2017 Offerings warrants to purchase a number of
shares of common stock equal to 100% of the shares of common stock into which such investor’s shares of
Series A Preferred Stock or Series B Preferred Stock were initially convertible (including shares of common
stock issuable as payment of dividends or the Make-Whole Payment, assuming that all such dividends and
the Make-Whole Payment are made in common stock), representing warrants to purchase 14,768,380
shares of common stock in the aggregate for all investors (collectively, the May 2017 Cash Warrants). The
exercise price of the May 2017 Cash Warrants is subject to standard adjustments as well as full-ratchet
anti-dilution protection for any issuance by the Company of equity or equity-linked securities during the
three-year period following the issuance of such warrants (May 2017 Dilution Period) at a per share price
less than the then-current exercise price of the May 2017 Cash Warrants, subject to certain exceptions. As
of December 31, 2017, the exercise prices of the May 2017 Cash Warrants were $4.40 per share and no

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May 2017 Cash Warrants had been exercised. As of December 31, 2018, the exercise prices of the May 2017
Cash Warrants were $4.40 per share and 8,523,560 May 2017 Cash Warrants had been exercised (see
“April 2018 Warrant Transactions” and “August 2018 Warrant Transactions” above).

In addition, the Company issued to each investor a warrant, with an exercise price of $0.0015 per share
as of December 31, 2018 (collectively, the May 2017 Dilution Warrants), to purchase a number of shares of
common stock sufficient to provide the investor with full-ratchet anti-dilution protection for any issuance
by the Company of equity or equity-linked securities during the May 2017 Dilution Period at a per share
price less than $6.30, the effective per share price paid by the investors for the shares of common stock
issuable upon conversion of their Series A Preferred Stock or Series B Preferred Stock (including shares of
common stock issuable as payment of dividends or the Make-Whole Payment, assuming that all such
dividends and the Make-Whole Payment are made in common stock) subject to certain exceptions. As of
December 31, 2018, the May 2017 Dilution Warrants were exercisable for an aggregate of 6,377,466 shares
based on an effective per share price of $4.40 per share, of which 6,329,488 warrants had been exercised,
resulting in a $64.1 million reduction in derivative liability. See “April 2018 Warrant Transactions” and
“August 2018 Warrant Transactions” above regarding the cancellation of certain May 2017 Dilution
Warrants.

The May 2017 Warrants each have a term of five years from the date such warrants initially became
exercisable upon the receipt and effectiveness of the July 2017 Stockholder Approval. The exercise of the
May 2017 Warrants (other than the May 2017 Warrants held by DSM) is subject to the May 2017 Offerings
Beneficial Ownership Limitation. In connection with the entry by the Company and Foris into a warrant
exercise agreement in August 2018 and related transactions (see “August 2018 Warrant Transactions”
above), the Company and Foris amended Foris’s May 2017 Cash Warrants and May 2017 Dilution Warrant
to remove the May 2017 Offerings Beneficial Ownership Limitation from such warrants. The May 2017
Cash Warrants are freestanding financial instruments that are accounted for as derivative liabilities and
recognized at their fair value on the date of issuance of $39.5 million. As of December 31, 2018, the fair
value of the May 2017 Cash Warrants was $24.1 million, as determined with the assistance of an
independent third-party appraisal.

For the years ended December 31, 2018 and 2017, the Company recorded a loss of $13.5 million and
$40.4 million, respectively, to reflect change in fair value of the May 2017 Cash Warrants (including the
anti-dilution protection feature). Subsequent changes to the fair value of the May 2017 Cash Warrants will
continue to be recorded in earnings until the warrants are exercised or expire in July 2022.

July 2017 Stockholder Approval

In connection with the May 2017 Offerings, the Company agreed to solicit from its stockholders (i) any
approval required by the rules and regulations of the NASDAQ Stock Market, including without limitation
for the issuance of common stock upon conversion of the Series A Preferred Stock in excess of the
May 2017 Exchange Cap, upon conversion of the Series B Preferred Stock and upon exercise of the
May 2017 Warrants (the NASDAQ Approval) and (ii) approval to effect the Reverse Stock Split
(collectively, the July 2017 Stockholder Approval) at an annual or special meeting of stockholders to be held
on or prior to July 10, 2017, and to use commercially reasonable efforts to secure the July 2017 Stockholder
Approval. The Reverse Stock Split was approved by the Company’s stockholders in May 2017 and the
NASDAQ Approval was obtained on July 7, 2017.

August 2017 DSM Offering — Related Party

On August 7, 2017, the Company issued and sold the following securities to DSM in a private

placement (August 2017 DSM Offering):

•

25,000 shares of Series B Preferred Stock (August 2017 DSM Series B Preferred Stock) at a price
of $1,000 per share;

a warrant to purchase 3,968,116 shares of common stock at an initial exercise price of $6.30 per
share expiring in five years (August 2017 DSM Cash Warrant); and

the August 2017 DSM Dilution Warrant (as described below).

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Net proceeds to the Company were $25.9 million after payment of offering expenses and the allocation

of total fair value received to the elements in the arrangement.

The exercise price of the August 2017 DSM Cash Warrant is subject to standard adjustments as well as
full-ratchet anti-dilution protection for any issuance by the Company of equity or equity-linked securities
during the three-year period following August 7, 2017 (DSM Dilution Period) at a per share price less than
the then-current exercise price of the August 2017 DSM Cash Warrant, subject to certain exceptions. As of
December 31, 2018, the exercise price of the August 2017 DSM Cash Warrant was $4.40 per share.

The August 2017 DSM Dilution Warrant allows DSM to purchase a number of shares of common
stock sufficient to provide DSM with full-ratchet anti-dilution protection for any issuance by the Company
of equity or equity-linked securities during the DSM Dilution Period at a per share price less than $6.30,
the effective per share price paid by DSM for the shares of common stock issuable upon conversion of its
Series B Preferred Stock (including shares of common stock issuable as payment of dividends or the
Make-Whole Payment (as defined below), assuming that all such dividends and the Make-Whole Payment
are made in common stock), subject to certain exceptions and subject to a price floor of $0.10 per share
(Dilution Floor). The August 2017 DSM Dilution Warrant expires five years from the date it is initially
exercisable.

In connection with the August 2017 DSM Offering, the Company also agreed that, subject to certain
exceptions, it would not (i) issue any shares of common stock or securities convertible into or exercisable or
exchangeable for common stock prior to October 31, 2017, (ii) effect any issuance of securities involving a
variable rate transaction until May 11, 2018 or (iii) issue any shares of common stock or securities
convertible into or exercisable or exchangeable for common stock at a price below the Dilution Floor
without DSM’s consent. On November 19, 2018, the Company entered into an agreement to reduce the
exercise price of the August 2017 DSM Cash Warrant from $6.30 to $4.40 to compensate DSM for failure
to obtain its consent to reduce the exercise price of the Vivo Warrant discussed in the “August 2018
Warrant Transactions” section of this Note 7 “Stockholders’ Deficit”. The Company determined the fair
value of this agreement to be $6.8 million and recorded a legal settlement expense for the period ended
December 31, 2018 in that amount. See Note 4, “Fair Value Measurement” for additional information. The
accounting treatment for this transaction was evaluated in conjunction with the other November 2018
transactions discussed in Note 11, “Related Party Transactions”. Also, upon execution of this agreement
the August 2017 DSM Dilution Warrant became exercisable for 1,713,565 shares based on an effective per
share price of $0.0001 per share, all of which were exercised in November 2018.

In connection with the August 2017 DSM Offering, the Company and DSM also entered into an
amendment to the stockholder agreement dated May 11, 2017 (DSM Stockholder Agreement) between the
Company and DSM (Amended and Restated DSM Stockholder Agreement). Under the DSM Stockholder
Agreement, DSM was granted the right to designate one director selected by DSM, subject to certain
restrictions and a minimum beneficial ownership level of 4.5%, to the Board. Furthermore, DSM has the
right to purchase additional shares of capital stock of the Company in connection with a sale of equity or
equity-linked securities by the Company in a capital raising transaction for cash, subject to certain
exceptions, to maintain its proportionate ownership percentage in the Company. Pursuant to the DSM
Stockholder Agreement, DSM agreed not to sell or transfer any of the Series B Preferred Stock or warrants
purchased by DSM in the May 2017 Offerings (as defined below), or any shares of common stock issuable
upon conversion or exercise thereof, other than to its affiliates, without the consent of the Company
through May 2018 and to any competitor of the Company thereafter. DSM also agreed that, subject to
certain exceptions, until three months after there is no DSM director on the Board, DSM will not, without
the prior consent of the Board, acquire common stock or rights to acquire common stock that would result
in DSM beneficially owning more than 33% of the Company’s outstanding voting securities at the time of
acquisition. Under the DSM Stockholder Agreement, the Company agreed to use its commercially
reasonable efforts to register, via one or more registration statements filed with the Securities and Exchange
Commission (SEC) under the Securities Act of 1933, as amended (Securities Act), the shares of common
stock issuable upon conversion or exercise of the securities purchased by DSM in the May 2017 Offerings.
The Amended and Restated DSM Stockholder Agreement provides that (i) DSM has the right to designate
a second director to the Board, subject to certain restrictions and a minimum beneficial ownership level of

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10%, and (ii) the shares of common stock issuable upon conversion or exercise of the securities purchased
by DSM in the August 2017 DSM Offering are (a) entitled to the registration rights provided for in the
DSM Stockholder Agreement and (b) subject to the transfer restrictions set forth in the DSM Stockholder
Agreement.

In addition, pursuant to the Amended and Restated DSM Stockholder Agreement, the Company and
DSM agreed to negotiate in good faith regarding an agreement concerning the development of certain
products in the Health & Wellness field and, in the event that the parties did not reach such agreement prior
to 90 days after the closing of the August 2017 DSM Offering (August 2017 DSM Closing), (a) certain
exclusive negotiating rights granted to DSM in connection with the entry into the DSM Stockholder
Agreement would expire and (b) on the first anniversary of the August 2017 DSM Closing and each
subsequent anniversary thereof, the Company would make a $5.0 million cash payment to DSM, provided
that the aggregate amount of such payments would not exceed $25.0 million. In September 2017, the
Company and DSM entered into such agreement, and in connection therewith an intellectual property
escrow agreement relating to certain intellectual property licenses granted by the Company to DSM upon
the August 2017 DSM Closing became effective.

In connection with the August 2017 DSM Offering and its $25.9 million in net proceeds, the Company
also entered into a separate intellectual property license with DSM for consideration of $9.0 million in cash,
which DSM remitted to the Company on October 28, 2017, and a credit letter (DSM Credit Letter) to be
applied against future collaboration and royalty payments owed by DSM to the Company beginning in
2018. The DSM Credit Letter had a fair value of $7.1 million and was recorded as deferred revenue on the
transaction date. The total fixed consideration of $34.0 million was allocated to each of the August 2017
DSM Series B Preferred Stock, August 2017 DSM Cash Warrant, August 2017 DSM Dilution Warrant and
DSM Credit Letter at fair value based on level 3 inputs. The August 2017 DSM Series B Preferred Stock
was recognized at its fair value on the date of issuance of $15.6 million, net of issuance costs of
$0.2 million. The August 2017 Make-Whole Payment met the criteria to be classified in permanent equity
and was not bifurcated from the preferred stock but will be recognized as a deemed dividend upon
conversion, increasing the net loss attributable to Amyris, Inc. common stockholders. The August 2017
DSM Cash Warrant and August 2017 DSM Dilution Warrant are freestanding financial instruments and
were initially recognized at their fair value of $10.6 million. The August 2017 DSM Cash Warrant and
August 2017 DSM Dilution Warrant have been reported together as derivative liabilities. Changes in the fair
value of the warrant derivatives for the years ended December 31, 2018 and 2017 have been recorded in
earnings as a $7.5 million loss and $4.0 million loss, respectively.

As of December 31, 2018, all the August 2017 Series B Preferred Shares have been converted into

common stock.

The DSM Credit Letter was initially recorded as deferred revenue at its $7.1 million fair value, which
was determined based on the assumptions that DSM would realize its credit over the next 18 months to
4 years with a 50% to 90% likelihood the credit will be utilized, fully discounted at the Company’s 8.6%
average cost of debt. After allocating the $34.0 million in fixed consideration to the financial instruments
noted above and the DSM Credit Letter, $7.8 million was available for recognition as revenue related to the
intellectual property licenses delivered to DSM, of which $3.3 million was recognized as license revenue
during the year ended December 31, 2017. The DSM Credit Letter was terminated in December 2017,
resulting in the reversal of the remaining unrecognized $4.5 million deferred revenue liability previously
recorded as consideration for the DSM License and Collaboration transaction. See Note 10, “Revenue
Recognition” for additional information.

August 2017 Vivo Offering — Related Party

On August 3, 2017, the Company issued and sold the following securities to Vivo in a private
placement (August 2017 Vivo Offering), resulting in net proceeds to the Company of $24.8 million after
payment of offering expenses.

•

2,826,711 shares of common stock at a price of $4.26 per share;

12,958 shares of Series D Preferred Stock at a price of $1,000 per share;

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•

warrants to purchase an aggregate of 5,575,118 shares of common stock at an initial exercise price
of $6.39 per share, expiring in five years (August 2017 Vivo Cash Warrants); and

the August 2017 Vivo Dilution Warrants (as described below).

Each share of Series D Preferred Stock has a stated value of $1,000 and, subject to the August 2017
Vivo Offering Beneficial Ownership Limitation (as defined below), is convertible at any time, at the option
of the holders, into common stock at a conversion price of $4.26 per share. The Series D Conversion Rate is
subject to adjustment in the event of any dividends or distributions of the common stock, or any stock
split, reverse stock split, recapitalization, reorganization or similar transaction.

Prior to declaring any dividend or other distribution of its assets to holders of common stock, the
Company shall first declare a dividend per share on the Series D Preferred Stock equal to $0.0001 per share.
In addition, the Series D Preferred Stock will be entitled to participate with the common stock on an
as-converted basis with respect to any dividends or other distributions to holders of common stock. There
were no dividends declared as of December 31, 2018 or 2017.

Unless and until converted into common stock in accordance with its terms, the Series D Preferred
Stock has no voting rights, other than as required by law or with respect to matters specifically affecting the
Series D Preferred Stock. The Series D Preferred Stock is classified as permanent equity, as the Company
controls all actions or events required to settle the optional conversion feature in shares.

these derivative liabilities from the date of

The August 2017 Vivo Cash Warrants and August 2017 Vivo Dilution Warrants are freestanding
derivative instruments in connection with the issuance of equity instruments, which have been recorded as
derivative liabilities. These warrants were recognized at their initial fair value upon issuance of $13.0 million
as determined by management with the assistance of an independent third party appraisal based on level 3
inputs. Changes in the fair value of
issuance through
December 31, 2018 have been recorded in earnings, with losses of $7.7 million and $3.0 million recorded for
the years ended December 31, 2018 and 2017, respectively. The remaining $12.0 million of the $25.0 million
in gross proceeds received was allocated on a relative fair value basis, resulting in $5.6 million of proceeds,
net of $0.2 million in issuance costs being allocated to the common stock sold in the August 2017 Vivo
Offering and $6.2 million allocated to the Series D Preferred Stock. The Series D Preferred Stock includes a
beneficial conversion feature of $5.8 million as the full fair value of the Series D Preferred Stock of
$12.0 million was greater than the $6.2 million allocated to the Series D Preferred Stock. The $5.8 million
beneficial conversation feature was recorded as a reduction to Additional Paid in Capital and a deemed
dividend increasing net loss attributable to Amyris, Inc. common stockholders upon conversion in the third
quarter of 2017.

At December 31, 2018 and 2017, 8,280 and 12,958 shares, respectively of Series D Preferred Stock were
outstanding. In the third quarter of 2018 Vivo converted 4,678 shares of August 2017 Offerings Series D
Preferred Stock and the Company recognized a $6.8 million deemed dividend for the unamortized
discounts created from the allocation of proceeds, as a reduction to Additional Paid in Capital and
increasing net loss attributable to Amyris, Inc. common stockholders.

In the event of a Fundamental Transaction, the holders of the Series D Preferred Stock will have the
right to receive the consideration receivable as a result of such Fundamental Transaction by a holder of the
number of shares of common stock for which the Series D Preferred Stock is convertible immediately prior
to such Fundamental Transaction (without regard to whether such Series D Preferred Stock is convertible
at such time), which amount shall be paid pari passu with all holders of common stock. A Fundamental
Transaction is defined in the Certificate of Designation of Preferences, Rights and Limitations relating to
the Series D Preferred Stock as any of the following: (i) merger with or consolidation into another legal
entity; (ii) sale, lease, license, assignment, transfer or other disposition of all or substantially all of the
Company’s assets in one or a series of related transactions; (iii) purchase offer, tender offer or exchange
offer of the Company’s common stock pursuant to which holders of the Company’s common stock are
permitted to sell, tender or exchange their shares for other securities, cash or property and has been
accepted by the holders of 50% or more of
the outstanding common stock; (iv) reclassification,
reorganization or recapitalization of the Company’s stock; or (v) stock or share purchase agreement that
results in another party acquiring more than 50% of the Company’s outstanding shares of common stock.

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Upon any liquidation, dissolution or winding-up of the Company, the holders of the Series D
Preferred Stock shall be entitled to receive out of the assets of the Company the same amount that a holder
of common stock would receive if the Series D Preferred Stock were fully converted to common stock
immediately prior to such liquidation, dissolution or winding-up (without regard to whether such Series D
Preferred Stock is convertible at such time), which amount shall be paid pari passu with all holders of
common stock.

The conversion of the Series D Preferred Stock is subject to a beneficial ownership limitation of 9.99%
(August 2017 Vivo Offering Beneficial Ownership Limitation), which limitation may be waived by the
holders on 61 days’ prior notice.

The exercise price of the August 2017 Vivo Cash Warrants is subject to standard adjustments as well as
full-ratchet anti-dilution protection for any issuance by the Company of equity or equity-linked securities
during the three-year period following August 3, 2017 (Vivo Dilution Period) at a per share price less than
the then-current exercise price of the August 2017 Vivo Cash Warrants, subject to certain exceptions. In
connection with the entry by the Company and Vivo into warrant exercise agreements in August 2018 and
related transactions (see “August 2018 Warrant Transactions” above), the Company and Vivo amended the
August 2017 Vivo Cash Warrants to (i) reduce the exercise price of such warrants from $6.39 per share to
$4.40 per share and (ii) remove the August 2017 Vivo Offering Beneficial Ownership Limitation from such
warrants.

The August 2017 Vivo Dilution Warrants allow Vivo to purchase a number of shares of common stock
sufficient to provide Vivo with full-ratchet anti-dilution protection for any issuance by the Company of
equity or equity-linked securities during the Vivo Dilution Period at a per share price less than $4.26, the
effective per share price paid by Vivo for the shares of common stock issuable upon conversion of the
Series D Preferred Stock, subject to certain exceptions and subject to the Dilution Floor. The August 2017
Vivo Dilution Warrants expire five years from the date they are initially exercisable.

As of December 31, 2017, none of the August 2017 Vivo Warrants were exercised. As of December 31,
2018, 5,575,118 of the August 2017 Vivo Cash Warrants had been exercised and the August 2017 Vivo
Dilution Warrants were not exercisable for any shares upon cancellation as part of the August 2018
transaction. See “August 2018 Warrant Transactions” above regarding the exercise of the August 2017 Vivo
Cash Warrants and the cancellation of the August 2017 Vivo Dilution Warrants.

In connection with the August 2017 Vivo Offering, the Company agreed that it would not issue any
shares of common stock or securities convertible into or exercisable or exchangeable for common stock at a
price below the Dilution Floor without Vivo’s consent.

In connection with the August 2017 Vivo Offering, the Company and Vivo also entered into a
Stockholder Agreement (Vivo Stockholder Agreement) setting forth certain rights and obligations of Vivo
and the Company. Pursuant to the Vivo Stockholder Agreement, Vivo will have the right, subject to certain
restrictions and a minimum beneficial ownership level of 4.5%, to (i) designate one director selected by Vivo
to the Board and (ii) appoint a representative to attend all Board meetings in a nonvoting observer capacity
and to receive copies of all materials provided to directors, subject to certain exceptions. Furthermore, Vivo
will have the right to purchase additional shares of capital stock of the Company in connection with a sale
of equity or equity-linked securities by the Company in a capital raising transaction for cash, subject to
certain exceptions, to maintain its proportionate ownership percentage in the Company. Vivo agreed not to
sell or transfer any of the shares of common stock, Series D Preferred Stock or warrants purchased by Vivo
in the August 2017 Vivo Offering, or any shares of common stock issuable upon conversion or exercise
thereof, other than to its affiliates, without the consent of the Company through August 2018 and to any
competitor of the Company thereafter. Vivo also agreed that, subject to certain exceptions, until the later of
(i) three years from the closing of the August 2017 Vivo Offering and (ii) three months after there is no Vivo
director on the Board, Vivo will not, without the prior consent of the Board, acquire common stock or
rights to acquire common stock that would result in Vivo beneficially owning more than 33% of the
Company’s outstanding voting securities at
the time of acquisition. Under the Vivo Stockholder
Agreement, the Company agreed to use its commercially reasonable efforts to register, via one or more
registration statements filed with the SEC under the Securities Act, the shares of common stock purchased
in the August 2017 Vivo Offering as well as the shares of common stock issuable upon conversion or
exercise of the Series D Preferred Stock and warrants purchased by Vivo in the August 2017 Vivo Offering.

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May 2017 Exchange of Common Stock for Series C Convertible Preferred Stock — Related Party

In May 2017, Foris and Naxyris agreed to exchange (May 2017 Exchange) their outstanding shares of
common stock, representing a total of 1,394,706 shares, for 20,921 shares of the Company’s Series C
Convertible Preferred Stock, par value $0.0001 per share (Series C Preferred Stock) in a private exchange.

Each share of Series C Preferred Stock had a stated value of $1,000 and would automatically convert
into common stock, at a conversion price of $15.00 per share (Series C Conversion Rate), upon the
approval by the Company’s stockholders and implementation of a reverse stock split.

The shares of Series C Preferred Stock automatically converted to common stock on June 6, 2017 in
connection with the effectiveness of the Reverse Stock Split. The Company accounted for the Series C
Preferred Stock and the May 2017 Exchange as a non-monetary transaction that had no impact on the
consolidated financial statements.

July 2015 PIPE Warrants

In July 2015, the Company entered into a securities purchase agreement with certain purchasers,
including entities affiliated with members of the Board, under which the Company agreed to sell 1,068,379
shares of common stock at a price of $23.40 per share, for aggregate proceeds to the Company of
$25.0 million. In connection with the sale, the Company granted to each of the purchasers a warrant,
exercisable at a price of $0.15 per share, to purchase of a number of shares of common stock equal to 10%
of the shares of common stock purchased by such investor. As of December 31, 2018 and 2017, such
warrants had been exercised with respect to 25,643 shares of common stock and warrants with respect to
81,197 shares of common stock were outstanding.

For information regarding issuances of equity securities subsequent to December 31, 2018, see Part II,

Item 8, “Subsequent Events”.

Right of First Investment to Certain Investors

In connection with investments in the Company has granted certain investors, including Vivo and
DSM, a right of
the Company proposes to sell securities in certain financing
transactions. With these rights, such investors may subscribe for a portion of any such new financing and
require the Company to comply with certain notice periods, which could discourage other investors from
participating in, or cause delays in its ability to close, such a financing.

first investment if

8. Net Loss per Share Attributable to Common Stockholders

The Company computes net loss per share in accordance with ASC 260, “Earnings per Share.” Basic
net loss per share of common stock is computed by dividing the Company’s net loss attributable to Amyris,
Inc. common stockholders by the weighted-average number of shares of common stock outstanding during
the period. Diluted net loss per share of common stock is computed by giving effect to all potentially
dilutive securities, including stock options, restricted stock units, convertible preferred stock, convertible
promissory notes and common stock warrants, using the treasury stock method or the as converted
method, as applicable. For the years ended December 31, 2018 and 2017, basic net loss per share was the
same as diluted net loss per share because the inclusion of all potentially dilutive securities outstanding was
anti-dilutive. As such, the numerator and the denominator used in computing both basic and diluted net
loss were the same for those years.

The Company follows the two-class method when computing net loss per common share when shares
are issued that meet the definition of participating securities. The two-class method requires income
available to common stockholders for the period to be allocated between common stock and participating
securities based upon their respective rights to receive dividends as if all income for the period had been
distributed. The two-class method also requires losses for the period to be allocated between common stock
and participating securities based on their respective rights if the participating security contractually
participates in losses. The Company’s convertible preferred stock are participating securities as they
contractually entitle the holders of such shares to participate in dividends and contractually require the
holders of such shares to participate in the Company’s losses.

117

The following table presents the calculation of basic and diluted net loss per share of common stock

attributable to Amyris, Inc. common stockholders:

Years Ended December 31,
(In thousands, except shares and per share amounts)

2018

2017

(As Restated,
Note 2)

Net loss attributable to Amyris, Inc.

. . . . . . . . . . . . . . . . . . . . . . . . . . . . .

(230,235)

(155,982)

Less deemed dividend related to beneficial conversion feature on Series A

preferred stock . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .