2013 Proxy Statement

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 SCHEDULE 14A (RULE 14a-101) INFORMATION REQUIRED IN PROXY STATEMENT SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. _______) Filed by the Registrant x Filed by a Party other than the Registrant o Check the appropriate box: o Preliminary Proxy Statement o Confidential, for Use of the Commission Only (as permitted by Rule 14a-6(e)(2) x Definitive Proxy Statement o Definitive Additional Materials o Soliciting Material Pursuant to § 240.14a-12 AMYRIS, INC. (Name of Registrant as Specified in its Charter) (Name of Person(s) Filing Proxy Statement, if Other Than the Registrant) Payment of Filing Fee (Check the appropriate box): x No fee required. o Fee computed on table below per Exchange Act Rules 14a-6(i)(1) and 0-11. (1) Title of each class of securities to which transaction applies: (2) Aggregate number of securities to which transaction applies: (3) Per unit price or other underlying value of transaction computed pursuant to Exchange Act Rule 0-11 (set forth the amount on which the filing fee is calculated and state how it was determined): (4) Proposed maximum aggregate value of transaction: (5) Total fee paid: o Fee paid with preliminary materials. o Check box if any part of the fee is offset as provided by Exchange Act Rule 0-11(a)(2) and identify the filing for which the offsetting fee was paid previously. Identify the previous filing by registration statement number, or the Form or Schedule and date of its filing. (1) Amount Previously Paid: (2) Form, Schedule or Registration Statement No.: (3) Filing Party: (4) Date Filed: April 16 , 2013 Dear Amyris stockholder: You are cordially invited to attend our 2013 Annual Meeting of Stockholders to be held on Thursday, May 9, 2013 at 3:00 p.m. Pacific Time at our headquarters located at 5885 Hollis Street, Suite 100, Emeryville, California. You can find directions to our headquarters on our company website at http://www.amyris.com/en/about-amyris/contact. The accompanying Notice of Annual Meeting of Stockholders and Proxy Statement describe the matters to be voted on at the meeting. At this year’s meeting, you will be asked to elect Class III directors, approve an amendment to our certificate of incorporation to increase our authorized shares, and ratify the appointment of PricewaterhouseCoopers LLP as our independent registered public accounting firm for 2013. 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 by mailing a completed proxy card or voter 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 CEO Emeryville, California 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 by completing, signing, dating and returning the accompanying proxy card or voter information form as promptly as possible. 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 a broker, bank or other custodian, nominee, trustee or fiduciary and you wish to vote at the meeting, you must obtain a proxy issued in your name from that record holder. AMYRIS, INC. 5885 Hollis Street, Suite 100 Emeryville, California 94608 NOTICE OF ANNUAL MEETING OF STOCKHOLDERS To Be Held May 9, 2013 The 2013 Annual Meeting of Stockholders of Amyris, Inc. will be held on Thursday, May 9, 2013 at 3:00 p.m. Pacific Time at our headquarters located at 5885 Hollis Street, Suite 100, Emeryville, California for the following purposes: 1. To elect the three Class III directors nominated by our Board of Directors (the “Board”) and named herein to serve on the Board for a three-year term. 2. To approve an amendment to our certificate of incorporation to increase the number of total authorized shares from 105,000,000 to 205,000,000 and the number of authorized shares of common stock from 100,000,000 to 200,000,000. 3. To ratify the appointment of PricewaterhouseCoopers LLP as our independent registered public accounting firm for the fiscal year ending December 31, 2013. 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 record date for the annual meeting is March 28, 2013. 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 in Emeryville, California 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 by completing, signing, dating and returning the accompanying proxy card or voter information form as promptly as possible. Under recent regulatory changes, if you have not given your broker specific instructions to do so, your broker will NOT be able to vote your shares with respect to most proposals, including the election of directors and approval of the amendment to our certificate of incorporation. If you do not provide voting instructions over the Internet, by telephone, or by returning a proxy card or voter 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 a broker, bank or other custodian, nominee, trustee or fiduciary and you wish to vote at the meeting, you must obtain a proxy issued in your name from that record holder. Important Notice Regarding the Availability of Proxy Materials for the Annual Meeting of Stockholders to be held on May 9, 2013: the Proxy Statement and our 2012 Annual Report to Stockholders are available at http://www.allianceproxy.com/amyris/2013. BY ORDER OF THE BOARD OF DIRECTORS Gary Loeb SVP, General Counsel and Secretary Emeryville, California April 16 , 2013 Table of Contents Table of Contents i Information Regarding Solicitation and Voting 1 Questions and Answers 1 Forward-Looking Statements 5 Proposal 1 - Election of Directors 6 General 6 Vote Required and Board Recommendation 6 Business Experience and Qualifications of Directors 7 Arrangements Concerning Selection of Directors 10 Independence of Directors 11 Board Leadership Structure 12 Role of the Board in Risk Oversight 12 Meetings of the Board and Committees 13 Committees of the Board 14 Stockholder Communications with Directors 18 Proposal 2 - Approval of Amendment to Certificate of Incorporation to Increase Number of Authorized Shares 19 General 19 Vote Required and Board Recommendation 19 Purpose of Proposed Amendment 20 Potential Adverse Effects of Proposed Amendment 21 Risks to Stockholders of Non-Approval 21 Interests of Our Directors and Executive Officers in the Amendment 21 Text of Proposed Amendment 22 Proposal 3 - Ratification of Appointment of Independent Registered Public Accounting Firm 23 General 23 Vote Required and Board Recommendation 23 Independent Registered Public Accounting Firm Fee Information 23 Audit Committee Pre-Approval of Services Performed by our Independent Registered Public Accounting Firm 24 Report of the Audit Committee* 25 Corporate Governance 26 Corporate Governance Principles 26 Code of Business Conduct and Ethics 26 Security Ownership of Certain Beneficial Owners and Management 27 Section 16(a) Beneficial Ownership Reporting Compliance 30 Equity Compensation Plan Information 30 Executive Compensation 32 Compensation Discussion and Analysis 32 i Leadership Development and Compensation Committee Report* 45 Summary Compensation Table 46 Grants of Plan-Based Awards in Fiscal 2012 48 Narrative Disclosure to Summary Compensation and Grants of Plan-Based Awards Tables 50 Outstanding Equity Awards as of December 31, 2012 51 Option Exercises and Stock Vested During Fiscal 2012 52 Pension Benefits 53 Non-Qualified Deferred Compensation 53 Potential Severance Payments upon Termination and upon Termination Following a Change in Control 53 Agreements with Executives 56 Limitation of Liability and Indemnification 56 Rule 10b5-1 Sales Plans 57 Director Compensation 58 Director Compensation for Fiscal Year 2012 58 Narrative to Director Compensation Tables 60 Compensation Committee Interlocks and Insider Participation 61 Transactions with Related Persons 62 Total Transactions 62 Private Placement Financings 66 Indemnification Arrangements 69 Executive Compensation and Employment Arrangements 70 Investors’ Rights Agreement and Registration Rights Agreements 70 Related Person Transaction Policy 70 Householding of Proxy Materials 70 Available Information 70 Incorporation of Information by Reference 71 Stockholder Proposals to be Presented at Next Annual Meeting 71 Other Matters 71 ii AMYRIS, INC. PROXY STATEMENT 2013 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 (“Amyris” or the “company”), for our 2013 Annual Meeting of Stockholders to be held at 3:00 p.m.

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