On September 3, 2012, Codexis, Inc. (the "Company") entered into an Agreement (the "New Shell Agreement") with Equilon Enterprises LLC dba Shell Oil Products US ("Shell US"). The New Shell Agreement, among other things, (i) amends the Amended and Restated License Agreement, effective November 1, 2006, as amended March 4, 2009, by and between Shell US and the Company (the "Shell License Agreement") and (ii) amends the Amended and Restated Collaboration Agreement, effective November 1, 2006, as amended March 4, 2009, February 23, 2010 and July 10, 2012, by and between Shell US and the Company (the "Shell Research Agreement").

Under the New Shell Agreement, Shell US provides the Company with royalty-bearing, non-exclusive rights and licenses to develop, manufacture, use and sell biocatalysts and microbes in the field of converting cellulosic biomass into fermentable sugars on a worldwide basis, except for Brazil, where such sugars are converted into liquid fuels, fuel additives or lubricants (the "Field of Use"). Raízen Energia Participações S.A. ("Raízen") holds the exclusive rights to use the Company's biocatalysts and microbes for converting cellulosic biomass into fermentable sugars in Brazil, where such sugars are converted into liquid fuels, fuel additives or lubricants. Following the date on which the Company, its affiliates and/or its customers produce sugars using biocatalysts in the Field of Use sufficient to produce 30,000,000 gallons of liquid fuel, the Company will be required to pay Shell US a royalty on the Company's sales to third parties of biocatalysts and microbes in the Field of Use, equal to a low single-digit percentage of net sales and the Company will also be required to pay Shell US a royalty on the use by the Company or its affiliates of catalysts in the Field of Use, equal to a low single-digit percentage of the Company's historical net sales of such biocatalysts or microbes or such amounts as are otherwise agreed by the parties. Shell US is also entitled to discounted pricing under the New Shell Agreement for biocatalysts purchased from the Company by Shell US for use in the Field of Use, but the Company is under no obligation to sell such biocatalysts to Shell US.

Shell US has also agreed not to sell any biocatalysts arising out of its collaboration with the Company to any third parties in the Field of Use, provided that such biocatalysts constitute improvements to any and all biocatalysts that are derived from technology developed under the Company's separate collaboration with Shell US, Shell Chemicals Canada Limited (together with Shell US, "Shell") and Iogen Energy Corporation ("Iogen"), and such improvements are made outside of that separate collaboration. Such restriction will not apply (i) to organizations for contract manufacture with respect to the manufacture of biocatalysts solely for use by Shell US or (ii) to Shell US or its affiliates or sublicensees with respect to activities in Brazil. The New Shell Agreement also provides a grant by the Company to Shell US of a non-exclusive, royalty-free license to manufacture, use and import, solely for the use of Shell US and its affiliates, (i) enzymes developed by the Company during the ten year period following August 31, 2012 outside of the Shell Research Agreement for use in the Field of Use and (ii) improvements to any microbe developed by the Company during the ten year period following August 31, . . .

The information set forth under "Item 1.01 Entry into a Material Definitive Agreement" of this Current Report on Form 8-K with respect to the termination of the Shell Research Agreement is incorporated into this Item 1.02 by reference.

On August 28, 2012, the Board committed to implementing a workforce reduction that includes the termination of the employment of approximately 133 employees. The Company began notifying affected employees on or around August 31, 2012. The Company is undertaking the workforce reduction to conserve cash for its ongoing and future programs following the termination of the Shell Research Agreement and the corresponding loss of ongoing funding for FTEs under the Shell Research Agreement. The Company expects that the workforce reduction will be completed by October 30, 2012. All affected employees will receive advance notice of their employment loss in accordance with applicable law.

The Company estimates that it will incur total charges of up to $3.6 million in the second half of 2012 with respect to the workforce reduction, including $2.9 million in continuation of salary and benefits of certain employees until their work is completed and their positions are eliminated and $0.7 million of one-time termination and miscellaneous costs, all of which will result in future cash expenditures.

This Item 2.05 contains forward-looking statements relating to the completion date of the workforce reduction, the Company's ability to conserve cash for its ongoing and future programs, the nature and amounts of charges to be incurred in connection with the workforce reduction and the amount of such charges that will result in future cash expenditures. You should not place undue reliance on these forward-looking statements because they involve known and unknown risks, uncertainties and other factors that are, in some cases, beyond the Company's control and that could materially affect actual results. Factors that could materially affect actual results include the possibility that the Company may need more cash and/or may need to incur greater charges than anticipated for its workforce reduction; the need to undertake additional restructuring efforts as a result of the loss of ongoing funding from Shell US; the need to retain key employees of the Company; and the need for substantial additional capital in the future in order to execute the Company's strategy. Additional factors that could materially affect actual results can be found in the Company's Quarterly Report on Form 10-Q for the period ended June 30, 2012 filed with the Securities and Exchange Commission on August 9, 2012, including under the caption "Risk Factors." The Company expressly disclaims any intent or obligation to update these forward-looking statements, except as required by law.

On September 3, 2012, the Company entered into a Rights Agreement between the Company and Wells Fargo Bank, N.A., as Rights Agent (as amended from time to time, the "Rights Agreement").

In connection with the Rights Agreement, a dividend was declared of one preferred stock purchase right (individually, a "Right" and collectively, the "Rights") for each share of common stock, par value $0.0001 per share (the "Common Stock"), of the Company outstanding at the close of business on September 18, 2012 (the "Record Date"). Each Right will entitle the registered holder thereof, after the Rights become exercisable and until September 2, 2013 (or the earlier redemption, exchange or termination of the Rights), to purchase from the Company one one-thousandth of a share of Series A Junior Participating Preferred Stock, par value $0.0001 per share (the "Series A Preferred"), of the Company at a price of $11.35 per one one-thousandth of a share of Series A Preferred (the "Purchase Price"). Until the earlier to occur of (i) the close of business on the tenth business day following a public announcement that a person or group of affiliated or associated persons has acquired, or obtained the right to acquire, beneficial ownership of 15% or more of the Common Stock (an "Acquiring Person") or (ii) the close of business on the tenth business day (or such later date as may be determined by action of the Board prior to such time as any person or group of affiliated or associated persons becomes an Acquiring Person) following the commencement or announcement of an intention to make a tender offer or exchange offer the consummation of which would result in the beneficial ownership by a person or group of affiliated or associated persons of 15% or more of the Common Stock (the earlier of (i) and (ii) being called the "Distribution Date"), the Rights will be evidenced, with respect to any of the Common Stock certificates outstanding as of the Record Date, by such Common Stock certificates, or, with respect to any uncertificated Common Stock registered in book entry form, by notation in book entry, in either case together with a copy of the Summary of Rights attached as Exhibit C to the Rights Agreement.

The Rights Agreement provides that any person who beneficially owned 15% or more of the Common Stock immediately prior to the first public announcement of the adoption of the Rights Agreement, together with any affiliates and associates of that person (each an "Existing Holder"), shall not be deemed to be an "Acquiring

The Rights will be transferred only with the Common Stock until the Distribution Date (or earlier redemption, exchange, termination or expiration of the Rights). As soon as practicable following the Distribution Date, separate certificates evidencing the Rights ("Right Certificates") will be mailed to holders of record of the Common Stock as of the close of business on the Distribution Date and such separate Right Certificates alone will evidence the Rights.

The Rights are not exercisable until the Distribution Date. The Rights will expire on September 2, 2013, subject to the Company's right to extend such date, unless earlier redeemed or exchanged by the Company or terminated. The Rights will at no time have any voting rights.

Each share of Series A Preferred purchasable upon exercise of the Rights will be entitled, when, as and if declared, to a minimum preferential quarterly dividend . . .

(c) Effective September 4, 2012, the Board appointed David O'Toole as the Company's Senior Vice President and Chief Financial Officer. Mr. O'Toole will also be replacing Mark Ho as principal accounting officer effective as of that date.

Mr. O'Toole, age 53, joins the Company from Response Genetics, Inc., a publicly traded molecular diagnostics company, where he served as Vice President and Chief Financial Officer from May 2010 to August 2012. From May 2008 to July 2009, Mr. O'Toole served as Executive Vice President and Chief Financial Officer of Abraxis Bioscience, Inc., a publicly traded biotechnology company. Prior to that time, Mr. O'Toole spent sixteen years with the accounting firm Deloitte & Touche LLP, including twelve years as a partner. During Mr. O'Toole's last eight years working in public accounting, his industry focus was in life sciences and biotechnology. Mr. O'Toole started his public accounting career in 1984 with Arthur Andersen & Co. where he worked for eight years. Since April 2012, Mr. O'Toole has also served as a member of the board of directors of MediciNova, Inc., a publicly traded pharmaceutical company, where Mr. O'Toole also serves as chairman of its audit committee. Mr. O'Toole received a B.S. in Accounting from the University of Arizona and is a Certified Public Accountant.

On August 31, 2012, Mr. O'Toole and the Company entered into an employment offer letter (the "Offer Letter") in connection with his appointment as Senior Vice President and Chief Financial Officer. The Offer Letter provides Mr. O'Toole with a one-time sign-on bonus of $50,000, which will have to be repaid to the Company in

Also in connection with his appointment as Senior Vice President and Chief Financial Officer, Mr. O'Toole is entering into a change of control severance agreement with the Company in the form entered into between the Company and certain of its officers, as filed as Exhibit 10.23 to the Company's Registration . . .

To the extent applicable, the information set forth under "Item 3.03 Material Modification to Rights of Security Holders" of this Current Report on Form 8-K with respect to the Certification of Designation and the Series A Preferred is incorporated into this Item 5.03 by reference.

On September 4, 2012, the Company issued a press release announcing the New Shell Agreement, the workforce reduction, the Rights Agreement, and a separate press release announcing the appointment of Mr. O'Toole as Senior Vice President and Chief Financial Officer. Copies of these press releases are furnished as Exhibits 99.1 and 99.2 to this Current Report on Form 8-K and incorporated by reference herein.

The information furnished pursuant to this Item 7.01 of this report, including Exhibits 99.1 and 99.2 attached hereto, shall not be deemed "filed" for purposes of Section 18 of the Securities Exchange Act of 1934, as amended, or otherwise subject to the liability of that section, nor shall it be deemed incorporated by reference in any filing under the Securities Act of 1933, as amended, or under the Securities Exchange Act of 1934, as amended, regardless of any general incorporation language in any such filing, unless the Company expressly sets forth in such filing that such information is to be considered "filed" or incorporated by reference therein.

(d) Exhibits

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Exhibit No.                                  Description

 3.1              Certificate of Designations of Series A Junior Participating
                  Preferred Stock of Codexis, Inc., filed with the Secretary of
                  State of the State of Delaware on September 4, 2012.

 4.1              Rights Agreement, dated as of September 3, 2012, between Codexis,
                  Inc. and Wells Fargo Bank, N.A., which includes the Form of
                  Certificate of Designations of Series A Junior Participating
                  Preferred Stock as Exhibit A, the Form of Right Certificate as
                  Exhibit B and the Summary of Rights to Purchase Preferred Shares
                  as Exhibit C.

99.1              Press release.

99.2              Press release.