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                                                                    Exhibit 3.2


               AMENDED AND RESTATED CERTIFICATE OF INCORPORATION

                                       OF

                         KOSAN BIOSCIENCES INCORPORATED

                             A DELAWARE CORPORATION

Daniel V. Santi and Blair W. Stewart hereby certify that:

     1. They are the President and Secretary, respectively, of Kosan
Biosciences Incorporated, a Delaware Corporation (the "Corporation").

     2. The Certificate of Incorporation of the Corporation, filed with the
Secretary of State of the State of Delaware on September __, 2000, is hereby
amended and restated in its entirety to read as follows:

     "FIRST: The name of the corporation is Kosan Biosciences Incorporated
(the "Corporation").

     SECOND: The address of the Corporation's registered office in the State of
Delaware is Corporation Trust Center, 1209 Orange Street, in the City of
Wilmington, County of New Castle, Delaware, 19801. The name of its registered
agent at such address is The Corporation Trust Company.

     THIRD: The nature of the business or purposes to be conducted or promoted
by the Corporation is to engage in any lawful act or activity for which
corporations may be organized under the General Corporation Law of Delaware.

     FOURTH: This Corporation is authorized to issue two classes of shares
designated Common Stock and Preferred Stock.

     1. The Corporation is authorized to issue 200,000,000 shares of Common
Stock, par value $0.001 per share (the "Common Stock"), and 10,000,000 shares of
Preferred Stock, par value $0.001 per share (the "Preferred Stock").

     2. The shares of Preferred Stock may be issued from time to time in one or
more series pursuant to a resolution or resolutions providing for such issue
duly adopted by the Board of Directors. The Board of Directors of the
Corporation is expressly authorized, by filing a certificate pursuant to the
applicable law of the State of Delaware, to: (i) establish from time to time the
number of shares to be included in each such series; (ii) fix the rights,
preferences, restrictions and designations of the shares of each such series,
including but not limited to the fixing or alteration of the dividend rights,
dividend rate, conversion rights, conversion rate, voting rights, rights and
terms of redemption (including sinking fund provisions), redemption price or
prices, voting rights and

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liquidation preferences of any series of Preferred Stock for which no shares
have been issued and are outstanding; (iii) increase number of shares of any
series at any time; and (iv) decrease the number of shares of any series prior
or subsequent to the issue of shares of that series, but not below the number of
shares of such series then outstanding. In case the number of shares of any
series shall be so decreased, the shares constituting such decrease shall resume
the status which they had prior to the adoption of the resolution originally
fixing the number of shares of such series.

     FIFTH: In furtherance and not in limitation of the powers conferred by
statute, the Board of Directors is expressly authorized to make, alter, amend,
or repeal the Bylaws of the Corporation.

     SIXTH: Advance notice of new business and stockholder nominations for the
election of directors shall be given in the manner and to the extent provided in
the Bylaws of the Corporation. Election of directors need not be by written
ballot unless the Bylaws of the Corporation shall so provide.

     SEVENTH: Meetings of stockholders may be held within or without the State
of Delaware, as the Bylaws may provide. No action that is required or permitted
to be taken by the stockholders of the Corporation at any annual or special
meeting of stockholders may be effected by written consent of stockholders in
lieu of a meeting of stockholders. The books of the Corporation may be kept
(subject to any provision contained in the statutes) outside of the State of
Delaware at such place or places as may be designated from time to time by the
Board of Directors or in the Bylaws of the Corporation. The directors of the
Corporation need not be elected by written ballot unless a stockholder demands
election by written ballot at the meeting and before voting begins, or unless
the Bylaws so provide.

     EIGHTH: The Corporation reserves the right to amend, alter, change or
repeal any provision contained in this Certificate of Incorporation, in the
manner now or hereafter prescribed by statute, and all rights conferred upon the
stockholders herein are granted subject to this right.

     NINTH: Subject to the provisions of the General Corporation Law of the
State of Delaware, the number of Directors of the Corporation shall be
determined as provided by the Bylaws.

     TENTH: The Board of Directors shall be divided into three classes
consisting of as nearly equal numbers of directors as possible, and designated
Class A, Class B, and Class C. The term of office of Class A shall expire at the
first annual meeting of stockholders following the effectiveness of this
Article, and each third annual meeting of stockholders thereafter; the term of
office of Class B shall expire at the second annual meeting of stockholders
following the effectiveness of this Article, and each third annual meeting of
stockholders thereafter; and the term of office of Class C shall expire at the
third annual meeting of stockholders following the effectiveness of this
Article, and each third annual meeting of stockholders thereafter. Directors
added to the board of directors between annual meetings of stockholders by
reason of an increase in the authorized number of directors shall belong to the
class designated by the Board of Directors; provided however that the number of
board seats designated to belong to Class A, Class B and Class C must be as
nearly equal in number as possible. Following the effectiveness of this Article,
stockholders may effect the

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removal of a director only for cause. This provision shall supersede any
provision to the contrary in the Corporation's Bylaws.

     ELEVENTH: The Corporation shall indemnify and hold harmless any director,
officer, employee or agent of the Corporation from and against any and all
expenses and liabilities that may be imposed upon or incurred by him in
connection with, or as a result of, any proceeding in which he may become
involved, as a part or otherwise, by reason of the fact that he is or was such a
director, officer, employee or agent of the Corporation, whether or not he
continues to be such at the time such expenses and liabilities shall have been
imposed or incurred, to the extent permitted by the laws of the State of
Delaware, as they may be amended from time to time.

     TWELFTH: The liability of the directors of the Corporation for monetary
damages shall be eliminated to the fullest extent permissible under Delaware
law.

     A director of the Corporation shall not be personally liable to the
Corporation or its stockholders for monetary damages for any breach of
fiduciary duty as a director, except for liability (i) for any breach of the
director's duty of loyalty to the Corporation or its stockholders, (ii) for
acts or omissions not in good faith or which involve intentional misconduct
or a knowing violation of law, (iii) under Section 174 of the Delaware
General Corporation Law, or (iv) for any transaction from which the director
derived an improper personal benefit. If the Delaware General Corporation Law
is amended after approval by the stockholders of this Article to authorize
corporate action further eliminating or limiting the personal liability of
directors, then the liability of a director shall be eliminated or limited to
the fullest extent permitted by the Delaware General Corporation Law, as so
amended.

     Any repeal or modification of this TWELFTH Article shall be prospective and
shall not affect the rights under this TWELFTH Article in effect at the time
of the alleged occurrence of any act or omission to act giving rise to liability
or indemnification.

     3. The foregoing Amended and Restated Certificate of Incorporation has
been duly approved by the board of directors of the Corporation in accordance
with the provisions of Sections 242 and 245 of the Delaware General
Corporation Law.

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     4. The foregoing Amended and Restated Certificate of Incorporation has
been duly approved by the required vote of the stockholders in accordance
with the Certificate of Incorporation and the provisions of Sections 242 and
245 of the Delaware General Corporation Law.

     The undersigned hereby acknowledges that the foregoing Amended and
Restated Certificate of Incorporation is his act and deed and that the facts
stated herein are true.

     Executed at Palo Alto, CA, this ___ day of September, 2000.



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Daniel V. Santi, President                 Blair W. Stewart, Secretary





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