AMENDED ANDRESTATED SUBSCRIPTION AGREEMENT

Exhibit 4.3

THE SHARES OF COMMON STOCK SUBSCRIBED FOR BY THIS AGREEMENT HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR REGISTERED OR QUALIFIED UNDER ANY STATE SECURITIES LAWS, AND TRANSFER OF SUCH SHARES IS RESTRICTED BY THE TERMS OF THIS AGREEMENT.

AMENDED AND RESTATED

SUBSCRIPTION AGREEMENT

THIS AMENDED AND RESTATED SUBSCRIPTION AGREEMENT, is dated as of May 2, 2014 (this “Agreement”), by and between the investor signatories hereto (each, an “Investor” and together, the “Investors”) and Pfenex Inc., a Delaware corporation (the “Company”).

W I T N E S S E T H

WHEREAS, the Company and the Investors are parties to a Subscription Agreement dated as of December 1, 2009 (the “Prior Agreement”);

WHEREAS, subject to the terms and conditions of the Prior Agreement, each Investor subscribed for and acquired the number of shares of Common Stock set forth next to such Investor’s name on Exhibit A hereto (with respect to each Investor, the “Shares”); and

WHEREAS, the Company and the Investors now desire to amend and restate the Prior Agreement in the manner set forth in this Agreement in order to clarify the Company’s repurchase rights regarding the Shares.

NOW, THEREFORE, in order to implement the foregoing and in consideration of the covenants and agreements contained herein, and for other good and valuable consideration, the receipt and adequacy of which are hereby acknowledged, the parties agree as follows:

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1.3.1    Deposit. As security for the faithful performance of this Agreement, each Investor delivered the certificate(s) representing the Shares, together with five (5) copies of a stock power form (the “Stock Powers”), to the Secretary of the Company or to another designee of the Company (the “Escrow Agent”) following the Closing (as defined in the Prior Agreement) under the Prior Agreement. These documents shall be held by the Escrow Agent pursuant to the Joint Escrow Instructions of the Company and the Investors dated December 1, 2009 (the “Escrow Instructions”), which instructions are incorporated into this Agreement by this reference.

1.3.2    Rights in Escrow Shares. Subject to the terms hereof, each Investor shall have all the rights of a stockholder with respect to such Shares while they are held in escrow, including without limitation, the right to vote the Shares. If, from time to time, there is (i) any stock dividend, stock split or other change in the Shares, (ii) any dividend of cash or other property on the Shares, or (iii) subject to the terms hereof, any Change in Control of the Company, any and all new, substituted or additional securities or cash or other consideration to which such Investor is entitled by reason of such Investor’s ownership of the Shares shall immediately become subject to this escrow, deposited with the Escrow Agent and included thereafter as “Shares” for purposes of this Agreement and the Company’s repurchase option set forth in this Section 1.

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or such other address as may be designated in writing hereafter, in the same manner, by such person.

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IN WITNESS WHEREOF, the parties have hereby executed this Amended and Restated Subscription Agreement as of the day set forth above.

IN WITNESS WHEREOF, the parties have hereby executed this Amended and Restated Subscription Agreement as of the day set forth above.

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IN WITNESS WHEREOF, the parties have hereby executed this Amended and Restated Subscription Agreement as of the day set forth above.

IN WITNESS WHEREOF, the parties have hereby executed this Amended and Restated Subscription Agreement as of the day set forth above.

EXHIBIT A

Investors