ZY / Zymergen Inc - Pemfailan SEC, Laporan Tahunan, Penyata Proksi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 15 CERTIFICATION AND NOTICE OF TERMINATION OF REGISTRATION UNDER SECTION 12(g) OF THE SECURITIES EXCHANGE ACT OF 1934 OR SUSPENSION OF DUTY TO FILE REPORTS UNDER SECTIONS 13

15-12G 1 d389575d1512g.htm 15-12G UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 15 CERTIFICATION AND NOTICE OF TERMINATION OF REGISTRATION UNDER SECTION 12(g) OF THE SECURITIES EXCHANGE ACT OF 1934 OR SUSPENSION OF DUTY TO FILE REPORTS UNDER SECTIONS 13 AND 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934. Commission File No. 001-40354 Zymergen Inc. (Exact name of regist

ZY / Zymergen Inc. / SB INVESTMENT ADVISERS (UK) LTD - SC 13G/A Passive Investment

Securities and Exchange Commission Washington, D.C. 20549 Schedule 13G (Rule 13d-102) Information to be Included in Statements Filed Pursuant to ? 240.13d-1(b), (c) and (d) and Amendments Thereto Filed Pursuant to ? 240.13d-2 UNDER THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No. 1)* Zymergen Inc. (Name of Issuer) Common Stock (Title of Class of Securities) 98985X100 (CUSIP Number) October 19, 2

As filed with the Securities and Exchange Commission on October 19, 2022

As filed with the Securities and Exchange Commission on October 19, 2022 Registration No.

Ginkgo Bioworks Completes Acquisition of Zymergen

Exhibit 99.1 Ginkgo Bioworks Completes Acquisition of Zymergen BOSTON, MA and EMERYVILLE, CA ? October 19, 2022 ? Today, Ginkgo Bioworks (NYSE: DNA), the leading horizontal platform for cell programming, and Zymergen (Nasdaq: ZY) announced that Ginkgo has completed its previously announced acquisition of Zymergen. The acquisition is expected to significantly enhance Ginkgo?s platform by integratin

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): October 18, 2022 Zymergen Inc. (E

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): October 18, 2022 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Number)

Sixth Amended and Restated Certificate of Incorporation of Zymergen Inc.

Exhibit 3.1 SIXTH AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF ZYMERGEN INC. A PUBLIC BENEFIT CORPORATION 1. The name of this corporation is Zymergen Inc. (the ?Corporation?). 2. The registered office of this Corporation in the State of Delaware is located at: c/o The Corporation Trust Company, 1209 Orange Street, Corporation Trust Center, Wilmington, County of New Castle, DE 19801. The na

As filed with the Securities and Exchange Commission on October 19, 2022

As filed with the Securities and Exchange Commission on October 19, 2022 Registration No.

As filed with the Securities and Exchange Commission on October 19, 2022

As filed with the Securities and Exchange Commission on October 19, 2022 Registration No.

Second Amended and Restated Bylaws of Zymergen Inc.

Exhibit 3.2 SECOND AMENDED AND RESTATED BYLAWS OF ZYMERGEN INC. (THE ?CORPORATION?) Section 1. LAW, CERTIFICATE OF INCORPORATION AND BYLAWS 1.1. These bylaws are subject to the certificate of incorporation of the Corporation (the ?Certificate of Incorporation?). In these bylaws, references to law, the Certificate of Incorporation and bylaws mean the law, the provisions of the Certificate of Incorp

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): October 17, 2022 Zymergen Inc. (E

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): October 17, 2022 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Number)

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): October 17, 2022 Zymergen Inc. (E

425 UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): October 17, 2022 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Num

Other Events

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): October 12, 2022 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Number)

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): October 12, 2022 Zymergen Inc. (E

425 UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): October 12, 2022 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Num

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. )

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. ) Filed by the Registrant ? Filed by a Party other than the Registrant ? Check the appropriate box: ? Preliminary Proxy Statement ? Confidential, for Use of the Commission Only (as permitted by Rule 14

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): August 25, 2022 Zymergen Inc. (Ex

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): August 25, 2022 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Number)

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, Costs Associated with Exit or Disposal Activities

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): August 25, 2022 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Number)

Filed by Ginkgo Bioworks Holdings, Inc.

Filed by Ginkgo Bioworks Holdings, Inc. pursuant to Rule 425 under the Securities Act of 1933 and deemed filed pursuant to Rule 14a-12 under the Securities Exchange Act of 1934 Subject Company: Zymergen Inc. Commission File No.: 001 ? 40354 Date: August 16, 2022 The following are excerpts from the transcript for the earnings call held by Ginkgo Bioworks Holdings, Inc. for the quarter ended June 30

Filed by Ginkgo Bioworks Holdings, Inc.

Filed by Ginkgo Bioworks Holdings, Inc. pursuant to Rule 425 under the Securities Act of 1933 and deemed filed pursuant to Rule 14a-12 under the Securities Exchange Act of 1934 Subject Company: Zymergen Inc. Commission File No.: 001 - 40354 Date: August 15, 2022 The following are slides from a presentation given by Ginkgo Bioworks Holdings, Inc. in connection with its earnings call for the quarter

Form of Retention Agreement.

Exhibit 10.1 [Zymergen Letterhead] August , 2022 [Name] [Address] [City, State, Zip] Re: Retention Awards Dear , As previously announced, on July 24, 2022, Zymergen Inc. (the ?Company?), entered into an Agreement and Plan of Merger (the ?Merger Agreement?) with Ginkgo Bioworks Holdings, Inc., a Delaware corporation (?Parent?), and certain other parties named therein, pursuant to which the Company

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

TABLE OF CONTENTS UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2022 OR ? TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For transition period from to Commission File Number 001-403

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Filed by Ginkgo Bioworks Holdings, Inc. pursuant to Rule 425 under the Securities Act of 1933 and deemed filed pursuant to Rule 14a-12 under the Securities Exchange Act of 1934 Subject Company: Zymergen Inc. Commission File No.: 001-40354 Date: July 25, 2022 Blog post made available by Ginkgo Bioworks Holdings, Inc. (?Ginkgo?) on July 25, 2022 at https://www.ginkgobioworks.com/2022/07/25/exciting-

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Filed by Ginkgo Bioworks Holdings, Inc. pursuant to Rule 425 under the Securities Act of 1933 and deemed filed pursuant to Rule 14a-12 under the Securities Exchange Act of 1934 Subject Company: Zymergen Inc. Commission File No.: 001-40354 Date: July 25, 2022 On July 25, 2022, Ginkgo Bioworks Holdings, Inc. (?Ginkgo?) made available the following communications. * * * * * Email to customers Dear [c

Ginkgo to Acquire Zymergen Frequently Asked Questions (FAQ) for Zymergen Employees

Filed by Zymergen Inc. Pursuant to Rule 425 of the Securities Act of 1933 and deemed filed pursuant to Rule 14a-12 of the Securities Exchange Act of 1934 Subject Company: Zymergen Inc. Commission File No.: 001-40354 Date: July 26, 2022 On July 26, 2022, Zymergen Inc. made available to its employees the below communication. Ginkgo to Acquire Zymergen Frequently Asked Questions (FAQ) for Zymergen Em

1

Filed by Ginkgo Bioworks Holdings, Inc. pursuant to Rule 425 under the Securities Act of 1933 and deemed filed pursuant to Rule 14a-12 under the Securities Exchange Act of 1934 Subject Company: Zymergen Inc. Commission File No.: 001-40354 Date: July 25, 2022 Transcript of the webcast ?M&A Strategy Update?, which was made available by Ginkgo Bioworks Holdings, Inc. on July 25, 2022 and can be acces

VOTING AGREEMENT

Exhibit 99.2 Execution Version VOTING AGREEMENT This Voting Agreement (this ?Agreement?), dated as of July 24, 2022, is made and entered into by and between Ginkgo Bioworks Holdings, Inc., a Delaware corporation (?Parent?), and SVF Excalibur (Cayman) Limited (the ?Stockholder?), a stockholder of Zymergen Inc., a Delaware public benefit corporation (the ?Company?). Parent and Stockholder are someti

ALL-EMPLOYEE EMAIL

Filed by Zymergen Inc. Pursuant to Rule 425 of the Securities Act of 1933 and deemed filed pursuant to Rule 14a-12 of the Securities Exchange Act of 1934 Subject Company: Zymergen Inc. Commission File No.: 001-40354 Date: July 25, 2022 ALL-EMPLOYEE EMAIL To: All Zymergen Employees Cc: All Zymergen Executives From: Jay Flatley Subject: All Hands Follow-Up: Gingko Acquisition, Layoffs Hi all, As dis

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Filed by Ginkgo Bioworks Holdings, Inc. pursuant to Rule 425 under the Securities Act of 1933 and deemed filed pursuant to Rule 14a-12 under the Securities Exchange Act of 1934 Subject Company: Zymergen Inc. Commission File No.: 001-40354 Date: July 25, 2022 On July 25, 2022, Ginkgo Bioworks Holdings, Inc. (?Ginkgo?) made available the following communications. * * * * * Communication to Ginkgo Em

Agreement and Plan of Merger, dated as of July 24, 2022, by and among Ginkgo Bioworks Holdings, Inc., a Delaware corporation, Pepper Merger Subsidiary Inc., a Delaware corporation and indirect wholly owned subsidiary of Ginkgo Bioworks Holdings, Inc., and Zymergen Inc., a Delaware public benefit corporation.*

Exhibit 2.1 Execution Version July 24, 2022 GINKGO BIOWORKS HOLDINGS, INC. PEPPER MERGER SUBSIDIARY INC. ZYMERGEN INC. AGREEMENT AND PLAN OF MERGER Contents Clause PAGE Article I DEFINITIONS & INTERPRETATIONS 2 1.1 Certain Definitions 2 1.2 Index of Defined Terms 21 1.3 Certain Interpretations 23 Article II THE MERGER 25 2.1 The Merger 25 2.2 The Effective Time 25 2.3 The Closing 25 2.4 Effect of

VOTING AGREEMENT

Exhibit 99.2 Execution Version VOTING AGREEMENT This Voting Agreement (this ?Agreement?), dated as of July 24, 2022, is made and entered into by and between Ginkgo Bioworks Holdings, Inc., a Delaware corporation (?Parent?), and SVF Excalibur (Cayman) Limited (the ?Stockholder?), a stockholder of Zymergen Inc., a Delaware public benefit corporation (the ?Company?). Parent and Stockholder are someti

VOTING AGREEMENT

Exhibit 99.4 Execution Version VOTING AGREEMENT This Voting Agreement (this ?Agreement?), dated as of July 24, 2022, is made and entered into by and among Ginkgo Bioworks Holdings, Inc., a Delaware corporation (?Parent?), and the stockholders of Zymergen Inc., a Delaware public benefit corporation (the ?Company?), identified on Exhibit A (each, a ?Stockholder? and collectively, the ?Stockholders?)

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): July 24, 2022 Zymergen Inc. (Exac

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): July 24, 2022 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Number) (I

Filed by Ginkgo Bioworks Holdings, Inc. pursuant to Rule 425 under the Securities Act of 1933 and deemed filed pursuant to Rule 14a-12 under the Securities Exchange Act of 1934 Subject Company: Zymergen Inc. Commission File No.: 001-40354 Date: July

Filed by Ginkgo Bioworks Holdings, Inc. pursuant to Rule 425 under the Securities Act of 1933 and deemed filed pursuant to Rule 14a-12 under the Securities Exchange Act of 1934 Subject Company: Zymergen Inc. Commission File No.: 001-40354 Date: July 25, 2022 M&A Strategy Update Accelerating scale to better deliver for our customers July 25, 2022 Disclaimer Forward Looking Statements This communica

VOTING AGREEMENT

Exhibit 99.3 Execution Version VOTING AGREEMENT This Voting Agreement (this ?Agreement?), dated as of July 24, 2022, is made and entered into by and among Ginkgo Bioworks Holdings, Inc., a Delaware corporation (?Parent?), and the stockholders of Zymergen Inc., a Delaware public benefit corporation (the ?Company?), identified on Exhibit A (each, a ?Stockholder? and collectively, the ?Stockholders?)

VOTING AGREEMENT

Exhibit 99.4 Execution Version VOTING AGREEMENT This Voting Agreement (this ?Agreement?), dated as of July 24, 2022, is made and entered into by and among Ginkgo Bioworks Holdings, Inc., a Delaware corporation (?Parent?), and the stockholders of Zymergen Inc., a Delaware public benefit corporation (the ?Company?), identified on Exhibit A (each, a ?Stockholder? and collectively, the ?Stockholders?)

VOTING AGREEMENT

Exhibit 99.3 Execution Version VOTING AGREEMENT This Voting Agreement (this ?Agreement?), dated as of July 24, 2022, is made and entered into by and among Ginkgo Bioworks Holdings, Inc., a Delaware corporation (?Parent?), and the stockholders of Zymergen Inc., a Delaware public benefit corporation (the ?Company?), identified on Exhibit A (each, a ?Stockholder? and collectively, the ?Stockholders?)

Ginkgo to Acquire Zymergen

Exhibit 99.1 Ginkgo to Acquire Zymergen ? Acquisition is expected to accelerate the development of Ginkgo?s innovative horizontal synthetic biology platform ? Expect integration of Zymergen?s complementary automation, software, and data science tools as well as biological assets to significantly enhance the capacity, capabilities, and efficiency of Ginkgo?s platform for its diverse customer base a

Filed by Zymergen Inc.

Filed by Zymergen Inc. Pursuant to Rule 425 of the Securities Act of 1933 and deemed filed pursuant to Rule 14a-12 of the Securities Exchange Act of 1934 Subject Company: Zymergen Inc. Commission File No.: 001-40354 Date: July 25, 2022 On July 25, 2022, Zymergen Inc. (?Zymergen?) hosted a business update call, a script of which is reproduced below. Carrie Mendivil, Investor Relations Good morning.

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, Entry into a Material Definitive Agreement, Financial Statements and Exhibits, Costs Associated with Exit or Disposal Activities, Other Events

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): July 24, 2022 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Number) (I

Agreement and Plan of Merger, dated as of July 24, 2022, by and among Ginkgo Bioworks Holdings, Inc., a Delaware corporation, Pepper Merger Subsidiary Inc., a Delaware corporation and indirect wholly owned subsidiary of Ginkgo Bioworks Holdings, Inc., and Zymergen Inc., a Delaware public benefit corporation.*

Exhibit 2.1 Execution Version July 24, 2022 GINKGO BIOWORKS HOLDINGS, INC. PEPPER MERGER SUBSIDIARY INC. ZYMERGEN INC. AGREEMENT AND PLAN OF MERGER Contents Clause PAGE Article I DEFINITIONS & INTERPRETATIONS 2 1.1 Certain Definitions 2 1.2 Index of Defined Terms 21 1.3 Certain Interpretations 23 Article II THE MERGER 25 2.1 The Merger 25 2.2 The Effective Time 25 2.3 The Closing 25 2.4 Effect of

Ginkgo to Acquire Zymergen

Exhibit 99.1 Ginkgo to Acquire Zymergen ? Acquisition is expected to accelerate the development of Ginkgo?s innovative horizontal synthetic biology platform ? Expect integration of Zymergen?s complementary automation, software, and data science tools as well as biological assets to significantly enhance the capacity, capabilities, and efficiency of Ginkgo?s platform for its diverse customer base a

Submission of Matters to a Vote of Security Holders

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): June 2, 2022 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Number) (IR

As filed with the Securities and Exchange Commission on May 27, 2022

As filed with the Securities and Exchange Commission on May 27, 2022 Registration No.

Power of Attorney (included on the signature page of the Registration Statement)

As filed with the Securities and Exchange Commission on May 12, 2022 Registration No.

Filing Fee Table

Exhibit 107 Calculation of Filing Fee Tables FORM S-3 (Form Type) ZYMERGEN INC. (Exact Name of Registrant as Specified in its Charter) Table 1: Newly Registered Securities Security Type Security Class Title Fee Calculation Rule Amount Registered Proposed Maximum Offering Price Per Share Maximum Aggregate Offering Price Fee Rate Amount of Registration Fee Fees to Be Paid Equity Common Stock, par va

Form of Indenture

Exhibit 4.4 Zymergen Inc. and [ ], Trustee INDENTURE Dated as of [ ], 20[ ] Cross-Reference Table Between Trust Indenture Act of 1939 and Indenture. Section of Trust Indenture Act of 1939, as amended Section of Indenture Section 310 (a)(1) 5.09 (a)(2) 5.09 (a)(3) NOT APPLICABLE (a)(4) NOT APPLICABLE (a)(5) 5.09 (b) 5.08 Section 311 (a) 5.13 (b) 5.13 Section 312 (a) 3.06 (b) 3.06 (c) 3.06 Section 3

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): May 12, 2022 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Number) (IR

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

TABLE OF CONTENTS UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2022 OR ? TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For transition period from to Commission File Number 001-40

Zymergen Reports Preliminary First Quarter 2022 Financial Results

Zymergen Reports Preliminary First Quarter 2022 Financial Results Emeryville, Calif.

Employment Separation Letter Agreement with

Exhibit 10.1 April 1, 2022 Aaron Kimball Re: Employment Separation Letter Agreement Dear Aaron: This letter agreement (this ?Letter Agreement?) confirms the termination of your employment with Zymergen Inc. (the ?Company?) and your resignation from all positions and offices with the Company and any of its affiliates, in each case, to take effect on April 1, 2022 (the ?Separation Date?). In connect

SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. )

SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No.

SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. )

SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K

TABLE OF CONTENTS 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, 2021 OR ? TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For transition period from to Commission File Number 001-40354 Z

Exhibit 4.3

Exhibit 4.3 DESCRIPTION OF REGISTRANT?S SECURITIES REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934 The following summary describes the common stock, $0.001 par value per share, of Zymergen Inc. (the ?Company,? ?we,? ?us? and ?our?), which is the only class of securities of the Company registered pursuant to Section 12 of the Securities Exchange Act of 1934, as amended (the

As filed with the Securities and Exchange Commission on March 30, 2022

As filed with the Securities and Exchange Commission on March 30, 2022 Registration No.

List of Subsidiaries of the Company.

Exhibit 21.1 Subsidiaries of Zymergen Inc. as of December 31, 2021 Name Direct Parent Jurisdiction 1776 Pharmaceuticals LLC Zymergen Inc. Delaware enEvolv, Inc. Zymergen Inc. Delaware Genesis Acquisition Sub, LLC Zymergen Inc. Delaware Lodo Therapeutics Corporation Zymergen Inc. Delaware Zymergen International HoldCo Inc. Zymergen Inc. Delaware Zymergen Japan GK Zymergen Inc. Japan Zymergen Spain,

Filing Fee Table

Exhibit 107 Calculation of Filing Fee Tables Form S-8 (Form Type) Zymergen Inc. (Exact name of Registrant as Specified in its Charter) Type 1?Newly Registered Securities Security Type Security Class Title Fee Calculation Rule Amount Registered(1) Proposed Maximum Offering Price per Unit(2) Maximum Aggregate Offering Price Fee Rate Amount of Registration Fee Equity Common Stock, $0.001 par value pe

Zymergen Reports Preliminary Fourth Quarter and Full Year 2021 Financial Results

Zymergen Reports Preliminary Fourth Quarter and Full Year 2021 Financial Results Emeryville, Calif.

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): March 22, 2022 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Number) (

Financial Statements and Exhibits, Other Events

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): March 8, 2022 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Number) (I

Forward Looking Statements Certain statements in this presentation and the accompanying oral commentary are forward-looking statements regarding Zymergen Inc. (“Zymergen”) within the meaning of federal securities laws. These statements relate to futu

Exhibit 99.1 Partner with nature to make better products, a better way, for a better world. Jay Flatley March 8, 2022 Cowen Healthcare Conference Forward Looking Statements Certain statements in this presentation and the accompanying oral commentary are forward-looking statements regarding Zymergen Inc. (?Zymergen?) within the meaning of federal securities laws. These statements relate to future p

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): March 1, 2022 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Number) (I

JOINT FILING AGREEMENT

Exhibit 99 JOINT FILING AGREEMENT In accordance with Rule 13d-1(k)(1) promulgated under the Securities Exchange Act of 1934, as amended, the undersigned hereby agree that they are jointly filing this statement on Schedule 13G.

CA:TOU / Tourmaline Oil Corp / SB INVESTMENT ADVISERS (UK) LTD - SC 13G Passive Investment

Securities and Exchange Commission Washington, D.C. 20549 Schedule 13G (Rule 13d-102) Information to be Included in Statements Filed Pursuant to ? 240.13d-1(b), (c) and (d) and Amendments Thereto Filed Pursuant to ? 240.13d-2 UNDER THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No. )* Zymergen Inc. (Name of Issuer) Common Stock (Title of Class of Securities) 98985X100 (CUSIP Number) December 31, 2

CA:TOU / Tourmaline Oil Corp / Data Collective II, L.P. - SCHEDULE 13G Passive Investment

SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULES 13d-1 (b), (c) AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO 13d-2 (b) (Amendment No. ) * Zymergen Inc. (Name of Issuer) Common Stock, par value $0.001 (Title of Class of Securities) 98985X100 (CUSIP Number) December 31, 2021 (Date of Event Which Requires Filin

CA:TOU / Tourmaline Oil Corp / True Ventures IV, L.P. - SC 13G Passive Investment

SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULES 13d-1 (b), (c) AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO 13d-2 (b) (Amendment No. )* Zymergen Inc. (Name of Issuer) Common Stock, $0.001 par value per share (Title of Class of Securities) 98985X100 (CUSIP Number) December 31, 2021 (Date of Ev

CA:TOU / Tourmaline Oil Corp / GIC Private Ltd Passive Investment

SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No.1)* Zymergen Inc. (Name of Issuer) Common Stock, $0.001 par value per share (Title of Class of Securities) 98985X100 (CUSIP Number) December 31, 2021 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the rule pursuant to which t

Zymergen, Inc. Investor Presentation

Financial Statements and Exhibits, Other Events

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): January 10, 2022 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Number)

. 1, W

Exhibit 10.3 [***] Certain information in this document has been excluded pursuant to Regulation S-K, Item (601)(b)(10). Such excluded information is not material and would likely cause competitive harm to the registrant if publicly disclosed. Execution Version AMENDMENT NO. 1, WAIVER AND CONSENT TO AMENDED AND RESTATED CREDIT AGREEMENT AND GUARANTY This AMENDMENT NO. 1, WAIVER AND CONSENT TO AMEN

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

TABLE OF CONTENTS UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2021 OR ? TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For transition period from to Commission File Number 00

Zymergen Reports Preliminary Third Quarter 2021 Financial Results and Provides Business Update

Zymergen Reports Preliminary Third Quarter 2021 Financial Results and Provides Business Update Emeryville, Calif.

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): November 3, 2021 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Number)

Entry into a Material Definitive Agreement, Costs Associated with Exit or Disposal Activities, Other Events

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): October 20, 2021 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Number)

Other Events

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): September 23, 2021 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Numbe

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

TABLE OF CONTENTS UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2021 OR ? TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For transition period from to Commission File Number 001-403

Letter Agreement with Jay Flatley.

Exhibit 10.1 August 2, 2021 Jay Flatley Dear Jay: On behalf of the Board of Directors, it is my pleasure to offer you the position of Acting Chief Executive Officer (?Acting CEO?) of Zymergen Inc. (?Zymergen? or the ?Company?), effective as of August 2, 2021 (your ?Start Date?). The time period for this role is anticipated to be up to when a permanent Chief Executive Officer commences employment w

Employment Separation Letter Agreement with Josh Hoffman.

Exhibit 10.2 August 2, 2021 Josh Hoffman Re: Employment Separation Letter Agreement Dear Josh: This letter agreement (this ?Letter Agreement?) confirms the termination of your employment with Zymergen Inc. (the ?Company?) and your resignation from all positions and offices with the Company and any of its affiliates, including from the board of directors of the Company, in each case, to take effect

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): July 28, 2021 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Number) (I

Zymergen Provides Business Update Jay Flatley, Chairman of the Board, Appointed Acting CEO; Josh Hoffman to Step Down Conference Call to be Held at 2:00 p.m. Pacific Time / 5:00 p.m. Eastern Time Today

EX-99.1 4 tm2123868d1ex99-1.htm EXHIBIT 99.1 Exhibit 99.1 Zymergen Provides Business Update Jay Flatley, Chairman of the Board, Appointed Acting CEO; Josh Hoffman to Step Down Conference Call to be Held at 2:00 p.m. Pacific Time / 5:00 p.m. Eastern Time Today EMERYVILLE, Calif., August 3, 2021 - Zymergen Inc. (“Zymergen” or the “Company”), today provided a business update regarding its commercial

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q

TABLE OF CONTENTS UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2021 OR ? TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For transition period from to Commission File Number 001-40

Zymergen Reports Preliminary First Quarter 2021 Financial Results

Zymergen Reports Preliminary First Quarter 2021 Financial Results Emeryville, Calif.

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): May 24, 2021 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Number) (IR

SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No.__)* Zymergen Inc. (Name of Issuer) Common Stock, par value $0.001 per share (Title of Class of Securities) (CUSIP Number)

SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No.)* Zymergen Inc. (Name of Issuer) Common Stock, par value $0.001 per share (Title of Class of Securities) 98985X100 (CUSIP Number) April 26, 2021 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the rule pursuant to which this

Amendments to Articles of Incorporation or Bylaws; Change in Fiscal Year, Material Modification to Rights of Security Holders, Financial Statements and Exhibits

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of Earliest Event Reported): April 26, 2021 Zymergen Inc. (Exact Name of Registrant as Specified in Charter) Delaware 001-40354 46-2942439 (State or Other Jurisdiction of Incorporation) (Commission File Number) (

Amended and Restated Bylaws of Zymergen Inc.

Exhibit 3.2 AMENDED AND RESTATED BYLAWS OF ZYMERGEN INC. A PUBLIC BENEFIT CORPORATION TABLE OF CONTENTS ARTICLE PAGE NO. Article I Corporate Offices 1 1.1 Registered Office. 1 1.2 Other Offices. 1 Article II Meetings of Stockholders 1 2.1 Annual Meeting. 1 2.2 Special Meeting. 1 2.3 Notice of Stockholders? Meetings. 1 2.4 Manner of Giving Notice; Affidavit of Notice. 2 2.5 Quorum. 2 2.6 Adjourned

Amended and Restated Certificate of Incorporation of Zymergen Inc.

Exhibit 3.1 AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF ZYMERGEN INC. A PUBLIC BENEFIT CORPORATION (Pursuant to Sections 242 and 245 of the General Corporation Law of the State of Delaware) Zymergen Inc. (the ?Corporation?), a corporation organized and existing under the General Corporation Law of the State of Delaware (as the same exists or may hereafter be amended, the ?DGCL?), does her

2021 Employee Stock Purchase Plan.

Exhibit 99.3 ZYMERGEN INC. EMPLOYEE STOCK PURCHASE PLAN ARTICLE 1 PURPOSE The Plan?s purpose is to assist employees of the Company and its Designated Companies in acquiring a stock ownership interest in the Company, and to help such employees provide for their future security and to encourage them to remain in the employment of the Company and its Subsidiaries. The Plan consists of two components:

16,130,000 Shares

TABLE OF CONTENTS Filed pursuant to Rule 424(b)(4) Registration No. 333-254612 PROSPECTUS 16,130,000 Shares ? Common Stock This is Zymergen Inc.?s initial public offering. We are offering 16,130,000 shares of our common stock to be sold in this offering. The initial public offering price is $31.00 per share of common stock. Prior to this offering, there has been no public market for our common sto

2021 Incentive Award Plan.

EXHIBIT 99.2 ZYMERGEN INC. 2021 INCENTIVE AWARD PLAN ARTICLE I PURPOSE The Plan?s purpose is to enhance the Company?s ability to attract, retain and motivate persons who make (or are expected to make) important contributions to the Company by providing these individuals with equity ownership opportunities. ARTICLE II DEFINITIONS As used in the Plan, the following words and phrases have the meaning

- FORM S-8

As filed with the Securities and Exchange Commission on April 22, 2021 Registration No.

- S-1MEF

As filed with the Securities and Exchange Commission on April 21, 2021. Registration No. 333- UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM S-1 REGISTRATION STATEMENT UNDER THE SECURITIES ACT OF 1933 Zymergen Inc. (Exact name of registrant as specified in its charter) Delaware 8731 46-2942439 (State or other jurisdiction of incorporation or organization) (Primary Stand

[Signature Page Follows]

April 19, 2021 VIA EDGAR Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.

- 8-A12B

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 8-A FOR REGISTRATION OF CERTAIN CLASSES OF SECURITIES PURSUANT TO SECTION 12(b) OR (g) OF THE SECURITIES EXCHANGEACT OF 1933 Zymergen Inc.

April 19, 2021

April 19, 2021 VIA EDGAR U.S. Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.E. Washington, D.C. 20549 Attention: Katherine Bagley Re: Zymergen Inc. Registration Statement on Form S-1 (File No. 333-254612) Request for Acceleration of Effective Date Dear Ms. Bagley: Pursuant to Rule 461 under the Securities Act of 1933, as amended, Zymergen Inc. (the ?Company?) h

AMENDED AND RESTATED BYLAWS ZYMERGEN INC. A PUBLIC BENEFIT CORPORATION TABLE OF CONTENTS

Exhibit 3.4 AMENDED AND RESTATED BYLAWS OF ZYMERGEN INC. A PUBLIC BENEFIT CORPORATION TABLE OF CONTENTS ARTICLE PAGE NO. Article I Corporate Offices 1 1.1 Registered Office. 1 1.2 Other Offices. 1 Article II Meetings of Stockholders 1 2.1 Annual Meeting. 1 2.2 Special Meeting. 1 2.3 Notice of Stockholders? Meetings. 1 2.4 Manner of Giving Notice; Affidavit of Notice. 2 2.5 Quorum. 2 2.6 Adjourned

AMENDED AND RESTATED CERTIFICATE OF INCORPORATION ZYMERGEN INC. A PUBLIC BENEFIT CORPORATION (Pursuant to Sections 242 and 245 of the General Corporation Law of the State of Delaware)

Exhibit 3.2 AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF ZYMERGEN INC. A PUBLIC BENEFIT CORPORATION (Pursuant to Sections 242 and 245 of the General Corporation Law of the State of Delaware) Zymergen Inc. (the ?Corporation?), a corporation organized and existing under the General Corporation Law of the State of Delaware (as the same exists or may hereafter be amended, the ?DGCL?), does her

Form of Stock Option Grant Notice and Stock Option Agreement under the 2021 Incentive Award Plan.

Exhibit 10.7 ZYMERGEN INC. 2021 INCENTIVE AWARD PLAN GLOBAL STOCK OPTION GRANT NOTICE Zymergen Inc., a Delaware corporation, (the ?Company?), pursuant to its 2021 Incentive Award Plan, as may be amended from time to time (the ?Plan?), hereby grants to the holder listed below (?Participant?), an option to purchase the number of shares of Common Stock (the ?Shares?), set forth below (the ?Option?).

Form of Indemnification Agreement between the Company and each of its directors and executive officers.

Exhibit 10.3 ZYMERGEN INC. INDEMNIFICATION AGREEMENT This Indemnification Agreement (this ?Agreement?) is made as of, April , 2021 by and between Zymergen Inc., a Delaware corporation (the ?Company?), and a member of the Board of Directors or an officer of the Company (?Indemnitee?). RECITALS The Company and Indemnitee recognize the increasing difficulty in obtaining liability insurance for direct

Employee Stock Purchase Plan.

Exhibit 10.9 ZYMERGEN INC. EMPLOYEE STOCK PURCHASE PLAN ARTICLE 1 PURPOSE The Plan?s purpose is to assist employees of the Company and its Designated Companies in acquiring a stock ownership interest in the Company, and to help such employees provide for their future security and to encourage them to remain in the employment of the Company and its Subsidiaries. The Plan consists of two components:

2021 Incentive Award Plan.

EXHIBIT 10.6 ZYMERGEN INC. 2021 INCENTIVE AWARD PLAN ARTICLE I PURPOSE The Plan?s purpose is to enhance the Company?s ability to attract, retain and motivate persons who make (or are expected to make) important contributions to the Company by providing these individuals with equity ownership opportunities. ARTICLE II DEFINITIONS As used in the Plan, the following words and phrases have the meaning

- S-1/A

S-1/A 1 nt10018776x8s1a.htm S-1/A TABLE OF CONTENTS As filed with the Securities and Exchange Commission on April 14, 2021. Registration No. 333-254612 UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 AMENDMENT NO. 2 TO FORM S-1 REGISTRATION STATEMENT UNDER THE SECURITIES ACT OF 1933 Zymergen Inc. (Exact name of registrant as specified in its charter) Delaware 8731 46-2942439

Form of Restricted Stock Unit Award Grant Notice and Restricted Stock Unit Award Agreement under the 2021 Incentive Award Plan.

Exhibit 10.8 ZYMERGEN INC. 2021 INCENTIVE AWARD PLAN GLOBAL RESTRICTED STOCK UNIT AWARD GRANT NOTICE Zymergen Inc. a Delaware corporation, (the ?Company?), pursuant to its 2021 Incentive Award Plan, as amended from time to time (the ?Plan?), hereby grants to the holder listed below (the ?Participant?), an award of restricted stock units (?Restricted Stock Units? or ?RSUs?). Each vested Restricted

RESTATED CERTIFICATE OF INCORPORATION ZYMERGEN INC. (Pursuant to Sections 242 and 245 of the General Corporation Law of the State of Delaware)

Exhibit 3.1 RESTATED CERTIFICATE OF INCORPORATION OF ZYMERGEN INC. (Pursuant to Sections 242 and 245 of the General Corporation Law of the State of Delaware) Zymergen Inc., a corporation organized and existing under and by virtue of the provisions of the General Corporation Law of the State of Delaware (the ?General Corporation Law?), DOES HEREBY CERTIFY: FIRST: That the name of this corporation i

Non-Employee Director Compensation Policy

Exhibit 10.10 ZYMERGEN INC. NON-EMPLOYEE DIRECTOR COMPENSATION POLICY Adopted April 2021 The Board of Directors (the ?Board?) of Zymergen Inc. (the ?Company?) has approved the following Non-Employee Director Compensation Policy (?Policy?) to provide all non-employee members of the Board compensation for their service on the Board This Policy shall be effective as of the date the Company?s registra

ZYMERGEN INC. [●] Shares of Common Stock Underwriting Agreement

Exhibit 1.1 ZYMERGEN INC. [?] Shares of Common Stock Underwriting Agreement [?], 2021 J.P. Morgan Securities LLC Goldman Sachs & Co. LLC As representatives of the several Underwriters listed in Schedule 1 hereto c/o J.P. Morgan Securities LLC 383 Madison Avenue New York, New York 10179 c/o Goldman Sachs & Co. LLC 200 West Street New York, NY 10282 Ladies and Gentlemen: Zymergen Inc., a Delaware co

CONFIDENTIAL TREATMENT REQUESTED BY ZYMERGEN INC.

CONFIDENTIAL TREATMENT REQUESTED BY ZYMERGEN INC. VIA EDGAR CORRESPONDENCE CERTAIN PORTIONS OF THIS LETTER AS FILED VIA EDGAR HAVE BEEN OMITTED AND FILED SEPARATELY WITH THE COMMISSION. CONFIDENTIAL TREATMENT HAS BEEN REQUESTED PURSUANT TO 17 CFR 200.83 WITH RESPECT TO THE OMITTED PORTIONS. OMITTED INFORMATION HAS BEEN REPLACED IN THIS LETTER AS FILED VIA EDGAR WITH A PLACEHOLDER IDENTIFIED BY THE

- S-1/A

TABLE OF CONTENTS As filed with the Securities and Exchange Commission on March 26, 2021.

The Corporation shall furnish without charge to each stockholder who so requests a statement of the powers, designations, preferences and relative, participating, optional or other special rights of each class of stock of the Corporation or series th

EX-4.2 2 nt10018776x5ex4-2.htm EXHIBIT 4.2 Exhibit 4.2 D E L A W A R E Z Y M R G E N , I C . C O E R P O R A N T E SEALApril 24,2013 ZY This certifies that is the record holder ofFULLY PAID AND NONASSESSABLE SHARES OF COMMON STOCK, $0.001 PAR VALUE PER SHARE, OFZymergen, Inc., a public benefit corporationtransferable on the books of the Corporation in person or by duly authorized attorney upon sur

Zymergen Inc. requests that the information contained in this letter, marked by brackets, be treated as confidential information pursuant to 17 C.F.R. §200.83.

VIA EDGAR CORRESPONDENCE CONFIDENTIAL TREATMENT REQUESTED BY ZYMERGEN INC.: ZY CERTAIN PORTIONS OF THIS LETTER AS FILED VIA EDGAR HAVE BEEN OMITTED AND FILED SEPARATELY WITH THE COMMISSION. CONFIDENTIAL TREATMENT HAS BEEN REQUESTED PURSUANT TO 17 CFR 200.83 WITH RESPECT TO THE OMITTED PORTIONS. OMITTED INFORMATION HAS BEEN REPLACED IN THIS LETTER AS FILED VIA EDGAR WITH A PLACEHOLDER IDENTIFIED BY

Warrant to Purchase Common Stock, dated November 17, 2014, between Zymergen Inc. and Silicon Valley Bank.

Exhibit 4.3 THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE "ACT"), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AS SET FORTH IN SECTIONS 5.3 AND 5.4 BELOW, MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND LAWS OR IN FORM AND SUBSTANCE SATISFACTORY TO THE COMPANY, S

Amended and Restated Credit Agreement and Guaranty, dated as of February 26, 2021, by and among Zymergen Inc., the Subsidiary Guarantors from time to time party thereto, the Lenders from time to time party thereto and Perceptive Credit Holdings II, LP., as the Administrative Agent.

Exhibit 10.1 including conformed signatures of the parties [***] Certain information in this document has been excluded pursuant to Regulation S-K, Item (601)(b)(10). Such excluded information is not material and would likely cause competitive harm to the registrant if publicly disclosed. AMENDED AND RESTATED CREDIT AGREEMENT AND GUARANTY dated as of February 26, 2021 by and among ZYMERGEN INC., a

Warrant to Purchase Series C Preferred Stock, dated December 19, 2019, between Zymergen Inc. and Perceptive Credit Holdings II, LP.

Exhibit 4.7 Execution Version WARRANT TO PURCHASE SERIES C PREFERRED STOCK THIS WARRANT AND THE SECURITIES ISSUABLE UPON EXERCISE OF THIS WARRANT HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR QUALIFIED UNDER ANY STATE OR FOREIGN SECURITIES LAWS AND MAY NOT BE OFFERED FOR SALE, SOLD, PLEDGED, HYPOTHECATED OR OTHERWISE TRANSFERRED OR ASSIGNED UNLESS (I) A REGISTRATION STA

Form of Stock Certificate for Common Stock of the Registrant.

Exhibit 4.2

Subsidiaries of Registrant

Exhibit 21.1 Subsidiaries of Registrant None.

Amended and Restated Investors’ Rights Agreement, dated July 29, 2020, by and among the Company and certain Investors listed therein.

Exhibit 4.1 ZYMERGEN INC. AMENDED AND RESTATED INVESTORS? RIGHTS AGREEMENT July 29, 2020 TABLE OF CONTENTS Page 1. Definitions 3 2. Registration Rights 5 2.1 Request for Registration 5 2.2 Company Registration 7 2.3 Form S-3 Registration 8 2.4 Obligations of the Company 10 2.5 Information from Holder 11 2.6 Expenses of Registration 12 2.7 Delay of Registration 12 2.8 Indemnification 12 2.9 Reports

Warrant to Purchase Common Stock, dated April 30, 2018, between Zymergen Inc. and Silicon Valley Bank.

Exhibit 4.6 THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE ?ACT?), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AS SET FORTH IN SECTIONS 5.3 AND 5.4 BELOW, MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND LAWS OR IN FORM AND SUBSTANCE SATISFACTORY TO THE COMPANY, S

Registration Statement - S-1

TABLE OF CONTENTS As filed with the Securities and Exchange Commission on March 23, 2021.

RESTATED CERTIFICATE OF INCORPORATION ZYMERGEN INC.

Exhibit 3.1 RESTATED CERTIFICATE OF INCORPORATION OF ZYMERGEN INC. (Pursuant to Sections 242 and 245 of the General Corporation Law of the State of Delaware) Zymergen Inc., a corporation organized and existing under and by virtue of the provisions of the General Corporation Law of the State of Delaware (the "General Corporation Law"), DOES HEREBY CERTIFY: FIRST: That the name of this corporation i

Form of Stock Option Grant Notice and Stock Option Agreement under the 2014 Stock Plan.

Exhibit 10.5 Zymergen, Inc 2014 Stock Plan Notice of Stock Option Grant (Installment Exercise with Acceleration) The Optionee has been granted the following option to purchase shares of the Common Stock of Zymergen, Inc.: Name of Optionee: ###PARTICIPANTNAME### Total Number of Shares: ###TOTALAWARDS### Type of Option: ###DICTIONARYAWARDNAME### Exercise Price per Share: ###GRANTPRICE### Date of Gra

Warrant to Purchase Common Stock, dated August 5, 2015, between Zymergen Inc. and Silicon Valley Bank.

Exhibit 4.4 THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE ?ACT?), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AS SET FORTH IN SECTIONS 5.3 AND 5.4 BELOW, MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND LAWS OR IN FORM AND SUBSTANCE SATISFACTORY TO THE COMPANY, S

Warrant to Purchase Common Stock, dated November 14, 2017, between Zymergen Inc. and Silicon Valley Bank.

Exhibit 4.5 THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE ?ACT?), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AS SET FORTH IN SECTIONS 5.3 AND 5.4 BELOW, MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND LAWS OR IN FORM AND SUBSTANCE SATISFACTORY TO THE COMPANY, S

AMENDED AND RESTATED BYLAWS OF ZYMERGEN, INC. (A DELAWARE CORPORATION) TABLE OF CONTENTS

Exhibit 3.3 AMENDED AND RESTATED BYLAWS OF ZYMERGEN, INC. (A DELAWARE CORPORATION) TABLE OF CONTENTS Page ARTICLE I OFFICES 1 1.1 Registered Office 1 1.2 Offices 1 ARTICLE II MEETINGS OF STOCKHOLDERS 1 2.1 Location 1 2.2 Timing 1 2.3 Notice of Meeting 1 2.4 Stockholders? Records 1 2.5 Special Meetings 2 2.6 Notice of Meeting 2 2.7 Business Transacted at Special Meeting 2 2.8 Quorum; Meeting Adjour

Strategic Partnership Agreement, dated as of April 9, 2019, by and between Registrant and Sumitomo Chemical Co. LTD.

Exhibit 10.2 [***] Certain information in this document has been excluded pursuant to Regulation S-K, Item (601)(b)(10). Such excluded information is not material and would likely cause competitive harm to the registrant if publicly disclosed. STRATEGIC PARTNERSHIP AGREEMENT BETWEEN ZYMERGEN INC. AND SUMITOMO CHEMICAL CO. LTD. STRATEGIC PARTNERSHIP AGREEMENT This Strategic Partnership Agreement (t

Form of Employment Agreement.

Exhibit 10.11 ZYMERGEN INC. EMPLOYMENT AGREEMENT This Employment Agreement (the ?Agreement?), is made and entered into by and between Zymergen Inc., a Delaware corporation (the ?Company?) and [] (?Executive? and, together with the Company, the ?Parties?). This Agreement will become effective as of immediately prior to the time the Company?s registration statement relating to the initial public off

2014 Stock Plan, as amended.

Exhibit 10.4 ZYMERGEN, INC. 2014 STOCK PLAN ADOPTED ON JULY 21, 2014, AS AMENDED TABLE OF CONTENTS Page SECTION 1. ESTABLISHMENT AND PURPOSE 1 SECTION 2. ADMINISTRATION 1 (a) Committees of the Board of Directors 1 (b) Authority of the Board of Directors 1 SECTION 3. ELIGIBILITY 1 (a) General Rule 1 (b) Ten-Percent Stockholders 1 SECTION 4. STOCK SUBJECT TO PLAN 2 (a) Basic Limitation 2 (b) Additio

STRATEGIC PARTNERSHIP AGREEMENT ZYMERGEN INC. SUMITOMO CHEMICAL CO. LTD. STRATEGIC PARTNERSHIP AGREEMENT

Exhibit 10.2 [***] Certain information in this document has been excluded pursuant to Regulation S-K, Item (601)(b)(10). Such excluded information is not material and would likely cause competitive harm to the registrant if publicly disclosed. STRATEGIC PARTNERSHIP AGREEMENT BETWEEN ZYMERGEN INC. AND SUMITOMO CHEMICAL CO. LTD. STRATEGIC PARTNERSHIP AGREEMENT This Strategic Partnership Agreement (t

Subsidiaries of Registrant

Exhibit 21.1 Subsidiaries of Registrant None.

[***] Certain information in this document has been excluded pursuant to Regulation S-K, Item (601)(b)(10). Such excluded information is not material and would likely cause competitive harm to the registrant if publicly disclosed.

Exhibit 10.1 including conformed signatures of the parties [***] Certain information in this document has been excluded pursuant to Regulation S-K, Item (601)(b)(10). Such excluded information is not material and would likely cause competitive harm to the registrant if publicly disclosed. AMENDED AND RESTATED CREDIT AGREEMENT AND GUARANTY dated as of February 26, 2021 by and among ZYMERGEN INC., a

ZYMERGEN INC. EMPLOYMENT AGREEMENT

Exhibit 10.11 ZYMERGEN INC. EMPLOYMENT AGREEMENT This Employment Agreement (the ?Agreement?), is made and entered into by and between Zymergen Inc., a Delaware corporation (the ?Company?) and [] (?Executive? and, together with the Company, the ?Parties?). This Agreement will become effective as of immediately prior to the time the Company?s registration statement relating to the initial public off

ZYMERGEN INC. AMENDED AND RESTATED INVESTORS’ RIGHTS AGREEMENT July 29, 2020 TABLE OF CONTENTS

Exhibit 4.1 ZYMERGEN INC. AMENDED AND RESTATED INVESTORS? RIGHTS AGREEMENT July 29, 2020 TABLE OF CONTENTS Page 1. Definitions 3 2. Registration Rights 5 2.1 Request for Registration 5 2.2 Company Registration 7 2.3 Form S-3 Registration 8 2.4 Obligations of the Company 10 2.5 Information from Holder 11 2.6 Expenses of Registration 12 2.7 Delay of Registration 12 2.8 Indemnification 12 2.9 Reports

-

TABLE OF CONTENTS As confidentially submitted to the Securities and Exchange Commission on March 8, 2021.

* * *

VIA EDGAR CORRESPONDENCE Silicon Valley 2710 Sand Hill Road Menlo Park CA 94025 T +1 650 618 9250 (Switchboard) E sarah.

-

TABLE OF CONTENTS As confidentially submitted to the Securities and Exchange Commission on January 25, 2021.

EX-4.2

Exhibit 4.2

WARRANT TO PURCHASE COMMON STOCK

Exhibit 4.3 THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE "ACT"), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AS SET FORTH IN SECTIONS 5.3 AND 5.4 BELOW, MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND LAWS OR IN FORM AND SUBSTANCE SATISFACTORY TO THE COMPANY, S

WARRANT TO PURCHASE COMMON STOCK

Exhibit 4.5 THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE ?ACT?), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AS SET FORTH IN SECTIONS 5.3 AND 5.4 BELOW, MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND LAWS OR IN FORM AND SUBSTANCE SATISFACTORY TO THE COMPANY, S

WARRANT TO PURCHASE COMMON STOCK

Exhibit 4.4 THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE ?ACT?), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AS SET FORTH IN SECTIONS 5.3 AND 5.4 BELOW, MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND LAWS OR IN FORM AND SUBSTANCE SATISFACTORY TO THE COMPANY, S

WARRANT TO PURCHASE SERIES C PREFERRED STOCK

Exhibit 4.7 Execution Version WARRANT TO PURCHASE SERIES C PREFERRED STOCK THIS WARRANT AND THE SECURITIES ISSUABLE UPON EXERCISE OF THIS WARRANT HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED, OR QUALIFIED UNDER ANY STATE OR FOREIGN SECURITIES LAWS AND MAY NOT BE OFFERED FOR SALE, SOLD, PLEDGED, HYPOTHECATED OR OTHERWISE TRANSFERRED OR ASSIGNED UNLESS (I) A REGISTRATION STA

RESTATED CERTIFICATE OF INCORPORATION ZYMERGEN INC.

Exhibit 3.1 RESTATED CERTIFICATE OF INCORPORATION OF ZYMERGEN INC. (Pursuant to Sections 242 and 245 of the General Corporation Law of the State of Delaware) Zymergen Inc., a corporation organized and existing under and by virtue of the provisions of the General Corporation Law of the State of Delaware (the "General Corporation Law"), DOES HEREBY CERTIFY: FIRST: That the name of this corporation i

WARRANT TO PURCHASE COMMON STOCK

Exhibit 4.6 THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE ?ACT?), OR THE SECURITIES LAWS OF ANY STATE AND, EXCEPT AS SET FORTH IN SECTIONS 5.3 AND 5.4 BELOW, MAY NOT BE OFFERED, SOLD, PLEDGED OR OTHERWISE TRANSFERRED UNLESS AND UNTIL REGISTERED UNDER SAID ACT AND LAWS OR IN FORM AND SUBSTANCE SATISFACTORY TO THE COMPANY, S

AMENDED AND RESTATED BYLAWS OF ZYMERGEN, INC. (A DELAWARE CORPORATION) TABLE OF CONTENTS

Exhibit 3.3 AMENDED AND RESTATED BYLAWS OF ZYMERGEN, INC. (A DELAWARE CORPORATION) TABLE OF CONTENTS Page ARTICLE I OFFICES 1 1.1 Registered Office 1 1.2 Offices 1 ARTICLE II MEETINGS OF STOCKHOLDERS 1 2.1 Location 1 2.2 Timing 1 2.3 Notice of Meeting 1 2.4 Stockholders? Records 1 2.5 Special Meetings 2 2.6 Notice of Meeting 2 2.7 Business Transacted at Special Meeting 2 2.8 Quorum; Meeting Adjour