Exhibit 4.2



[Form of   Preferred Stock Certificate] UNLESS THIS CERTIFICATE IS PRESENTED BY AN   AUTHORIZED REPRESENTATIVE OF THE DEPOSITORY TRUST COMPANY, A NEW YORK   CORPORATION (“DTC”), TO THE CORPORATION OR THE TRANSFER AGENT, AND ANY   CERTIFICATE ISSUED IS REGISTERED IN THE NAME OF THE HOLDER OR IN SUCH OTHER   NAME AS IS REQUESTED BY AN AUTHORIZED REPRESENTATIVE OF DTC (AND ANY PAYMENT   IS MADE TO THE HOLDER, OR TO SUCH OTHER ENTITY AS IS REQUESTED BY AN   AUTHORIZED REPRESENTATIVE OF DTC), ANY TRANSFER, PLEDGE OR OTHER USE HEREOF   FOR VALUE OR OTHERWISE BY OR TO ANY PERSON IS WRONGFUL INASMUCH AS THE   REGISTERED OWNER HEREOF HAS AN INTEREST HEREIN. TRANSFERS OF THIS GLOBAL   SECURITY SHALL BE LIMITED TO TRANSFERS IN WHOLE, BUT NOT IN PART, TO NOMINEES   OF DTC OR TO A SUCCESSOR THEREOF OR SUCH SUCCESSOR’S NOMINEE. THE CORPORATION   IS AUTHORIZED TO ISSUE MORE THAN ONE CLASS OF STOCK AND MORE THAN ONE SERIES   OF ITS CLASS OF PREFERRED STOCK. THE CORPORATION WILL FURNISH WITHOUT CHARGE   TO EACH STOCKHOLDER WHO SO REQUESTS THE POWERS, DESIGNATIONS, PREFERENCES AND   RELATIVE PARTICIPATING, OPTIONAL OR OTHER SPECIAL RIGHTS OF EACH CLASS OF   STOCK OR SERIES THEREOF AND THE QUALIFICATIONS, LIMITATIONS OR RESTRICTIONS   OF SUCH PREFERENCES AND/OR RIGHTS. Incorporated under the laws of the State of   Delaware, September 1998 Certificate Number: [] Initial Number of Shares of   Series A Convertible Preferred Stock: [ ] CUSIP [ ISIN [ ] ] YIELD10   BIOSCIENCE, INC. Yield10 Bioscience, Inc. (the “Corporation”) hereby   certifies that [ ] (the “Holder”) is the registered owner of [ ] fully paid   and non-assessable shares of the Corporation’s designated Series A   Convertible Preferred Stock, par value $0.01 per share (the “Series A   Preferred Stock”), transferable on the books and records of the Transfer   Agent, in person or by a duly authorized attorney, upon surrender of this   certificate duly endorsed or assigned and in proper form for transfer. This   Certificate and the shares represented hereby are issued and shall be held   subject to all the provisions of the Amended and Restated Certificate of   Incorporation and the Amended and Restated Bylaws of the Corporation and any   amendments thereto, including the provisions of the Certificate of   Designation of Preferences, Rights and Limitations, dated [ ], as the same   may be amended from time to time (the “Certificate of Designations”).   Capitalized terms used herein but not defined shall have the meaning given   them in the Certificate of Designations. The shares of the Series A Preferred   Stock shall be convertible in the manner and accordance with the terms set   forth in the Certificate of Designations. Reference is hereby made to the   provisions of the Series A Preferred Stock set forth in the Certificate of   Designations, which provisions shall for all purposes have the same effect as   if set forth at this place. Upon receipt of this executed certificate, the   Holder is bound by the Certificate of Designations and is entitled to the   benefits thereunder. [Unless the Transfer Agent has properly countersigned,   these shares of the Series A Preferred Stock shall not be entitled to any   benefit under the Certificate of Designations or be valid or obligatory for   any purpose.] 


    




 










IN WITNESS   WHEREOF the said Corporation has caused this Certificate to be signed by its   duly authorized officers as of [ ]. By: Name: Title: By: Name: Title:   COUNTERSIGNATURE These are shares of the Series A Convertible Preferred Stock   referred to in the within-mentioned Certificate of Designations. Dated:   American Stock Trust & Transfer Company, as Transfer Agent By: Name:   Title: