Exhibit 10.01
SECOND AMENDMENT TO PROMISSORY NOTE AND PARTNERSHIP AGREEMENT

This Second Amendment to Promissory Note and Partnership Agreement (this “Second
Amendment”) is made as of August 10, 2020 by and between Amyris, Inc., a
Delaware corporation (the “Company”), and Ginkgo Bioworks, Inc., a Delaware
corporation (“Ginkgo”), pursuant to the terms of (i) that certain Promissory
Note, dated October 20, 2017 (as amended, the “Note”), issued by the Company to
Ginkgo, (ii) that certain Partnership Agreement, dated October 20, 2017 (as
amended, the “Partnership Agreement”), by and between the Company and Ginkgo,
(iii) that certain Waiver Agreement and Amendment to Promissory Note Issued
October 20, 2017, dated September 29, 2019 (the “First Note Amendment”), by and
between the Company and Ginkgo, (iv) that certain Waiver Agreement and
Amendment, dated March 11, 2020 (the “First Partnership Amendment”), by and
between the Company and Ginkgo, and (v) that certain Waiver Agreement, dated May
6, 2020 (the “Waiver”), by and between the Company and Ginkgo. Capitalized terms
used but not otherwise defined herein shall have the meanings given to such
terms in the Note, the Partnership Agreement or the Waiver, as applicable.

RECITALS

A.    Pursuant to Section 2.1(b) of the Note, the Company is required to make
monthly interest payments to Ginkgo beginning on November 30, 2017 and
continuing on the last day of each month thereafter, through and including the
Maturity Date (each, an “Interest Payment”).

B.    Pursuant to Section 4.3(a) of the Partnership Agreement, the Company is
required to pay Ginkgo monthly fees beginning on March 31, 2020 and continuing
on the last day of each month thereafter, through and including October 31, 2021
(each, a “Partnership Payment”).

C.    The Company and Ginkgo desire to amend the Note, the Partnership Agreement
and the Waiver in order to adjust the payment terms of these agreements
effective as of May 31, 2020.

D.     Pursuant to Section 10.7 of the Note, any modification to the Partnership
Agreement shall only be effective if made in a writing signed by the Company and
Ginkgo.

E.    Pursuant to Section 9.4 of the Partnership Agreement, any modification to
the Partnership Agreement shall only be effective if made in a writing signed by
the Company and Ginkgo.

AGREEMENT

In consideration of the mutual covenants and agreements set forth herein, and
for other good and valuable consideration, the receipt and sufficiency of which
are hereby acknowledged, the parties hereto, intending to be legally bound,
agree as follows:

1.    Note Amendment. Effective May 31, 2020, the following amendments are
hereby made to the Note:

a.The definition of “Applicable Rate” in the Note is hereby amended to read as
follows:

“Applicable Rate” means (i) from October 20, 2017 to September 30, 2019
(inclusive), a rate equal to the lower of: (a) the Highest Lawful Rate; and (b)
ten and one half of one percent (10.5%) per annum; (ii)

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from and after October 1, 2019, a rate equal to the lower of: (a) the Highest
Lawful Rate; and (b) twelve percent (12%) per annum; and (iii) conditioned upon
timely Payment of Interest on September 30, 2020 and December 31, 2020, from and
after January 1, 2021, a rate equal to the lower of: (a) the Highest Lawful
Rate; and (b) nine percent (9%) per annum.

b.The definition of “Default Rate” in the Note is hereby amended to read as
follows:

“Default Rate” (i) from October 20, 2017 to September 30, 2019 (inclusive), a
rate equal to the lower of (a) the Highest Lawful Rate; and (b) fifteen and one
half of one percent (15.5%) per annum; (ii) from and after October 1, 2019, a
rate equal to the lower of: (a) the Highest Lawful Rate; and (b) seventeen
percent (17%) per annum; and (iii) conditioned upon timely Payment of Interest
on September 30, 2020 and December 31, 2020, from and after January 1, 2021, a
rate equal to the lower of: (a) the Highest Lawful Rate; and (b) fourteen
percent (14%) per annum.

c.Section 2.1 (b) of the Note is hereby amended to read as follows:

Payment of Interest.
(i)Beginning on November 30, 2017 and continuing on the last day of each month
thereafter, through and including February 29, 2019, the Company shall pay
monthly payments of interest in the amount of $105,000 (subject to Section
2.1(c), below), or such lower amount as represents payment of interest at a
fixed per annum rate equal to the Applicable Rate.
(ii)Between March 31, 2019 and August 10, 2020, the Company shall make one
payment of interest in the aggregate amount of $2,756,671 (subject to Section
2.1(c), below).
(iii)On each of September 30, 2020 and December 31, 2020, the Company shall pay
interest in the amount of $360,000 (subject to Section 2.1(c), below), or such
lower amount as represents payment of interest at a fixed per annum rate equal
to the Applicable Rate.
(iv)Beginning on March 31, 2021 and continuing on the last day of each quarter
thereafter, through the Maturity Date, the Company shall pay quarterly payments
of interest at the Applicable Rate (subject to Section 2.1(c), below).

d.Section 2.1 (c) of the Notes is hereby amended to read as follows:

Default Rate of Interest. Immediately upon the occurrence and during the
continuance of an Event of Default, the Company shall pay monthly interest at a
fixed per annum rate equal to the Default Rate. Payment or acceptance of the
increased interest rate provided in this Section 2.1(c) is not a permitted
alternative to timely payment and shall not constitute a waiver of any Event of
Default or otherwise prejudice or limit any rights or remedies of the Holder.

2.    Partnership Agreement Amendment. Effective May 31, 2020, the following
amendments are hereby made to the Partnership Agreement:

e.Section 4.3, “Partnership Payments,” is hereby amended so that the first
paragraph thereof reads as follows:

(a) Regardless of whether the Parties terminate this Agreement pursuant to
Section 5.2 (or for any other reason), the Company shall pay directly to Ginkgo
an aggregate of $4,188,610 on or before August 10, 2020, for unpaid Partnership
Payments, interest, and any fees accrued through that date. The Parties further
agree that the Company shall pay directly to Ginkgo an
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aggregate of $2,120,625 in quarterly Partnership Payments, beginning on
September 30, 2020 and continuing on the last day of each quarter thereafter,
through and including September 30, 2022 (“Partnership Payment Term”), with
Partnership Payments in the amount of $292,500 through and including December
31, 2020, and of $219,375 thereafter during the Partnership Payment Term
provided that, if Amyris does not make timely payment of any Partnership Payment
due by December 31, 2020, the quarterly Partnership Payments due beginning
January 1, 2021 shall be $292,500; and (iii) an aggregate of $9,750,000 on
October 19, 2022 (the “End of Term Payment”); provided that, if Amyris does not
prepay the entire Balance of the Note, as amended, by April 19, 2022, the End of
Term Payment shall be in the amount of $10,350,00.

3.    Waiver Amendment. Effective May 31, 2020, the following amendments are
hereby made to the Waiver:

a.Section 3, “May 2020 Payment,” is hereby deleted, and the payments set forth
in Section 3 of the Waiver are replaced by the payments set forth in Sections 1
and 2 of this Second Amendment.

4.    Full Force and Effect. Except as expressly modified by this Second
Amendment, the terms of the Note (as amended), the Partnership Agreement (as
amended), and the Waiver (as amended) shall remain in full force and effect.

5.    Release. In consideration of the agreements contained in this Second
Amendment and other good and valuable consideration, the Company unconditionally
and irrevocably releases, waives, and forever discharges Ginkgo, together with
its respective predecessors, successors, assigns, subsidiaries, affiliates,
agents, employees, directors, officers, attorneys, and attorneys’ consultants
(collectively, the “Released Parties”), from (x) any and all liabilities,
obligations, duties, promises, or indebtedness of any kind (if any) of the
Released Parties to the Company or any of its affiliates, which existed, arose,
or occurred at any time from the beginning of the world to the date of this
Second Amendment; and (y) all claims, offsets, causes of action, suits, or
defenses of any kind whatsoever (if any), which the Company or any of its
affiliates might otherwise have against the Released Parties, or any of them; in
either case of (x) or (y) on account of any condition, act, omission, event,
contract, liability, obligation, indebtedness, claim, cause of action, defense,
circumstance, or matter of any kind, which existed, arose, or occurred at any
time from the beginning of the world to the date of this Second Amendment,
whether at law or in equity, whether based upon statute, common law or
otherwise, whether matured, contingent or non-contingent, whether direct or
indirect, whether known or unknown, whether suspected or unsuspected, which the
Company ever had, now has, or may claim to have against, arising out of, based
on, asserted in, or in connection with any agreement or event.

6.    Section 1542 Waiver. In consideration of the agreements contained in this
Second Amendment and other good and valuable consideration, the Company
unconditionally and irrevocably waives any rights it has or may have pursuant to
California Civil Code Section 1542, which provides as follows:

A general release does not extend to claims that the creditor or releasing party
does not know or suspect to exist in his or her favor at the time of executing
the release and that, if known by him or her, would have materially affected his
or her settlement with the debtor or released party.

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7.    Attorneys’ Fees. The Company promises to pay to Ginkgo immediately upon
receipt of an invoice any and all reasonable attorneys’ and other professionals’
fees and expenses incurred by Ginkgo in connection with the Note (as amended),
the Partnership Agreement (as amended), and Second Amendment, including, without
limitation, with respect to the administration, collection, enforcement,
amendment or modification of any of them; and with respect to any waiver,
consent, release, termination, litigation, administrative proceeding,
arbitration, bankruptcy proceeding, or dispute resolution. Any failure by the
Company to make timely payment as set forth in this Section 7 shall render all
waivers set forth in this Second Amendment null and void.

8.    Acknowledgement. Ginkgo hereby acknowledges and agrees that the defaults
described in the First Note Amendment, the First Partnership Amendment and the
Waiver have been cured as of this date.

9.    Integration. This Second Amendment, the Note (as amended), the Partnership
Agreement (as amended), and the Waiver (as amended) shall constitute the entire
agreement and understanding of the parties with respect to the subject matter
hereof, and supersede all prior understandings and agreements, whether oral or
written, between the parties hereto with respect to the specific subject matter
hereof.

10.    Counterparts. This Second Amendment may be executed in one (1) or more
counterparts, each of which shall be deemed an original, but all of which
together shall constitute one and the same instrument. This Second Amendment may
be executed and delivered by facsimile, or by email in portable document format
(.pdf) or other electronic format, and delivery of any signature page by any
such method will be deemed to have the same effect as if the original signature
page had been delivered to the other party.

[Signature pages follow]
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IN WITNESS WHEREOF, the parties hereto have executed this Second Amendment as of
the date first above written.

AMYRIS, INC.

By: /s/ Han Kieftenbeld
Name: Han Kieftenbeld
Title: Chief Financial Officer

[Signature Page - Second Amendment]

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IN WITNESS WHEREOF, the parties hereto have executed this Second Amendment as of
the date first above written.

GINKGO BIOWORKS, INC.

By: /s/ Jason Kelly
Name: Jason Kelly
Title: CEO

[Signature Page - Second Amendment]