Valery Vasilievich. Samsonov et al.

Patent Trials and Appeals Board

Dec 10, 2019

15165606 - (D) (P.T.A.B. Dec. 10, 2019)

UNITED STATES PATENT AND TRADEMARK OFFICE
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
15/165,606 05/26/2016 Valery Vasilievich Samsonov US-547 3374
38108 7590 12/10/2019
CERMAK NAKAJIMA & MCGOWAN LLP
127 S. PEYTON STREET
SUITE 210
ALEXANDRIA, VA 22314
EXAMINER
EPSTEIN, TODD MATTHEW
ART UNIT PAPER NUMBER
1652
NOTIFICATION DATE DELIVERY MODE
12/10/2019 ELECTRONIC
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address(es):
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PTOL-90A (Rev. 04/07)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________

Ex parte VALERY VASILIEVICH SAMSONOV,
NATALIA SERGEEVNA EREMINA, and
NATALIA VIKTOROVNA STOYNOVA
____________

Appeal 2018-007422
Application 15/165,606
Technology Center 1600
____________

Before FRANCISCO C. PRATS, TAWEN CHANG, and
JOHN E. SCHNEIDER, Administrative Patent Judges.

PRATS, Administrative Patent Judge.

DECISION ON APPEAL
Pursuant to 35 U.S.C. § 134(a), Appellant1 appeals from the
Examiner’s decision to reject claims 1–3, 6–8, 13, and 14. We have
jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM.

1 We use the word “Appellant” to refer to “applicant” as defined in 37
C.F.R. § 1.42. Appellant identifies Ajinomoto Co., Inc., a corporation of
Japan, as the Real Party in Interest. Appeal Br. 3.
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STATEMENT OF THE CASE
The sole rejection before us for review is the Examiner’s rejection of
claims 1–3, 6–8, 13, and 14 under 35 U.S.C. § 103(a) as being unpatentable
over Takikawa,2 Park,3 Marquardt,4 and Uniprot (Accession No. D6ICC5,
2013, www.uniprot.org)5 (Ans. 3–7).
Claim 1, the sole independent claim on appeal, is representative and
reads as follows:
1. A method for producing an L-amino acid comprising:
(i) cultivating an L-amino acid-producing bacterium of
the family Enterobacteriaceae in a culture medium to produce
the L-amino acid in the culture medium, the bacterium, or both;
and
(ii) collecting said L-amino acid from the culture
medium, the bacterium, or both,
wherein said bacterium has been modified to attenuate
expression of a gshA gene, and
wherein said L-amino acid is a branched-chain L-amino
acid.
Appeal Br. 10.

2 US 2011/0212496 A1 (published Sept. 1, 2011). The Examiner’s Answer,
the Appeal Brief, and the Reply Brief, all provide an incorrect document
number for the Takikawa reference, apparently due to a typographical error.
See Ans. 3; Appeal Br. 5; Reply Br. 3.
3 Jin Hwan Park et al., Metabolic engineering of Escherichia coli for the
production of L-valine based on transcriptome analysis and in silico gene
knockout simulation, 104 PNAS 7797–7802 (2007).
4 US 5,120,654 (issued June 9, 1992).
5 The Uniprot reference of record cited by the Examiner has the accession
number D6ICC5.
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DISCUSSION
The Examiner’s Rejection
The Examiner cited Takikawa as teaching a process of producing an
L-amino acid (L-glutamic acid) by culturing a bacterium belonging to the
family Enterobacteriaceae (E. coli), in which the E. coli strain was modified
to attenuate expression of the gshA gene, as recited in Appellant’s
representative claim 1. Ans. 4. The Examiner noted in particular
Takikawa’s teaching that reducing or eliminating expression of the gshA
gene enhanced production of glutamic acid. See id. (citing Takikawa ¶ 101).
The Examiner cited the Uniprot reference as evidence that “the gshA
gene from strains of E. coli encodes a protein identical to SEQ ID NO: 2”
recited in Appellant’s claim 8, which depends from representative claim 1.
Ans. 4.
The Examiner conceded that Takikawa differs from Appellant’s
representative claim 1 in that Takikawa did not teach that its process
produced valine, the L-amino acid produced by the process of claim 1. See
Ans. 4. (“Takikawa et al. do not indicate an E.coli strain having deletion of
the gshA gene for valine production, a branched-chain L-amino acid.”).
The Examiner cited Park as evidence that it would have been obvious
to produce valine using an E. coli strain modified to attenuate expression of
the gshA gene, as recited in Appellant’s claim 1. See Ans. 4–5.
Specifically, the Examiner cited Park as teaching that, when
producing valine in E. coli, the immediate precursor compound in the
biosynthetic pathway to valine is 2-ketoisovalerate, and that valine is formed
by an enzyme (ilvE) that transfers an amine group to 2-ketoisovalerate from
an amine-containing compound. Ans. 5.
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The Examiner cited Marquardt as evidence that, in E. coli, valine is
synthesized by transferring “[an] amino group from glutamate to the keto
compound 2-ketoisovalerate. As such, all valine produced by E.coli
including the L-valine production strain described by Park et al. contains an
amino group originating from glutamate, such that an intracellular pool of
glutamate is necessary for the production of valine.” Ans. 5.
The Examiner reasoned, therefore, that when using E. coli to produce
valine as taught in Park, a skilled artisan would have been motivated to
attenuate the expression of the gshA gene as taught in Takikawa, and recited
in Appellant’s representative claim 1, in order to increase the amount of
glutamic acid available for the synthesis of valine:
[T]he skilled artisan at the time of the invention would have
readily recognize[d] that sufficient amounts of glutamate to
support the activity of the transferase encoded by the ilvE gene
is required for L-valine biosynthesis. As such, the skilled
artisan at the time of filing would have been motivated to delete
the gshA gene in the L-valine production strain taught by Park
et al. to achieve the benefit of increased availability of
glutamate substrate for the transferase encoded by the ilvE gene
required for L-valine biosynthesis.
Ans. 5–6.
Analysis
As stated in In re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992):
[T]he examiner bears the initial burden . . . of presenting a
prima facie case of unpatentability. . . .
After evidence or argument is submitted by the applicant
in response, patentability is determined on the totality of the
record, by a preponderance of evidence with due consideration
to persuasiveness of argument.

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In the present appeal, having carefully considered the arguments and
evidence advanced by Appellant and the Examiner, Appellant does not
persuade us that the preponderance of the evidence fails to support the
Examiner’s conclusion of obviousness. To the contrary, we adopt as our
own the Examiner’s findings of fact, and conclusion of obviousness based
thereon. We address Appellant’s arguments below, providing the following
analysis for emphasis.
Park describes a process of producing valine, a branched amino acid
encompassed by Appellant’s representative claim 1, by culturing an
engineered strain of E. coli, a bacterium of the family Enterobacteriaceae
encompassed by claim 1. See Park 7797 (“The L-valine production strain of
Escherichia coli was constructed by rational metabolic engineering and
stepwise improvement based on transcriptome analysis and gene knockout
simulation of the in silico genome-scale metabolic network.”) (abstract).
Park explains that its approach to increasing valine production in E.
coli was to increase the concentration of valine precursors and thereby drive
enhanced valine yields. See Park 7797 (“The ilvA, leuA, and panB genes
were deleted to make more precursors available for L-valine biosynthesis.”);
see also id. at 7798 (“L-valine production was enhanced by increasing the
carbon flux toward L-valine formation. The availability of pyruvate and
2-ketoisovalerate is important because it can influence the flux toward
L-valine formation.”).
Park’s process differs from the process of Appellant’s claim 1 only in
that Park’s bacterium was not modified to attenuate expression of a gshA
gene.
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However, as the Examiner points out, and Appellant does not dispute,
it was known in the art that, in E. coli, the final enzymatic step in the
biosynthesis of valine is the transfer of an amino group from glutamate to
2-ketoisovalerate, catalyzed by a branched chain amino acid
aminotransferase encoded by the ilvE gene. See Park 7798 (Fig. 1); see also
Marquardt 1:60–64 (“The aliphatic aminotransferase from E. coli ATCC
11303, for which the ilvE gene codes, synthesizes valine . . . from the
relevant keto precursor[] by transferring an amino group from glutamate.”).
As the Examiner also points out, Takikawa discloses that production
of glutamate, the immediate precursor to valine in E. coli, can be increased
by reducing or eliminating the activity of the gshA gene:
Examples of L-glutamic acid-producing bacteria and
parent strains which can be used to derive L-glutamic acid-
producing bacteria also include strains in which activity of an
enzyme that catalyzes synthesis of a compound other than L-
glutamic acid by directing synthesis away from the biosynthetic
pathway of L-glutamic acid, or activity of an enzyme that
catalyzes a reaction of decomposing or consuming L-glutamic
acid, is reduced or eliminated. Examples of these enzymes
include . . . γ-glutamylcysteine synthetase (gshA) . . . .
Takikawa ¶ 101.
Thus, to summarize, Park teaches the desirability of enhancing valine
production in E. coli by increasing the concentration of valine precursors
through elimination of relevant enzymatic reactions, and Takikawa teaches
that reducing or eliminating the activity of the gshA gene in E. coli improves
the production of glutamate, an immediate precursor to valine in Park’s
process. Given these teachings, we agree with the Examiner that a skilled
artisan had motivation for, and a reasonable expectation of success in,
modifying Park’s process by using an E. coli strain with reduced or
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eliminated the gshA gene activity, thereby increasing the concentration of
the valine precursor glutamate available for the formation of valine, and
ultimately improving the yield of valine. We, therefore, also agree with the
Examiner that the process recited in Appellant’s representative claim 1
would have been obvious to a skilled artisan.
We acknowledge, but are not persuaded by, Appellant’s contention
that, because of the complexity of the biosynthetic pathways, a skilled
artisan “would not have concluded from these disparate and unrelated
disclosures that by increasing the amount of intracellular L-glutamic acid,
L-valine production can be increased.” Appeal Br. 7; see also id. at 8
(“Appellant’s argument is simply that the synthesis pathways for various
L-amino acids are complex and hence outcomes cannot be readily or easily
predicted based on that which is known in the prior art”); Reply Br. 5
(“[T]hat amino acid biosynthetic pathways are complex and involve multiple
and varied conditions, enzymes, and catalysts is a well-known fact. This
fact is learned in basic high school or low-college level biochemistry and
biology course, and can be found in any basic textbook for the same.”).
It is well settled that “[o]bviousness does not require absolute
predictability of success . . . . all that is required is a reasonable expectation
of success.” In re Kubin, 561 F.3d 1351, 1360 (Fed. Cir. 2009) (quoting In
re O’Farrell, 853 F.2d 894, 903–04 (Fed. Cir. 1988) (emphasis removed).
Here, as noted above, despite the complexity of the biosynthetic
pathway to valine alleged by Appellant, Park nonetheless describes
performing precisely the type of genetic modification to the valine-
producing E. coli strain posited by the Examiner—reduction or elimination
of an enzymatic activity to increase the concentration of a valine precursor.
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See Park 7797 (“The ilvA, leuA, and panB genes were deleted to make more
precursors available for L-valine biosynthesis.”); see also id. at 7798
(“L-valine production was enhanced by increasing the carbon flux toward
L-valine formation. The availability of pyruvate and 2-ketoisovalerate is
important because it can influence the flux toward L-valine formation.”).
That is, Park expressly teaches that, when producing valine in E. coli,
it was desirable to modify, genetically, the valine-producing strain by
reducing or eliminating genes to increase the concentration of valine
precursors. Given the absence of any persuasive evidence contradicting
Park’s approach to enhancing valine production in E. coli, we are not
persuaded that the alleged complexity in the valine biosynthetic pathway
would have dissuaded a skilled artisan from genetically modifying Park’s E.
coli strain in a manner expected to increase the availability of a valine
precursor, such as glutamate.
To the contrary, because Park teaches the desirability of enhancing
valine production in E. coli by increasing the concentration of valine
precursors through elimination of relevant enzymatic reactions, and because
Takikawa teaches that reducing or eliminating the activity of the gshA gene
in E. coli improves the production of glutamate, an immediate precursor to
valine in Park’s process, we agree with the Examiner that a skilled artisan
had motivation for, and a reasonable expectation of success in, modifying
Park’s process by using an E. coli strain with reduced or eliminated the gshA
gene activity, as recited in Appellant’s claim 1.
We are also unpersuaded by Appellant’s argument that, because
glutamate is ultimately regenerated, a skilled artisan would not have
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considered it obvious to increase the amount of glutamate available for
valine formation by the E. coli strain. See Appeal Br. 7–8; Reply Br. 4–5.
In particular, Appellant contends initially that a skilled artisan would
not have been aware that the valine precursor glutamate would have been
regenerated in Park’s process, suggesting an argument in relation to
unexpected results. See Appeal Br. 7–8 (“That is, L-glutamic acid is
regenerated and used for L-valine biosynthesis, which could not have been
predicted or surmised from the cited disclosures. Hence, a skilled artisan
would not have concluded that increasing the intracellular pool of L-
glutamic acid would be effective for L-valine production.”) (emphasis
added).
Then, in the Reply Brief, Appellant contends, to the contrary, that a
skilled artisan would have been aware that glutamate was regenerated. See
Reply Br. 4 (“As the Examiner has acknowledged and we agree,
regeneration and reuse of L-glutamic acid, that is, repeated use of L-
glutamic acid as an amino group carrier, is known.”) (emphasis added).
Ultimately, as we understand it, Appellant contends that, because a
skilled artisan knew that glutamate was regenerated in E. coli, a skilled
artisan would not have considered it obvious to increase the amount of
glutamate available for valine formation by the E. coli strain:
[A] person of ordinary skill in the art would have known and
expected that native L-glutamic acid is present in an amount
required as an amino group carrier; and hence the native
L-glutamic acid can be repeatedly used for L-valine synthesis.
It can also be surmised that the person of ordinary skill in the
art would not have concluded that increasing the intracellular
pool of L-glutamic acid would be effective for L-valine
production.
Reply Br. 4.
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We are not persuaded. Appellant fails to identify any persuasive
evidence suggesting that, in processes such as that described in Park, when
making genetic modifications to increase precursor amounts to drive
production of an amino acid such as valine, skilled artisans would not have
sought to increase the overall amount of a regenerated precursor. In
particular, Appellant fails to identify any persuasive evidence suggesting
that, because glutamate was regenerated in E. coli, glutamate was present in
such an ample supply that, when increasing the amounts of other valine
precursors as taught by Park, a skilled artisan would have failed to consider
genetic modifications to increase the amount of glutamate available for
valine formation.
To the contrary, given Park’s focus on increasing the overall
concentration of valine precursors, the fact that the immediate valine
precursor glutamate was known to be regenerated does not persuade us that
a skilled artisan lacked motivation for, or a reasonable expectation of
success in, increasing the overall concentration of glutamate when seeking to
drive valine production. Given Park’s focus on increasing the concentration
of valine precursors, we find that the evidence of record suggests that a
skilled artisan would have found it desirable to use known methods of
increasing the concentration of the valine precursor glutamate, including by
reducing or eliminating the activity of the gshA gene in E. coli, as taught in
Takikawa and recited in Appellant’s representative claim 1.
In sum, for the reasons discussed, we find that the preponderance of
the evidence supports the Examiner’s conclusion of obviousness as to
Appellant’s claim 1. We, therefore, affirm the Examiner’s rejection of claim
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1 over Takikawa, Park, Marquardt, and Uniprot. Claims 2, 3, 6–8, 13, and
14 fall with claim 1. See 37 C.F.R. § 41.37(c)(1)(iv).

CONCLUSION
In summary:

Claims
Rejected
35 U.S.C.
§
Reference(s)/Basis Affirmed Reversed
1–3, 6–8, 13,
14
103(a) Takikawa, Park,
Marquardt, Uniprot
1–3, 6–8, 13,
14

TIME PERIOD
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a).

AFFIRMED