Ex Parte DOI et al

Patent Trial and Appeal Board

Mar 9, 2018

12691211 (P.T.A.B. Mar. 9, 2018)

United States Patent and Trademark Office
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
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APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
12/691,211 01/21/2010 HIDETAKA DOI US-420 9313
38108 7590 03/13/2018
CERMAK NAKAJIMA MCGOWAN LLP
127 S. Peyton Street
Suite 210
ALEXANDRIA, VA 22314
EXAMINER
ROBINSON, HOPE A
ART UNIT PAPER NUMBER
1652
NOTIFICATION DATE DELIVERY MODE
03/13/2018 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 HIDETAKA DOI and TAKUJIUEDA
Appeal 2017-005484
Application 12/691,2111
Technology Center 1600
Before RICHARD M. LEBOVITZ, RICHARD J. SMITH, and
TIMOTHY G. MAJORS, Administrative Patent Judges.
LEBOVITZ, Administrative Patent Judge.
DECISION ON APPEAL
This appeal under 35 U.S.C. § 134 involves claims directed to a
method of producing L-lysine comprising culturing an Escherichia coli
bacterium. The Examiner rejected the claims as unpatentable under 35
U.S.C. § 103. We have jurisdiction under 35 U.S.C. § 6(b). The § 103
rejection is affirmed.
1 The Appeal Brief (“Br.”) 3 identifies Ajinomoto Co., Inc., as the real-
party-in-interest.
Appeal 2017-005484
Application 12/691,211
STATEMENT OF THE CASE
Claims 18, 19, and 21-28 stand rejected by the Examiner under 35
U.S.C. § 103 as obvious in view of Kim2, Ajinomoto,3 Kojima4, Wehrmann5,
and Cahyanto6. Final Act. 3.
Claim 18, the only independent claim on appeal, reads as follows:
2 Kim et al., Cloning and Sequencing of the ddh gene involved in the Novel
Pathway of Lysine Biosynthesis from Brevibacterium Lactofermentum, 5 J
Microbiology and Biotechnology 5,250-56 (1995).
3 Ajinomoto is a Japanese patent application in the Japanese language.
Neither the Examiner nor Appellants directed us to a full translation of it.
However, it appears from this record that the Kojima patent cited in the
rejection claims the benefit of the Ajinomoto Japanese patent application
and that both Examiner and Appellants rely on it instead, even though both
repeatedly refer to “Ajinomoto”. Thus, for the purpose of this Appeal,
“Ajinomoto” is shorthand for the Kojima patent.
4 Kojima et al., US 6,040,160, issued March 21, 2000 (“Kojima”).
5 Wehrmann et al., Different Modes of Diaminopimelate Synthesis and Their
Role in Cell Wall Integrity: a Study with Corynebacterium glutamicum,
180J. Bacteriology 12,3159-65 (June 1998).
6 Cahyanto et al., Regulation of aspartokinase, aspartate semialdehyde
dehydrogenase, dihydrodipicolinate synthase and dihydrodipicolinate
reductase in Lactobacillus plantarum 152 Microbiology 105-112 (2006).
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Application 12/691,211
18. A method for producing L-lysine comprising: culturing in a medium an
Escherichia coli bacterium that has the ability to produce L-lysine; and
collecting L-lysine from the medium,
wherein said bacterium has been modified to decrease the
activity of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-
succinyltransferase [dapD] by a method selected from the
group consisting of:
a) decreasing expression of the gene
encoding 2,3,4,5-tetrahydropyridine-2,6-
dicarboxylate N-succinyltransferase, and
b) disrupting the gene encoding 2,3,4,5-
tetrahydropyridine-2,6-dicarboxy late N -
succinyltransferase, and
wherein a gene coding for diaminopimelate
dehydrogenase [ddh] has been introduced into said bacterium.
Br. 12 (Claims Appendix) (indentations and bracketed abbreviations
added for clarity).
REJECTION
Claim 18 is directed to a method for producing lysine comprising
culturing an Escherichia coli that has the ability to make lysine. The
bacterium is recited in the claims to have two genetic modifications:
1) decreased activity in the enzyme coded for by the dapD gene by
decreasing the gene’s expression or disrupting the gene; and
2) the introduction of the ddh gene into the E. coli strain.
The biosynthetic pathway of L-lysine in prokaryotes is reproduced
below.7 The figure is annotated by highlighting the dapD and ddh genes,
7 The diagram is reproduced from Roh et al., Mol. Cells, 4:296-99, 1994
(“Roh”), which has overlapping authorship with Kim. Kim also had a figure
depicting the pathways, but the copy in our electronic database was illegible.
Roh was accessed from the Internet and is attached to this Decision.
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Application 12/691,211
and adding in the names of the enzymes which mediate the first steps of the
process:
L-faprtate
I LysC (encodes aspartokiaase)
t dspar iy f pmphs t*i /
L'Aspsrtata l-sesslsldphydg
I DapA (encodes DDPS)
L~2» 3- Dihpdrodlpseol tmU
As shown in the figure reproduced above, there are three pathways for
producing lysine in prokaryotes. Roh 296. Pathway B (the DAP pathway)
operates in E. coli, and uses the dapD, dapC, dapE, and dapF enzymes. Id.
Pathway C (the DDH pathway) uses the ddh enzyme and involves fewer
steps than the DAP pathway. Id. Certain bacteria, such as B. sphaericus and
C. glutamicum, use both the DAP and DDH pathways. Id.
The Examiner found that Kim discloses cloning the ddh gene utilizing
an E. coli strain deficient in dapD. Final Act. 3.
The following findings of fact (“FF”) are pertinent:
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Application 12/691,211
FF1. Kim introduced genomic fragments from B. lactofermentum
into the dapD deficient E. coli (AT986). Kim 252.
FF2. Ddh activity is normally absent from E. coli. Roh 296; Kim
254.
FF3. The appearance of ddh activity in the dapD deficient E. coli
strain was determined using an enzyme assay for ddh. Kim 251, 254.
FF4. Kim identified a clone comprising a genomic fragment from B.
lactofermentum that conferred ddh activity on the dapD deficient strain of E.
coli, indicating that it contained the gene for ddh. Kim 252-53.
The Examiner found that although the E. coli strain described in Kim
has both genetic characteristics of the claimed E. coli, namely deficient in
dapD activity and comprising an introduced ddh gene, Kim does not teach
utilizing the strain to make lysine. Final Act. 4. However, the Examiner
found that Ajinomoto discloses “replacement of dapD with a gene coding for
ddh (diaminopimelate dehydrogenase) and the resulting effect of increased
L-lysine production (see column 14 of the patent).” Id.
The pertinent disclosure from Ajinomoto is as follows:
FF5
For this purpose, as shown in Example 6 described below, the
order of rate determining steps of the L-lysine biosynthesis
system has been elucidated by introducing, into E. coli, genes
of the L-lysine biosynthesis system originating from E. coli in a
stepwise manner. In this elucidation, four genes of dapC
succinyldiaminopimelate transaminase[,] dapD
(tetrahydrodipicolinate succinylase gene)[,] dapE
(succinyldiaminopimelate deacylase gene), and dapF
(diaminopimelate epimerase gene) located downstream in the
biosynthesis pathway were replaced with a gene DDH coding
for DDH (diaminopimelate dehydrogenase) of Brevibacterium
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Application 12/691,211
lactofermentum capable of catalyzing reactions participated by
these gene products by itself.
Ajinomoto, col. 14,11. 48-61 (underlining added).
FF6. “An enhancing effect on the L-lysine productivity was observed
only in DDH, and it was found that the reaction catalyzed by DDH was the
fourth rate determining step.” Id. at col. 36,11. 13-16.
The Examiner found that it would have been obvious to have used
Kim’s strain to produce lysine, based on the teaching in Ajinomoto that ddh
enhances lysine production (Final Act. 4; FF6) “to obtain high L-lysine
productivity.” Final Act. 5. The Examiner further found:
Additionally, one of ordinary skill in the art could easily
conceive of obtaining E. coli capable of synthesizing
diaminopimelic acid using the DDH pathway instead of the
DAP pathway by deleting genes such as dapD involved in the
DAP pathway, and introducing the ddh gene in E. coli, and of
producing L-lysine by culturing those E. coli with a reasonable
expectation of success as evidenced by the Ajinomoto Co., Inc.,
patent.
Final Act. 5.
The Examiner also found that Kim teaches “the four-step enzymatic
reaction [using the DAP pathway] can be reduced to one step [using the
DDH pathway], and therefore is advantageous.” Id. at 4. Specifically, as
found by the Examiner, Figure 1 from Roh reproduced above shows that the
DDH pathway goes directly from Tetrahydrodipicolinate to meso-
Diaminopimelate using only the ddh enzyme, while the DAP pathway makes
the same transformation but using four different enzymes, dapD, dapC,
dapE, and dapF.
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Application 12/691,211
As found by the Examiner, Kim contains the following teaching
regarding the “merit” of the DDH pathway as compared to the DAP
pathway:
It has been well know that L-lysine biosynthesis proceeds
in prokaryotes through three different pathways ... (Fig. 1).
One of them, the diaminopimelate (DAP) pathway
involving succinylated intermediates requires four steps from
tetrahydrodipieolinate (THDP) to M;wo-diaminopimelate
(mesa-DAP) and has been extensively studied in E. coll.... In
Bacillus sphaericus, THDP is converted by a single enzymatic
step to meso-DAP, catalyzed by meso-DAP dehydrogenase
(DDH).... We refer to this step as the DDH pathway. It has
been supposed that the DDH pathway has more merit by not
requiring aeetyl-CoA or succinyl-CoA and abbreviating the
enzymatic reaction of four steps as found in the DAP pathway.
Kim 250.
The Examiner also found that there would have been a reasonable
expectation of success of using Kim’s E. coli strain to make lysine based on
the teaching in Wehrmann that, when dapD is inactivated, and the bacteria is
forced to use on the DDH pathway, lysine is made. Final Act. 6.
Appellants contend that “it has not been previously reported that when
DDH is expressed in an Escherichia bacterium, decreasing the activity of an
enzyme belonging to the meso-DAP synthesis pathway can be effective for
increasing L-lysine production.” Br. 6.
Appellants contend that Ajinomoto describes two alternative
pathways for improving L-lysine synthesis. Br. 7. First, the introduction of
the ddh gene into the E. coli (the DDH pathway), and second is
overexpression of dapD and dapE genes, which encode enzymes of the DAP
pathway. Id. Appellants assert that the claimed method is directly the
opposite, that is, “enhancement of DDH in combination with a decrease in
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the activity of DapD.” Id. For this reason, Appellants contend that
Ajinomoto “clearly teaches away from the present invention, and one skilled
in the art could not have expected that decreasing the activity of any
enzyme(s) of the meso-DAP synthesis pathway in combination with the
introduction of DDH would result in improved L-lysine production.” Id.
Appellants also contend that the Examiner erred in finding that
Ajinomoto discloses that “the native dapD gene of a host bacterium was
replaced with DDH gene, or that L-lysine production was increased by such
a replacement.” Id. at 8 (emphasis added).
Appellants acknowledge that Ajinomoto states dap genes were
“replaced” by the ddh gene, but contend that when Ajinomoto is read in its
entirety, it is evident that gene replacement was not accomplished, but rather
“replaced” means replacing the function of the DAP pathway with the DDH
pathway. Br. 8-9. Appellants provided a declaration under 37 C.F.R. § 132
by the co-inventors (“132 Decl.”; dated July 14, 2015) in which they averred
that, in Ajinomoto “the dapC, dapD dapE, and dapF genes are still present in
the cell and the pathway; no gene deletion or excision is described in”
Ajinomoto. 132 Decl. ^ 5. Therefore, Appellants state:
the person of ordinary skill in the art would not have expected
that the strain disclosed in Kim, that is, a stain deficient in
dapD gene and introduced with ddh gene, would have the
ability to produce L-lysine equivalent to a strain in which both
dapD and dapE genes are ‘replaced’.
Br. 10.
DISCUSSION
We agree with Appellants that, when Ajinomoto is read in its entirety,
it is evident that the normal DAP pathway present in E. coli is still active in
the strains in which the DDH gene is introduced. We could not identify
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Application 12/691,211
disclosure in Ajinomoto of deleting, excising, or otherwise decreasing the
expression of the genes present in the DAP pathway. The only teaching, as
indicated by Appellants, is of increasing their expression by the addition of
additional gene copies of the dap genes. Br. 7.
The Examiner relied on the literal language in Ajinomoto at col. 14,11.
48-61 in finding that dap gene expression was disrupted. But this
interpretation is inconsistent with the actual experiments performed by
Ajinomoto upon which the description at column 14 relied upon by the
Examiner was based. It is more reasonable and factually consistent to read
“replaced” in column 14 of Ajinomoto to mean that the function to make
lysine by the DAP pathway was superseded by the DDH pathway. Thus, we
agree with Appellants that the Examiner erred in finding that Ajinomoto
teaches that expression of the dap genes were decreased. Ans. 12-14.
Nonetheless, we do not agree that this error undermines the rejection.
The Examiner explicitly found it would have been obvious with a reasonable
expectation of success to have used Kim’s strain to produce lysine.8 The
Examiner also gave a reason for it: because Kim specifically teaches the
merits of using the DDH pathway which uses only one enzyme opposed to
the four enzymes in the DAP pathway. Final Act. 4; Kim 250 (reproduced
above). Appellants did not persuasively identify a flaw in this reasoning.
8 “one of ordinary skill in the art could easily conceive of obtaining E. coli
capable of synthesizing diaminopimelic acid using the DDH pathway instead
of the DAP pathway by deleting genes such as dapD involved in the DAP
pathway, and introducing the ddh gene in E. coli, and of producing L-lysine
by culturing those E. coli with a reasonable expectation of success.” Final
Act. 5.
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With respect to the expectation of success, the Examiner found that it
would have been reasonably expected that the bacteria would produce lysine
in view of the teaching in Wehrmann of bacteria lacking dapD, which
produce lysine using the DDH pathway, and Ajinomoto which also teaches
that ddh expression leads to lysine production. Final Act. 6. Appellants did
not identify an error in the Examiner’s finding, but rather acknowledged
Wehrmann’s teaching (Br. 8). Thus, since Wehrmann teaches a bacteria
with the same genetic characteristics as claimed and taught by Kim, i.e.,
dapD knocked out and a functional ddh gene, the preponderance of the
evidence on this record indicates that the E. coli strain of Kim would be
effective for producing lysine. Consequently, we do not agree with
Appellants that it would be unexpected that Kim’s strain would produce
lysine. Br. 10. There is no requirement that a strain be a better producer of
lysine because Kim provides a reason to use it, i.e., to obtain the benefit of
the one-step DDH pathway, instead of the four-step DAP pathway.
Appellants argue that Ajinomoto “teaches away” from the claimed
subject matter because it teaches enhancing the activity of the DAP pathway,
not decreasing it as claimed. Br. 7. We do not agree. As recognized by
Appellants, Ajinomoto teaches “two alternative ways for improving L-lysine
production.” Br. 7. The second way is utilizing the DDH pathway. Id. The
reason to use the DDH pathway, and decrease or knock out the DAP
pathway, is to avoid the additional steps of the DAP pathway. The
Examiner expressly relied upon Kim for this teaching. Final Act. 4-5.
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SUMMARY
The obviousness of claim 18 is affirmed. Claims 19 and 21-28 were
not argued separately and fall with claim 18. 37 C.F.R. § 41.37(c)(l)(iv).
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)(l)(iv).
AFFIRMED
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