Ex Parte Nakamura et al

Board of Patent Appeals and Interferences

Nov 22, 2010

10720177 (B.P.A.I. Nov. 22, 2010)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte JUN NAKAMURA and KAYO AKIYAMA
__________

Appeal 2010-002880
Application 10/720,177
Technology Center 1600
__________

Before CAROL A. SPIEGEL, LORA M. GREEN, and
MELANIE L. McCOLLUM, Administrative Patent Judges.

GREEN, Administrative Patent Judge.

DECISION ON APPEAL1
This is a decision on appeal under 35 U.S.C. § 134 from the
Examiner’s rejection of claims 1, 4, 5, 12-16, and 18-21. Claims 8-11 are
also pending, but stand withdrawn from consideration. (App. Br. 3.) We
have jurisdiction under 35 U.S.C. § 6(b).

1 The two-month time period for filing an appeal or commencing a civil
action, as recited in 37 C.F.R. § 1.304, or for filing a request for rehearing,
as recited in 37 C.F.R. § 41.52, begins to run from the “MAIL DATE”
(paper delivery mode) or the “NOTIFICATION DATE” (electronic delivery
mode) shown on the PTOL-90A cover letter attached to this decision.
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STATEMENT OF THE CASE
Claim 1 is the only independent claim on appeal and reads as follows:
1. An isolated coryneform bacterium having L-glutamine-producing
ability, wherein said bacterium has been modified by disrupting or mutating
a glutaminase gene on the chromosome so that the glutaminase activity of
the bacterium is reduced to 0.1 U/mg of cellular protein or less, wherein said
glutaminase gene is selected from the group consisting of:
a) a DNA comprising the DNA sequence of SEQ ID NO: 1, and
b) a DNA which is able to hybridize with the DNA of SEQ ID NO: 1
under stringent conditions of 1 X SSC, 0.1% SDS, at 60°C, and is 95% or
more homologous to SEQ ID NO: 1.

The following grounds of rejection are before us on appeal:
I. Claims 1, 4, 5, 12-16, and 18-21 stand rejected under 35 U.S.C.
§ 112, second paragraph.
II. Claims 1, 4, 5, 12-16, 18, 19, and 21 stand rejected under 35
U.S.C. § 112, first paragraph, as failing to comply with the written
description requirement.
III. Claims 1, 4, 5, 12-16, and 18-21 stand rejected under 35 U.S.C.
§ 112, first paragraph, as failing to comply with the enablement
requirement.
IV. Claims 1, 4, 5, 13-16, and 19-21 stand rejected under 35 U.S.C.
§ 103(a) as being rendered obvious by the combination of
Nakamura,2 Pompejus,3 Jakoby,4 Nakagawa,5 and Durán.6

2 Nakamura, EP 1 229 121 A2, published August 7, 2002.
3 Pompejus, WO 01/00843 A2, published January 4, 2001.
4 Jakoby et al., Isolation of the Corynebacterium glutamicum glnA gene
encoding glutamine synthetase I, 154 FEMS MICROBIOLOGY LETTERS 81-88
(1997).
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We reverse rejections I, II, and III, but affirm rejection IV.
ISSUE I
Has the Examiner set forth a prima facie case that the use of the term
“homology” renders the claims on appeal indefinite?

FINDINGS OF FACT
FF1 The Examiner’s statement of the rejection may be found at pages 3-13
of the Examiner’s Answer.
FF2 Specifically, the Examiner finds that claims “1, 5 and 16 . . . are
indefinite in the recitation of ‘95% or more homologous to SEQ ID NO:
X.’” (Ans. 3.)
FF3 According to the Examiner, as the Specification
does not provide the specific parameters/methods intended in
the calculation of sequence homology (e.g., PAM matrices),
one of skill in the art cannot determine the scope of the term
“95% homologous” because a percent sequence homology
value for a set of sequences is variable depending on the
parameters used in the calculation and Appellant has not set
forth the intended method/parameters for that calculation.

(Id. at 3-4.)

FF4 The Examiner then set forth two different alignments using different
parameters (id. at 4-15), finding that one set of parameters finds that the

5 Nakagawa, EP 1 108 790 B1, published June 20, 2001.
6 Durán et al., The role of glutaminase in Rhizobium etli: studies with a new
mutant, 141 MICROBIOLOGY 2883-2889 (1995).
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sequences are 95.4% homologous, while another set of parameters finds that
the sequences are 96.1% homologous (id. at 37).

PRINCIPLES OF LAW
“The test for definiteness is whether one skilled in the art would
understand the bounds of the claim when read in light of the specification.”
Miles Laboratories, Inc. v. Shandon, Inc., 997 F.2d 870, 875 (Fed. Cir.
1993). Claims are in compliance with 35 U.S.C. § 112, second paragraph, if
“the claims, read in light of the specification, reasonably apprise those
skilled in the art both of the utilization and scope of the invention, and if the
language is as precise as the subject matter permits.” Hybritech, Inc. v.
Monoclonal Antibodies, Inc., 802 F.2d 1367, 1385 (Fed. Cir. 1986).

ANALYSIS
Appellants argue that “standardized and well-practiced methods for
determining homology between sequences [are] known to those of skill in
the art,” such as through the use of the BLAST program. (App. Br. 8.)
We agree with Appellants. The results shown by the Examiner
demonstrate that the use of different parameters may result in a conclusion
that two sequences may be 95.4% homologous or 96.1% homologous.
Given that the difference is only 0.7% and given that the use of alignment
programs such as BLAST is well known and routine with the art, the skilled
artisan would reasonably understand the metes and bounds of the claim
limitation “95% or more homologous to SEQ ID NO: 1.”

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CONCLUSION OF LAW
We conclude that the Examiner has not set forth a prima facie case
that the use of the term “homology” renders the claims on appeal indefinite.
We thus reverse the rejection of claims 1, 4, 5, 12-16, and 18-21 under 35
U.S.C. § 112, second paragraph.

ISSUE II
Has the Examiner established a prima facie case that the Specification
fails to describe the claims on appeal within the meaning of 35 U.S.C. § 112,
first paragraph?

FINDINGS OF FACT
FF5 The Examiner’s statement of the rejection may be found at pages 13-
15 of the Answer.
FF6 The Examiner notes that the “claims require a precise reduction in
glutaminase activity to a specific level of glutaminase activity (0.1 U/mg or
0.01 U/mg) and a precise ratio of glutamine synthetase activity to
glutaminase activity (2:1) obtained by any means.” (Ans. 14, original
emphasis.)
FF7 The Examiner finds that neither the Specification nor the prior art
provides an “adequate description of the genus of methods by which one
could achieve the required activity levels.” (Id.)
FF8 The Examiner finds further that as “the claims require a precise level
of reduction in enzymatic activity and/or a precise ratio of enzymatic
activities,” that the Specification
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should provide some description as to how one of skill in the art
should mutate the recited glutaminase genes such that those
mutations would result in that precise level of enzymatic
activity reduction in any coryneform bacterium as recited . . . .
[as well as ] adequate description as to the modifications that
can be made to a coryneform bacterium as recited such that one
could achieve the desired ratio.
(Id.)
FF9 The Examiner also finds, citing Witkowski7 for the proposition that
“even a single conservative substitution can result in enzymatic activity
changes,” that the Specification and prior art do not “provide a
structure/function correlation for glutaminases or glutamine synthetases that
would allow one of skill in the art to envision the structural modifications
required in the recited genes to obtain the desired reduction in glutaminase
activity, or the desired ratio of glutaminase to glutamine synthetase activity.”
(Id. at 15.)

PRINCIPLES OF LAW
“The burden of showing that the claimed invention is not described in
the application rests on the PTO in the first instance.” In re Edwards, 568
F.2d 1349, 1354 (CCPA 1978).

[T]he determination of what is needed to support generic
claims to biological subject matter depends on a variety
of factors, such as the existing knowledge in the
particular field, the extent and content of the prior art,
the maturity of the science or technology, the

7 Witkowski et al., Conversion of a β-Ketoacyl Synthase to a Malonyl
Decarboxylase by Replacement of the Active-Site Cysteine with Glutamine,
38 BIOCHEMISTRY 11643-11650 (1999).
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predictability of the aspect at issue, and other
considerations appropriate to the subject matter.

Capon v. Eshhar, 418 F.3d 1349, 1359 (Fed. Cir. 2005).

ANALYSIS
Appellants argue that a “precise” reduction in glutaminase activity, or
a precise ratio of glutaminase to glutamine synthetase activity is not required
by the claims, but that the claims set an upper limit and encompass activities
below those limits. (App. Br. 10-11.)
We agree with Appellants that the Examiner appears to be interpreting
the claims to require a “precise” reduction in glutaminase activity or a
“precise” ratio of glutaminase to glutamine synthetase activity. The claims,
however, do not require a precise glutaminase activity or a precise ratio of
glutaminase to glutamine synthetase activity, but set an upper limit, and
anything that falls below that upper limit is encompassed by the claim.

CONCLUSION OF LAW
We conclude that the Examiner has not established a prima facie case
that the Specification fails to describe the claims on appeal within the
meaning of 35 U.S.C. § 112, first paragraph. We are thus compelled to
reverse the rejection of claims 1, 4, 5, 12-16, 18, 19, and 21 under 35 U.S.C.
§ 112, first paragraph, as failing to comply with the written description
requirement.

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ISSUE III
Has the Examiner established a prima facie case that the Specification
fails to enable the full scope of the claims on appeal?
FINDINGS OF FACT
FF10 The Examiner’s statement of the rejection may be found at pages 15-
20 of the Answer.
FF11 Specifically, according to the Examiner, the Specification,
while being enabling for a C. glutamicum cell, wherein said cell
has been modified to reduce the endogenous glutaminase
activity and to increase glutamine synthetase activity, wherein
the reduction in glutaminase activity is due to an inactivating
deletion in the endogenous glutaminase gene of said C.
glutamicum cell, wherein the endogenous glutaminase gene
comprises SEQ ID NO: 1 prior to the introduction of the
deletion, and the increase in glutamine synthase activity is due
to (i) an increase in the copy number of the C. glutamicum glnA
gene of SEQ ID NO: 3, or (ii) an increase in expression of the
C. glutamicum glnA gene of SEQ ID NO: 3 by placing said
gene under the control of a heterologous promoter, does not
reasonably provide enablement for (1) a coryneform bacterium
modified to reduce glutaminase activity to less than 0.1 U/mg
protein or 0.01 U/mg protein in said bacterium by mutating any
region of a glutaminase gene comprising SEQ ID NO: 1 or a
structural homolog thereof, (2) the coryneform bacterium of (1)
further modified in any way to modulate any glutamine
synthetase activity such that the recited ratio (2 to 1) of
glutamine synthetase activity to glutaminase activity is
achieved, or (3) the coryneform bacterium of (1) further
modified by increasing the expression of a glutamine synthetase
gene which is a structural homolog of the nucleic acid of SEQ
ID NO: 3, wherein said increase in expression is obtained by
increasing the copy number of the glutamine synthetase gene or
by replacing the endogenous promoter of the glutamine
synthetase gene with a stronger promoter.
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(Ans. 15-16.)
FF12 The Examiner finds that the teachings of the Specification are not
commensurate in scope with the claimed subject matter as the Specification
does not teach:
(A) the mutations which would result in (1) a coryneform
bacterium to have a glutaminase activity which is 0.1/0.01
U/mg cellular protein or less, or (2) a coryneform bacterium to
have the recited glutaminase activity and the recited ratio of
glutaminase to glutamine synthetase activity, (B) the structure
of any glutamine synthetase gene and mutations required to
modulate the expression of said gene so that the recited ratio of
glutaminase to glutamine synthetase is obtained, and (C) the
structural features required in any structural variant of the
polynucleotide of SEQ ID NO: 3 such that it can encode a
protein having glutamine synthetase activity.

(Id. at 17.)
FF13 As with the written description rejection, the Examiner also
finds that the Specification lacks any disclosure of mutations that
would lead to the precise reduction in glutaminase activity, as well as
those mutations that would result in the precise glutaminase to
glutamine synthetase activity. (Id. at 18.)
FF14 The Examiner also reiterates that neither the Specification nor
the art provides a structure/function correlation, “such that one of skill
in the art can envision the structure of any nucleic acid encoding a
glutamine synthetase,” or “such that one of skill in the art would know
which structural modifications are required to obtain the desired effect
in glutaminase and glutamine synthetase activity.” (Id.)
FF15 The Examiner also finds:
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While methods of generating or isolating variants of a
polynucleotide were known in the art at the time of the
invention, it was not routine in the art to screen by a trial and
error process for any number of polynucleotides and determine
which ones encode glutamine synthetases. In addition, it was
not routine in the art to screen by trial and error for (1)
essentially an infinite number of mutations in either the
regulatory region of a gene or in the coding region of a gene to
determine which ones result in reduced glutaminase activity or
enhanced glutamine synthetase activity, as recited in the claims,
(2) all possible enhancers of glutamine synthetase activity such
as chemicals and the products of other genes, or (3) all possible
transcription enhancers of genes encoding glutamine
synthetases such as chemicals and the products of other genes.

(Id. at 19.)

PRINCIPLES OF LAW
[A] specification disclosure which contains a teaching of the
manner and process of making and using the invention in terms
which correspond in scope to those used in describing and
defining the subject matter sought to be patented must be taken
as in compliance with the enabling requirement of the first
paragraph of § 112 unless there is reason to doubt the objective
truth of the statements contained therein which must be relied
on for enabling support.

In re Marzocchi, 439 F.2d 220, 223 (CCPA 1971) (emphasis added).
“[I]t is incumbent upon the Patent Office, whenever a rejection on this
basis is made, to explain why it doubts the truth or accuracy of any statement
in a supporting disclosure and to back up assertions of its own with
acceptable evidence or reasoning which is inconsistent with the contested
statement.” Id. at 224.
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ANALYSIS
Appellants reiterate their argument that a “precise” reduction in
glutaminase activity, or a precise ratio of glutaminase to glutamine
synthetase activity is not required by the claims, but that the claims set an
upper limit and encompass activities below those limits. (App. Br. 12-13.)
We agree with Appellants. As noted above with respect to the written
description requirement, the claims do not require a precise glutaminase
activity or a precise ratio of glutaminase to glutamine synthetase activity, but
set an upper limit, and anything that falls below that upper limit is
encompassed by the claim. In addition, the Specification teaches different
methods of reducing glutaminase [GLS] activity (see Spec. 9-10), and as
also noted by the Examiner in the obviousness rejection, “inactivation of
genes by introducing deletions/insertions if the sequence of the target gene is
known is well known and widely practiced in the art” (Ans. 34.) Thus, it
would have been well within the level of skill of the art to disrupt
glutaminase. In addition, Nakamura teaches coryneform bacterium having
increased glutamine synthetase activity. Moreover, the Specification teaches
assays for determining glutaminase and glutamine synthetase activity (see
Specification, Examples, pp. 20-33). Moreover, there is no requirement that
the Specification enable all possible ways of achieving the claimed subject
matter, which the Examiner is apparently requiring. (See, e.g., FF15.)

CONCLUSION OF LAW
We conclude that the Examiner has not established a prima facie case
that the Specification fails to enable the full scope of the claims on appeal.
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We are thus compelled to reverse the rejection of claims 1, 4, 5, 12-16, and
18-21 under 35 U.S.C. § 112, first paragraph, as failing to comply with the
enablement requirement.

ISSUE IV
Has the Examiner established by a preponderance of the evidence that
the combination of references cited renders obvious the coryneform
bacterium of claim 1?

FINDINGS OF FACT
FF16 The Examiner’s statement of the rejection may be found at pages 21-
35 of the Answer. As Appellants have not argued the claims separately, we
focus our analysis on claim 1, and claims 4, 5, 13-16, and 19-21 stand or fall
with that claim. 37 C.F.R. § 41.37(c)(1)(vii).
FF17 The Examiner cites Nakamura for teaching a method of “producing L-
glutamine by fermentation of an L-glutamine producing C. glutamicum
cell,” wherein the cell has been modified to increase the copy number of the
gene encoding glutamine synthetase. (Ans. 21.)
FF18 Specifically, Nakamura:
relates to an L-glutamine producing bacterium belonging to
coryneform bacteria and a method for producing L-glutamine.
L-Glutamine is an industrially useful amino acid as an
ingredient of seasonings, liver function promoting agents,
amino acid transfusions, comprehensive amino acid
preparations, and so forth.

(Nakamura, ¶1.)
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FF19 The Examiner notes that Nakamura does not teach “a method for
producing L-glutamine wherein glutaminase activity is reduced.” (Ans. 21.)
FF20 The Examiner cites Durán for teaching that “glutaminase degrades
glutamine to yield glutamate and ammonium.” (Id.)
FF21 The Examiner finds that Durán teaches a Rhizobium mutant, “wherein
the chromosomal glutaminase gene is disrupted by Tn5 mutagenesis,” and
that the mutants have increased levels of glutamine as compared to wild-
type. (Id. at 21-22.)
FF22 The Examiner thus finds that Durán “clearly teach[es] that by
reducing glutaminase activity, there is an increase in glutamine levels.” (Id.
at 44.)
FF23 Specifically, Durán teaches:
Since the low glutaminase activity observed in the LM16
mutant should result in impairment of the catabolism of
glutamine to glutamate, we measured the intracellular
glutamine and glutamate pools in LM16 under different growth
conditions. In comparison with the wild-type strain, LMl6
showed a 53-fold higher glutamine content and a threefold
lower glutamate content when grown on glutamine as nitrogen
and carbon source, a sixfold higher glutamine and a twofold
lower glutamate content when grown on glutamine plus
succinate, a twofold higher glutamine and a threefold lower
glutamate content when grown on ammonium plus succinate
and a twofold higher glutamine and similar glutamate content
when grown on PY-rich medium (Table 1). This indicates that
the inability of LMl6 to grow on glutamine as nitrogen and
carbon source is not due to the lack of transport of this amino
acid.

(Durán, p. 2886 (first column).) Durán thus concludes that the metabolic
block is in the degradation of glutamine. (Id. at 2887, first column.)
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FF24 The Examiner notes that Durán does not teach “a C. glutamicum or
coryneform bacterium deficient in glutaminase.” (Ans. 22.)
FF25 The Examiner cites Jakoby for teaching a glutamine synthetase gene
from C. glutamicum that has 99.1% identity to SEQ ID NO: 3. (Id.)
FF26 The Examiner further cites Pompejus for teaching a glutaminase gene
from C. glutamicum that has 99.1% identity to nucleotides 827-1687 of SEQ
ID NO: 1. (Id. at 25.) The Examiner cites Nakagawa for teaching the
remaining structure of the glutaminase gene of Pompejus. (Id. at 28-29.)
FF27 The Examiner concludes that it would have been obvious to disrupt or
modify the glutaminase gene in C. glutamicum because Nakamura teaches a
C. glutamicum for the production of glutamine, and Durán teaches that
disruption of glutaminase results in higher levels of glutamine. (Id. at 34.)

PRINCIPLES OF LAW
A rejection for obviousness must include “articulated reasoning with
some rational underpinning to support the legal conclusion.” KSR Int’l Co.
v. Teleflex Inc., 550 U.S. 398, 418 (2007), quoting In re Kahn, 441 F.3d 977,
988 (Fed. Cir. 2006). The proper question to ask is whether a person of
ordinary skill in the art, facing the wide range of needs created by
developments in the field of endeavor, would have seen a benefit to
combining the prior art teachings. KSR, 550 U.S. at 424; see also In re
Fulton, 391 F.3d 1195, 1200 (Fed. Cir. 2004) (the desirability of the
combination may arise from nature of the problem, teachings of references,
or the ordinary knowledge of those skilled in the art). In addition,
[w]hen there is a design need or market pressure to solve a
problem and there are a finite number of identified, predictable
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solutions, a person of ordinary skill has good reason to pursue
the known options within his or her technical grasp. If this
leads to the anticipated success, it is likely the product not of
innovation but of ordinary skill and common sense. In that
instance, the fact that a combination was obvious to try might
show it was obvious under §103.

KSR, 550 U.S. at 421.

ANALYSIS
Appellants argue that “Duran only teaches uptake of glutamine added
to the medium by the bacterial cells, and does not show production of
glutamine by the LM16 strain in the culture medium.” (App. Br. 15.)
According to Appellants, “it is known that glutamine is synthesized from
glutamate and ammonium via the catalytic effect of glutamine synthetase,”
and thus the ordinary artisan “would know that the production of glutamine
decreases when the intracellular glutamate concentration decreases.” (Id.)
Appellants further assert that from Figure 3 of Durán, the ordinary artisan
would understand that “glutaminase is clearly not involved, or involved very
minimally, in the degradation of glutamine.” (Id. at 16.)
Appellants’ arguments have been carefully considered, but are not
found to be convincing. As found by the Examiner, Nakamura teaches a
method of using a C. glutamicum to produce L-glutamine. (See FF17.)
Nakamura teaches that the L-glutamine can then be obtained from the
medium. (Nakamura, ¶54.) Durán teaches that glutaminase is involved in
the breakdown of L-glutamine to yield glutamate and ammonium. (See
FF20.) Thus, we agree with the Examiner that it would have been obvious
to the ordinary artisan to suppress glutaminase activity by disrupting or
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mutating the gene for glutaminase on the chromosome in order to suppress
the breakdown of L-glutamine to glutamate and ammonium.
As to Appellants’ argument that glutamine is synthesized from
glutamate and ammonium via the catalytic effect of glutamine synthetase, as
taught by Nakamura, many carbon sources are known, such as “glucose,
glycerol, fructose, sucrose, maltose, mannose, galactose, starch
hydrosolysate and molasses, and organic acids such as acetic acid and citric
acid, and alcohols such as ethanol.” (Nakamura, ¶56.) In addition, the
disruption of the glutaminase gene would merely prevent the desired
product, L-glutamine, from being degraded to glutamate and ammonium.
Finally, as to Appellants’ argument that Figure 3 of Durán demonstrates that
glutaminase is not involved, or involved very minimally, in the degradation
of glutamine, this is contrary to the specific teachings of Durán, as Durán
clearly teaches that “glutamine is also degraded by a glutaminase which
catalyses its hydrolytic deamidation to yield glutamate and ammonium.”
(Durán, p. 2884, first column.)
Appellants further assert that Durán uses a rhizobial strain, asserting
that “[i]t is known that the rizobial [sic] strains use nitrogen assimilation
similar to that used and studied in plants,” and that “later review papers
which describe the nitrogen metabolism of other types of bacteria such as
the Corynebacterium and E. coli, do not describe the glutaminase as
described in Duran.” (App. Br. 16.) Appellants also argue that in the
Rhizobium bacterium of Durán, that when glutamine is used as the sole
carbon source, an enzyme called GOGAT would not work, whereas when
glucose is added to the medium, that enzyme would have a greater
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contribution to the degradation of glutamine. (Id. at 17.) Thus, Appellants
assert, Durán does not “teach or suggest an increased glutamine level in a
glutaminase-deficient bacterium when glucose is present in the medium,”
and as such, actually teaches away from the claimed invention. (Id.)
Appellants’ arguments are again not convincing. While Appellants
argue that later reviews apparently distinguish the glutaminase of
Corynebacterium and E. Coli from that of the rhizobial strain of Durán,
Appellants have not provided those review papers, and arguments of counsel
cannot take the place of evidence in the record. In re Scarbrough, 500 F.2d
560, 566 (CCPA 1974). Similarly, Appellants have not provided any
evidence to support their arguments based on the role of the GOGAT
enzyme, such that the ordinary artisan would not expect that disruption of
the glutaminase gene would not inhibit breakdown of the desired product, L-
glutamine.
Finally, our mandate is to give claims their broadest reasonable
interpretation. In re American Academy Of Science Tech Center, 367 F.3d
1359, 1364 (Fed. Cir. 2004). Claim 1 is drawn to “[a]n isolated coryneform
bacterium having L-glutamine-producing ability,” thus any coryneform
bacterium that has the ability to produce L-glutamine, as long as it meets the
remaining limitations of the claim, would be encompassed by claim 1.

CONCLUSION OF LAW
We conclude that the Examiner established by a preponderance of the
evidence that the combination of references cited renders obvious the
coryneform bacterium of claim 1. We thus affirm the rejection of claims 1,
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4, 5, 13-16, and 19-21 under 35 U.S.C. § 103(a) as being rendered obvious
by the combination of Nakamura, Pompejus, Jakoby, Nakagawa, and Durán.

SUMMARY
We reverse the rejections under 35 U.S.C. § 112 of claims 1, 4, 5, 12-
16, and 18-21, but affirm the obviousness rejection of claims 1, 4, 5, 13-16,
and 19-21.

TIME PERIOD FOR RESPONSE
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a)(1)(iv)(2006).

AFFIRMED-IN-PART

cdc

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SPIEGEL, Administrative Patent Judge. Concurring-in-part and Dissenting-
in-part.

I agree with the decision of the majority of this panel to reverse the
ground of rejection under 35 U.S.C. § 112, second paragraph (definiteness),
and to affirm the obviousness rejection under 35 U.S.C. § 103(a). However,
I respectfully disagree with respect to the grounds of rejection under 35
U.S.C. § 112, first paragraph (written description and enablement), which I
would affirm. I focus my attention on claims 1 and 14.
A. Representative Claims
Claim 1, the sole independent claim on appeal, and claim 14 are
representative and read as follows (App. Br. 20-21).
1. An isolated coryneform bacterium having L-
glutamine-producing ability, wherein said
bacterium has been modified by disrupting or
mutating a glutaminase gene on the chromosome
so that the glutaminase activity of the bacterium is
reduced to 0.1 U/mg of cellular protein or less,
wherein said glutaminase gene is selected from the
group consisting of:
a) a DNA comprising the DNA sequence
of SEQ ID NO:1, and
b) a DNA which is able to hybridize
with the DNA of SEQ ID NO: 1 under stringent
conditions of 1 X SSC, 0.1% SDS, at 60oC, and is
95% or more homologous to SEQ ID NO: 1.

14. The bacterium of claim 1, wherein the
glutaminase activity of the bacterium is reduced to
0.01 U/mg of cellular protein or less.

A. Written Description
1. Positions of Appellants and the Examiner
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The Examiner agrees with Appellants "that disruption of the
glutaminase gene … would result in no glutaminase activity (0 U/mg), and 0
U/mg protein is a species of the genus of levels of [reduced] glutaminase
activity recited" (Ans. 39). However, the Examiner correctly points out that
the claims encompass not only bacteria lacking glutaminase activity, but also
bacteria mutated to achieve a specified reduced level of glutaminase activity
of 0.1 U/mg cellular protein (claim 1) or 0.01 U/mg cellular protein (claim
14) (id.). According to the Examiner, since these levels of glutaminase
activity "are the main embodiments of the genus of glutaminase activity
levels recited, one of skill in the art would expect, at a minimum, that the
specification would adequately describe those embodiments which are
considered representative of the genus" (id.).
Appellants argue that claim 1 "does not require one to achieve exactly
[a glutaminase activity of] exactly 0.1 U/mg, … only that the [glutaminase]
gene is disrupted or mutated so that the level falls below this activity
number" (App. Br. 10-11). According to Appellants, "disruption and/or
mutation of genes are well-known procedures in the art, and the teachings of
the specification combined with these well-known methods clearly
demonstrate that the claimed invention is adequately described" (id. at 11).
Appellants further argue that, based on the submitted amino acid
alignment of various glutaminases (Exhibit A), one of ordinary skill in the
art "would clearly recognize which regions are important for the enzymatic
activities of the proteins … and would be able to reduce the activities of the
proteins by introducing amino acid mutations at such regions" (id.).
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According to the Examiner, Appellants' amino acid sequence
alignment data is unpersuasive because conserved amino acid regions may
be evolutionary artifacts which are not necessarily related to enzyme activity
and, therefore, do not provide guidance/suggestion as to the effect of making
a particular modification on enzymatic activity levels absent additional
structure/function correlation information (Ans. 39-40). The Examiner cites
Seffernick8 and Witkowski (see n.7 supra) as evidence that two proteins
having 98% sequence identity can have two different functions, i.e., catalyze
two different reactions, and that even a single conservative can result in
enzymatic activity changes, respectively (Ans. 15, 40-41). Thus, the
Examiner maintains that, absent some structure/function correlation or some
guidance as to which mutations are required to obtain the desired reduction
in glutaminase activity, one of skill in the art cannot reasonably conclude
that the claimed invention is adequately described in the Specification (id. at
15).
These are not new arguments. The Examiner and Appellants have
maintained substantially the same positions throughout prosecution of the
instant Application. For example, on page 3 of the Pre-Appeal Brief
Request for Review filed June 17, 2008, Appellants argued that based on
the alignment of the protein sequences of
glutaminase (gls) (Exhibit A …), one of ordinary
skill in the art would clearly recognize which
regions are important for the enzymatic activities
of the proteins, and would be able to reduce the

8 Seffernick et al., Melamine Deaminase and Atrazine Chlorohydrolase: 98
Percent Identical but Functionally Different, 183 JOURNAL OF
BACTERIOLOGY 2405-2410 (2001) ("Seffernick").
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activities of the proteins by introducing amino acid
mutations at such regions, and hence the claims are
fully and adequately described. Furthermore, one
of ordinary skill in the art would be able to readily
ascertain expression regulatory sequence of the
recited glutaminase gene on the chromosome of a
coryneform bacterium based on the sequence
information for glutaminase genes, and would be
able to mutate or disrupt the expression regulatory
sequence of the recited glutaminase gene. That is,
one of ordinary skill in the art would be able to
obtain a coryneform bacterium in which
gluatminase activity is reduced to 0.1U/mg of
cellular protein or less, by mutating or disrupting
the recited glutaminase gene … and/or by mutating
or disrupting expression regulatory sequence of the
recited glutaminase gene, based on the known
sequence information for glutaminase genes, the
teaching of the specification, and the knowledge
and level of skill in this art. No undue
experimentation is required to determine such
information, and the invention is fully and
adequately described ….

Similarly, on pages 6-7 of the Office action mailed October 16, 2008, prior
to mailing of the Answer, the Examiner stated that
as previously indicated, the written description
issue … is the fact that the claims require a precise
reduction in glutaminase activity to a specific level
of glutaminase activity (0.1 U/mg or 0.01 U/mg)
…obtained by any means. … However, in view of
the fact that the claims require a precise level of
reduction in enzymatic activity, the specification
should provide some description as to how one of
skill in the art should mutate the recited
glutaminase genes such that those mutations would
result in that precise level of enzymatic activity
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23
reduction in any coryneform bacterium as recited,
or how should one [sic] modulate expression of the
recited genes to obtain the desired level of
enzymatic activity. …
With regard to the alignments …, it is
unclear … how one could look at the conserved
regions in the alignments and determine which
modifications would result in the desired effect if
(1) there is no structure/function correlation that
would provide one of skill in the art with some
suggestion as to the effect of making a particular
modification on function, (2) the art as previously
discussed [i.e., Seffernick and Witkowski] teaches
the unpredictability of determining a priori the
effect of structural changes on a protein's function
based solely on structural similarity, and (3) …
there is no indication as to how these conserved
regions are related to the enzymatic activity
required by the claims.

Thus, the Examiner's position as to coryneform bacteria having
reduced glutaminase activity (which is required by all of the claims on
appeal) is two-fold. First, the claims expressly recite bacteria having two
ranges of reduced activity extending from no enzyme activity to a precise
upper limit -- "0.1 U/mg cellular protein or less" (claim 1) and "0.01 U/mg
cellular protein or less" (claim 14) -- but the Specification only describes
bacteria with inactivated glutaminase activity. Second, the Specification
only describes reducing glutaminase activity by totally disrupting the gene
which encodes the glutaminase, while the claimed invention (but for claim
20) encompasses any method for reducing glutaminase activity, including
mutating the gene at an unknown position(s) to produce a modified protein
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of desired activity from 0 U/mg cellular protein to 0.01 U/mg cellular
protein (claim 14) or to 0.1 U/mg cellular protein (claim 1).
Appellants' position, on the other hand, is that the claims do not
require bacteria having the exact upper limit of reduced glutaminase activity
recited in the claims. Instead, the claims simply require bacteria having
reduced glutaminase activity less than the "precise" upper limit recited in the
claims. According to Appellants, the alignments of glutaminase amino acid
sequences (Exhibit A), the teachings of the Specification, and the ordinary
level of skill in the art adequately describe the claimed invention.
2. Issue
At issue is whether the Specification describes the invention of claims
1 and 14 as required by the first paragraph of § 112.
3. Legal principles
To fulfill the written description requirement, a
patent specification must describe an invention and
do so in sufficient detail that one skilled in the art
can clearly conclude that "the inventor invented
the claimed invention." Lockwood v. American
Airlines, Inc. …([Fed. Cir.] 1997); In re Gosteli,
… (Fed. Cir. 1989). . . . Thus, an applicant
complies with the written description requirement
"by describing the invention, with all its claimed
limitations, not that which makes it obvious,” and
by using "such descriptive means as words,
structures, figures, diagrams, formulas, etc., that
set forth the claimed invention." Lockwood, …

Regents of the University of California v. Eli Lilly & Co., 119 F.3d 1559,
1566 (Fed. Cir. 1997). "The description requirement of the patent statute
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requires a description of an invention, not an indication of a result that one
might achieve if one made that invention." Id. at 1568.
To satisfy the written description requirement in a
case of a chemical or biotechnological genus, more
than a statement of the genus is normally required.
One must show that one had possession, as
described in the application, of sufficient species to
show that he or she invented and disclosed the
totality of the genus.

Carnegie Mellon University v. Hoffmann-La Roche Inc., 541 F.3d 1115,
1126 (Fed. Cir. 2008).
4. Additional findings of fact
FF28 SEQ ID NO: 1 of the Specification is the gene encoding the
glutaminase of Brevibacterium flavum strain ATCC 14067
(Specification 8).
FF 29 The Specification describes a modified strain of B. flavum
strain ATCC 14067 wherein the gene encoding glutaminase has
been disrupted (Specification 23-27).
FF30 The Examiner found that neither the Specification nor the prior
art provides a structure/function correlation for glutaminases.
(Ans. 15).
5. Analysis
Claim 1 broadly recites a genus of isolated coryneform bacteria which
have been modified such that their glutaminase activity is reduced to a level
of 0.1 U/mg cellular protein or less, wherein the gene encoding the
glutaminase protein comprises the DNA of SEQ ID NO: 1 or a DNA at least
95% homologous thereto under hybridization conditions recited in claim 1.
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SEQ ID NO: 1 is nucleotide sequence encoding the glutaminase of
Brevibacterium flavum strain ATCC 14067 (FF 28). Thus, claim 1
encompasses modified coryneform bacteria having glutaminase activities
between 0.1 U/mg cellular protein and no glutaminase activity. In other
words, contrary to Appellants' position, claim 1 does not just encompass
bacteria which have been modified to having a reduced level of glutaminase
activity vis-à-vis the parent strains, but also bacteria which have been
modified to specified levels of glutaminase activity, i.e., 0.1 U/mg cellular
protein and 0.01 U/mg cellular protein as expressly recited in claims 1 and
14.
The Specification describes a modified coryneform bacterium at one
end of the recited range, i.e., no glutaminase activity due to the disruption of
the gene encoding the protein (FF 29). However, the Specification does not
describe a modified coryneform bacterium with glutaminase activity at the
upper end of glutaminase activity expressly recited in claims 1 and 14.
Thus, Appellants have not shown that they had possession, as described in
the Specification, of sufficient species to show that they invented and
disclosed the totality of the genus recited in claim 1 (or in claim 14).
Carnegie Mellon University v. Hoffmann-La Roche, 541 F.3d at 1126.
6. Conclusion
The Specification does not describe the totality of the genus of
modified bacteria recited in claims 1 and 14 as required by the first
paragraph of § 112. Contrary to Appellants' argument that claim 1 only
requires that the glutaminase gene is "disrupted or mutated so that the level
falls below this activity number" as argued by Appellants (App. Br. 10-11),
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for example, the genus of claim 1 clearly includes a bacteria modified to
achieve a glutaminase activity of exactly 0.1 U/mg cellular protein as
correctly interpreted by the Examiner.
B. Enablement
1, Positions of Appellants and the Examiner
The Examiner acknowledges that the Specification enables complete
inactivation of the gene encoding glutaminase (Ans. 15). However,
according to the Examiner,
[t]he enablement provided [by the Specification] is
not commensurate in scope with the claims due to
the lack of information as to (A) the mutations
which would result in (1) a coryneform bacterium
to have a glutaminase activity which is 0.1/0.01
U/mg cellular protein or less, … [Ans. 17.]

Appellants argue that
one of ordinary skill in the art would be able to
obtain a coryneform bacterium in which
glutaminase activity is reduced to 0.1 U/mg of
cellular protein or any level below this activity
level, by mutating or disrupting the recited
glutaminase gene on the chromosome of a
coryneform bacterium and/or by mutating or
disrupting expression regulatory sequence of the
recited glutaminase gene, based on the known
sequence information for glutaminase genes, the
teaching of the specification, and the knowledge
and level of skill in this art. No undue
experimentation is required to determine such
information, particularly in view of the knowledge
in the prior art regarding the sequences. [App. Br.
13-14, original emphasis.]

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Again, these are not new arguments. The Examiner and Appellants
have maintained substantially the same positions throughout most of the
prosecution of the instant Application. For example, on page 3 of the Pre-
Appeal Brief Request for Review filed June 17, 2008, Appellants argue
one of ordinary skill in the art would be able to
obtain a coryneform bacterium in which
glutaminase activity is reduced to 0.1 U/mg of
cellular protein or less, by mutating or disrupting
the recited glutaminase gene on the chromosome of
a coryneform bacterium and/or by mutating or
disrupting expression regulatory sequence of the
recited glutaminase gene, based on the known
sequence information for glutaminase genes, the
teaching of the specification, and the knowledge
and level of skill in the art. No undue
experimentation is required to determine such
information, ….

Similarly, on page 10 of the Office action mailed October 16, 2008,
prior to mailing of the Answer, the Examiner maintained that
(1) there is no structure/function correlation that
would provide one of skill in the art with some
suggestion as to the effect of making a particular
modification on function, (2) the art as previously
discussed clearly teaches the unpredictability of
determining a priori the effect of structural
changes on a protein's function based solely on
structural similarity, and (3) the conserved regions
shown in the alignment are the regions which are
conserved among the proteins used in the
alignment and there is no indication as to how
these conserved regions are related to the
enzymatic activity required by the claims. Thus,
contrary to Applicant's assertion, alignments such
as those provided by Applicant would not provide
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the necessary structure/function correlation which
would allow one of skill in the art to determine a
priori which modifications are most likely to result
in the desired effect. Therefore, to enable the
entire scope of the claims, one of skill in the art
would have to test an infinite number of mutations
to determine which ones result in the desired
enzymatic activity ….(original emphasis).

2. Issue
At issue is whether the Specification enables the full scope of claims 1
and 14 as required by the first paragraph of § 112.
3. Legal principles
"[T]o be enabling, the specification … must teach those skilled in the
art how to make and use the full scope of the claimed invention without
'undue experimentation.'" In re Wright, 999 F.2d 1557, 1561 (Fed. Cir.
1993). "That some experimentation may be required is not fatal; the issue is
whether the amount of experimentation required is 'undue.'" In re Vaeck,
947 F.2d 488, 495 (Fed. Cir. 1991) (original emphasis). Some
experimentation, even if a considerable amount, is not "undue" if, for
example the specification provides a reasonable amount of guidance as to
the direction in which the experimentation should proceed. In re Wands,
858 F.2d 731, 737 (Fed. Cir. 1988).
4. Additional findings of fact
FF31 According to the Specification, glutaminase activity may be
reduced by treating bacteria with UV radiation or a
mutagenzing agent and/or by gene disruption and then
screening for bacteria with the desired level of residual
glutaminase activity (Specification 9-10).
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5. Analysis
Claims 1 and 14 encompass coryneform bacteria modified by any type
of mutation to a glutaminase gene to reduce glutaminase activity to a
specific level of 0.1 or 0.01 U/mg cellular protein, respectively. The
Specification generally describes mutating bacteria by UV irradiation, with a
mutagenizing agent, and by gene disruption (FF 31). One of skill in the art
would reasonably expect that disrupting the glutaminase gene would result
in expression of an inactive glutaminase protein, if any glutaminase protein
at all. Furthermore, one of skill in the art would reasonably expect that
mutagenesis of the glutaminase gene of a bacterium would encode a
glutaminase with reduced activity vis-à-vis that of the unmodified parent
bacterium. However, this is the precise point at which the Examiner and
Appellants part company. Appellants emphasize that claims 1 and 14
encompass modified bacteria having less than 0.1 and 0.01 U glutaminase
activity/mg cellular protein and, therefore, general knowledge in the art,
including a nucleotide sequence a glutaminase gene from a coryneform
bacterium and well-known methods of gene mutagenesis suffice to enable a
skilled artisan to make and use the subject matter of claims 1 and 14. The
Examiner, however, correctly emphasizes that claims 1 and 14 include
modified bacteria having precisely 0.1 and 0.01 U glutaminase activity/mg
cellular protein, not merely any reduction in glutaminase activity vis-à-vis
the unmodified bacteria.
Given the breadth of claims 1 and 14, including bacteria having the
expressly recited upper level of glutaminase activity, the evidence of
unpredictability submitted by the Examiner, and the lack of any specific
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structure/function guidance in the Specification, I agree with the Examiner
that it would require undue experimentation to modify a coryneform
bacterium to obtain the precise level of glutaminase activity encompassed by
the scope of claims 1 and 14. In other words, mutating a bacterium and then
screening for mutants with a desired level of residual glutaminase activity is
insufficient to enable full scope of claims 1 and 14 absent undue
experimentation.
6. Conclusion
The Specification does not enable the full scope modified bacteria
recited in claims 1 and 14 as required by the first paragraph of § 112 because
it would require undue experimentation to make bacteria modified to
achieve a glutaminase activity of exactly 0.1 or 0.01 U/mg cellular protein as
included in the scope of claims 1 and 14.

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