Ex Parte Nishio et al

Patent Trial and Appeal Board

Jan 10, 2013

10933280 (P.T.A.B. Jan. 10, 2013)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte YOSUKE NISHIO, EIICHIRO KIMURA, YOSHIHIRO USUDA,
KAZUHO IKEO, YOJI NAKAMURA, TAKASHI GOJOBORI,
YUTAKA KAWARABAYASHI, YUMI HINO, EIICHI HORI,
and JUN YAMAZAKI
__________

Appeal 2011-010490
Application 10/933,280
Technology Center 1600
__________

Before ERIC GRIMES, MELANIE L. McCOLLUM, and
ULRIKE W. JENKS, Administrative Patent Judges.

GRIMES, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a method
of modifying a protein, which have been rejected for obviousness. We have
jurisdiction under 35 U.S.C. § 6(b). We reverse.
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STATEMENT OF THE CASE
“[T]hermostable enzymes[ ] are advantageous over those that are
inactivated at high temperatures because they do not need to be cooled to be
active” (Spec. 1, ¶ 6). The Specification discloses that
amino acid substitutions which might be involved in
temperature resistance could be precisely predicted by
comparing a large number of amino acid sequences of
orthologous genes extracted from the genome sequences of two
types of closely related bacteria showing different optimum
growth temperatures, that is, bacteria of a thermophilic type and
a mesophilic type.
(Id. at 6, ¶ 21.)
Claims 1 and 3-5 are on appeal. Claim 1 is the only independent
claim and reads as follows (emphasis added):
1. A method for modifying the thermostability of a protein, comprising
(a) selecting 1000 or more genes from the genome of a first
microorganism, and selecting 1000 or more genes from the genome of a
second microorganism, wherein the genes from the first microorganism are
orthologs to the genes from the second microorganism, and wherein the
second microorganism is closely related to the first microorganism, but
grows differently under an optimum growth condition wherein the optimum
growth condition is the optimum growth temperature when compared with
the first microorganism, and
(b) comparing an amino acid sequence encoded by one of the said
1000 or more genes from the first microorganism to an amino acid sequence
encoded by the orthologous gene from the second microorganism,
(c) detecting substitutions between the amino acid sequence encoded
by one of the said 1000 or more genes from the first microorganism and the
amino acid sequence encoded by the orthologous gene from the second
microorganism for each pair of orthologous genes,
(d) compiling the detected amino acid substitutions for each amino
acid substitution type,
(e) calculating the frequency of each amino acid substitution type,
wherein for each detected amino acid substitution type, a correction is made
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by subtracting the total number of substitution types which occur from the
first microorganism to the second microorganism from the total number of
the same substitution type which occurs in the reverse direction, or from the
second microorganism to the first microorganism,
(f) identifying and labelling the amino acid substitutions which occur
at a high frequency, and
(g) modifying the thermostability of said protein by introducing one or
more mutations into a gene encoding said protein so that the amino acid
substitutions identified in (f) occur.

The Examiner has rejected all of the claims on appeal under 35 U.S.C.
§ 103(a) as obvious based on Akihiko
1
and Gianese
2
(Answer 3). The
Examiner finds that Akihiko discloses a method of improving the thermo-
stability of a protein by “comparing the amino acid sequences of proteins
from two or more species, which evolutionarily correspond to each other . . .
to infer an ancestral amino acid sequence” and modifying a protein to match
the sequence of the ancestral protein (id. at 5). The Examiner finds that
Gianese discloses the analysis required by step e) of claim 1 (id. at 6-7).
The Examiner acknowledges that Akihiko does not teach selecting
1000 or more genes from each of the two species but concludes that it
suggests this limitation because “the selection of two or more species to
compare, in a sense is selecting two or more genomes from which to select a
gene and its protein/amino acid sequence to compare” (id. at 5-6). The
Examiner concludes that it would have been obvious

1
Akihiko Yamagishi, EP 1 182 253 A2, published Feb. 27, 2002. The
Examiner and Appellants refer to this reference as Akihiko, so we do as
well.
2
Gianese et al., Structural adaption of enzymes to low temperatures, 14
PROTEIN ENGINEERING 141-148 (2001).
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to have selected 1000 or more genes from the genomes of the
two or more species from which to select a gene and its
protein/amino acid sequence to compare for modification
[because] . . . [s]electing more potential genes, i.e. 1000 or
more from each microorganism, from which to select a single
gene to compare has no patentable significance.
(Id. at 6.)
Appellants argue that “the methods of Akihiko and Gianese are quite
different from each other, because, as shown in schemes II to IV . . . ., they
are directed to completely different techniques” (Appeal Br. 9). Appellants
also argue that “Scheme V of Exhibit A demonstrates further advantages
which are not taught or suggested by Akihiko or Gianese. Such advantages
and/or features of the claimed method are not disclosed nor suggested by the
distinctly different methods taught by Akihiko and Gianese.” (Id. at 9-10.)
We agree with Appellants that the Examiner has not persuasively
shown that Akihiko and Gianese would have made obvious a method having
all of the features of the claimed method. See In re Oetiker, 977 F.2d 1443,
1445 (Fed. Cir. 1992) (“[T]he examiner bears the initial burden, on review
of the prior art or on any other ground, of presenting a prima facie case of
unpatentability. If that burden is met, the burden of coming forward with
evidence or argument shifts to the applicant.”).
Claim 1 requires selecting at least 1000 orthologous pairs of genes
from two different microorganisms, comparing the amino acid sequences
encoded by the genes, and “detecting substitutions . . . for each pair of
orthologous genes” (claim 1; see also Appeal Br. Exhibit A (Scheme V):
“more than a thousand types of protein pairs are used”). The substitutions
are then compiled, the frequency of each is calculated and corrected to
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identify substitutions that occur at high frequency, and a protein is modified
to include the substitution(s) to modify its thermostability (claim 1). The
Specification describes an example of the claimed method (Spec. 17-21)
using 1430 orthologous pairs of genes (id. at 18, ¶ 66) to predict “the amino
acid substitutions involved in the higher thermostability of Corynebacterium
efficiens in comparison with Corynebacterium glutamicum” (id. at 21, ¶ 70).
Akihiko discloses that “the ancestors common to eubacteria,
eukaryotes and archaebacteria might be ultra-thermophilic bacteria” and
therefore “for designing and producing a thermostable protein, it is more
important that the amino acid sequence of ancestral protein is estimated and
mimicked” (Akihiko 2, ¶ 5). Akihiko discloses a method for improving
thermostability of proteins by “comparing amino acid sequences of proteins
derived from two or more species which evolutionarily correspond to each
other,” “estimating an amino acid sequence of an ancestral protein
corresponding to” the compared proteins, and modifying one of the
compared proteins to match the sequence of the ancestral protein (id. at 2,
¶ 6). Akihiko provides an example that compares the amino acid sequences
of 3-isopropylmalate dehydrogenase (IPMDH; id. at 2, ¶ 2) from seven
species and the amino acid sequences of isocitrate dehydrogenase (ICDH;
id.) from four species, to predict the amino acid sequence of a single
ancestral protein (id. at 6-8).
Gianese discloses comparison of the amino acid sequences of 21
enzymes from different psychrophilic (cold-adapted) organisms with
homologous proteins from mesophiles and thermophiles (Gianese 141).
Specifically, Gianese compares each of 21 specific enzymes, from any of 17
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psychrophilic species, to between 2 and 51 homologs from mesophilic or
thermophilic species, for a total of 427 comparisons (id. at 144, Table I).
Gianese states that its “analysis is aimed at detecting general features of
structural adaptation of enzymes to low temperatures” (id. at 143, right col.).
Thus, neither Akihiko nor Gianese describes a process that compares
a large number of genes from one particular (e.g., thermostable) species with
a large number of orthologous genes in a second (e.g., non-thermostable)
species to identify substitutions that are characteristic of proteins from a
species with a particular optimum growth temperature. We agree with
Appellants (Appeal Br. Exhibit A, Scheme V) that it is hard to get the idea
of comparing at least 1000 protein pairs from the disclosures of Akihiko and
Gianese. In other words, the Examiner has not provided an adequate basis
for concluding that it would have been obvious, based on Akihiko and
Gianese, to compare the amino acid sequences of at least 1000 pairs of
orthologous proteins from two different species in order to identify amino
acid substitutions that are characteristic of thermostable proteins.
SUMMARY
We reverse the rejection of claims 1 and 3-5 as obvious based on
Akihiko and Gianese.

REVERSED

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