Ex Parte Mashko et al

Board of Patent Appeals and Interferences

Sep 1, 2010

11002141 (B.P.A.I. Sep. 1, 2010)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte SERGEI VLADIMIROVICH MASHKO and
DANILA VADIMOVICH ZIMENKOV
__________

Appeal 2009-010864
Application 11/002,141
Technology Center 1600
__________

Before ERIC GRIMES, JEFFREY N. FREDMAN, and
STEPHEN WALSH, Administrative Patent Judges.

FREDMAN, Administrative Patent Judge.

DECISION ON APPEAL1
This is an appeal under 35 U.S.C. § 134 involving claims to a method
of controlling gene expression and an expression control sequence. The
Examiner rejected the claims as obvious. We have jurisdiction under 35
U.S.C. § 6(b). We reverse.

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
The invention concerns a “prokaryotic artificial regulatory system
providing increase of the controlled gene expression as the result of increase
of an intracellular concentration of the sense amino acid” (Spec. 5, ll. 17-
20).
Claims 11-16 and 24-26 are on appeal (see App. Br. 2). The
claims have not been argued separately and therefore stand or fall
together. 37 C.F.R. § 41.37(c)(1)(vii). Independent claim 11 is
representative and reads as follows:
11. A method for controlling expression of a
target gene, comprising
transforming a bacterium with a genetic
construct comprising an expression control
sequence,
cultivating said bacterium in a culture
medium, and changing an intracellular
concentration of an amino acid on which
expression control by the expression control
sequence depend, to control expression of the
target gene,
wherein the expression control sequence is
an expression control sequence which controls
expression of a target gene linked downstream of
the expression control sequence depending on an
intracellular concentration of an amino acid,
wherein in a bacterium which harbors a
DNA construct comprising the expression control
sequence, a promoter linked upstream of the
expression control sequence and the target gene
linked downstream of the expression control
sequence, frequency of termination in the
expression control sequence when transcription
initiates from the promoter is decreased due to an
increase in the intracellular concentration of an
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amino acid, whereby expression of the target gene
increases,
wherein said expression control sequence
comprises a region coding for a leader peptide
comprising said amino acid and a ρ independent
terminator, wherein when translation of the leader
peptide stops at codon of said amino acid in the
course of the translation in case of starvation of
said amino acid, a base pairing structure of the ρ
independent terminator is formed in a transcript of
the expression control sequence, whereby the
frequency of termination in the expression control
sequence, of the transcription increases;
wherein said expression control sequence
comprises five segments which are from an
attenuator of a tryptophan operon of Escherichia
coli and an attenuator of a histidine operon of
Escherichia coli when the five segments are
numbered in order from an upstream side, the first
and second segments, and a coding region for the
leader peptide comprise the corresponding part of
the attenuator of the tryptophan operon, the fourth
and fifth segments comprise the corresponding part
of the attenuator of the histidine operon, and the
third segment comprises a combination of the
corresponding parts of the attenuators of the
tryptophan operon and the histidine operon;
wherein the first segment overlaps with
codon of the amino acid in the leader peptide; and
wherein the sequence of each segment or a
part thereof and the sequence of the adjacent
segment or a part thereof constitute an inverted
repeat sequence.

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The issue2
The Examiner rejected claims 11-16 and 24-26 under 35 U.S.C. §
103(a) as obvious over Lu,3 Gish,4 and Landick5 (Ans. 3-7).
The Examiner concludes it would have been obvious
to combine the construct as taught by Lu with elements of the
expression control sequence that is regulated by tryptophan
as taught by Gish with a rearrangement of the well described
terminator and antiterminator sequences of the his operon
taught by Landick, so that expression control sequence
comprising a promoter and target gene is regulated and
increased by intracellular amino acid concentration,
particularly tryptophan. One would have been motivated to
combine these teachings in order to obtain the expected
benefit of an efficient inducible expression construct for the
expression of heterologous DNA.

(Ans. 6.)
Appellants contend that “even if the skilled artisan were to combined
the disclosures of Lu et al, Gish et al, and Landick et al, the concept of an
anti-attenuator would not have been expected” (App. Br. 7-8). Appellants

2 The Examiner does not restate the claim objection, so we will
treat this objection as withdrawn.
3 Chung-Dar Lu and Ahmed T. Abdelal, The gdhB Gene of
Pseudomonas aeruginosa Encodes an Arginine-Inducible NAD+-
Dependent Glutamate Dehydrogenase Which is Subject to
Allosteric Regulation, 183 J. BACTERIOLOGY 490-499 (2001).
4 Kurt Gish and Charles Yanofsky, Evidence Suggesting cis Action
by the TnaC Leader Peptide in Regulating Transcription
Attenuation in the Tryptophanase Operon of Escherichia coli, 177
J. BACTERIOLOGY 7245-7254 (1995).
5 Robert Landick and Charles Yanofsky, Transcription Attenuation
in ESCHERICHIA COLI AND SALMONELLA TYPHIMURIUM CELLULAR
AND MOLECULAR BIOLOGY 1276-1301 (F. Niedhardt Ed., 1987).
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contend that “the transcript of an anti-attenuator takes the antitermination
configuration when the amount of the final product is adequate (i.e.,
sufficient). Thus, the response to the final product in an anti-attenuator (i.e.,
the present invention) is the exact opposite of the response in an attenuator
(i.e., that disclosed by Landick et al)” (id. at 9).
Appellants contend that
even assuming arguendo that the artisan would have been
motivated to combine the disclosure of Lu et al, Gish et al,
and Landick et al to obtain an efficient inducible expression
construct for the expression of heterologous DNA, at best
the resulting expression construct will be an attenuator based
on a combination of the attenuators disclosed in the cited
references.

(Id. at 10.)
The issue with respect to this rejection is: Does the evidence of record
support the Examiner’s conclusion that the cited prior art renders obvious a
method of controlling expression with an anti-attenuator expression control
sequence as required by Claim 11?
Findings of Fact (FF)
1. The Specification teaches an artificial regulatory system, which
“unlike the natural attenuators of amino acid operons, provides not decrease,
but increase of the controlled gene expression in case of excess of the sense
amino acid intracellular concentration” (Spec. 5, l. 27 to 6, l. 4).
2. Specification Figure 1 is reproduced below:
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“Fig. 1 shows the explanatory scheme of the structures and properties of the
native attenuators and the expression control sequence (artificial anti-
attenuator)” (Spec. 11, ll. 2-5).
3. Table 1 of the Specification is reproduced below:

“Table 1. Determination of CAT activity in the strains carrying the
recombinant plasmids with the tested regulatory elements” (Spec. 25, ll. 8-
10).
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4. The Specification shows that the native trpL attenuator
increases expression during starvation of the amino acid tryptophan relative
to the expression in conditions of excess tryptophan, while the “anti-
attenuators” show increased levels of expression during tryptophan excess
relative to tryptophan starvation (see Spec. 25, Table 1).
5. Lu teaches a recombinant plasmid with the gdhB operon which
when “grown in LB supplemented with 20 mM arginine, had a 28-fold-
higher NAD-GDH activity than the control strain” (Lu 492, col. 2).
6. The Examiner finds that Lu teaches a regulatory operon which
“comprises at least 3 segments capable of forming base pair structures . . .
The sequence taught contains an inverted repeat sequences (Id. ‘GTTG’, in
sequence line ‘70’)” (Ans. 5).
7. Gish teaches that “[e]levated levels of tryptophan induce
transcription antitermination at one or more Rho factor-dependent
termination sites in the leader region of the operon” (Gish 7245, abstract).
8. Gish teaches “plasmids containing the intact tna operon
(pKG1), a translational fusion of tnaA to lacZ driven by the tna promoter . . .
or the tet promoter” (Gish 7248, col. 1).
9. Gish teaches that in tests “with a plasmid containing the intact
tna operon, there was appreciable induction by DL-1-methyltryptophan and
L-tryptophan” (Gish 7248, col. 1).
10. Gish teaches that “these data support the conclusion that the
predicted RNA secondary structures are not responsible for tryptophan
induction” (Gish 7251, col. 1).
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11. Landick teaches regarding the his operon that “segments of the
leader transcript theoretically can fold into two alternative secondary
structures: one has a potential Rho-independent terminator at its 3’ end, and
the other structure could function as an antiterminator” (Landick 1283, col.
2).
Principles of Law
The Examiner has the initial burden of establishing a prima facie case
obviousness under 35 U.S.C. § 103. In re Oetiker, 977 F.2d 1443, 1445
(Fed. Cir. 1992).
“[R]ejections on obviousness grounds cannot be sustained by mere
conclusory statements; instead, there must be some articulated reasoning
with some rational underpinning to support the legal conclusion of
obviousness.” KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 418 (2007).
Analysis
The Examiner acknowledges that Landick “does not teach how to
modify an attenuator to impart anti-attenuator activity” (Ans. 8). The
Examiner nevertheless contends that “one would have been motivated to
combine these references, and the attenuators, in order to obtain the expected
benefit of an efficient inducible expression construct for the expression of
heterologous DNA” (id.).
The Examiner’s statement is not an articulated reason to make an anti-
attenuator, nor is there any underpinning to support this conclusion. The
Examiner, while identifying a teaching of the his operon (FF 11), does not
even provide evidence that the trp operon is taught in the prior art.
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The Examiner also argues that “the name of the composition does not
matter . . . the references teach that the frequency of termination in the
expression control sequence is decreased, leading to gene expression that is
increased due to an increase in amino acid concentration” (Ans. 9-10).
We are not persuaded since this is not what claim 11 requires for the
expression control sequence. Claim 11 is directed towards a method for
controlling target gene expression using an expression control sequence
which increases the frequency of termination of translation “in case of
starvation of amino acid” (see Claim 11). Thus, as Appellants contend, the
“attenuator attenuates translation as an amino acid increases, whereas the
anti-attenuator attenuates translation as an amino acid decreases” (App. Br.
10).
We agree with Appellants that the Examiner has not adequately
explained how the references would have suggested modifying an attenuator
into an anti-attenuator as required by Claim 11. The Examiner has not
pointed to any disclosure in Lu, Gish, or Landick that provides any
disclosure of an anti-attenuator like activity. Although the Examiner
concludes that this limitation would have been obvious based on Landick,
the Examiner has not pointed out any part of Landick that would have
suggested to one of skill in the art the formation of an anti-attenuator. The
Examiner has not explained how Landick’s “could function” (FF 11)
statement provided sufficient information.
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Conclusion of Law
The evidence of record does not support the Examiner’s conclusion
that the cited prior art renders obvious a method of controlling expression
with an anti-attenuator expression control sequence as required by Claim 11.
SUMMARY
In summary, we reverse the rejection of claims 11-16 and 24-26 under
35 U.S.C. § 103(a) as obvious over Lu, Gish, and Landick.

REVERSED

cdc

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