Ex Parte Jones et al

Patent Trial and Appeal Board

Nov 15, 2017

13059230 (P.T.A.B. Nov. 15, 2017)

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.
13/059,230 05/16/2011 Louise Jones BAT // PI 1611US00 8147
22885 7590 11/17/2017
MCKEE, VOORHEES & SEASE, P.L.C.
801 GRAND AVENUE
SUITE 3200
DES MOINES, IA 50309-2721
EXAMINER
KOVALENKO, MYKOLA V
ART UNIT PAPER NUMBER
1662
NOTIFICATION DATE DELIVERY MODE
11/17/2017 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):
patatty@ipmvs.com
michelle. woods @ ipmvs. com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte LOUISE JONES, GWENDOLINE LEACH, and STEVE COATES
Appeal 2017-001237
Application 13/059,230
Technology Center 1600
Before JEFFREY N. FREDMAN, DEVON ZASTROW NEWMAN, and
DAVID COTTA, Administrative Patent Judges.
FREDMAN, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal1 under 35U.S.C. § 134 involving claims to a genetic
construct. The Examiner rejected the claims as obvious. We have
jurisdiction under 35 U.S.C. § 6(b). We affirm.
Statement of the Case
Background
“A primary target in increasing the flavour of flue-cured tobacco is
the production of the amino acid threonine. Accumulation of high levels of
threonine in the leaves of mutant tobacco plants gives significant flavour and
1 Appellants identify British American Tobacco (Investments) Limited as the
Real Party in Interest (see App. Br. 3).
Appeal 2017-001237
Application 13/059,230
aroma benefits” (Spec. 1:10—12). “Normally, however, threonine production
is tightly regulated .... Therefore, modification of the biosynthetic pathway
which produces threonine is required” (Spec. 1:15—18). “[TJransgenic plants
containing feedback-insensitive aspartate kinase, and which are able to
overproduce threonine in comparison with wild-type plants, grew poorly and
demonstrated a catastrophic fitness cost if such plants were homozygous for
that mutation” (Spec. 1:29-32).
“The inventors ... set out to provide a transgenic plant which is able
to accumulate threonine in leaves by overcoming the feedback inhibition
loop discussed above, but ideally without any cost to its fitness” (Spec. 2:4—
7). “Consequently, the inventors have developed a series of genetic
constructs in which the feedback insensitive aspartate kinase (AK) activity is
expressed only after the plant has entered senescence” (Spec. 3:16—18).
The Claims
Claims 1—21 and 24—30 are on appeal. Independent claim 1 is
representative and reads as follows:
1. A genetic construct comprising:
a senescence specific promoter operably linked to a
coding sequence encoding a polypeptide having threonine
insensitive aspartate kinase (AK) activity.
The Issue
The Examiner rejected claims 1—21 and 24—30 under 35
U.S.C.
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Appeal 2017-001237
Application 13/059,230
§ 103(a) as obvious over Shaul,2 Liu,3 Amasino,4 Wen,5 Phukan,6
and Paris7 (Final Act. 4—17).
The Examiner finds Liu teaches “to increase threonine levels
within tobacco plants (and cured tobacco leaves) for the production
of tobacco blends having improved taste and aroma” (Final Act. 6).
The Examiner finds Shaul teaches “overexpression of a threonine
insensitive aspartate kinase from Escherichia coli in tobacco leaves
and the resulting increase in threonine levels within leaves of those
overexpressing tobacco plants” (id.).
The Examiner finds Shaul teaches “experimental plants
having leaves that achieved a very high level of threonine — an
8 3-fold increase in free threonine as compared to controls — also
exhibited the altered phenotypes of wrinkled upper leaves, delayed
flowering and partial sterility” (id.). The Examiner finds Liu also
2 Orit Shaul & Gad Galili, Threonine Overproduction in Transgenic
Tobacco Plants Expressing a Mutant Desensitized Aspartate Kinase of
Escherichia coli, 100 Plant Pathology 1157-63 (1992).
3 Liu et al., US 7,173,170 B2, issued Feb. 6, 2007.
4 Amasino et al., US 6,359,197 Bl, issued Mar. 19, 2002.
5 Jiang-Qi Wen et al., Changes in Protein and Amino Acid Levels during
Growth and Senescence ofNicotiana rustica Callus, 148 J. Plant
Physiology 707-10 (1996).
6 Rupa Phukan, Changes In Amino Acid And Protein Content In Tobacco
Leaves From Maturity To Senescence Stage, 19 Ad. Plant Sci. 99—101
(2006).
7 Stephane Paris et al., Mechanism of Control of Arabidopsis thaliana
Aspartate Kinase-Homoserine Dehydrogenase by Threonine, 278 J. Biol.
Chem. 5361-66 (2003).
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Application 13/059,230
teaches “a 150-fold increase of threonine will result in a plant
having stunted stature and that is sterile” (Final Act. 7).
The Examiner finds Amasino teaches a “sense[en]ce-specific, leaf-
and-flower-parts-specific Arabidopsis SAG 12 promoter” that “directs
sequence expression in a sense[en]ce-specific manner and within leaves and
flower parts of tobacco” (Final Act. 8). The Examiner finds Paris teaches “a
Glutamine to Alanine substitution at either of the Arabidopsis AK-HSDH’s
threonine binding sites (Gin443 and Gin524) results in threonine feedback
inhibition insensitivity” (id.).
The Examiner finds
Because together Liu et al. and Shaul et al. teach an about
2- to 10-fold increase in threonine levels may be achieved
(Shaul et al. by transgenic methods), because threonine
precursors are available during tobacco leaf senescence
(Phukan et al. and Wen et al.), and because threonine levels
within senescing tobacco leaves naturally rise by about 2.5-fold
(Wen et al. Table 1 at Page 709); a person with ordinary skill in
the art at the time the present invention was made would
reasonably expect and select a tobacco plant for having an at
least 3-fold increase in threonine levels within its senescing
tobacco leaves wherein the senescing tobacco leaves express a
threonine insensitive AK-HS DH under the control of a SAG 12
functional variant/fragment.
(Final Act. 10).
The issue with respect to this rejection is: Does the evidence of record
support the Examiner’s conclusion that Shaul, Liu, Amasino, Wen, Phukan,
and Paris render the genetic construct of claim 1 obvious?
Findings of Fact
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Application 13/059,230
1. Liu teaches: “Nicotiana tobacum comprising a higher than
average threonine content. These plants are useful for developing tobacco
blends which have improved taste and aroma” (Liu 1:17—19).
2. Liu teaches “sensitivity of AK [aspartate kinase] to feedback
inhibition is the major limiting factor for threonine synthesis” (Liu 22:38—
39).
3. Liu teaches a plant with a variant aspartate kinase enzyme that
is insensitive to feedback inhibition “in which the concentration of threonine
was about 150 times as much as that in K326, the parent control. Although
generally healthy, this plant was stunted and sterile” (Liu 22:38—60).
4. Liu teaches “novel lines of N. tobacum that produce unusually
high levels of aspartic acid in flue-cured tobacco leaves. . . . [with] a 72% to
184% increase in free aspartic acid production over unmodified N. tobacum
parent line, which normally produces about 1.48 nmoles of free aspartic acid
per milligram of dry leaf weight of flue-cured leaf material” (Liu 15:52—63).
5. Shaul teaches: “To study the potential of increasing threonine
production in plants by genetic engineering, we have expressed a mutant
desensitized AK derived from Escherichia coli in transgenic tobacco plants”
(Shaul 1157, col. 2).
6. Shaul teaches: “Plants expressing the chloroplastic-type E. coli
AK exhibited a significant increase in the level of free threonine, ranging
from about 2- to 9-fold higher than in control plants” (Shaul 1160, col. 1).
7. Shaul teaches: “Homozygous E-26 and E-15 plants, which
accumulated the highest level of threonine, exhibited an altered phenotype,
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Appeal 2017-001237
Application 13/059,230
including wrinkled upper leaves, delayed flowering, and partial sterility”
(Shaul 1160, col. 1)
8. Shaul teaches “the use of tissue-specific promoters would
enable the expression of the desensitized AK in desirable tissues, such as
seeds, thereby overcoming phenotypic problems associated with constitutive
AK expression” (Shaul 1162, col. 1).
9. Amasino teaches “a genetic construct comprising a senescence-
specific promoter operably linked to a foreign gene sequence that is not
natively associated with the promoter” (Amasino 3:10—13).
10. Amasino teaches “senescence-specific expression permits the
expression in plants of genes which might be disruptive of plant morphology
or productivity if expressed at any other stage of plant development”
(Amasino 7:9—12).
11. Amasino teaches “if one wished to obtain expression of a
protein that is deleterious to plant cells, it may be useful to place the gene
encoding the protein under the control of a senescence specific promoter so
that the protein will be produced only after the leaf reaches the end of its
useful photosynthetic life span” (Amasino 7:32—37).
12. Wen teaches “threonine accounted for more than 60 % of the
total amino acids in the calli before day 30. Thereafter, it gradually declined
to about 40 % on day 40” (Wen 710, col. 1).
13. Table 1 of Phukan is reproduced below:
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Appeal 2017-001237
Application 13/059,230
Ags of leaves idays)
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sad J 4 1 4* 4 * |: 4 4 4 4 4 4 1
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4 1 * 4 ■4 1 * 4 4 4 + ■ 4 1+ I * 4 '4 j 4 4 4 4 4 4 f
Ot-amfewbutyifc sdcf | j - — j 4 4 j
DL-pls&tyfatafssm* j | 4 4 4 1 ^ 4* « *sv jtdeucma ■4 i +. 4 -v* X* ^ i
TrypSopJvsn- - 1 ** « - 4 4 1
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DUespartfcacfcS ■HK 1 + i - ' " «* »» ~ I
1-trgSn!*** I ~ - „ «* 4 |
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l-iyrestee 1 W ! .w 4. 4 4 |
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Table 1 shows “Amino acid content of tobacco leaves during different stages
of growth” (Phukan 100).
14. Phukan teaches: “Depletion in the level of alanine and
threonine and appearance of arginine and tryptophan in the senescent leaves
as observed in the present study, may also play some role in the subsequent
decline in protein in the old leaves” (Phukan 100).
15. Paris teaches “mutation of lie442 (and not lie522) by alanine leads
to a loss of threonine sensitivity for the AK activity” (Paris 5366, col. 1).
Principles of Law
A prima facie case for obviousness “requires a suggestion of all
limitations in a claim,” CFMT, Inc. v. Yieldup Int’l Corp., 349 F.3d 1333,
1342 (Fed. Cir. 2003) and “a reason that would have prompted a person of
ordinary skill in the relevant field to combine the elements in the way the
claimed new invention does.” KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398,
418 (2007).
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Analysis
We adopt the Examiner’s findings of fact and reasoning regarding the
scope and content of the prior art (Final Act. 4—17; FF 1—15) and agree that
the claims are rendered obvious by Shaul, Fiu, Amasino, Wen, Phukan, and
Paris. We address Appellants’ arguments below.
Appellants contend
the alleged motivation to combine the elements disclosed in the
art to arrive at a threonine insensitive aspartate kinase (AK)
under the control of a senescence- specific promoter in a plant,
with a reasonable expectation of success, does not exist given
that multiple references cited by the Office that are inconsistent
and would have dissuaded a skilled practitioner from arriving at
the presently claimed subject matter.
(App. Br. 13.)
We find this argument unpersuasive. Fiu teaches that tobacco leaves
with increased threonine contend “have improved taste and aroma” (FF 1)
but that threonine levels are limited by feedback inhibition of the aspartate
kinase enzyme (FF 2). Fiu teaches that this feedback inhibition may be
overcome by use of a variant aspartate kinase enzyme that is insensitive to
feedback inhibition to result in significantly increased threonine levels, but
that negative side effects of these variant aspartate kinase enzymes is that the
“plant was stunted and sterile” (FF 3).
Shaul also teaches threonine expression in tobacco plants can be
increased by using an insensitive aspartate kinase enzyme (FF 5—6) and also
recognizes that plants with high threonine levels have negative side effects
including “wrinkled upper leaves, delayed flowering, and partial sterility”
(FF 7).
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Application 13/059,230
Shaul suggests that to retain the benefits of an insensitive aspartate
kinase enzyme without the negative side effects, “the use of tissue-specific
promoters would enable the expression of the desensitized AK in desirable
tissues . . . thereby overcoming phenotypic problems associated with
constitutive AK expression” (FF 8).
Thus, the combination of Liu and Shaul reasonably suggests that the
ordinary artisan, interested in increasing threonine levels for improved taste
and aroma of tobacco, would have had reason to express known variant
aspartate kinase enzymes that increased threonine levels in a tissue specific
manner to avoid the known phenotypic problems associated with
constitutive AK expression such as stunted, sterile or wrinkled plants (FF 1—
8).
Liu and Shaul do not specifically identify all tissue specific promoters
that would be desirable for expressing the variant aspartate kinase enzymes
that result in increased threonine levels.
Amasino teaches the use of senescence-specific promoters to express
genes of interest (FF 9) and specifically suggests that use of senescence-
specific promoters “permits the expression in plants of genes which might be
disruptive of plant morphology or productivity if expressed at any other
stage of plant development” (FF 10). Amasino specifically explains that “if
one wished to obtain expression of a protein that is deleterious to plant
cells,” such as insensitive variants of aspartate kinase, “it may be useful to
place the gene encoding the protein under the control of a senescence
specific promoter so that the protein will be produced only after the leaf
reaches the end of its useful photosynthetic life span” (FF 3, 7, 11).
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Application 13/059,230
Thus, the ordinary artisan would have had reason to select the
senescence specific promoter of Amasino as the “tissue-specific promoter”
suggested by Shaul (FF 8) because Liu and Shaul recognize that aspartate
kinase is a protein deleterious to plant cells (FF 3, 7) and expression of the
insensitive variant of aspartate kinase to increase threonine levels for
improved taste of tobacco leaves may therefore occur after the leaf reaches
the end of its useful photo synthetic life span without damaging the plant
during growth and reproduction (FF 11).
Appellants contend:
overexpressing threonine to [a] level higher in a modified plant
than a nonmodified plant must overcome three feedback
inhibition loops, must have enough precursor aspartate
available, and must subsequently overcome negative feedback
inhibition from the threonine itself. This is an extremely
delicate and unpredictable balance that must be achieved.
Appellants overcame this feedback inhibition by using a
threonine insensitive aspartate kinase, but the other feedback
inhibition and aspartate pressure issues remain unpredictable.
(App. Br. 14; cf Reply Br. 2—3).
We find this argument unpersuasive. Liu and Shaul expressly
demonstrate that expression of a threonine insensitive aspartate kinase
predictably results in increased threonine expression (FF 2, 3, 6). Also,
claim 1, drawn to genetic constructs, does not require any degree of increase
in threonine expression. See In re Self, 671 F.2d 1344, 1348 (CCPA 1982)
(“[AJppellanf s arguments fail from the outset because . . . they are not based
on limitations appearing in the claims.”) If this argument is intended to
address claim 24, both Liu and Shaul teach more than three-fold higher
expression of threonine (FF 3, 6).
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Application 13/059,230
Appellants contend “expressing feedback insensitive aspartate kinase
und[er] the control of a leaf specific constitutive promoter resulted in a
severe fitness cost” and that “one can only conclude that results of increased
threonine are unpredictable as different references and different authors
reported different phenotypic effects” (App. Br. 15—16).
We are not persuaded. Liu and Shaul acknowledge that expression of
aspartate kinase results in phenotypic problems for tobacco plants, but Shaul
specifically suggests that tissue-specific promoters will predictably
overcome “phenotypic problems associated with constitutive AK
expression” (FF 8) and Amasino teaches that senescence-specific promoters
are a specific type of tissue-specific promoter that are useful for expression
of proteins “deleterious to plant cells” (FF 11). Thus, contrary to
Appellants’ arguments, the prior art suggests that the use of senescence-
specific promoters would predictably avoid the phenotypic problems that
were associated with constitutive aspartate kinase expression. “Obviousness
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) (citation omitted).
Appellants contend that “it is unpredictable to determine which
pathways are up and down regulated at senescence to determine if an
increase in production of a desired protein such as threonine may be created
using a senescence specific promoter” (App. Br. 16—17; cf. Reply Br. 5—7).
In particular, Appellants contend
One of skill in the art would not expect to be able to increase[]
threonine levels in senescence when aspartate levels (the
required precursor) does not also increase while lysine a
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Application 13/059,230
feedback inhibitor increases. In fact, Wen et al. teaches that
after day 30 there is a sharp decline in levels of total free amino
acids. The disclosure of Wen casts considerable doubt on the
availability of substrate for the aspartate kinase.
(App. Br. 17). Appellants also contend that “from the disclosure of Phukan
that aspartate may not be available as a precursor for threonine synthesis via
the aspartate kinase biosynthetic pathway during senescence” {id. at 18).
Appellants contend “the increase in levels of certain free amino acids (such
as threonine) during senescence is due to the degradation of proteins by
proteases, rather than an increase in amino acid synthesis” {id. at 19).
We are not persuaded. The issue is not the natural result of the
threonine synthesis pathway, but rather whether the vector comprising a
senescence-specific promoter regulating expression of a threonine
insensitive aspartate kinase enzyme rendered obvious by Liu, Shaul, and
Amasino would result in increased threonine production in tobacco relative
to the amount of threonine naturally present in tobacco leaves.
Consistent with Appellants’ own argument that free amino acids are
expected to be available during senescence {see App. Br. 19) and the
Examiner’s finding that “the necessary amino acids would be available to
support said expression during senescence” (Ans. 22), we conclude that the
evidence reasonably supports the position that some amount of the precursor
amino acid aspartic acid would have been available in senescent tobacco
leaves. Whether that availability is due to protein degradation or amino acid
synthesis does not detract from the obvious expression of a threonine-
insensitive aspartate kinase enzyme with a senescence-specific promoter of
Amasino (FF 11) to increase threonine levels, as shown occurs by Fiu and
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Shaul (FF 3, 6), in order to obtain the benefits of increased threonine taught
by Liu (FF 1).
Conclusion of Law
The evidence of record supports the Examiner’s conclusion that
Shaul, Liu, Amasino, Wen, Phukan, and Paris render the genetic construct of
claim 1 obvious.
SUMMARY
In summary, we affirm the rejection of claim 1 under 35 U.S.C.
§ 103(a) as obvious over Shaul, Liu, Amasino, Wen, Phukan, and Paris.
Claims 2—21 and 24—30 fall with claim 1.
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
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