Justin M. Lira et al.

Patent Trials and Appeals Board

Jan 16, 2020

12517906 - (D) (P.T.A.B. Jan. 16, 2020)

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.
12/517,906 01/18/2011 Justin M. Lira P12791.1US(64593A-
US-PCT)
1695
80834 7590 01/16/2020
Magleby Cataxinos & Greenwood/Dow AgroSciences LLC
170 S. Main Street
Suite 1100
Salt Lake City, UT 84101
EXAMINER
KOVALENKO, MYKOLA V
ART UNIT PAPER NUMBER
1662
NOTIFICATION DATE DELIVERY MODE
01/16/2020 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):
ptomail@mcgiplaw.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte JUSTIN M. LIRA, TERRY R. WRIGHT, SEAN M. RUSSELL,
DONALD J. MERLO, STEVEN ROBERT WEBB, NICOLE L. ARNOLD,
ANDREW E. ROBINSON, and KELLEY A. SMITH 1
Appeal 2018-003927
Application 12/517,906
Technology Center 1600
Before ERIC B. GRIMES, JOHN G. NEW, and JAMIE T. WISZ,
Administrative Patent Judges.
GRIMES, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134(a) involving claims related to
phosphinothricin-resistant transgenic plant cells, which have been rejected as
obvious. We have jurisdiction under 35 U.S.C. § 6(b).
We REVERSE.

1 Appellant identifies the real party in interest as Dow AgroSciences, LLC.
Appeal Br. 2. We use the word Appellant to refer to “applicant” as defined
in 37 C.F.R. § 1.42(a).
Appeal 2018-003927
Application 12/517,906
2
STATEMENT OF THE CASE
The invention relates to a gene referred to in the Specification as
DSM-2 and “plant-optimized genes, encoding DSM-2 proteins.” Spec. 5.
“The DSM-2 protein is distantly related to PAT and BAR” (id. at 3), which
are both phosphinothricin acetyltransferase enzymes (id. at 2). “DSM-2 can
be useful as a transgenic trait to impart tolerance to plants to the herbicides
glufosinate, phosphinothricin, and bialaphos.” Id.
Claims 1, 5, 7–11, 31, 48, 49, 58, 59, 68, and 73–75 are on appeal.
Claims 1 and 5, reproduced below, are illustrative:
1. A phosphinothricin-resistant transgenic plant cell
comprising between 1 and 3 copies of the polynucleotide of
SEQ ID NO:3 integrated in the genomic DNA of the plant cell,
wherein the plant cell is resistant to glufosinate when applied at
a rate of 560 g ai/ha.

5. A method of selecting for a transgenic plant cell, the
method comprising:
transforming a plurality of plant cells with a low copy
number vector comprising a polynucleotide operably linked to a
promoter operable in the plant cells, wherein the polynucleotide
is SEQ ID NO:3, thereby producing transgenic plant cells
comprising a low copy number of the polynucleotide; and
growing the plurality of plant cells in a concentration of
bialaphos or glufosinate that permits cells that express the
polynucleotide to grow, while killing or inhibiting the growth
of cells that do not express the polynucleotide,
thereby selecting a transgenic plant cell that is resistant to
glufosinate when applied at a rate of 560 g ai/ha.

Appeal 2018-003927
Application 12/517,906
3
OPINION
Obviousness
Claims 1, 5, 7–11, 31, 48, 49, 58, 59, 68, and 73–75 stand rejected
under 35 U.S.C. § 103(a) as obvious based on Leemans I,2 Leemans II,3
UniProt,4 GenBank,5 Bedford,6 Wright,7 Kohli,8 and Dudits.9 Ans. 3. The
Examiner finds that Leemans I discloses transgenic plant cells comprising
DNA encoding a phosphinothricin acetyltransferase enzyme and “a method
of producing a plant cell tolerant to phosphinothricin and other glutamine
synthetase inhibitors.” Id. at 4. The Examiner finds that Leemans II teaches
similar transgenic plant cells comprising phosphinothricin acetyltransferase-
encoding DNA stably integrated into the genome. Id. at 5.
The Examiner finds that the Leemans references do not teach
transgenic plant cells comprising 1–3 copies of the polynucleotide of SEQ
ID NO: 3, as recited in the claims. Id. However, the Examiner finds that
Bedford discloses a “gene from Streptomyces coelicolor A3(2) conferring
bialaphos resistance,” which is shown by GenBank to be the same as SEQ
ID NO: 1 of Appellant’s Specification. Id. at 7. The Examiner finds that
“[t]he instant specification teaches that SEQ ID NO: 3 represents a plant-
optimized version of SEQ ID NO: 1 and that both nucleic acid sequences

2 US 5,646,024; July 8, 1997.
3 US 5,561,236; Oct. 1, 1996.
4 UniProt Accession Number JH0246 (submitted on September 10, 1999).
5 GenBank Accession Number M62753 (submitted on April 26, 1993).
6 Bedford et al., Characterization of a gene conferring bialaphos resistance in
Streptomyces coelicolor A3(2), Gene 104:39–45 (1991).
7 US 7,838,733 B2; Nov. 23, 2010.
8 Kohli et al., Transgene integration, organization and interaction in plants,
Plant Mol. Biol. 52:247–258 (2003).
9 US 6,284,945 B1; Sept. 4, 2001.
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Application 12/517,906
4
encod[e] the same protein, SEQ ID NO: 2.” Id. at 8. (The Examiner cites
UniProt as evidence that Bedford’s gene encodes SEQ ID NO: 2. Id. at 5–6.)
The Examiner finds that Wright teaches “codon optimizing bacterial
genes for expression in plants,” and specifically teaches transgenic plants
encoding an enzyme making them tolerant to 2,4-D and a method of
controlling weeds. Id. at 8. The Examiner finds that Wright also teaches
“screening out transgenic lines that had high copy number of the transgene.”
Id. The Examiner finds that Kohli teaches that “low copy number transgene
loci result in improved stability of expression” and that “Agrobacterium-
mediated transformation gives rise to lower transgene copy numbers
compared to direct transformation.” Id. at 8–9. Finally, the Examiner finds
that Dudits teaches “expression of a pat [phosphinothricin acetyltransferase]
gene in maize plants conferred resistance to 2.0 kg of active ingredient per
hectare of glufosinate.” Id. at 9.
The Examiner concludes that it would have been obvious “to modify
the teachings of Leemans-I and II using the polynucleotide sequence of . . .
Bedford . . . , to obtain the plants, plant cells, and seeds comprising a
polynucleotide encoding a protein with phosphinothricin acetyltransferase
activity.” Id. The Examiner also concludes that modifying the sequence
to codon-optimize it for expression in plants would have been
prima facie obvious given the teachings of Wright et al. The
sequence thus obtained and the instant SEQ ID NO: 3 would be
considered obvious variant[s] of each other, given that they
would encode the same protein (SEQ ID NO: 2).
Id.
The Examiner also concludes that
[s]electing the transgenic plants, cells and seeds for low copy
number of the transgene, as taught by Wright et al, would have
been obvious given the direct suggestion of Wright et al. Given
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Application 12/517,906
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the advantages of having a transgene integrated at low copy
number, as taught by Kohli et al . . . , one would have been
motivated to screen for transgenic plants and cells with 1–3
copies of the transgene . . . and one would have reasonably
expected to obtain such low copy number transformants using
the art-standard Agrobacterium-based transformation.
Id. at 9–10. The Examiner reasons that “[o]ne would have been motivated to
combine the above teachings because of the known agronomic advantages of
transgenic plants resistant to glutamine synthase inhibitors, such as
phosphinothricin or bialaphos.” Id. at 11.
We agree with the Examiner that the cited references support a prima
facie case of obviousness. Leemans I discloses a gene from Streptomyces
hygroscopicus that inactivates bialaphos. Leemans I at 2:36–39.10 Leemans I
discloses “DNA fragments capable, when introduced into plant cells and
plants, to confer on them protection against Bialaphos or PPT
[phosphinothricin].” Id. at 5:56–58. Leemans I also discloses recombinant
DNAs comprising its DNA fragments and heterologous DNA; “[p]referred
recombinant DNA contains heterologous DNA compatible with plant cells,
particularly Ti-plasmid DNA.” Id. at 6:63–65, 7:26–27.
Bedford discloses the bar gene from Streptomyces coelicolor A3(2).
Bedford 39, abstract. Bedford states that “[a]lthough S. coelicolor is
sensitive to low levels of Bp [bialaphos] (2 µg/ml), bar confers high-level
resistance to Bp (500 µg/ml) when cloned on a high-copy-number plasmid
in this species.” Id. at 43, bridging sentence. Bedford discloses that “[t]he Km
for PPT [phosphinothricin] of the S. coelicolor bar gene product is approx.
l mM, a concentration nearly 20-fold higher than the Km of the S.

10 Leemans I is a divisional of Leemans II, so their disclosures are
substantively identical. We therefore discuss only Leemans I.
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Application 12/517,906
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hygroscopicus enzyme (0.06 mM . . .).” Id. at 43, right col. Bedford states
that
the S. coelicolor chromosomal copy of bar does not confer
appreciable resistance to Bp. Moreover, high levels of identity
(> 70%) are usually found between the products of genes
encoding resistance to the same antibiotic in different
Streptomyces species. . . . In contrast, the product of the S.
coelicolor bar gene shows only approx. 30% similarity to
products of the bar/pat genes associated with the Bp
biosynthetic clusters.
Id. Bedford states that “[t]hese considerations may imply that the
physiological substrate of the bar gene product is not PPT, but a structurally
related compound.” Id.
Wright discloses transgenic plants producing an enzyme (AAD-1) that
makes them tolerant to the herbicide 2,4-D. Wright 3:58 to 4:9, 4:33–35.
Wright states that its “invention also relates to ‘plant optimized’ genes that
encode proteins of the subject invention.” Id. at 20:16–18. The “microbial
gene has been redesigned such that the protein is encoded by codons having
a bias toward both monocot and dicot plant usage (hemicot).” Id. at 20:10–
12. Wright states that “the exemplified rebuilt gene was more efficacious in
conveying herbicide resistance to the plant, as compared to the bacterial
gene.” Id. at 20:19–21. Wright provides an example of a “plant-optimized”
AAD-1 gene comprising specific codons at specific frequencies. Id. at col.
57–58 (Table 12).
The Examiner finds that Genbank shows that Appellant’s SEQ ID
NO: 1 is identical to the S. coelicolor gene disclosed by Bedford, and that
UniProt shows that Appellant’s SEQ ID NO: 2 is the amino acid sequence
encoded by both Bedford’s gene and SEQ ID NO: 3. Ans. 5–7. Appellant
does not dispute this finding. See, e.g., Appeal Br. 10 (“[T]he DSM-2 (SEQ
Appeal 2018-003927
Application 12/517,906
7
ID NO:2) polypeptide [is] encoded by the claimed SEQ ID NO:3 and the
bacterial gene of Bedford.”). Nor does Appellant dispute that SEQ ID NO: 3,
recited in the claims, would be an obvious plant-optimized variant of
Bedford’s gene. Id. at 14–16.
Kohli states that one of the two alternative strategies for producing
transgenic plants “exploits the natural ability of Agrobacterium tumefaciens
to transfer DNA from a resident plasmid into the plant genome.” Kohli 247,
left col. More specifically, “Agrobacterium tumefaciens can transfer a small
segment of DNA (known as T-DNA) from a resident Ti plasmid into the
plant genome.” Id. at 252, right col. “Generally Agrobacterium-mediated
transformation gives rise to lower transgene copy numbers compared to
direct transformation methods.” Id. at 253, left col. Kohli states that, in one
experiment, “more than one third contained a single T-DNA insert, half
contained 2–3 copies and the remainder contained 4–5 copies.” Id.
Based on the above disclosures, it would have been obvious to a
skilled artisan to make transgenic plants expressing the enzyme encoded by
Bedford’s bar gene, because Bedford discloses that expression of the gene
(albeit on a high-copy-number vector) conferred resistance to
phosphinothricin (PPT) on PPT-sensitive bacteria. PPT resistance is a
desirable trait in transgenic crop plants because Leemans I discloses that
PPT and bialaphos are nonselective herbicides that inhibit growth of all
(PPT-sensitive) plant species present, causing their total destruction.
Leemans I at 1: 62–67.
In addition, it would have been obvious to modify the gene disclosed
by Bedford to use codons optimized for plant expression, as taught by
Wright, because Wright teaches that such a rebuilt gene is more efficacious
in conveying herbicide resistance to plants, as compared to the bacterial
Appeal 2018-003927
Application 12/517,906
8
gene. Finally, Kohli teaches that using Agrobacterium-mediated
transformation is one of two alternative strategies for making transgenic
plants, and therefore it would have been an obvious choice as a method for
making transgenic plants comprising the modified bar gene. Agrobacterium-
mediated transformation transfers the transgenic DNA into the plant genome
(Kohli 252, right col.) and results in a high percentage of low copy-number
transformants (1–3 copies of the transgene) (id. at 253, left col.), as recited
in claims 1 and 5.
Finally, Dudits teaches transgenic maize plants expressing
phosphinothricin acetyltransferase (PAT) that are resistant to
phosphinothricin at a concentration corresponding to 2.0 kg/ha (Dudits
19:10–42), which is more than the 560 g/ha glufosinate required by claims 1
and 5. Thus, the claimed references would have made obvious a transgenic
plant cell, and a method of selecting for transgenic plant cells, meeting all of
the limitations of claim 1 and 5.
Appellant argues, however, that the claimed invention provides
unexpectedly superior results. Appeal Br. 16–20.11 Appellant argues that
the person of ordinary skill could never have expected that
DSM-2 would be a superior selectable marker to PAT, given
the fact that Bedford reports its affinity to be 20x lower for the
common substrate, PPT. In contrast, . . . Appellants have found
that this protein actually is a very favorable PPT resistance
marker.
Id. at 16–17 (citing Wright Decl.12 ¶ 23).

11 Appellant also argues that the cited references do not support a prima facie
case of obviousness but, for the reasons discussed below, we need not
address those arguments.
12 Declaration under 37 C.F.R. § 1.132 of Terry Wright, filed Oct. 21, 2016.
Appeal 2018-003927
Application 12/517,906
9
We agree with Appellant that the Wright Declaration provides
persuasive evidence of unexpected results for the claimed invention. The
evidence of record supports Appellant’s position that a person of ordinary
skill in the art would have had relatively low expectations for the
performance of DSM-2 (encoded by SEQ ID NO: 3) as a transgene for
conferring phosphinothricin (PPT) resistance in plants.
Those expectations would have been informed by Bedford, which
states that the chromosomal copy of the gene in S. coelicolor does not confer
resistance, instead requiring expression on a high copy-number plasmid to
do so. Bedford 43, right col. Bedford also states that the Km for the enzyme
is twenty-fold higher than the Km for the comparable S. hygroscopicus
enzyme, and that the S. coelicolor enzyme has a significantly lower degree
of amino acid sequence similarity to the S. hygroscopicus and
S. viridochromogenes enzymes (BAR and PAT, respectively) than is
“usually found between the products of genes encoding resistance to the
same antibiotic in different Streptomyces species.” Id. In view of these
considerations, Bedford suggests that the physiological substrate of its
enzyme may not even be PPT, but a related compound. Id.
Thus, Bedford would have led a skilled artisan to expect that DSM-2
could provide resistance to PPT when expressed at a high level, but a skilled
artisan would not reasonably have expected that DSM-2 would provide PPT
resistance equivalent to PAT when both were expressed in low copy
number. The Wright Declaration supports this conclusion. Dr. Wright states
that,
[p]rior to the disclosure of the present application, PAT was
considered the best available PPT selectable marker in plant
cells. No proteins having such a low level of sequence identity
Appeal 2018-003927
Application 12/517,906
10
as DSM2 to PAT . . . had been shown prior to the present
application to provide useful activity in plants.
Wright Decl. ¶ 23.
Dr. Wright also states that “[w]hen tested in the model plant system,
Arabidopsis, it was found that each of PAT . . . and DSM2 provided some
PPT resistance with low copy number (relative ranking PAT>DSM2 . . .).”
Id. “From this result, it was expected that a greater copy number of DSM2
would be required to obtain equivalent activity to that observed with PAT.”
Id.
The Wright Declaration, however, provides evidence that “even
though DSM2 was worse than PAT at conferring PPT resistance in bacteria,
it was equivalent to PAT at providing PPT tolerance in whole plants in the
greenhouse. Appendix 1, at pp. 14–15.” Id.13 Page 14 of Appendix 1
provides results for a “[s]ide by side comparison” of DSM-2 and PAT in
canola. At 840 g/ha glufosinate,14 the average injury for PAT is 5.0%, while
the lowest comparable result for DSM-2 is 7.3%; at 1680 g/ha glufosinate,
the average injury for PAT is 17.5%, and the best result for DSM-2 is
11.0%. Appendix 1, page 14. The results are said to show that “[t]olerance is
surprisingly equivalent to PAT.” Id.
Page 15 of Appendix 1 provides results for a “[s]ide by side
comparison” of DSM-2 and PAT in soybeans. The results of plant growth at
0, 411, 822, and 1644 g ae/ha glufosinate are shown visually for DSM-2,
PAT, and a control, and the results are said to show that “[t]olerance is

13 Appendix 1 was entered into the record Oct. 21, 2016, separately from but
concurrently with the Wright Declaration.
14 “[T]he term ‘glufosinate’ is synonymous with ‘phosphinothricin.’” Ans.
16.
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Application 12/517,906
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surprisingly equivalent to PAT in greenhouse.” Id., page 15. The growth of
the plants shown supports the statement that glufosinate tolerance is
equivalent for DSM-2 and PAT.
Dr. Wright also states that the “equivalence has translated to whole
plant tolerance in the field to high glufosinate rates. Appendix 1, at p. 16.”
Wright Decl. ¶ 23. Page 16 of Appendix 1 reproduces the greenhouse results
shown on page 15, and beneath them shows field results for DSM-2 and
PAT, in % injury, at 542 and 1084 g ae/ha. Appendix 1, page 16. The results
are said to show that “[t]olerance is surprisingly equivalent to PAT in
greenhouse” “[a]nd the field.” Id.
In addition to the data regarding PPT resistance, the Wright
Declaration and Appendix 1 present results for transformation frequency of
DSM-2 and PAT. Wright Decl. ¶ 23; Appendix 1, page 13. Dr. Wright states
that, “[w]hen compared in plant cells, it was surprisingly found that DSM2
was actually superior to PAT as a selectable marker in culture yielding 50–
100% improvement in canola transformation efficiency and 125%
improvement in soybean in side-by-side comparisons. Appendix 1, at p. 13”
Id.
Dr. Wright declares that “[n]one of these experimental results would
have been foreseen, let alone reasonably expected, by a person of ordinary
skill in the art at the time of the present application.” Id.
In summary, Bedford described the enzyme encoded by SEQ ID
NO: 3 of the instant claims, noting its high Km and low sequence similarity
to enzymes with similar activity, and expressing doubt about whether the
physiological substrate of the enzyme was phosphinothricin at all. The
Wright Declaration, however, provides evidence that DSM-2 (the product of
SEQ ID NO: 3) functions as well as PAT in providing resistance to
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12
glufosinate in transgenic plants, both in the greenhouse and in the field, and
also provides superior transformation frequency compared to PAT in canola
and soybeans.
Dr. Wright has stated that the transformation results were surprising,
and that neither the transformation frequency nor the PPT resistance in
plants would have been expected. Wright Decl. ¶ 23. “Mere improvement in
properties does not always suffice to show unexpected results. . . .
[H]owever, when an applicant demonstrates substantially improved results
. . . and states that the results were unexpected, this should suffice to
establish unexpected results in the absence of evidence to the contrary.” In
re Soni, 54 F.3d 746, 751 (Fed. Cir. 1995) (emphasis in original).
Here, the Examiner addresses Appellant’s data with respect to the
comparison of DSM-2 with a phosphinothricin acetyltransferase identified in
a search of annotated sequences (designated DSM-1, and not discussed
above). Ans. 22. The Examiner, however, does not point to evidence or
provide persuasive reasoning to show that a skilled artisan would have
expected DSM-2, having the same amino acid sequence as Bedford’s
enzyme, to provide PPT resistance equivalent to that of PAT when
expressed in plants. In view of Appellant’s showing of unexpected results,
we conclude that the rejection under 35 U.S.C. § 103(a) is not supported by
a preponderance of the evidence of record.
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DECISION SUMMARY
In summary:
Claims
Rejected
35 U.S.C. § Reference(s)/Basis Affirmed Reversed
1, 5, 7–11,
31, 48, 49,
58, 59, 68,
73–75
103(a) Leemans I, Leemans II,
UniProt, GenBank,
Bedford, Wright,
Kohli, Dudits
1, 5, 7–11,
31, 48, 49,
58, 59, 68,
73–75

REVERSED