Ex Parte Livshits et alDownload PDFPatent Trials and Appeals BoardMar 22, 201915185371 - (D) (P.T.A.B. Mar. 22, 2019) Copy Citation UNITED STA TES p A TENT AND TRADEMARK OFFICE APPLICATION NO. FILING DATE 15/185,371 06/17/2016 38108 7590 03/26/2019 CERMAK NAKAJIMA MCGOWAN LLP 127 S. Peyton Street Suite 210 ALEXANDRIA, VA 22314 FIRST NAMED INVENTOR Vitaliy Arkadyevich Livshits 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 ATTORNEY DOCKET NO. CONFIRMATION NO. US-126C 9962 EXAMINER STEADMAN, DAVID J ART UNIT PAPER NUMBER 1656 NOTIFICATION DATE DELIVERY MODE 03/26/2019 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): cgoode@cnmiplaw.com ip@cnmiplaw.com scermak@cnmiplaw.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte VIT ALIY ARKADYEVICH LIVSHITS, NATALIAPAVLOVNAZAKATAEVA, VLADIMIR VENIAMINOVICH ALESHIN, ALLA V ALENTINOVNA BELAREV A, and IRINA L YVOVNA TOKHMAKOV A 1 Appeal2018-001581 Application 15/185,371 Technology Center 1600 Before RICHARD M. LEBOVITZ, JEFFREY N. FREDMAN, and JOHN G. NEW, Administrative Patent Judges. LEBOVITZ, Administrative Patent Judge. DECISION ON APPEAL This appeal involves claims directed to methods for producing amino acids in Escherichia. The Examiner rejected the claims as lacking written description and enablement under 35 U.S.C. § 112, as obvious under 35 U.S.C. § 103, and under obviousness-type double-patenting. Pursuant to 35 U.S.C. § 134, Appellant appeals the Examiner's determination that the claims are unpatentable. We have jurisdiction under 35 U.S.C. § 6(b ). The Examiner's decision is AFFIRMED. 1 The Appeal Brief ("Br." entered Jun. 2, 2017) lists Ajinomoto Co., Inc., as the real party in interest. Appeal2018-001581 Application 15/185,371 STATEMENT OF THE CASE The Examiner finally rejected the claims as follows: 1. Claims 1-7 under 35 U.S.C. § 112 (pre-AIA), first paragraph, as failing to comply with the written description requirement. Ans. 2. 2. Claims 2 and 4--6 under 35 U.S.C. § 112 (pre-AIA), first paragraph, as failing to enable the full scope of the claim. Ans. 13. 3. Claims 1--4 and 7 under 35 U.S.C. § I03(a) as obvious in view of Debabov et al. (US Patent 4,321,325, issued Mar. 23, 1982) ("Debabov"), Vrlijc et al. (US Patent 6,858,406 Bl, issued Feb. 22, 2005) ("Vrlijc"), and Zakataeva et al. (FEES Lett. 452:228-232, 1999) ("Zakataeva"). Ans. 21. 4. Claims 4--7 under 35 U.S.C. § I03(a) as obvious in view of Nakano et al. (US Patent 5,629,180, issued May 13, 1997) ("Nakano") and Zakataeva. Ans. 28. 5. Claims 1-7 under the judicially created doctrine of obviousness- type double-patenting as obvious over claims 1-6 of U.S. Patent 9,394,346 B2, issued Jul. 19, 2016). Ans. 33. Appellants did not provide arguments as to why the obviousness-type double-patenting rejection should be reversed. Accordingly, we summarily affirm the rejection for the reasons set forth by the Examiner. Final Act. 43- 45. Independent claim 1, which is illustrative of the rejected claims, is reproduced below: 2 Appeal2018-001581 Application 15/185,371 1. A method for producing the amino acid L-homoserine or L- threonine, comprising the steps of: i) cultivating a bacterium belonging to the genus Escherichia, which has the ability to produce the amino acid, in a culture medium, to produce and accumulate the amino acid in the medium, and ii) recovering the amino acid from the medium, wherein L-threonine resistance of said bacterium is enhanced by increasing the activity of a first protein in said bacterium as compared to a corresponding wild-type Escherichia bacterium by increasing the copy number of a DNA encoding said first protein or replacing a promoter sequence of said DNA, wherein said first protein is selected from the group consisting of: (A) a protein comprising the amino acid sequence shown in SEQ ID NO: 4; and (B) a protein comprising the amino acid sequence shown in SEQ ID NO: 4, but which includes deletion, substitution, insertion or addition of one amino acid in the amino acid sequence, and which has the activity of conferring resistance to L-threonine to the bacterium wherein the DNA encoding said first protein is selected from the group consisting of: (a) a DNA comprising nucleotides 187 to 804 in SEO ID NO: 3; and (b) a DNA which hybridizes with the complete complement of the nucleotide sequence of nucleotides 187 to 804 in SEQ ID NO: 3 under conditions of washing at 60°C, and at a salt concentration of 1 x SSC and 0.1 % SDS, and wherein said DNA encodes a protein having the activity of conferring resistance to L-threonine to the bacterium. THE CLAIMS Independent claim 1 is directed to a method for producing the amino acid L-homoserine or L-threonine. The method comprises cultivating Escherichia to produce the amino acid. L-threonine resistance is enhanced in the Escherichia by increasing the activity of: 3 Appeal2018-001581 Application 15/185,371 (A) a protein comprising the amino acid sequence of SEQ ID NO: 4, which is encoded by a DNA comprising nucleotides 187 to 804 in SEO ID NO: 3; or (B) a protein comprising the amino acid sequence of SEQ ID NO: 4, "but which includes deletion, substitution, insertion or addition of one amino acid in the amino acid sequence, and which has the activity of conferring resistance to L-threonine to the bacterium", and which is encoded by "a DNA which hybridizes with the complete complement of the nucleotide sequence of nucleotides 187 to 804 in SEQ ID NO: 3" (emphasis added) under specifically recited washing conditions. The activity is increased "by increasing the copy number of a DNA encoding said first protein or replacing a promoter sequence of said DNA." SEQ ID NOS: 3 (nucleotide sequence) and 4 (amino acid sequence) correspond to the rhtC gene which codes for a protein having resistance to threonine or "Rt" activity. Spec. ,r,r 31, 35, 36, 41. Independent claim 4 has the same steps as claim 1, but further comprises cultivating Escherichia to produce an amino acid using an amino acid sequence of SEQ ID NO: 2. The claim comprises: (1) utilizing a DNA coding for a protein of SEQ ID NO: 4 or a protein as in part (B) of claim 1; and (2) (C) a protein comprising the amino acid sequence shown in SEQ ID NO: 2 and (D) "a protein comprising the amino acid sequence of SEQ ID NO: 4, but which includes deletion, substitution, insertion or addition of one amino acids in the amino acid sequence shown in SEQ ID NO: 2, and which has the activity of conferring resistance to L-threonine to the bacterium." 4 Appeal2018-001581 Application 15/185,371 (D), unlike (B) is claim 1, is not limited to hybridization to a DNA sequence. SEQ ID NO: 2 corresponds to the rhtB gene and represents a protein having resistance to L-homoserine or "Rh" activity. Spec. ,r,r 31, 36, 37. WRITTEN DESCRIPTION REJECTION The Examiner rejected claims 1-7 under 35 U.S.C. § 112, first paragraph, as failing to comply with the written description requirement. Part (B) of claim 1 recites that the protein of SEQ ID NO: 4 (the rhtC gene) "includes deletion, substitution, insertion or addition of one amino acid in the amino acid sequence." The claim also recites that the DNA coding for (B) must be either SEQ ID NO: 3 or a DNA which hybridizes to it under specific washing conditions. The Examiner found that the term "includes" is open-ended language that would encompass proteins having more than one deletion, substitution, etc., of an amino acid. Final Act. 7-8. The Examiner thus construed the claim scope to include numerous species, limited only by the ability to confer resistance to L-threonine and to hybridize to SEQ ID NO: 3. Independent claim 4 has similar breadth to claim 1, but is directed to an embodiment utilizing the DNA sequence coding for SEQ ID NO: 2 (protein sequence of the rhtB gene), and amino acid modifications of it. Claim 4 is does not limit the DNA coding for SEQ ID NO: 2 to DNAs that hybridize to its coding nucleotide sequence as does claim 1. Although each of the claims define a genus of rhtC and rhtB proteins, the Examiner found that the Specification only discloses one representative species of each, namely an Escherichia coli transformed with vectors 5 Appeal2018-001581 Application 15/185,371 comprising a DNA coding for the amino acid sequence of SEQ ID NO: 4 and/or SEQ ID NO 2. Final Act. 15-16. The Examiner therefore concluded that the claimed genus of rhtB and rhtC proteins are not described in the Specification. Discussion 35 U.S.C. § 112 requires a patentee to provide a written description of the claimed subject matter that allows a person of ordinary skill in the art to recognize that the patentee invented what is claimed. Ariad Pharms., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1351 (Fed. Cir. 2010) (en bane). In University of California v. Eli Lilly & Co. ("Lilly"), 119 F.3d 1559 (Fed. Cir. 1997), the Federal Circuit set forth a test for compliance with the written description requirement when a genus of recombinant nucleotide sequences is claimed. In Lilly, only a single cDNA to rat insulin was described in the patent specification, but the Patentee had claims that covered broader genera of cDNAs, coding for mammalian and vertebrate insulins, respectively. Lilly, 119 F.3d at 1563, 1567. In an infringement suit, the validity of these claims was challenged. The Lilly court held the claims invalid for failing to provide an adequate written description of the claimed genus. The court wrote: In claims to genetic material, however, a generic statement such as "vertebrate insulin cDNA" or "mammalian insulin cDNA," without more, is not an adequate written description of the genus because it does not distinguish the claimed genus from others, except by function. It does not specifically define any of the genes that fall within its definition. It does not define any structural features commonly possessed by members of the genus that distinguish them from others. One skilled in the art therefore cannot, as one can do with a fully described genus, visualize or recognize the identity of the members of the genus. 6 Appeal2018-001581 Application 15/185,371 Id. at 119 F.3d at 1568. Consistent with Lilly, it was held in Enzo Biochem, Inc. v. Gen-Probe Inc., 323 F.3d 956, 964 (Fed. Cir. 2002): [T]he written description requirement can be met by "show[ing] that an invention is complete by disclosure of sufficiently detailed, relevant identifying characteristics ... i.e., complete or partial structure, other physical and/or chemical properties, functional characteristics when coupled with a known or disclosed correlation between function and structure, or some combination of such characteristics." In sum, to meet the written description requirement, the Specification must describe "structural features commonly possessed by members of the genus that distinguish them from others" (Lilly, 119 F.3d at 1568), such as "a known or disclosed correlation between function and structure." Enzo Biochem, 323 F.3d at 964. In this case, the Specification discloses only a single protein species for each genus of rhtB and rhtC proteins, namely SEQ ID NOS: 2 and 4, respectively. A representative number of species for each genus has not been disclosed. Appellants have provided no guidance on where amino acid modifications can be made in the protein without destroying its activity. Appellants have also not described "structural features commonly possessed by members of the [ claimed] genus [ of rhtB and rhtC proteins] that distinguish them from others" (Lilly, 119 F.3d at 1568), such as "a known or disclosed correlation between function [ amino acid efflux] and [protein] structure." Enzo Biochem, 323 F.3d at 964. Final Act. 17-18. Thus, the Examiner's decision to reject the claims as lacking a written description is supported by a preponderance of the evidence. 7 Appeal2018-001581 Application 15/185,371 Appellants contend that the Examiner misconstrued the claims and that the claims allow only one amino acid alteration. Br. 8. Appellants argue: the current language of the claims omits the phrase 'or several', the language clearly indicates that only one amino acid can be altered. If the interpretation as alleged by the Examiner were adopted, this would be in direct contradiction to the specification, which states that one or several amino acids can be altered as alternative embodiments. Br. 8-9. During patent examination proceedings, claim terms are given "the broadest reasonable meaning ... in their ordinary usage as they would be understood by one of ordinary skill in the art, taking into account whatever enlightenment by way of definitions or otherwise that may be afforded by the written description contained in the applicant's specification." In re Morris, 127 F.3d 1048, 1054 (Fed. Cir. 1997). However, "a particular embodiment appearing in the written description may not be read into a claim when the claim language is broader than the embodiment." SuperGuide Corp. v. DirecTV Enters., Inc., 358 F.3d 870, 875 (Fed. Cir. 2004). Appellants' interpretation improperly attempts to import a limitation into the claim from the Specification. The claim expressly states "includes," which the Examiner interpreted to be open-ended and permit additional amino acid alterations. Appellants have not explained why this definition is incorrect. Appellants have also not provided an adequate reason, based on the actual language in the claim, to interpret "includes deletion, substitution, insertion or addition of one amino acid in the amino acid sequence" to exclude more than one amino acid modification when "includes" is understood to be an open-ended, inclusive term. Had Appellants intended 8 Appeal2018-001581 Application 15/185,371 the claim to exclude all other amino acid modifications, the claim language could have been amended to replaced "includes" with "consisting of," or otherwise made clear by the claim language that only one modification of the protein sequence is permitted. 2 Even if Appellants' interpretation is adopted, there are still numerous species encompassed by the claims because a single deletion, substitution, insertion, or addition of an amino acid could occur anywhere in the sequence, and comprise any one of the twenty naturally-occurring amino acids. Yet, as stated above, Appellants have provided no guidance on where in the protein amino acid modification can be made without destroying its activity. Appellants have also not described "structural features commonly possessed by members of the [ claimed] genus [ of rhtB and rhtC proteins] that distinguish them from others" (Lilly, 119 F.3d at 1568), such as "a known or disclosed correlation between function and structure." Enzo Biochem, 323 F.3d at 964. Appellants argue "that description of a representative number of species does not require the description to be of such specificity that it would provide individual support for each species that the genus embraces." Br. 10. However, there is only single species disclosed for each genus. A representative number has not been disclosed. 2 "[T]he PTO gives a disputed claim term its broadest reasonable interpretation during patent prosecution .... The 'broadest reasonable interpretation' rule recognizes that 'before a patent is granted the claims are readily amended as part of the examination process.' Burlington Indus. v. Quigg, 822 F.2d 1581, 1583 (Fed. Cir. 1987). Thus, a patent applicant has the opportunity and responsibility to remove any ambiguity in claim term meaning by amending the application." In re Bigio, 381 F.3d 1320, 1324 (Fed. Cir. 2004). 9 Appeal2018-001581 Application 15/185,371 For the foregoing reason, we affirm the Examiner's determination that claims 1-7 lack a written description as required by 35 U.S.C. § 112, first paragraph. ENABLEMENT REJECTION Claims 2 and 4---6 stand rejected by the Examiner for lack of enablement. The Examiner states the claims involve expression of both rhtC (SEQ ID NO: 4) and rhtB (SEQ ID NO: 2). Ans. 14. The Examiner found the claims do not limit the DNA coding for the amino acid alterations in the amino acid sequence of SEQ ID NO: 2 to a DNA which hybridizes to SEQ ID NO: 2 under specific washing conditions and therefore lack enablement because, without a hybridization restriction, the claim scope "encompass any conceivable mutants or variants of the amino acid sequence of SEQ ID NO: 2, provided the protein confers the phenotype of resistance to L- homoserine." Ans. 17. The Examiner considered the factors set forth in In re Wands, 858 F .2d 731 (Fed. Cir. 1988) for determining whether undue experimentation was required to enable the full scope of the claims. Final Act. 19-20. After reviewing all the factors (id. at 20, 23-25), the Examiner determined that there was "a high level of unpredictability in altering the sequence of SEQ ID NO: 2" while still "maintaining the desired activity" because of the broad scope of the claim, the lack of working examples, and the lack of guidance in what amino acids could be changed while still preserving the protein's rhtB efflux activity. Final Act. 25. Appellants do not identify a deficiency in the Examiner's findings nor reasoning. Instead, Appellants contend, as they did in the written description rejection, that the Examiner misconstrued the claim scope and 10 Appeal2018-001581 Application 15/185,371 that they are limited to alterations of only one amino acid at a time. Br. 11. For the reasons already discussed, this interpretation is not the broadest reasonable interpretation of the claim language. In sum, for the reasons set forth by the Examiner, the enablement rejection of claims 2 and 4---6 are affirmed. OBVIOUSNESS REJECTION BASED ON DEBABOV, VRLIJC, AND ZAKATAEVA The Examiner found that Debabov describes a method for producing L-threonine in Escherichia. Final Act. 32. The Examiner found that Debabov differs from the claim method in not over-expressing "a DNA encoding a threonine efflux protein of SEQ ID NO: 4." Id. The Examiner found that Vrlijc describes "enhancing expression of an L-amino acid export [efflux] polypeptide for improving L-amino acid production," but not the claimed threonine efflux protein of SEQ ID NO: 4. Id. at 33. However, the Examiner found that Zakataeva describes the rhtB and rhtC genes of E. coli that encode amino acid efflux proteins and confer resistance to homoserine and threonine, respectively. Id. at 33-34. The Examiner recognized that Zakataeva does not expressly disclose SEQ ID NO: 4, but found that the Specification discloses that SEQ ID NO: 4 corresponds to the rhtC gene, the same gene described in Zakataeva. Id. at 34. The Examiner determined that Vrlijc provides the reason to have used the rhtC amino acid efflux gene of Zakataeva in Debabov's method because Vrlijc teaches that increased expression of L-amino acid exporters result in increased accumulation of the amino acid in culture medium. Id. at 33. 11 Appeal2018-001581 Application 15/185,371 Appellants contend that "none of the references disclose or suggest ... [the rhtC gene's], or the encoded protein's, involvement in the increased production of amino acids, including L-threonine." Br. 12. Further, Appellants argue: [T]here is no teaching of the production of L-amino acids using the rhtC gene, nor that such production can be increased by increasing expression of this gene. Therefore, there is no motivation or reason to combine these references with each other. It certainly could not have been obvious to use the gene of Zakataeva in an effort to increase amino acid production since there is no suggestion or teaching of this function of the specific claimed sequence. Br. 13. This argument does not persuade us the Examiner erred in rejecting the claims as obvious. The Examiner set forth a detailed and well-reasoned explanation as to why the claimed method would have been obvious to one of ordinary skill in the art. Final Act. 32-37. Specifically, while there is no teaching of utilizing the claimed rhtC gene sequence to increase threonine production, the Examiner cited Vrlijc as a reason to have used the gene for this purpose. Vrlijc describes the microbial production of amino acid. Vrlijc 1: 10- 15. Vrlijc describes efforts to increase amino acid production by bacteria. Id. at 2:8-10. Vrlijc, as found by the Examiner (Final Act. 33), teaches that improving amino acid export is one approach to increasing amino acid production: However, as a further limitation basically also the export of the amino acids formed in the interior of a cell into the culture medium should be taken into consideration. As a result, it has been tried to improve this export and, consequently, the efficiency of the amino acid production. 12 Appeal2018-001581 Application 15/185,371 Vrlijc 2:10-13 (emphasis added). Vrlijc acknowledges: Altogether, the attempts to increase the secretion of amino- acids formed within the cell have all in common that an increase ejjlux of amino acids on the basis of the selected non- directed and non-specific methods could be achieved only accidentally. Vrlijc 2:25-29 ( emphasis added). However, Vrlijc addressed this problem in a directed way by identifying a gene responsible for amino acid export and found that its increased expression resulted in increased accumulation of the exported amino acid in the medium: It has now been found surprisingly that only a single specific gene is responsible for the export of amino acids so that, in accordance with the invention, for the first time a method for the microbial manufacture of amino acids is provided wherein clearly the export gene expression and/or the export carrier activity of a microorganism producing amino acids is increased. The increased export expression or respectively, activity of the export carrier resulting from this process leads to an increased secretion rate so that the export of the respective amino acid is increased. The microorganisms so modified also accumulate an increased part of the respective amino acid in the culture medium. Vrlijc 2:62-3:6. Zakataeva teaches that the product of the rhtC gene, the same gene which is claimed, provides resistance to threonine (Abstract) and "conducts the efflux of threonine" (Zakataeva 228, col. 2). Thus, as found by the Examiner, Vrlijc's teaching that an increase in amino acid ejjlux using an amino export carrier provides strong reason to have used the rhtC ejjlux 13 Appeal2018-001581 Application 15/185,371 gene of Zakataeva to improve amino acid production. Appellants do not identify a defect in the Examiner's factual findings or reasoning. Appellants' contention that it would not have been obvious "to use the gene of Zakataeva in an effort to increase amino acid production since there is no suggestion or teaching of this function of the specific claimed sequence" (Br. 13) is not persuasive because Zakataeva describes the function of the gene ("conducts the efflux of threonine") and the gene has the same sequence as the clamed SEQ NO: 4. Specifically, the Specification discloses that SEQ ID NO: 4 is derived from GenBank accession number M87049. Spec. ,r 41. Zakataeva teaches the same accession number. Zakataeva 229 (Section 3.1). Appellants' argument regarding the failure of Vrlijc to disclose the claimed sequence (Br. 12) ignores that Zakataeva discloses a clone having the same sequence as claimed. Appellants contend that "there is no evidence that the sequence taught by Zakataeva would function if expressed, nor what its function would be, other than generally involved in efflux, which is very different from production of amino acids which involves complex metabolic pathways." Br. 13. This argument is not supported by persuasive evidence. First, as explained above, Zakataeva expressly teaches that "the product of the rhtC gene conducts the efflux of threonine" (Zakataeva 228 (in section titled "Introduction"). Second, Vrlijc teaches that an amino acid exporter improved amino acid production, providing a reasonable expectation that the rhtC gene, which has the same basic function of the gene in Zakataeva, would likewise improve production of threonine. Appellants have not provided adequate evidence to the contrary, nor a reason why one of ordinary skill in the art would have doubted that the gene described in 14 Appeal2018-001581 Application 15/185,371 Zakataeva would increase amino acid production when expressed in Escherichia. For the foregoing reasons, the rejection of claim 1 is affirmed. Claims 2--4 and 7 fall with claim 1 because separate reason for their patentability were not provided. 37 C.F.R. § 4I.37(c)(iv)(l). OBVIOUSNESS REJECTION BASED ON NAKANOANDZAKATAEVA The Examiner rejected claims 4--7 as obvious in view of Nakano and Zakataeva. Independent claim 4 is similar to claim 1, but in addition to the requirement that L-threonine resistance is enhanced utilizing SEQ ID NO: 4, further requires enhanced L-homoserine resistance utilizing SEQ ID NO: 2. The Examiner found Nakano describes a method for producing L-amino acids in Escherichia. Final Act. 39. The Examiner recognized that Nakano does not teach "overexpress[ing] a DNA encoding a protein comprising the amino acid sequence of SEQ ID N0:4 and a DNA encoding a protein comprising the amino acid sequence of SEQ ID NO: 2" as required by claim 4. Id. at 39--40. The Examiner cited Zakataeva for teaching the rhtB and rhtC genes which have the same sequences recited in the claims. Id. at 40. The Examiner determined it would have been obvious to one of ordinary skill in the art to have utilized the rhtB and rhtC genes in Nakano's method to "avoid suppressing growth of the E. coli because Zakataeva teaches that exogenetic [exogenous] homo serine and threonine suppress growth of E. coli in a nutritional medium and rhtB and rhtC genes of E. coli confer resistance to homo serine and threonine." Id. at 41. 15 Appeal2018-001581 Application 15/185,371 Appellants contend that Zakataeva is deficient for the same reasons already argued in the first rejection. Br. 14. Accordingly, the rejection of claim 4 is affirmed for reasons set forth above and those set forth by the Examiner (Final Act. 37--42; Ans. 28-33). Claims 5-7 fall with claim 4 because separate reason for their patentability were not provided. 37 C.F.R. § 4I.37(c)(iv)(l). TIME PERIOD No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § 1.136(a)(l)(iv). AFFIRMED 16 Copy with citationCopy as parenthetical citation