Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
DETAILED ACTION
Claims 70-84 and 88 are pending. Claims 1-69 and 85-87 are cancelled. Claims 70-77 and 88 are withdrawn. Claims 78-84 are under examination on their merits.
Response to Arguments
Applicant's arguments filed 12/22/2025 have been fully considered but they are not persuasive.
Applicant argues against the rejection of claims under 35 U.S.C. 103 on the grounds that a methyl group can lead to an exponential increase in binding affinity for a methylated substrate per Barreiro et al. (Arguments, paragraph 1 on page 7).
In response, Applicant has not cited any specific portion of Barreiro et al. Furthermore, Barreiro is focused on medicinal chemistry and the binding of methylated compounds to receptors in the body, not the binding of methylated compounds to an enzyme active site. See, for example, Barreiro’s teaching that removal of the methyl group attached to the sp3 nitrogen of the benzylisoquinoline ring from morphine to generate normorphine causes a 6-fold reduction in in vivo analgesic activity (page 5218, left column, bottom paragraph). The methyl group of a sp3 nitrogen of a benzylisoquinoline is not analogous at all to the methyl group of 3M3SH. Barreiro also teaches that the methyl groups at positions in a hexahydronaphthalene ring and the butanoate side chain in the lactone subunit of lovastatin are responsible for important interactions with the target enzyme HMG-CoA reductase (page 5253, left column, first full paragraph). However, Barreiro teaches that the stereochemistry of the methyl group alpha to the carbonyl group does not influence the inhibitory activity of these compounds (page 5253, left column, paragraph 2). Again, this is a special circumstance pertaining to enzyme inhibition by an aromatic substrate with methyl groups. These teachings are not applicable to the instant application, especially given that Barreiro’s teachings regarding methyl groups pertain to methyl groups of heteroaromatic compounds whereas Cys-3MH and Cys-3M3SH are both linear, non-aromatic substrates.
Applicant argues that Figure 4D of Rudden depicts Cys-3M3SH computationally docked into a co-crystal structure of cycloserine and ShPatB (Staphylococcus hominis PatB) and that this co-structure is not representative of Cys-3M3SH or Cys-3SH binding to ShPatB due to the presence of cycloserine (Arguments, paragraph 2 on page 7).
In response, cycloserine is merely used to improve the mechanistic understanding of a reaction because Rudden was unable to capture reaction intermediates by soaking ShPatB with Cys-3M3SH (see page 5, paragraph 1). However, Rudden experimentally verifies that the Staphylococcus PatB enzymes catalyze reactions with the substrate Cys-3M3SH: see Fig. 3. Therefore, the person of ordinary skill in the art would have inferred based on the experimental results, not just the structural characterization work of Rudden, that the S. PatB enzymes would have also catalyzed reactions with Cys-3MH, which is structurally very similar to Cys-3M3SH.
Applicant argues against the rejection of claims under 35 U.S.C. 103 on the grounds that the person of ordinary skill in the art would not have been motivated to select an enzyme that preferentially cleaves tertiary thiols (i.e., Cys-3M3SH) given the unpleasant odor of compounds such as 3M3SH. Applicant argues further that the person of ordinary skill in the art would not have been motivated to use an enzyme directly implicated in human body odor (Arguments, paragraph 1 on page 8).
In response, this argument is not persuasive because Applicant has not provided any evidence that the substrate Cys-3M3SH is even present in beverage fermentation media. The person of ordinary skill in the art would not have expected an unpleasant smell from the use of the PatB enzyme unless the same substrates were present in fermentation media as the human body. In contrast, cysteinylated precursors including Cys-3MH are already known to be present in the grape-derived fermentation media of wines (Swiegers Abstract).
Applicant argues further against the rejection of claims under 35 U.S.C. 103 on the grounds that the person of ordinary skill in the art would not have been motivated to select an enzyme with high enzymatic activity in producing a specific product, like ShPatB, but rather would have been motivated to select an enzyme with general activity against a wide variety of thioalcohol substrates (Arguments, paragraph 2 on page 8).
In response, the claims are rejected over S. devriesei PatB not S. hominis PatB (ShPatB). Furthermore, Applicant has not provided any objective evidence to support this point. Given that 3SH has a pleasant odor, the person of ordinary skill in the art would have been motivated to increase the amount of this particular volatile compound.
Applicant concludes that the rejection is based upon hindsight reasoning because there is evidence lacking in the rejection to point a person of skill in the art to select PatB for use in a recombinant yeast for the production of palatable thiols (Arguments, paragraph bridging pages 8-9).
In response, this argument is not persuasive because Applicant has not pointed to any specific part of the Office’s rejection based upon information in Applicant’s disclosure (i.e. hindsight reasoning). Rather, the rejection is based purely on the cited references and is thus proper. Furthermore, Applicant’s assertion that multiple palatable thiols are required is not congruent with the claimed invention, which only requires that the recombinant yeast is capable of producing 3-sulfanyl-1-hexanol (3SH).
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
The following rejections are necessitated by the amendment, except for claim 84, which is a maintained rejection.
Claims 78-84 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 78 recites a recombinant yeast comprising a polynucleotide encoding PatB, wherein the PatB converts a non-volatile form of 3-sulfanyl-1-hexanol {3SH} to free 3SH in the yeast. Claim 78 is indefinite because although the method preamble seems to indicate that the statutory category of invention is a product (the yeast), the wherein clause recites an active method step, leading to ambiguity in the statutory category of invention.
Claims 79-84 are rejected for depending from a rejected base claim.
(Maintained Rejection) Claim 84 recites “Kluyveromyces/Lachance.” However, Lachancea is a new proposed genus distinct from Kluyveromyces (see Abstract of Kurtzman et al., FEMS Yeast Research, Volume 4, Issue 3, December 2003, Pages 233–245; cited in the Non-Final Action mailed on 8/27/2025), thus rendering claim 84 indefinite because it is unclear whether the claim scope is Kluyveromyces, Lachancea, or both. Applicant may consider amending the claim to recite Kluyveromyces and Lachancea in the alternative.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
The following rejections are necessitated by the amendment.
Claim 78-81 are rejected under 35 U.S.C. 103 as being unpatentable over Swiegers et al. (Yeast 24.7 (2007): 561-574) in view of Rudden et al. (Sci Rep. 2020 Jul 27;10(1):1250) and WP_107520157.1 (2020, website) as evidenced by PubChem1 (2005, website) and PubChem2 (2006, website).
Swiegers recombinantly expresses the E. coli tnaA gene, encoding a tryptophanase with strong cysteine β-lyase activity, in Saccharomyces cerevisiae under the control of PGK1 (Abstract). Swiegers teaches that the enzymatic release of aromatic thiols from grape-derived non-volatile cysteinylated precursors including Cys-3MH enhances the varietal characters of wines (Abstract). Swiegers teaches that the carbon-sulfur lyase activity releases 4MMP and 3MH during fermentation, which results in more intense passionfruit aroma (Abstract). 3MH stands for 3-mercaptohexan-1-ol, which is a synonym for 3-sulfanyl-1-hexanol.
Regarding claims 78-81, Swiegers does not teach that the recombinant Saccharomyces cerevisiae comprises PatB from Staphylococcus devriesei. Swiegers does not teach SEQ ID NO: 10.
Rudden teaches a family of enzymes called cysteine-thiol lyases selective for branched aliphatic thiolalcohol ligands such as the substrate Cys-3M3SH, which is the precursor for the volatile 3M3SH (page 3, “ShPatB is selective for branched aliphatic thioalcohol ligands” and Figure 1 panel B and caption). 3M3SH stands for 3-methyl-3-sulfanylhexan-1-ol, which is a synonym for 3-mercapto-3-methyl-1-hexanol or 3-sulfanyl-1-hexanol. Rudden teaches S. devriesei PatB has a high catalytic efficiency for 3M3SH (Figure 3).
WP_107520157.1 teaches the amino acid sequence of 3M3SH-releasing C-S lyase (i.e. cysteine-thiol lyase PatB) from S. devriesei. The amino acid sequence of WP_107520157.1 is 99.9% identical to SEQ ID NO: 10 (OA Appendix A of the Non-Final Action mailed on 8/27/2025), which is within the claimed range of at least 80% identical to SEQ ID NO: 10.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to replace Swiegers’s E. coli tnaA with the PatB from S. devriesei. The person of ordinary skill in the art would have been motivated to further increase the release of aromatic 3MH from Cys-3MH. The person of ordinary skill in the art would have been motivated to choose from the finite number of PatB enzymes that Rudden teaches in order to select the PatB with the highest specificity for Cys-3MH. The person of ordinary skill in the art would have had a reasonable expectation of success because PatB has a substrate pocket specific for hydrophobic branched aliphatic thioalcohol ligands (Rudden bottom two paragraphs on page 3) and the precursors for the volatiles Cys-3MH and Cys-3M3SH are both chemically and structurally similar since they differ only by a single methyl group, as evidenced by PubChem1 (see 2D Structure) and PubChem 2 (see 2D Structure).
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PubChem images of 3MH (left, cited as PubChem1 in the PTO-892 of the Non-Final Action mailed on 8/27/2025) and 3M3SH (right, cited as PubChem2 in the PTO-892 of the Non-Final Action mailed on 8/27/2025).
Although Rudden is not in the same field of endeavor as Swiegers, Rudden is still analogous art because Rudden teaches a solution to the problem faced by Swiegers and others in the fermentation industry. Swiegers discloses the enzymatic release of volatile compounds and Rudden discovers a new class of enzymes specifically capable of releasing volatile compounds structurally similar to those desired by Swiegers. See MPEP 2141.01(a)(I).
Claims 82-84 are rejected under 35 U.S.C. 103 as being unpatentable over Swiegers et al. (Yeast 24.7 (2007): 561-574) in view of Rudden et al. (Sci Rep. 2020 Jul 27;10(1):1250) and WP_107520157.1 (2020, website) as evidenced by PubChem1 and PubChem2, as applied to claims 78-81 above, further in view of Roop et al. (WO 2021/076917 A1). Roop is prior art under 35 U.S.C. 102(a)(2) because Roop has an effectively filed date of 16 October 2020, which is the international filing date of PCT/US2020/056022, whereas the instant application claims priority to U.S. provisional application 63/147,963, filed 10 February 2021. Therefore, Roop was effectively filed before the effective filing date of the claimed invention.
See discussion of Swiegers, Rudden, and WP_107520157.1 above, which is incorporated into this rejection as well.
Swiegers does not teach that the yeast is from a non-Saccharomyces genus.
Roop teaches genetically modified yeast cells that recombinantly express a gene encoding a mutant beta-lyase (Abstract). Roop’s yeast include Hanseniaspora uvarum, Hanseniaspora guillermondii, Hanseniaspora vinae, Metschnikowia pulcherrima, Kluyveromyces/Lachancea thermotolerans, Starmerella bacillaris (previously referred to as Candida stellata/Candida zemplinina), Saccharomycodes ludwigii, Zygosaccharomyces rouxii, Dekkera bruxellensis, Dekkera anomala, Brettanomyces custersianus, Brettanomyces naardenensis, Brettanomyces nanus, Wickerhamomyces anomalus, and Torulaspora delbrueckii (lines 19-24 on page 27), which Roop teaches are also used in the production of fermented beverages (lines 11-13 on page 27).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to recombinantly express the WP_107520157.1 PatB gene from S. devriesei under the control of the PGK1 in any of Roop’s yeast rather than S. cerevisiae. The person of ordinary skill in the art would have been motivated to increase the release of 3MH in other fermented beverages in order to improve their aromas. The person of ordinary skill in the art would have had a reasonable expectation of success in recombinantly expressing WP_107520157.1 PatB in any of Roop’s non-Saccharomyces yeast in the industry of fermented beverages.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CANDICE LEE SWIFT whose telephone number is (571)272-0177. The examiner can normally be reached M-F 8:00 AM-4:30 PM (Eastern).
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Louise Humphrey can be reached at (571)272-5543. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/CANDICE LEE SWIFT/Examiner, Art Unit 1657
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