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
The amendment filed 06/26/2026 has been entered. Claims 3-5, 7, 18-21, 23, 24, and 29-31 are cancelled. Claims 32 and 33 have been newly added. Claims 1, 2, 6, 8-17, 22, and 25-28 remain pending. Claims 1, 2, 6, 8-17, 22, and 25 remain withdrawn. Claims 26-28, 32, and 33 are under examination.
Response to Arguments
Applicant's arguments filed 06/26/2026 have been fully considered but they are not persuasive. With respect to the rejection of claims 27 and 28 under 35 USC 112(b), Applicant has amended claim 27 to recite “wherein the concentration of the small molecule in the culture medium during culturing is sufficient to activate the promoter”. However, it is still it is unclear if the earlier recited phrase, “responsive to”, means that the promoter activity is repressed, activated, or induced by the small molecule. Moreover, the phrase “the culture medium” still lacks antecedent basis.
Claim Rejections - 35 USC § 112(b)
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.
(MAINTAINED REJECTION)
Claims 27 and 28 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 27 recites that the one or more heterologous nucleic acids is positively regulated by the activity of a promoter responsive to the small molecule, wherein the concentration of the small molecule in the growth medium is sufficient to repress the promoter, and wherein the concentration of the small molecule in the culture medium during the culturing is sufficiently low that the promoter is activated. The claim language is confusing and it is unclear if “responsive to” means that the promoter activity is repressed, activated, or induced by the small molecule.
Claim 27 recites the limitation "the culture medium" in line 6. There is insufficient antecedent basis for this limitation in the claim.
Claim 28 is also rejected as it depends from claim 27.
Applicant may consider the following amendment, which has been drafted by the Examiner, to obviate the rejection:
Claim 27. The method of claim 26, further comprising: prior to the culturing, growing the population of genetically modified host cells in a growth medium comprising a small molecule, wherein expression of at least one of the one or more heterologous nucleic acids is positively regulated by the activity of a promoter that is repressed byis present in the growth mediumand binds to and represses the promoter, and whereinis absent in a and the promoter is induced
Claim Rejections - 35 USC § 103
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.
(NEW REJECTION NECESSITATED BY AMENDMENT)
Claims 26-28, and 32 are rejected under 35 U.S.C. 103 as being unpatentable over Raetz et al., (WO 2021/022216 A1; previously cited) in view of Liang et al. (Newly identified genes contribute to vanillin tolerance in Saccharomyces cerevisiae. Microb Biotechnol. 2021 Mar;14(2):503-516; previously cited) and Piotrowski et al., (US 2016/0333362 A1).
Under BRI, it is interpreted that a promoter that is repressed by a small molecule meets the limitations of claim 27.
Regarding claim 26, Raetz teaches genetically modified host cells and methods for improved production of vanillin and/or glucovanillin (Abstract). Raetz teaches that the host cell is genetically engineered to comprise one or more heterologous nucleic acids and/or biosynthetic pathway enzymes e.g., for a vanillin or glucovanillin compound (para. [00112]). Raetz teaches that the method for producing vanillin or glucovanillin involves culturing a population of host cells in a medium under conditions suitable for making vanillin or glucovanillin (para. [0009]). Raetz teaches that the host microbe is Saccharomyces cerevisiae (para. [0075]), i.e., a yeast host cell.
Raetz does not teach that GCY1 (glycerol dehydrogenase) gene expression or GCY1 protein activity is inhibited in the yeast host cell, or teach a deletion or disruption in the SKY1 gene or SKY1 protein.
Liang teaches a Saccharomyces cerevisiae strain in which the GCY1 gene was deleted (Table 1; p. 504, Results and Discussion, para. 1). Liang does not teach a deletion or disruption in the SKY1 gene or SKY1 protein.
Piotrowski teaches a recombinant S. cerevisiae strain that has been genetically engineered to exhibit a decreased level of functional SKY1 polypeptide (para. [0007]).
It would have been obvious to one of ordinary skill in the art, prior to the effective filing date of the claimed invention, to engineer the vanillin-producing yeast host cell of Raetz by deleting GCY1 gene, as taught by Liang, and by decreasing the level of functional SKY1 polypeptide, as taught by Piotrowski. One of ordinary skill in the art would have been motivated to delete GCY1 because Liang teaches that the GCY1 gene of S. cerevisiae encodes an enzyme, Gcy1p, with vanillin-reductase activity, i.e., Gcy1p catalyzes the conversion of vanillin to vanillyl alcohol (p. 505, col. 2, The NADPH-dependent vanillin reductase activity of Gcy1p contributes to vanillin tolerance in S. cerevisiae; Conclusion), while Raetz teaches that the host cell is S. cerevisiae (para. [0075]; para. [00131]). It would have been obvious to one of ordinary skill that deleting GCY1 in S. cerevisiae would result in an increase in vanillin accumulation, based on the teachings of Liang, as said deletion would decrease the conversion of vanillin to vanillyl alcohol. One of ordinary skill in the art would have been motivated to engineer the host cell of Raetz to exhibit a decreased level of functional SKY1 because Piotrowski teaches that yeast genetically modified as such exhibit improved fermentation rates relative to unmodified yeast (para. [0034]). One of ordinary skill in the art would have had a reasonable expectation of success because Raetz, Liang, and Piotrowski are in the same field of endeavor of S. cerevisiae engineering for industrial scale production.
Regarding claims 27 and 28, Raetz teaches promoters that are repressed by maltose, i.e., a small molecule, (para. [0067]). Raetz teaches that, in certain embodiments, the vanillin-producing enzymes are repressed by maltose during a growth phase of the cells, and the vanillin-producing enzymes are expressed during an expression phase of the fermentation (para. [0085]). Therefore, it would be obvious to one of ordinary skill in the art to use a maltose-repressible promoter to control expression of the heterologous nucleic acids encoding the vanillin biosynthesis genes, to grow the host cells expressing said genes in maltose-containing growth medium, and to culture and/or ferment said cells in a maltose-free or low maltose-containing culture medium to allow for vanillin biosynthesis enzyme production, based on the teachings of Raetz.
Regarding claim 32, Raetz teaches that the genetically modified host cell may comprise a nucleic acid expressing AroF (claim 7), which is phospho-2-dehydro-3-deoxyheptonate aldolase (para. [0027]).
Claim 33 is rejected under 35 U.S.C. 103 as being unpatentable over Raetz et al., (WO 2021/022216 A1), Liang et al. (Newly identified genes contribute to vanillin tolerance in Saccharomyces cerevisiae. Microb Biotechnol. 2021 Mar;14(2):503-516) and Piotrowski et al., (US 2016/0333362 A1) as applied to claim 26 above, and further in view of Eberhardt et al., (Strategy for deletion of complete open reading frames in Saccharomyces cerevisiae. 1995 Mar;27(4):306-8).
See discussion of Raetz, Liang, and Piotrowski, which is incorporated into this rejection as well.
Liang teaches a Saccharomyces cerevisiae strain in which the GCY1 gene was deleted but does not teach that the GCY1 mutant was developed by deleting the open reading frame.
Eberhardt teaches deletion of the entire open reading frame to generate S. cerevisiae knockout mutants (Abstract).
It would have been obvious to one of ordinary skill in the art, prior to the effective filing date of the claimed invention, to delete the S. cerevisiae open reading frame as taught by Eberhardt of the GYC1 gene to generate a GCY1 deletion mutant, as taught by Liang. One of ordinary skill in the art would have been motivated to do so because Eberhardt teaches that deleting the open reading frame allows for complete gene deletion, and allows for gene deletion without inserting a selection marker, which is relevant for industrial strains or for the construction of strains with multiple deletions (Introduction, para. 1, p. 308, col. 1, last paragraph). One of ordinary skill in the art would have had a reasonable expectation of success because Raetz, Liang, Piotrowski, and Eberhardt are in the same field of endeavor of S. cerevisiae engineering.
Conclusion
Applicant's amendment necessitated the new ground 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 RACHEL EMILY MARTIN whose telephone number is (703)756-1416. The examiner can normally be reached M-Th 8:30-16:00, F 8:30-10:00 EST.
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/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/RACHEL EMILY MARTIN/Examiner, Art Unit 1657
