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
Receipt is acknowledged of certified copies of priority papers required by 37 CFR 1.55. In the claim amendment filed on 4/16/2026, new claims 19-31 have been added.
Claims 15-31 are pending.
Information Disclosure Statement
The IDS filed on 4/22/24 has been fully considered except where references have been lined through.
Election/Restrictions
Applicant’s election without traverse of Group I, claims 15-18, and the species of ANB1 and SEQ ID NO 25, in the reply filed on 4/16/26 is acknowledged.
Claim 25 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 4/16/26. Claims 15-24 and 26-31 are examined.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 15 and 22-23 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 15 and 22-23 requires a function homologue of SEQ ID 25 having an 80% identity to SEQ ID NO 25. SEQ ID NO 25 is 679 amino acids long, which means that 80% identical still allows for a difference of 135 amino acids. As evidenced by Xue (Chem. Soc. Rev. 2018, 47, 1516), there are 800 naturally occurring amino acids and 1000s of unnatural amino acids (introduction). Therefore, one of ordinary skill in the arts understands that there is nearly an unlimited number of peptides that could be generated. Applicants have only reduced SEQ ID NO: 25 to practice and therefore are not in possession of the whole genus of 80% homology to SEQ ID NO 25. Additionally, there is no structure function relationship provided for in the specification. The specification does not provide any information on which amino acids can be varied or deleted while preserving the transketylase activity. Lacking art-recognized structure-function relationship of variants that comprise an amino acid substitution at specific positions in the instant SEQ ID NO:25, one of ordinary skill in the art would not be able to reasonably predict or envision all species of transketylase variants with 80% identity to SEQ ID NO:25 that would retain the transketylase activity.
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.
Claims 15-24 and 26-31 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.
Regarding claims 15, 28, and 30-31 the claims require enzyme names followed by an EC classification. The EC class is a narrower classification than the enzyme as one of ordinary skill in the arts understands that enzymes can go by a wide variety of names. Further, it is unclear if the claimed enzyme is limited to the claimed EC class, or if the claim limitation only extends to the enzyme name. Dependent claims 16-24, 26-27 and 29 are also rejected.
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.
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.
Claims 15-22, 24, and 28-30 are rejected under 35 U.S.C. 103 as being unpatentable over De Waal (WO2018172328A1) in view of Papapetridis (US20190249201A1).
De Waal and Papapetridis were published more than 1 year before the effective filing date of instant application and therefore is valid prior art under 35 USC 102(a)(1).
Regarding claim 15, De Waal teaches a recombinant yeast cell to produce ethanol (process for the production of ethanol) (abstract). De Waal teaches the yeast cell encodes a NAD+ dependent acetylating acetaldehyde dehydrogenase (EC 1.2.1.10) enzyme (abstract). De Waal teaches the yeast can further comprise overexpression of a transketolase EC 2.2.1.1 (p27, first full paragraph). De Waal teaches the fermentation can take place under anaerobic conditions (p3 4th full paragraph). De Waal teaches that glucose can be used as a substrate (carbon source) (p29 4th full paragraph).
De Waal does not specifically teach a promoter for the transketolase having an anaerobic-aerobic expression ratio of 2 or more.
Papapetridis teaches recombinant yeast (abstract). Papapetridis teaches the yeast can be used to produce ethanol (figs 2 and 6). Papapetridis teaches that transketolase EC 2.2.1.1 can be overexpressed ([0093]). Papapetridis teaches a carbon source can be used in the production of ethanol ([0029]). Papapetridis teaches promoters that enable higher expression under anaerobic conditions as compared to aerobic conditions can be used ([0025]). Papapetridis teaches that the promoter used can have an anaerobic-aerobic expression ratio of 2 or more ([0003] and claim 1). Papaetridis teaches that their yeast exhibits improved product yields and/or reduced side-product formation and/or improved propagation characteristics and/or absence of additives, such as antibiotics ([0003]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to incorporate the anaerobic promoter as taught by Papapetridis in the overexpression of transketolase as taught by De Waal. One of ordinary skill in the art would be motivated to do so because Papapetridis teaches this results in a yeast with improved product yields among other benefits. Further, one of ordinary skill in the art would be motivated to do so because these anaerobic promoters have been successfully used to overexpress proteins in recombinant yeast for ethanol production, and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination yielded nothing more than predictable results to one of ordinary skill in the art. There would be a reasonable expectation of success as both De Waal and Papapetridis are in the same field of endeavor of using recombinant yeast to produce ethanol.
Regarding claim 16, De Waal teaches that fermentation can be carried out at 60g/L glucose (p32 micro-/anaerobic cultivations section). This overlaps the claimed range and therefore the claimed range is prima facia obvious.
Regarding claims 17 and 18, De Waal teaches that glucoamylase can be used (p32, Media section).
Regarding claim 19, Papapetridis teaches ANB1 can be used (claim 5; [0016]).
Regarding claim 20, Papapetridis teaches a synthetic oligonucleotide can be used for the promoter ([0026]).
Regarding claim 21, De Waal teaches the engineered cell can over express transketolase via a promoter and that transketolase is naturally encoded by S. cerevisiae (p27 first full paragraph).
Regarding claim 22 and 24, De Waal teaches the overexpressed transketolase can be heterologous and controlled via a promoter (p27 first full paragraph).
Regarding claim 28, De waal teaches that the yeast can express genes encoding an NAD+-dependent alcohol dehydrogenase (EC 1.1.1.1) (p22 3rd full paragraph; claim 8).
Regarding claim 29, De Waal teaches that GPD can be deleted (p33 example 1).
Regarding claim 30, De Waal teaches the yeast can comprise a gene coding for a glycerol transporter (claim 1).
Claim 23 is rejected under 35 U.S.C. 103 as being unpatentable over De Waal (WO2018172328A1) and Papapetridis (US20190249201A1), as applied to claims 15-22, 24, and 28-30 above, and further in view of Schutter et al. (Direct Submission 05-May-2009; "Genome sequence of the recombinant protein production host Pichia pastoris." Nature biotechnology 27.6 (2009): 561-566).
Regarding claim 23, De Waal teaches that the heterologous genes used in the engineered yeast can come from foreign species (p8 2nd full paragraph). De Waal teaches that Pichia pastoris is widely used (p8 last partial paragraph).
De Waal and Papaetridis do not teach the instantly claimed SEQ ID NO 25.
Schutter teaches a 100% match to the instantly claimed SEQ ID NO:25 (appendix). Schutter teaches that the origin of the gene is a Pichia pastoris yeast (abstract). Schutter teaches that the yeast sequence comes from the most commonly used specie of yeast in recombinant protein production (p561 left column). Schutter teaches that the sequence of this yeast will result in improved strains and rapid development of protein expression hosts (discussion).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to incorporate SEQ ID NO: 25 of Schutter in the recombinant yeast cell of De Waal as modified by Papaetridis above. One of ordinary skill in the art would be motivated to do so because Schutter teaches that strain of yeast is the most common yeast used in industry for recombinant protein production, and this is a simple substitution of one known enzyme for another with predictable results to one of ordinary skill. There would be a reasonable expectation of success as De Waal, Papaetridis and Schutter are in the same field of endeavor of engineered yeast.
Claims 26 and 27 are rejected under 35 U.S.C. 103 as being unpatentable over De Waal (WO2018172328A1) and Papapetridis (US20190249201A1), as applied to claims 15-22, 24, and 28-30 above, and further in view of Matsushika et al. ("Characterization of non-oxidative transaldolase and transketolase enzymes in the pentose phosphate pathway with regard to xylose utilization by recombinant Saccharomyces cerevisiae." Enzyme and microbial technology 51.1 (2012): 16-25).
Regarding claim 26, De waal and Papapetridis do not
Matsushika studies transketolase in yeast (abstract). Matsushika teaches that strains that have the transketolase knocked out can exhibit higher rates of ethanol production than the control strains (p21 “3.3. Ethanol fermentation by TAL and TKL knockout mutant strains”, p21 left column 2nd full paragraph).
Regarding claim 27, Matsushika teaches that strains that express both the endogenous transketolase and a plasmid version of transketolase can be created (table 1). Matsushika teaches that some strains having both native and plasmid copies of transketolase can exhibit higher rates of ethanol production ( 3.4. Ethanol fermentation by TAL- and TKL-overexpressing strains, p22 left column last partial paragraph). Matsushika teaches that intensive studies regarding transketolase will be needed (discussion and p24 right column last full paragraph). Therefore, the knockout or overexpression of transketolase is a result effective variable and one of ordinary skill in the arts is motivated to experiment with the levels of gene expression.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the expression levels of transketolase via knockout (disruption or deletion) or addition of an extra copy to the endogenous transketolase as taught by Matsushika in the yeast of De Waal and Papapetridis above. One of ordinary skill in the art would be motivated to do so because Matsushika teaches that additional studies are needed and the effects on ethanol fermentation can be strain dependent. There would be a reasonable expectation of success as De Waal, Papapetridis, and Matsushika are in the same field of endeavor of using enginerred yeast to make ethanol.
Claim 31 is rejected under 35 U.S.C. 103 as being unpatentable over De Waal (WO2018172328A1) and Papapetridis (US20190249201A1), as applied to claims 15-22, 24, and 28-30 above, and further in view of Green (US20150159178A1).
Regarding claim 31, De Waal and Papapetridis do not
Green teaches methods for producing ethanol (claim 1). Green teaches the microorganism used can be a yeast ([0052]). Green teaches that the microorganism can express glucoamylase ([0040]). Green teaches the enzyme is in EC 3.2.1.3 (table 2). Green teaches these engineered organisms are uniquely efficient ([0006]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to incorporate the glucoamylase promoter as taught by Green in the yeast cell of De Waal and Papapetridis above. One of ordinary skill in the art would be motivated to do so because Green teaches this results in a yeast with unique efficency. Further, one of ordinary skill in the art would be motivated to do so because the glucoamylase has been successfully used in recombinant yeast for ethanol production, and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination yielded nothing more than predictable results to one of ordinary skill in the art. There would be a reasonable expectation of success as Green, De Waal and Papapetridis are in the same field of endeavor of using recombinant yeast to produce ethanol.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to TREVOR L KANE whose telephone number is (571)272-0265. The examiner can normally be reached M-F 7:00 am-4:00pm.
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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
/TREVOR KANE/Examiner, Art Unit 1657
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