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 1-18 are pending.
Election/Restrictions
Applicant’s election without traverse of claims 1-15 in the reply filed on 14 April 2026 is acknowledged.
Claims 16-18 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 14 April 2026.
Claims 1-15 are under examination.
Domestic Benefit
Acknowledgment is made of Applicant’s claim for the domestic benefit of the filing date of 12 December 2022 of US provisional application no. 63/387,035. The effective filing date is 12 December 2022.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 14 February 2024 is being considered by the examiner.
Examiner Comments on Patent Eligibility
The instant composition recited in claim 1 requires the combination of a bacterial host cell and a yeast host cell, wherein the bacterial host cell comprises metabolic pathways comprising polypeptides for converting pentoses or acetate into ethanol, for converting glycerol into dihydroxyacetone phosphate, and for converting pyruvate into ethanol; and wherein the yeast host cell comprises metabolic pathways comprising polypeptides for producing glycerol and for converting pentoses into ethanol.
After extensive searching, Examiner has not found any natural bacteria having all of the metabolic pathways comprising polypeptides for converting pentoses or acetate into ethanol, for converting glycerol into dihydroxyacetone phosphate, and for converting pyruvate into ethanol. Some naturally occurring bacteria are known to possess at least one of the aforementioned metabolic pathways, but no natural organism possess all of the metabolic pathways as claimed. The prior art shows that extensive genetic engineering is required to result in a bacterial host cell comprising all of the metabolic pathways as claimed. As such, the instant composition is not naturally occurring, and is patent eligible under 35 USC §101.
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.
Claim 7 is 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 7 recites the one or more third heterologous polypeptides comprise: a native or heterologous pyruvate decarboxylase and/or a native or heterologous alcohol dehydrogenase. It is unclear how the one or more third heterologous polypeptides are able to be native polypeptides.
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.
Claims 1-13 and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Kang et al. (Metabolic Engineering of a Glycerol-Oxidative Pathway in Lactobacillus panis PM1 for Utilization of Bioethanol Thin Stillage: Potential To Produce Platform Chemicals from Glycerol, Applied and Environmental Microbiology, December 2014, 80:24 p. 7631–7639, doi:10.1128/AEM.01454-14) in view of Wang et al. (Effects of carbon concentration, oxygen, and controlled pH on the engineering strain Lactiplantibacillus casei E1 in the production of bioethanol from sugarcane molasses, AMB Expr (2021) 11:95, doi:10.1186/s13568-021-01257-x), Suhaimi et al. (Bioconversion Of Glycerol For Bioethanol Production Using Isolated Escherichia Coli SS1, Brazilian Journal of Microbiology (2012): 506-516), Ruchala et al. (Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts, FEMS Microbiology Reviews, fuaa069, 45, 14 December 2020, 1-44, doi:10.1093/femsre/fuaa069), and Klein et al. (Glycerol metabolism and transport in yeast and fungi: established knowledge and ambiguities, Environmental Microbiology (2017) 19(3), 878–893 doi:10.1111/1462-2920.13617).
Claim 1 recites “for making ethanol from a biomass”, “for converting pentoses or acetate into ethanol”, “for converting glycerol into dihydroxyacetone phosphate”, “for converting pyruvate into ethanol”, “for producing glycerol”, and “for converting pentoses into ethanol”, which are interpreted as being intended uses of the claimed composition, but does not add any new structural limitations to the composition. Claims 4-5 recite similar limitations. If a composition in the prior art teaches all of the structural limitations of the claimed composition, claims 1 and 4-5 will be considered to be rendered obvious.
Regarding claims 1-2, 8-9, 13, and 15, Kang teaches a Lactiplantibacillus bacteria comprising a glycerol oxidative metabolic pathway capable of converting glycerol into dihydroxyacetone phosphate and ultimately into ethanol (Kang fig. 1). Kang also teaches these metabolic pathways are able to convert acetate into ethanol (Kang fig. 1).
Kang does not teach their Lactiplantibacillus bacteria comprises a heterologous metabolic pathway for converting pyruvate into ethanol.
Wang teaches a Lactiplantibacillus casei recombinant bacterial host cell used for ethanol fermentation from biomass (Wang Abstract). Wang teaches the recombinant Lactiplantibacillus casei comprises a metabolic pathway for converting pyruvate into ethanol with heterologous enzymes pyruvate decarboxylase and alcohol dehydrogenase (Wang pg. 3 para. 3).
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the present invention to genetically engineer Kang’s bacterial host cell comprising the glycerol to ethanol and acetate to ethanol conversion pathways to heterologously express Wang’s metabolic pathway for converting pyruvate into ethanol with heterologous enzymes pyruvate decarboxylase and alcohol dehydrogenase. One of ordinary skill in the art would have been motivated to do so because it would allow the modified Lactiplantibacillus bacterial cell to be a more efficient ethanol producer able to convert pentoses, acetate, and glycerol into ethanol.
Suhaimi teaches that glycerol is a known byproduct produced by biofuel production acting as a contaminant, but it is able to be converted into ethanol by a fermentative microorganism with anabolic pathway, and glycerol’s utilization to produce more ethanol adds more value to the biodiesel industry (Suhaimi Abstract, pg. 506 para. 1, and pg. 507 para. 1). Thus, one of ordinary skill in the art would have recognized the beneficial effect of adding the ability to convert excess pyruvate into additional ethanol by modifying Kang’s Lactiplantibacillus bacterial cell.
Kang and Wang do not teach a yeast host cell comprising a metabolic pathway comprising polypeptides for producing glycerol, or for converting pentoses into ethanol.
Ruchala teaches a Saccharomyces cerevisiae yeast cell engineered to comprise polypeptides for converting the pentose xylose into ethanol (Ruchala Table 1, Figs. 2-3, pg. 6 para. 1, and pg. 8 para. 2).
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the present invention to combine Kang and Wang’s genetically modified Lactiplantibacillus bacterial host cell with Ruchala’s genetically modified Saccharomyces cerevisiae yeast cell. One of ordinary skill in the art would have been motivated to do so with a reasonable expectation of success because doing so would maximize the amount of ethanol that can be produced through fermentation of a input biomass. Both Kang and Wang’s genetically modified Lactiplantibacillus bacterial host cell and Ruchala’s genetically modified Saccharomyces cerevisiae yeast cell were known to produce ethanol through biomass fermentation, with Kang and Wang’s bacterial cell able to produce ethanol through glycerol, pyruvate, and acetate conversion, and Ruchala’s yeast cell through xylose conversion into ethanol. Since both cells were known to be useful for the same purpose, one of ordinary skill in the art would have found it obvious to combine the two into a third composition useful for that same purpose of produce ethanol through biomass fermentation. See MPEP §2144.06(I).
Kang, Wang, and Ruchala do not teach a yeast host cell comprising a metabolic pathway comprising polypeptides for producing glycerol.
Klein teaches that Saccharomyces cerevisiae yeast cells produce waste glycerol through an anabolic glycerol 3-phosphate (G3P) pathway (Klein pg. 884).
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the present invention that Ruchala’s Saccharomyces cerevisiae yeast cell also comprises a glycerol production metabolic pathway because Klein teaches that Saccharomyces cerevisiae yeast cells produce waste glycerol through an anabolic glycerol 3-phosphate (G3P) pathway (Klein pg. 884). Thus, one of ordinary skill in the art would understand that Ruchala’s Saccharomyces cerevisiae yeast cell comprises both a glycerol production metabolic pathway and a xylose-to-ethanol fermentation pathway. Additionally, Kang and Wang’s genetically modified Lactiplantibacillus bacterial host cell engineered to be able to convert glycerol to ethanol would be reasonably expected by one of ordinary skill in the art to synergize with Ruchala’s genetically modified Saccharomyces cerevisiae yeast cell, which is known to produce glycerol through an anabolic glycerol 3-phosphate (G3P) pathway.
Regarding claims 3-4, Kang teaches the metabolic pathway comprises the acetate-to-acetyl CoA converting enzyme phosphotransacetylase (PTA), the acetyl CoA-to-acetaldehyde converting enzyme acetaldehyde dehydrogenase (abbrev. by Kang as ALDH), and the acetaldehyde-to-ethanol converting enzyme alcohol dehydrogenase (ADH) (Kang fig. 1).
Regarding claims 5-6, Kang teaches a glycerol dehydrogenation metabolic pathway that comprises the enzyme glycerol 3-phosphate dehydrogenase (abbrev. by Kang as GlpD) that produces dihydroxyacetone (Kang fig. 1).
Regarding claim 7, Wang teaches the recombinant Lactiplantibacillus casei was constructed with heterologous enzymes pyruvate decarboxylase and alcohol dehydrogenase (Wang pg. 3 para. 3).
Regarding claim 10, the claim recites “the bacterial host cell has a decreased lactate dehydrogenase activity and optionally at least one inactivated native gene coding for a lactate dehydrogenase”, which are interpreted as being intended property of the claimed bacterial host cell, but does not add any new structural limitations to the composition; thus, if a composition in the prior art teaches all of the structural limitations of the claimed composition, claim 10 will be considered to be rendered obvious.
Regarding claim 11, Klein teaches that Saccharomyces cerevisiae produces glycerol by using glycerol 3-phosphate dehydrogenase (cG3PDH) and glycerol 3-phosphatase (GPP) (Klein pg. 884 para. 1).
Regarding claim 12, Ruchala teaches Saccharomyces cerevisiae yeast has been engineered to comprise heterologous enzymes xylose reductase, xylose dehydrogenase, xylose isomerase, arabinose isomerase and ribulokinase (heterologous E. coli genes araA and araB, respectively), and ribulose-5-phosphate 4-epimerase (Ruchala Table 1, Figs. 3 and 7, pg. 6 para. 1, pg. 8 left col last para., and pg. 25 para. 1).
Claim 14 is rejected under 35 U.S.C. 103 as being unpatentable over Kang et al. (Applied and Environmental Microbiology, December 2014, 80:24 p. 7631–7639) in view of Wang et al. (AMB Expr 2021:11:95), and Suhaimi et al. (Brazilian Journal of Microbiology 2012: 506-516).
The claim recites the limitation “for making ethanol from a biomass comprising pentoses”, which is interpreted as being intended uses of the claimed composition, but does not add any new structural limitations to the composition; thus, if a composition in the prior art teaches all of the structural limitations of the claimed composition, claim 14 will be considered to be rendered obvious.
Kang teaches a Lactiplantibacillus bacteria comprising a glycerol oxidative metabolic pathway capable of converting glycerol into dihydroxyacetone phosphate and ultimately into ethanol (Kang fig. 1). Kang also teaches these metabolic pathways are able to convert acetate into ethanol (Kang fig. 1).
Kang does not teach their Lactiplantibacillus bacteria comprises a heterologous metabolic pathway for converting pyruvate into ethanol.
Wang teaches a Lactiplantibacillus casei recombinant bacterial host cell used for ethanol fermentation from biomass (Wang Abstract). Wang teaches the recombinant Lactiplantibacillus casei comprises a metabolic pathway for converting pyruvate into ethanol with heterologous enzymes pyruvate decarboxylase and alcohol dehydrogenase (Wang pg. 3 para. 3).
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the present invention to genetically engineer Kang’s bacterial host cell comprising the glycerol to ethanol and acetate to ethanol conversion pathways to heterologously express Wang’s metabolic pathway for converting pyruvate into ethanol with heterologous enzymes pyruvate decarboxylase and alcohol dehydrogenase. One of ordinary skill in the art would have been motivated to do so because it would allow the modified Lactiplantibacillus bacterial cell to be a more efficient ethanol producer able to convert pentoses, acetate, and glycerol into ethanol. Suhaimi teaches that glycerol is a known byproduct produced by biofuel production acting as a contaminant, but it is able to be converted into ethanol by a fermentative microorganisms with anabolic pathway, and glycerol’s utilization to produce more ethanol adds more value to the biodiesel industry (Suhaimi Abstract, pg. 506 para. 1, and pg. 507 para. 1). Thus, one of ordinary skill in the art would have recognized the beneficial effect of adding the ability to convert excess pyruvate into additional ethanol by modifying Kang’s Lactiplantibacillus bacterial cell.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-15 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3-10, 13, and 15-17 of copending Application No. 18/537,412 in view of Ruchala et al. (Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts, FEMS Microbiology Reviews, fuaa069, 45, 14 December 2020, 1-44, doi:10.1093/femsre/fuaa069).
Regarding instant claim 1, conflicting claim 1 recites a combination for making ethanol from a biomass comprising a bacterial host cell and a yeast host cell, wherein: the bacterial host cell has a first metabolic pathway comprising one or more first polypeptides for converting acetate into ethanol; a second metabolic pathway comprising one or more second polypeptides for the conversion of glycerol into dihydroxyacetone phosphate; and a third metabolic pathway comprising one or more third heterologous polypeptides for converting pyruvate into ethanol; and the yeast host cell has: a fourth metabolic pathway comprising one or more fourth polypeptides for producing glycerol; and a fifth metabolic pathway comprising one or more fifth polypeptides for generating acetate.
However, conflicting claim 1 does not recite the yeast host cell comprises a metabolic pathway comprising one or more polypeptides for converting pentoses into ethanol.
Ruchala teaches a Saccharomyces cerevisiae yeast cell engineered to comprise polypeptides for converting the pentose xylose into ethanol (Ruchala Table 1, Figs. 2-3, pg. 6 para. 1, and pg. 8 para. 2).
It would have been prima facie obvious to one of ordinary skill in the art to modify conflicting claim 1’s yeast host cell to express Ruchala’s engineered metabolic pathway comprising polypeptides for converting the pentose xylose into ethanol. One of ordinary skill in the art would have been motivated to do so because the goal of the conflicting claim’s composition was to produce ethanol from a biomass. Biomass is known to also comprise various pentoses (Ruchala Abstract); therefore one of ordinary skill in the art would have found it advantageous to genetically engineer the conflicting claim’s yeast host cell to further comprise a metabolic pathway that is able to convert those pentoses in the biomass into additional ethanol, thereby increasing the amount of recovered ethanol.
Regarding instant claim 2, Ruchala teaches that the biomass comprises lignocellulosic fibers (Ruchala Abstract) and the engineered yeast host cell is able to produce ethanol from xylose and arabinose pentoses (Ruchala Table 1). Conflicting claim 1 recites that the yeast host cell comprising a metabolic pathway for generating acetate; therefore the obvious yeast host cell is able to convert xylose and/or arabinose into ethanol, and is in combination with acetate and lignocellulosic fibers.
Regarding instant claim 3, conflicting claim 3 recites one or more native or heterologous enzymes for converting acetate into acetyl- CoA; and/or one or more native or heterologous enzymes for converting acetyl-CoA into acetaldehyde, and optionally acetaldehyde into ethanol.
Regarding instant claim 4, conflicting claim 4 recites the one or more native or heterologous enzymes for converting acetate into acetyl- CoA comprise a polypeptide having an acetate kinase (ACK) activity; a polypeptide having phosphotransacetylase (PTA) activity; and/or a polypeptide having acetyl coA-synthetase (ACS) activity; and the one or more native or heterologous enzymes for converting acetyl-CoA into acetaldehyde, and optionally acetaldehyde into ethanol comprise: a polypeptide having acetaldehyde-dehydrogenase (AADH) activity; a polypeptide having an alcohol dehydrogenase (ADH) activity); and/or a polypeptide having a bifunctional acetaldehyde/alcohol dehydrogenase (ADHE) activity.
Regarding instant claim 5, conflicting claim 5 recites the second metabolic pathway is for the dehydrogenation of glycerol.
Regarding instant claim 6, conflicting claim 6 recites the one or more second polypeptides comprise: a native or heterologous polypeptide having glycerol dehydrogenase (GLDA) activity or a combination of the native and the heterologous polypeptides having GLDA activity, a native or heterologous polypeptide having an ATP-dependent dihydroxyacetone kinase (DAK) activity, and/or a native or heterologous polypeptide having a PEP-dependent dihydroxyacetone kinase (DHAKLM) activity or a combination of a native and a heterologous polypeptides having DHAKLM activity.
Regarding instant claim 7, conflicting claim 7 recites the one of or more third heterologous polypeptides comprise: a native or heterologous polypeptide having pyruvate decarboxylase (PDC) activity, and/or a native or heterologous polypeptide having alcohol dehydrogenase (ADH) activity.
Regarding instant claim 8, conflicting claim 8 recites the bacterial host cell is a lactic acid bacterium.
Regarding instant claim 9, conflicting claim 9 recites the bacterial host cell is from Lactiplantibacillus sp.
Regarding instant claim 10, conflicting claim 10 recites the bacterial host cell has a decreased lactate dehydrogenase activity and optionally at least one inactivated native gene coding for a lactate dehydrogenase.
Regarding instant claim 11, conflicting claim 13 recites the one or more fourth polypeptides comprise: a native or heterologous polypeptide having glycerol-3-phosphate dehydrogenase activity, and/or a native or heterologous polypeptide having glycerol-3-phosphate phosphatase activity.
Regarding instant claim 12, Ruchala teaches Saccharomyces cerevisiae yeast has been engineered to comprise heterologous enzymes xylose reductase, xylose dehydrogenase, xylose isomerase, arabinose isomerase and ribulokinase (heterologous E. coli genes araA and araB, respectively), and ribulose-5-phosphate 4-epimerase (Ruchala Table 1, Figs. 3 and 7, pg. 6 para. 1, pg. 8 left col last para., and pg. 25 para. 1).
Regarding instant claim 13, conflicting claim 15 recites the yeast host cell is from Saccharomyces sp.
Regarding instant claim 14, conflicting claim 16 recites a bacterial host cell comprising a first metabolic pathway comprising one or more first polypeptides for converting acetate into ethanol; a second metabolic pathway comprising one or more second polypeptides for the conversion of glycerol into dihydroxyacetone phosphate; and a third metabolic pathway comprising one or more third heterologous polypeptides for converting pyruvate into ethanol.
Regarding instant claim 15, conflicting claim 17 recites a composition comprising the combination of conflicting claim 1 and a biomass comprising hexoses. However, conflicting claim 17 does not recite that the biomass comprises pentoses. Biomass is known to also comprise various pentoses (Ruchala Abstract).
This is a provisional nonstatutory double patenting rejection.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ALEXANDER M DURYEE whose telephone number is (571)272-9377. The examiner can normally be reached Monday - Friday 9:00 am - 5:00 pm.
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/Alexander M Duryee/Examiner, Art Unit 1657 /LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
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