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 15-30 are pending.
Examiner’s Comment
Two Claim 26 are presented in the claim set filed on 04/16/2026 and does not comply with 37 C.F.R. 1.126. For the purposes of examination only, the first claim 26 is hereafter referred to as 26(a) and the second claim 26 is hereafter referred to as claim 26(b). Note 37 CFR 1.126 requires the original numbering of the claims to be preserved throughout the prosecution.
Election/Restrictions
Applicant’s election without traverse of the species of ANB1 promoter, SEQ ID NO: 25, SEQ ID NO: 9, SEQ ID NO: 6, and SEQ ID NO: 1, in the reply filed on 4/16/2026 is acknowledged.
Claims 15-30 are examined herein.
The examiner’s preliminary search of the prior art resulted in examining the non-elected species of SEQ ID NO: 27, thus the requirement for a species election between SEQ ID NO: 1-25 and 27 is withdrawn.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. See [039]-[040] of the specification. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Objections
Claims 16, 23, and 25-29 are objected to because of the following informalities:
In claim 16, “a medium comprising glucose in a glucose concentration” is redundant and should be replaced with “a medium comprising a glucose concentration.”
In claim 19, the term “a promoter of a gene” is superfluous.
The hyphens in claims 23, 25, and 27-29 should be replaced with alphanumeric designations.
Regarding claims 25, Saccharomyces cerevisiae should be italicized.
The claim number 26 is repeated and claim numbers for claims 27-30 are thus incorrect.
Appropriate correction is required.
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.
Claims 15-30 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 15 is indefinite for the limitation “converting a carbon source using a recombinant yeast cell” because “using” is not a descriptive active verb. Applicant may consider amending claim 15 to recite “fermenting a carbon source with a recombinant yeast cell.” Claim 15 is further indefinite for the limitations, a nucleic acid sequence encoding a protein comprising phosphoketolase activity (EC 4.1.2.9 or EC 4.1.2.22), phosphotransacetylase (PTA) activity (EC 2.3.1.8), acetate kinase (ACK) activity (EC 2.7.2.12), and transketolase activity (EC 2.2.1.1). EC numbers are subject to change, which renders the claim scope indefinite. Furthermore, the EC numbers are in parentheses, so it is unclear whether they are part of the claimed invention.
Claim 29 is likewise indefinite for the limitations, a protein having glycerol dehydrogenase activity (E.C. 1.1.1.6) and a protein having dihydroxyacetone kinase activity (E.C. 2.7.1.28 or E.C. 2.7.1.29), for the same reason as above.
Claim 30 is likewise indefinite for the limitation, glucoamylase activity (EC 3.2.1.20 or 3.2.1.3), for the same reason as above.
Claim 16 recites “wherein the process is at least partly carried out in a medium” comprising glucose.” It is unclear whether “at least partly carried out” is requiring that the carbon source is glucose and at least part of the glucose is converted, whether at least one step of the process has glucose at a concentration of 25g/L or more, or whether at least part of the medium is glucose.
Similarly in claim 17, it is unclear whether the “at least partly carried out” refers to the steps of the process (at least one step of the process is carried out in the presence of the enzymes) or the step of converting the carbon (at least part of the duration of the step occurs in the presence of the enzyme).
Claim 22 is indefinite because it is unclear whether the claim is further limiting the nucleic acid sequence encoding a protein having transketolase activity to a heterologous nucleic acid sequence or whether the recombinant yeast cell further comprises a heterologous nucleic acid sequence encoding a protein having transketolase activity.
Claim 26(b) is indefinite because it is unclear whether the native protein having transketolase activity, the heterologous protein having transketolase activity, or both the native and the heterologous protein having transketolase activity are under the control of the promoter having an anaerobic/aerobic expression ratio for the transketolase of 2 or more.
Claims 16-30 are rejected for depending from a rejected base claim and not rectifying the source of indefiniteness discussed above.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 25 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 25 is rejected for failing to include all the limitations of the claim upon which it depends. Claim 25 recites the protein having transketolase activity comprises or consists of an amino acid sequence having in the range of equal to or more than 30% to equal to or less than 80% sequence identity with the amino acid sequence of SEQ ID NO: 9 or 10. However, claim 25 depends from claim 22, which requires that the protein having transketolase activity comprises or consists of SEQ ID NO: 11-25 or 27.
Applicant may cancel the claim, amend the claim to place the claim in proper dependent form, rewrite the claim in independent form, or present a sufficient showing that the dependent claim complies with the statutory requirements.
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, 22-23, 25, and 27-28 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.
Claim 23 recites a genus of functional homologues having at least 80% identity with SEQ ID NO: 11-25 and 27 (proteins having transketolase activity). Claim 23 also recites a genus of fragments of SEQ ID NO: 11-25 and 27 having transketolase activity (“the protein having transketolase activity comprises or consists of: an amino acid sequence of SEQ IDNO: 11…”).
Claim 25 recites a genus of proteins having transketolase activity comprising or consisting of an amino acid sequence having in the range of equal to or more than 30% or equal to or less than 80% sequence identity with the amino acid sequence of SEQ ID NO: 9. The broadest reasonable interpretation of claim 25 encompasses fragments of the SEQ ID NO: 9 (“an amino acid sequence”) as well as amino acid sequences comprising fragments of SEQ ID NO: 9.
Claim 27 recites a genus of functional homologues having at least 80% identity with SEQ ID NO: 1-4 (proteins having phosphoketolase activity). Claim 27 also recites a genus of fragments of SEQ ID NO: 1-4 having phosphoketolase activity (“the protein having phosphoketolase activity comprises or consists of an amino acid sequence of SEQ ID NO: 1…”).
Claim 28 recites a genus of functional homologues having at least 80% identity with SEQ ID NO: 5-8 (proteins having phosphotransacetylase activity). Claim 28 recites a genus of fragments of SEQ ID NO: 5-8 having phosphotransacetylase activity (“the protein having phosphotransacetylase activity comprises or consists of: an amino acid sequence of SEQ ID NO: 5…”).
The specification does not disclose any functional homologues (i.e. variants) of SEQ ID NO: 1-8, 11-25, and 27, nor does the specification disclose any fragments of these enzymes that retain activity.
The specification does not disclose the structure-function correlation between each of the enzymes and their activities. SEQ ID NO: 1-8, 11-25, and 27 are each sequences from different organisms: for example, SEQ ID NO: 1 is from Bifidobacterium animalis, SEQ ID NO: 5 is from Bacillus subtilis, and SEQ ID NO: 11 is from Komagataella phaffii.
Kochetov et al. (Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1844.9 (2014): 1608-1618) teaches that transketolase from S. cerevisiae is a homodimer of structurally identical subunits: the first two domains (amino acid residues 3-22 and 323-538) are involved in binding the coenzyme, whereas the function of the third domain is currently unknown but is believed to be involved in the regulation of the enzyme activity (page 1609, left column, 2. General structure of transketolase, paragraph 1; Fig. 2). Kochetov teaches that the residue Asp-477 interacts with the hydroxyl at C4 of substrate xylulose-5-phosphate (X5P), whereas His-263 and His-30 interact with the hydroxyl at C3 of the same substrate (page 1612, right column, bottom paragraph). Kochetov also teaches a Asp477Ala transketolase mutant (page 1612, right column, bottom paragraph). Kochetov concludes that the conserved residues of the substrate-harboring channel likely determine the stereospecificity of transketolase (page 1612, right column, bottom paragraph).
Suzuki et al. (Journal of Biological Chemistry 285.44 (2010): 34279-34287) teaches the crystal structure of phosphoketolase from Bifidobacterium breve (Abstract; note that the instant SEQ ID NO: 1-3 are all from Bifidobacterium spp.). Suzuki generates single amino acid substitutions of the phosphoketolase in order to verify the importance of key residues in substrate recognition and catalysis (page 34285, right column, paragraph 2 and Table 2). However, Suzuki teaches that there is no significant pattern that can predict the substrate preference to X5P and F6P (page 34284, right column, bottom paragraph). Suzuki concludes that surrounding residues that do not directly interact with the substrate may be responsible for the substrate specificity (page 34284, right column, bottom paragraph).
Ferry ("Acetate kinase and phosphotransacetylase." Methods in enzymology. Vol. 494. Academic Press, 2011. 219-231) teaches that the crystal structure of phosphotransacetylase from Streptococcus pyogenes and M. thermophila have been solved: both structures form a homodimer with each monomer consisting of two α/β domains and a cleft along the domain boundary that is the proposed active site bottom (bottom paragraph on page 228). Ferry also teaches that site-directed variants have been generated for M. thermophila (bottom paragraph on page 228). However, claim 28 requires functional homologues of SEQ ID NO: 5-8, which are not from the same organism.
To summarize, the specification does not disclose species of the claimed genus of functional homologues or fragments of transketolase, phosphoketolase, and phosphotransacetylase, nor does the specification disclose a structure-function correlation for each of the enzymes. The prior art teaches a high degree of unpredictability in the art with respect to the structure-function correlation of each of these enzymes.
Based on the above analysis, the person of ordinary skill in the art would not have recognized, at the time the application was filed, that the inventors had possession of the claimed genus of functional homologues or fragments of transketolase, phosphoketolase, or phosphotransacetylase.
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 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.
Claims 15-21, 27-28, and 30 are rejected under 35 U.S.C. 103 as being unpatentable over Miasnikov et al. (WO 2015148272 A1; cited in the IDS filed on 1/11/2024) in view of De Bont (US 20150176032 A1).
Miasnikov teaches a method of producing ethanol comprising the use of a fermentation composition in a fermentation process with a feedstock, wherein the fermentation composition comprises a recombinant yeast cell comprising at least one nucleic acid encoding a polypeptide having phosphoketolase activity, a polypeptide having phosphotransacetylase activity, and a transketolase wherein the composition further comprises glucose and glucoamylase (Miasnikov claims 1, 14, 17, and 21). Miasnikov teaches increasing transketolase activity allows more carbon flux towards fructose 6-phosphate and xylulose 5-phosphate via the non-oxidative branch of the pentose phosphate pathway, thereby increasing the eventual production of acetyl CoA and ethanol (lines 4-9 on page 21).
Miasnikov does not teach that the transketolase is under the control of the promoter ANB1, which is a promoter having an anaerobic/aerobic expression ratio for the transketolase of 2 or more (see instant claim 19).
De Bont teaches the ANB1 promoter is an anoxic promoter ([0036]) suitable for controlling expression of enzymes including transketolase for conversion of a pentose to a desired fermentation product such as ethanol or isoprenoid-derived products ([0039], [0074]). De Bont teaches overexpression of an enzyme from the non-oxidative part of the pentose phosphate pathway, including transketolase ([0074]).
Regarding claims 15 and 19, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the recombinant yeast cell in Miasnikov’s process for producing ethanol by expressing the transketolase under the control of the ANB1 promoter in order to increase expression of the enzyme. The person of ordinary skill in the art would have been motivated by the teaching of De Bont, who suggests that the anoxic ANB1 promoter is suitable for controlling expression of enzymes in the non-oxidative part of the pentose phosphate pathway such as transketolase. The person of ordinary skill in the art would have had a reasonable expectation of success in placing the transketolase under the control of the ANB1 promoter.
Regarding claim 16, Miasnikov teaches culturing recombinant yeast in medium containing 6% glucose (60 g/l glucose), which is within the claimed range of 25 g/l or more.
Regarding claims 17-18, the fermentation process is carried out in the presence of glucoamylase (Miasnikov claim 14).
Regarding claims 20-21, Miasnikov teaches increasing the activity of an endogenous (“native”) transketolase by replacing the transketolase gene promoter with a synthetic, high-expressing promoter (lines 16-20 on page 21). Promoters are oligonucleotide sequences.
Regarding claim 27¸ Miasnikov teaches transforming S. cerevisiae with SEQ ID NO: 37, which is the phosphoketolase from Bifidobacterium animalis (Table 8 on page 37). SEQ ID NO: 37 is 99.3% identical to the instant SEQ ID NO: 1 (OA Appendix A).
Regarding claim 28, Miasnikov teaches the transformation of S. cerevisiae with a recombinant vector comprising SEQ ID NO: 4, which is the nucleic acid encoding phosphotransacetylase from Lactobacillus plantarum (lines 12-14 on page 28). The amino acid translation of SEQ ID NO: 4 is 98.3% identical to the instant SEQ ID NO: 6 (OA Appendix B).
Regarding claim 30, Miasnikov teaches that the recombinant yeast further comprises a recombinant gene encoding a glucoamylase (lines 20-25 on page 5).
Claims 22-25 and 26(a)-(b) are rejected under 35 U.S.C. 103 as being unpatentable over Miasnikov et al. (WO 2015148272 A1) in view of De Bont (US20150176032 A1), as applied to claims 15-21, 27-28, and 30 above, further in view of Jacoby et al. (Current genetics 31.1 (1997): 15-21) as evidenced by AAB05935.1 (1996, website).
See discussion of Miasnikov and De Bont above, which is incorporated into this rejection as well.
Regarding claim 22, Miasnikov does not teach that the recombinant yeast further comprises a heterologous transketolase. Rather, Miasnikov teaches upregulating endogenous transketolase ([0064] and [0097]).
Jacoby teaches that Kluyveromyces lactis transketolase complements S. cerevisiae deficient in tk1 tikl2 double deletion mutant and restores transketolase activity (Abstract). Jacoby teaches the sequence of the Kluyveromyces lactis transketolase is U65983 (Fig. 2 caption), which encodes amino acid sequence GenBank AAB05935.1.
Regarding claims 22 and 26(a)-(b), it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to express the Kluyveromyces lactis transketolase in the yeast cell of Miasnikov in order to express a higher number of copies of the transketolase, thus increasing transketolase activity and ethanol production from the yeast cell. The person of ordinary skill in the art would have had a reasonable expectation of success.
Regarding claim 23. The amino acid sequence of AAB05935.1 is identical to the instant SEQ ID NO: 27 (OA Appendix C).
Regarding claim 24¸ Miasnikov does not teach expressing the heterologous transketolase under the control of a promoter having an anaerobic/aerobic expression ratio for the transketolase of 2 or more.
However, Miasnikov teaches increasing transketolase activity allows more carbon flux towards fructose 6-phosphate and xylulose 5-phosphate via the non-oxidative branch of the pentose phosphate pathway, thereby increasing the eventual production of acetyl CoA and ethanol (lines 4-9 on page 21).
De Bont teaches overexpression of an enzyme from the non-oxidative part of the pentose phosphate pathway, including transketolase ([0074]).
De Bont teaches the ANB1 promoter is an anoxic promoter ([0036]) suitable for controlling expression of enzymes including transketolase for conversion of a pentose to a desired fermentation product such as ethanol or isoprenoid-derived products ([0039], [0074]).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to express the heterologous Kluyveromyces lactis transketolase of Jacoby under the control of De Bont’s ANB1 promoter since De Bont teaches that the promoter is an anoxic promoter suitable for the controlling the expression of enzymes including transketolase. The person of ordinary skill in the art would have had a reasonable expectation of success. The ANB1 promoter necessarily has the required anaerobic/aerobic expression ratio (see dependent claim 19).
Regarding claim 25, Miasnikov teaches the recombinant yeast cell is Saccharomyces cerevisiae (lines 1-2 on page 5).
AAB05935.1 is identical to the instant SEQ ID NO: 27, which is 80.5% identical to the instant SEQ ID NO: 9 (OA Appendix D). Thus, the sequence AAB05935.1 is 80.5 % identical to the instant SEQ ID NO: 9, which is approaching the claimed range of equal to or more than 30% to equal to or less than 80%.
Regarding claim 26(a), Miasnikov does not teach the native nucleic acid sequence encoding for a protein having transketolase activity has been deleted.
Jacoby teaches that Kluyveromyces lactis transketolase complements S. cerevisiae deficient in tk1 tikl2 double deletion mutant and restores transketolase activity (Abstract).
It would have been obvious to the person of ordinary skill in the art before the effective filing date of the claimed invention to delete the native S. cerevisiae tk1 tikl2 transketolase genes and replace them with the Kluyveromyces lactis transketolase gene per the teaching of Jacoby. Jacoby teaches that the Kluyveromyces lactis transketolase complements the S. cerevisiae deficient in tk1 tikl2 double deletion mutant so they are art-recognized equivalents for the same purpose (they both encode a transketolase). See MPEP 2144.06(II).
Claim 29 is rejected under 35 U.S.C. 103 as being unpatentable over Miasnikov et al. (WO-2015148272-A1) in view of De Bont (US-20150176032-A1), as applied to claims 15-21, 27-28, and 30 above, further in view of Zhang et al. (Journal of Industrial Microbiology and Biotechnology 40.10 (2013): 1153-1160.
See discussion of Miasnikov and De Bont above, which is incorporated into this rejection as well.
Regarding claim 29, Miasnikov does not teach that the recombinant yeast further comprises glycerol dehydrogenase.
Zhang teaches that glycerol is a major by-product of industrial ethanol production (Abstract). Zhang teaches that overexpressing glycerol dehydrogenase and dihydroxyacetone kinase in the glycerol degradation pathway increases ethanol yield in S. cerevisiae (Abstract).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to overexpress glycerol dehydrogenase and dihydroxyacetone kinase in the recombinant yeast in the process of Miasnikov modified by De Bont in order to further enhance the yield of ethanol from the strain. The person of ordinary skill in the art would have had a reasonable expectation of success given the teaching of Zhang.
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 15-25 and 26(b)-30 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 18-19, 22, 24-27, 35-36 of copending Application No. 18/578,585 (reference application; hereafter ‘585) in view of Miasnikov et al. (WO-2015/148272-A1).
Claim 17 of ‘585 recites a process for the production of ethanol comprising converting a carbon source using a recombinant yeast cell, wherein the recombinant yeast cell functionally expresses a nucleic acid sequence encoding a native protein having transketolase activity and a nucleic acid sequence encoding a heterologous protein having transketolase activity.
Claim 26 of ‘585, which depends from claim 17 of ‘585, recites that expression of the nucleic acid sequence encoding the transketolase is under the control of a promoter having an anaerobic/aerobic expression ratio for the transketolase of 2 or more.
Claim 26 of ‘585 does not recite that the recombinant yeast cell further comprises a phosphoketolase, a phosphotransacetylase, or an acetate kinase.
Miasnikov teaches a method of producing ethanol comprising the use of a fermentation composition in a fermentation process with a feedstock, wherein the fermentation composition comprises a recombinant yeast cell comprising at least one nucleic acid encoding a polypeptide having phosphoketolase activity, a polypeptide having phosphotransacetylase activity, and a transketolase wherein the composition further comprises glucose and glucoamylase (Miasnikov claims 1, 14, 17, and 21). Miasnikov teaches the recombinant yeast cell is Saccharomyces cerevisiae (lines 1-2 on page 5).
Miasnikov teaches increasing transketolase activity allows more carbon flux towards fructose 6-phosphate and xylulose 5-phosphate via the non-oxidative branch of the pentose phosphate pathway, thereby increasing the eventual production of acetyl CoA and ethanol (lines 4-9 on page 21).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to further modify the recombinant yeast cell of the process of claim 26 of 585 by expressing phosphoketolase and phosphotransacetylase in the yeast cell. The person of ordinary skill in the art would have been motivated by the teaching of Miasnikov, who suggests that a recombinant yeast cell expressing phosphoketolase, phosphotransacetylase, and transketolase is capable of producing ethanol from a feedstock. The person of ordinary skill in the art would have had a reasonable expectation of success.
Instant claim 16 is obvious over claims 18 and 26 of ‘585 in view of Miasnikov.
Instant claim 17 is obvious over claims 19 and 26 of ‘585 in view of Miasnikov.
Instant claim 18 is obvious over claims 26 and 36 of ‘585 in view of Miasnikov.
Instant claim 19 is obvious over claims 25-27 of ‘585 in view of Miasnikov.
Regarding instant claim 20, claim 26 of ‘585 does not recite that the promoter is a synthetic oligonucleotide.
Miasnikov teaches increasing the activity of an endogenous transketolase by replacing the transketolase gene promoter with a synthetic, high-expressing promoter (lines 16-20 on page 21).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to synthesize the promoter of claim 26 of ‘585 for expression in the recombinant yeast of claim 26 of ‘585 per the teaching of Miasnikov. The person of ordinary skill in the art would have had a reasonable expectation in synthesizes the promoter. Promoters are oligonucleotide sequences.
Instant claims 21-22 and claim 26(b) are obvious over claim 26 of ‘585 in view of Miasnikov.
Instant claim 23 is obvious over claim 22 of ‘585 in view of Miasnikov for the embodiments in which the transketolase is SEQ ID NO: 3-11 (identical to instant SEQ ID NO: 11-19, respectively),
Instant claim 24 is obvious over claim 24 of ‘585 in view of Miasnikov.
Instant claim 25 is obvious over claim 22 of ‘585 in view of Miasnikov because SEQ ID NO: 3 of ‘585 (corresponding to instant SEQ ID NO: 11) is 37.2% identical to the instant SEQ ID NO; 9, which is within the claimed range equal to or more than 30% identity to equal to or more than 80% identity. Although claim 22 of ‘585 does not recite that the recombinant yeast cell is S. cerevisiae, Miasnikov teaches the recombinant yeast cell is Saccharomyces cerevisiae (lines 1-2 on page 5). Thus, it would have been obvious to the person of ordinary skill in the art before the effective filing date of the claimed invention to specifically use S. cerevisiae in the process of claim 22 of ‘585 modified by Miasnikov and the person of ordinary skill in the art would have had a reasonable expectation of success in doing so.
Regarding instant claim 27¸ Miasnikov teaches transforming S. cerevisiae with SEQ ID NO: 37, which is the phosphoketolase from Bifidobacterium animalis (Table 8 on page 37). SEQ ID NO: 37 is 99.3% identical to the instant SEQ ID NO: 1 (OA Appendix A).
Regarding instant claim 28, Miasnikov teaches the transformation of S. cerevisiae with a recombinant vector comprising the nucleic acid SEQ ID NO: 4 encoding phosphotransacetylase from Lactobacillus plantarum (lines 12-14 on page 28). The amino acid translation of SEQ ID NO: 4 of Miasnikov is 98.3% identical to the instant SEQ ID NO: 6, which overlaps with the claimed range of greater than 80% identity to SEQ ID NO: 6 (OA Appendix B).
Instant claim 29 is obvious over claims 26 and 35 of ‘585 in view of Miasnikov.
Instant claim 30 is obvious over claims 26 and 36 of ‘585 in view of Miasnikov.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 15-30 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 15-27 and 30-31 of copending Application No. 18/578,589 (reference application; hereafter ‘589) in view of Miasnikov et al. (WO-2015148272-A1).
Claim 15 of ‘589 recites a process for the production of ethanol, comprising converting a carbon source using a recombinant yeast cell, wherein the recombinant yeast cell functionally expresses: a) a nucleic acid sequence encoding a protein having NAD+ dependent acetylating acetaldehyde dehydrogenase activity and b) a nucleic acid sequence encoding a protein having transketolase activity, wherein the expression of the nucleic acid sequence encoding the protein having transketolase activity is under control of a promoter having an anaerobic/aerobic expression ratio for the transketolase of 2 or more.
Claim 15 of ‘589 does not recite that the recombinant yeast cell further comprises a nucleic acid sequence encoding a protein having phosphoketolase activity or a nucleic acid sequence encoding a protein having phosphotransacetylase activity.
Miasnikov teaches a method of producing ethanol comprising the use of a fermentation composition in a fermentation process with a feedstock, wherein the fermentation composition comprises a recombinant yeast cell comprising at least one nucleic acid encoding a polypeptide having phosphoketolase activity, a polypeptide having phosphotransacetylase activity, a polypeptide having acetylating acetaldehyde dehydrogenase activity, and a transketolase wherein the composition further comprises glucose and glucoamylase (Miasnikov claims 1, 14, 17, and 21).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the recombinant yeast cell of claim 15 of ‘589 by further expressing a nucleic acid sequence encoding a protein having phosphoketolase activity or a nucleic acid sequence encoding a protein having phosphotransacetylase activity. The person of ordinary skill in the art would have been motivated by the teaching of Miasnikov, who teaches a recombinant yeast cell for the production of ethanol comprising phosphoketolase, phosphotransacetylase, acetylating acetaldehyde dehydrogenase, and transketolase.
Instant claim 16-25 are each obvious over the conflicting claims 16-25 of ‘589, respectively, in view of Miasnikov.
Instant claim 26(a) is obvious over claim 26 of ‘589 in view of Miasnikov.
Instant claim 26(b) is obvious over claim 27 of ‘589 in view of Miasnikov.
Regarding instant claim 27¸ Miasnikov teaches transforming S. cerevisiae with SEQ ID NO: 37, which is the phosphoketolase from Bifidobacterium animalis (Table 8 on page 37). SEQ ID NO: 37 is 99.3% identical to the instant SEQ ID NO: 1 (OA Appendix A).
Regarding instant claim 28, Miasnikov teaches the transformation of S. cerevisiae with a recombinant vector comprising the nucleic acid SEQ ID NO: 4 encoding phosphotransacetylase from Lactobacillus plantarum (lines 12-14 on page 28). The amino acid translation of SEQ ID NO: 4 is 98.3% identical to the instant SEQ ID NO: 6, which overlaps with the claimed range of greater than 80% identity to SEQ ID NO: 6 (OA Appendix B).
Instant claim 29 is obvious over claim 30 of ‘589 in view of Miasnikov.
Instant claim 30 is obvious over claim 31 of ‘589 in view of Miasnikov.
Claims 15-21 and 27-30 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 11, and 16-17 of copending Application No. 18/578,590 (reference application; hereafter ‘590) in view of Miasnikov et al. (WO-2015148272-A1) and De Bont (US-20150176032-A1).
Claim 1 of ‘590 recites a recombinant yeast cell that functionally expresses a nucleic acid sequence encoding a protein having glycerol dehydrogenase activity, a nucleic acid sequence encoding a protein having dihydroxyacetone kinase activity, and a nucleic acid sequence encoding a protein having glycerol transporter activity, wherein expression of the nucleic acid sequence encoding the protein having glycerol transporter activity is under the control of a promoter that has an anaerobic/aerobic expression ratio for the glycerol transporter of 2 or more.
Claim 2 of ‘590 recites the promoter is the promoter of the ANB1 gene.
Claim 11 of ‘590 recites the recombinant yeast cell functionally expresses a nucleic acid sequence encoding a protein comprising phosphoketolase activity, phosphotransacetylase activity, and acetate kinase activity.
Claim 16 of ‘590 recites the recombinant yeast cell further functionally expresses a nucleic acid sequence encoding a protein having glucoamylase activity.
Claim 17 of ‘590 is drawn to a process for the production of ethanol comprising converting a carbon source using a recombinant yeast cell according to claim 1.
Claims 1-2, 11, and 16-17 of ‘590 do not recite that the recombinant yeast cell further comprises a transketolase.
Miasnikov teaches a method of producing ethanol comprising the use of a fermentation composition in a fermentation process with a feedstock, wherein the fermentation composition comprises a recombinant yeast cell comprising at least one nucleic acid encoding a polypeptide having phosphoketolase activity, a polypeptide having phosphotransacetylase activity, and a transketolase wherein the composition further comprises glucose and glucoamylase (Miasnikov claims 1, 14, 17, and 21).
Miasnikov teaches increasing transketolase activity allows more carbon flux towards fructose 6-phosphate and xylulose 5-phosphate via the non-oxidative branch of the pentose phosphate pathway, thereby increasing the eventual production of acetyl CoA and ethanol (lines 4-9 on page 21).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the recombinant yeast cell of claims 1-2, 11, and 16-17 of ‘590 by expressing the transketolase of Miasnikov and fermenting the yeast cell to produce ethanol. The person of ordinary skill in the art would have had a reasonable expectation of success given the teaching of Miasnikov that including a transketolase in the yeast cell increases the production of ethanol.
Regarding instant claims 15 and 19, claims 1-2, 11, and 16-17 of ‘590 do not recite that the transketolase is under the control of the promoter that has an anaerobic/aerobic expression ratio for the transketolase of 2 or more.
De Bont teaches overexpression of an enzyme from the non-oxidative part of the pentose phosphate pathway, including transketolase ([0074]).
De Bont teaches the ANB1 promoter is an anoxic promoter ([0036]) suitable for controlling expression of enzymes including transketolase for conversion of a pentose to a desired fermentation product such as ethanol or isoprenoid-derived products ([0039], [0074]).
It would have been further obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the recombinant yeast cell of claims 1-2, 11, and 16-17 of ‘590 modified by Miasnikov by putting the transketolase under the control of the ANB1 promoter in order to increase expression of the enzyme. The person of ordinary skill in the art would have been motivated by the teaching of De Bont, who suggests that the anoxic ANB1 promoter is suitable for controlling expression of enzymes in the non-oxidative part of the pentose phosphate pathway such as transketolase. The person of ordinary skill in the art would have had a reasonable expectation of success in placing the transketolase under the control of the ANB1 promoter.
Regarding instant claim 16, claims 1-2, 11, and 16-17 of ‘590 do not recite that the process is carried out in a medium comprising a glucose concentration of 25 g/L or more.
Miasnikov teaches culturing recombinant yeast in medium containing 6% glucose (60 g/l glucose), which is within the claimed range of 25 g/l or more.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to apply the teachings of Miasnikov regarding the glucose concentration in the culture conditions to the recombinant yeast in the process of claims 1-2, 11, and 16-17 of ‘590 modified by Miasnikov and De Bont per the teaching of Miasnikov and the person of ordinary skill in the art would have had a reasonable expectation of success in doing so.
Regarding instant claims 20-21, claims 1-2, 11, and 16-17 of ‘590 do not recite that the promoter for the transketolase is a synthetic oligonucleotide or that a native nucleic acid sequence encoding the transketolase is under the control of the promoter.
Miasnikov teaches increasing the activity of an endogenous (“native”) transketolase by replacing the transketolase gene promoter with a synthetic, high-expressing promoter (lines 16-20 on page 21).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to synthesize De Bont’s promoter (oligonucleotide sequence) and modify the yeast cell in the process of claims 1-2, 11, and 16-17 of ‘590 modified by Miasnikov and De Bont by expressing an endogenous transketolase under the control of the promoter. The person of ordinary skill in the art would have had a reasonable expectation of success in doing so.
Regarding instant claims 27-28, claims 1-2, 11, and 16-17 of ‘590 do not recite the sequence of the phosphoketolase or the phosphotransacetylase.
Regarding instant claim 27¸ Miasnikov teaches transforming S. cerevisiae with SEQ ID NO: 37, which is the phosphoketolase from Bifidobacterium animalis (Table 8 on page 37). SEQ ID NO: 37 is 99.3% identical to the instant SEQ ID NO: 1 (OA Appendix A).
Regarding instant claim 28, Miasnikov teaches the transformation of S. cerevisiae with a recombinant vector comprising the nucleic acid SEQ ID NO: 4 encoding phosphotransacetylase from Lactobacillus plantarum (lines 12-14 on page 28). The amino acid translation of SEQ ID NO: 4 is 98.3% identical to the instant SEQ ID NO: 6, which overlaps with the claimed range of greater than 80% identity to SEQ ID NO: 6 (OA Appendix B).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to apply the teaching of Miasnikov regarding the specific phosphoketolase and phosphotransacetylase sequences to the recombinant yeast in the process of claims 1-2, 11, and 16-17 of ‘590 modified by Miasnikov and De Bont. The person of ordinary skill in the art would have had a reasonable expectation of success in doing so.
Instant claim 29 is obvious over claim 17 of ‘590 in view of Miasnikov and De Bont.
Instant claims 17-18 and 30 are obvious over claim 16 of ‘590 in view of Miasnikov and De Bont.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 22-25 and 26(a)-(b) are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 11, and 16-17 of copending Application No. 18/578,590 (reference application; hereafter ‘590) in view of Miasnikov et al. (WO-2015148272-A1) and De Bont (US-20150176032-A1), as applied to claims 15-21 and 27-30 above, further in view of Jacoby et al. (Current genetics 31.1 (1997): 15-21) as evidenced by AAB05935.1 (1996, website).
See discussion of claims 1-2, 11, and 16-17 of ‘590, Miasnikov, and De Bont above, which is incorporated into this rejection as well.
Regarding claim 22, claims 1-2, 11, and 16-17 of ‘590 do not recite and Miasnikov does not teach that the recombinant yeast further comprises a heterologous transketolase. Rather, Miasnikov teaches upregulating endogenous transketolase ([0064] and [0097]).
Jacoby teaches that Kluyveromyces lactis transketolase complements S. cerevisiae deficient in tk1 tikl2 double deletion mutant and restores transketolase activity (Abstract). Jacoby teaches the sequence of the Kluyveromyces lactis transketolase is U65983, which encodes amino acid sequence GenBank AAB05935.1.
Regarding claims 22 and 26(b), it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to express the Kluyveromyces lactis transketolase in the yeast cell of the process of claims 1-2, 11, and 16-17 of ‘590 modified by Miasnikov and De Bont in order to express a higher number of copies of the transketolase, thus increasing transketolase activity and ethanol production from the yeast cell. The person of ordinary skill in the art would have had a reasonable expectation of success.
Regarding claim 23, Jacoby teaches the sequence of the Kluyveromyces lactis transketolase is U65983 (Fig. 2 caption), which encodes amino acid sequence GenBank AAB05935.1. AAB05935.1 is identical to the instant SEQ ID NO: 27 (OA Appendix C).
Regarding instant claim 24¸ claims 1-2, 11, and 16-17 of ‘590 do not recite and Miasnikov does not teach expressing the heterologous transketolase under the control of a promoter having an anaerobic/aerobic expression ratio for the transketolase of 2 or more.
However, Miasnikov teaches increasing transketolase activity allows more carbon flux towards fructose 6-phosphate and xylulose 5-phosphate via the non-oxidative branch of the pentose phosphate pathway, thereby increasing the eventual production of acetyl CoA and ethanol (lines 4-9 on page 21).
De Bont teaches overexpression of an enzyme from the non-oxidative part of the pentose phosphate pathway, including transketolase ([0074]).
De Bont teaches the ANB1 promoter is an anoxic promoter ([0036]) suitable for controlling expression of enzymes including transketolase for conversion of a pentose to a desired fermentation product such as ethanol or isoprenoid-derived products ([0039], [0074]).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to express the heterologous Kluyveromyces lactis transketolase of Jacoby under the control of De Bont’s ANB1 promoter in the recombinant yeast in the process of claims 1-2, 11, and 16-17 of ‘590 modified by Miasnikov and De Bont because De Bont teaches that the promoter is an anoxic promoter suitable for the controlling the expression of enzymes including transketolase. The person of ordinary skill in the art would have had a reasonable expectation of success. The ANB1 promoter necessarily has the required anaerobic/aerobic expression ratio (see dependent claim 19).
Regarding claim 25, AAB05935.1 is identical to the instant SEQ ID NO: 27, which is 80.5% identical to the instant SEQ ID NO: 9 (OA Appendix D). Thus, the sequence AAB05935.1 is 80.5 % identical to the instant SEQ ID NO: 9, which is approaching the claimed range of equal to or more than 30% to equal to or less than 80%. Although claims 1-2, 11, and 16-17 of ‘590 do not recite that the recombinant yeast cell is S. cerevisiae, Miasnikov teaches the recombinant yeast cell is Saccharomyces cerevisiae (lines 1-2 on page 5). Thus, it would have been obvious to the person of ordinary skill in the art before the effective filing date of the claimed invention to specifically use S. cerevisiae in the process of claims 1-2, 11, and 16-17 of ‘590 modified by Miasnikov, De Bont, and Jacoby and the person of ordinary skill in the art would have had a reasonable expectation of success in doing so.
Regarding claim 26(a), claims 1-2, 11, and 16-17 of ‘590 do not recite and Miasnikov does not teach the native nucleic acid sequence encoding for a protein having transketolase activity has been deleted.
Jacoby teaches that Kluyveromyces lactis transketolase complements S. cerevisiae deficient in tk1 tikl2 double deletion mutant and restores transketolase activity (Abstract). Jacoby teaches the sequence of the Kluyveromyces lactis transketolase is U65983 (Fig 2 caption), which encodes amino acid sequence GenBank AAB05935.1.
It would have been obvious to delete the native S. cerevisiae tk1 tikl2 transketolase genes in the recombinant yeast of the process of claims 1-2, 11, and 16-17 of ‘590 modified by Miasnikov and De Bont and replace them with the Kluyveromyces lactis transketolase gene because they are art-recognized equivalents for the same purpose (they both encode a transketolase). See MPEP 2144.06(II).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 15-21 and 27-30 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 9 of copending Application No. 18/704,739 (reference application; hereafter ‘739) in view of Miasnikov et al. (WO-2015148272-A1) and De Bont (US-20150176032-A1).
Claim 9 of ‘739 recites a process for production of ethanol comprising fermentation of a feed under anaerobic conditions in the presence of a recombinant yeast cell, wherein the recombinant yeast cell comprises a protein having phosphoketolase activity, a protein having phosphotransacetylase activity, a protein having acetate kinase activity, a protein having glycerol dehydrogenase activity, a protein having dihydroxyacetone kinase activity, and a protein having glycerol transporter activity.
Claim 9 of ‘739 does not recite that the recombinant yeast cell further comprises a transketolase.
Miasnikov teaches a method of producing ethanol comprising the use of a fermentation composition in a fermentation process with a feedstock, wherein the fermentation composition comprises a recombinant yeast cell comprising at least one nucleic acid encoding a polypeptide having phosphoketolase activity, a polypeptide having phosphotransacetylase activity, and a transketolase wherein the composition further comprises glucose and glucoamylase (Miasnikov claims 1, 14, 17, and 21).
Miasnikov teaches increasing transketolase activity allows more carbon flux towards fructose 6-phosphate and xylulose 5-phosphate via the non-oxidative branch of the pentose phosphate pathway, thereby increasing the eventual production of acetyl CoA and ethanol (lines 4-9 on page 21).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the recombinant yeast cell in the process of claim 9 of ‘739 by expressing the transketolase of Miasnikov. The person of ordinary skill in the art would have had a reasonable expectation of success given the teaching of Miasnikov that including a transketolase increases the production of ethanol.
Regarding instant claims 15 and 19, claim 9 of ‘739 does not recite that the expression of the nucleic acid sequence encoding the protein having transketolase activity is under the control of a promoter having an anaerobic/aerobic expression ratio for the transketolase of 2 or more.
De Bont teaches overexpression of an enzyme from the non-oxidative part of the pentose phosphate pathway, including transketolase ([0074]).
De Bont teaches the ANB1 promoter is an anoxic promoter ([0036]) suitable for controlling expression of enzymes including transketolase for conversion of a pentose to a desired fermentation product such as ethanol or isoprenoid-derived products ([0039], [0074]).
It would have been further obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the recombinant yeast cell in the process of claim 9 of ‘739 modified by Miasnikov by putting the transketolase under the control of the ANB1 promoter in order to increase expression of the enzyme. The person of ordinary skill in the art would have been motivated by the teaching of De Bont, who suggests that the anoxic ANB1 promoter is suitable for controlling expression of enzymes in the non-oxidative part of the pentose phosphate pathway such as transketolase. The person of ordinary skill in the art would have had a reasonable expectation of success in placing the transketolase under the control of the ANB1 promoter. The ANB1 promoter necessarily has an anaerobic/aerobic expression ratio for the transketolase of 2 or more (see instant dependent claim 19).
Regarding instant claim 17, claim 9 of ‘739 depends from claim 1 of ‘739, which recites that the recombinant yeast cell produces a glucosidase (saccharolytic enzyme), thus the process of claim 9 of ‘739, is carried out in the presence of a saccharolytic enzyme.
Regarding instant claim 16, claim 9 of ‘739 does not recite that the process is carried out in a medium comprising a glucose concentration of 25 g/L or more.
Regarding instant claim 18, claim 9 of ‘739 does not recite that the process is carried out in the presence of glucoamylase.
Regarding instant claim 30, claim 9 of ‘739 does not recite that the recombinant yeast further comprises a recombinant gene encoding a glucoamylase.
Miasnikov teaches culturing recombinant yeast in medium containing 6% glucose (60 g/l glucose), which is within the claimed range of 25 g/l or more.
Miasnikov teaches that the fermentation process is carried out in the presence of glucoamylase (Miasnikov claim 14).
Miasnikov teaches that the recombinant yeast further comprises a recombinant gene encoding a glucoamylase (lines 20-25 on page 5).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to apply the teachings of Miasnikov regarding the culture conditions (i.e. glucose concentration and the expression of glucoamylase) to the recombinant yeast in the process of claim 9 of ‘739 modified by Miasnikov and De Bont per the teaching of Miasnikov and the person of ordinary skill in the art would have had a reasonable expectation of success in doing so.
Regarding instant claims 20-21, claim 9 of ‘739 does not recite that the promoter for the transketolase is a synthetic oligonucleotide or that a native nucleic acid sequence encoding the transketolase is under the control of the promoter.
Miasnikov teaches increasing the activity of an endogenous (“native”) transketolase by replacing the transketolase gene promoter with a synthetic, high-expressing promoter (lines 16-20 on page 21).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to synthesize De Bont’s promoter (oligonucleotide sequence) and modify the yeast cell in the process of claim 9 of ‘739 modified by Miasnikov and De Bont by expressing an endogenous transketolase under the control of the promoter. The person of ordinary skill in the art would have had a reasonable expectation of success in doing so.
Regarding instant claims 27-28, claim 9 of ‘739 does not recite the sequence of the phosphoketolase or the phosphotransacetylase.
Regarding instant claim 27¸ Miasnikov teaches transforming S. cerevisiae with SEQ ID NO: 37, which is the phosphoketolase from Bifidobacterium animalis (Table 8 on page 37). SEQ ID NO: 37 is 99.3% identical to the instant SEQ ID NO: 1 (OA Appendix A).
Regarding instant claim 28, Miasnikov teaches the transformation of S. cerevisiae with a recombinant vector comprising the nucleic acid SEQ ID NO: 4 encoding phosphotransacetylase from Lactobacillus plantarum (lines 12-14 on page 28). The amino acid translation of SEQ ID NO: 4 is 98.3% identical to the instant SEQ ID NO: 6, which overlaps with the claimed range of greater than 80% identity to SEQ ID NO: 6 (OA Appendix B).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to apply the teaching of Miasnikov regarding the specific phosphoketolase and phosphotransacetylase sequences to the recombinant yeast in the process of claim 9 of ‘739 modified by Miasnikov and De Bont. The person of ordinary skill in the art would have had a reasonable expectation of success in doing so.
Instant claim 29 is obvious over claim 9 of ‘739 in view of Miasnikov and De Bont.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 22-25 and 26(a)-(b) are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 6 and 9 of copending Application No. 18/704,739 (reference application; hereafter ‘739) in view of Miasnikov et al. (WO-2015148272-A1) and De Bont (US-20150176032-A1), as applied to claims 15-21, 27-28, and 30 above, further in view of Jacoby et al. (Current genetics 31.1 (1997): 15-21) as evidenced by AAB05935.1 (1996, website).
See discussion of claim 9 of ‘539, Miasnikov, and De Bont above, which is incorporated into this rejection as well.
Regarding claim 22, claim 9 of ‘739 does not recite and Miasnikov does not teach that the recombinant yeast further comprises a heterologous transketolase. Rather, Miasnikov teaches upregulating endogenous transketolase ([0064] and [0097]).
Jacoby teaches that Kluyveromyces lactis transketolase complements S. cerevisiae deficient in tk1 tikl2 double deletion mutant and restores transketolase activity (Abstract). Jacoby teaches the sequence of the Kluyveromyces lactis transketolase is U65983, which encodes amino acid sequence GenBank AAB05935.1.
Regarding instant claims 22 and 26(b), it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to express the Kluyveromyces lactis transketolase in the yeast cell of the process of claim 9 of ‘739 modified by Miasnikov and De Bont in order to express a higher number of copies of the transketolase, thus increasing transketolase activity and ethanol production from the yeast cell. The person of ordinary skill in the art would have had a reasonable expectation of success.
Regarding instant claim 23, Jacoby teaches the sequence of the Kluyveromyces lactis transketolase is U65983 (Fig. 2 caption), which encodes amino acid sequence GenBank AAB05935.1. AAB05935.1 is identical to the instant SEQ ID NO: 27 (OA Appendix C).
Regarding instant claim 24¸ claim 9 of ‘739 does not recite and Miasnikov does not teach expressing the heterologous transketolase under the control of a promoter having an anaerobic/aerobic expression ratio for the transketolase of 2 or more.
However, Miasnikov teaches increasing transketolase activity allows more carbon flux towards fructose 6-phosphate and xylulose 5-phosphate via the non-oxidative branch of the pentose phosphate pathway, thereby increasing the eventual production of acetyl CoA and ethanol (lines 4-9 on page 21).
De Bont teaches overexpression of an enzyme from the non-oxidative part of the pentose phosphate pathway, including transketolase ([0074]).
De Bont teaches the ANB1 promoter is an anoxic promoter ([0036]) suitable for controlling expression of enzymes including transketolase for conversion of a pentose to a desired fermentation product such as ethanol or isoprenoid-derived products ([0039], [0074]).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to express the heterologous Kluyveromyces lactis transketolase of Jacoby under the control of De Bont’s ANB1 promoter in the recombinant yeast in the process of claim 9 of ‘739 modified by Miasnikov and De Bont because De Bont teaches that the promoter is an anoxic promoter suitable for the controlling the expression of enzymes including transketolase. The person of ordinary skill in the art would have had a reasonable expectation of success. The ANB1 promoter necessarily has the required anaerobic/aerobic expression ratio (see dependent claim 19).
Regarding claim 25, although claim 9 of ‘739 does not recite the species of yeast, claim 6 of ‘739 recites that the recombinant yeast cell is S. cerevisiae, thus it would have been obvious to the person of ordinary skill in the art before the effective filing date of the claimed invention to specifically use S. cerevisiae in the process of claim 9 of ‘739 modified by Miasnikov, De Bont, and Jacoby. Jacoby teaches the sequence of the Kluyveromyces lactis transketolase is U65983 (Fig. 2 caption), which encodes amino acid sequence GenBank AAB05935.1. AAB05935.1 is identical to the instant SEQ ID NO: 27 (OA Appendix C). AAB05935.1 is identical to the instant SEQ ID NO: 27, which is 80.5% identical to the instant SEQ ID NO: 9 (OA Appendix D). Thus, the sequence AAB05935.1 is 80.5 % identical to the instant SEQ ID NO: 9, which is approaching the claimed range of equal to or more than 30% to equal to or less than 80%.
Regarding claim 26(a), claim 9 of 739 does not recite and Miasnikov does not teach the native nucleic acid sequence encoding for a protein having transketolase activity has been deleted.
Jacoby teaches that Kluyveromyces lactis transketolase complements S. cerevisiae deficient in tk1 tikl2 double deletion mutant and restores transketolase activity (Abstract). Jacoby teaches the sequence of the Kluyveromyces lactis transketolase is U65983, which encodes amino acid sequence GenBank AAB05935.1.
It would have been obvious to delete the native S. cerevisiae tk1 tikl2 transketolase genes in the recombinant yeast of the process of claim 9 of ‘739 modified by Miasnikov and De Bont and replace them with the Kluyveromyces lactis transketolase gene because they are art-recognized equivalents for the same purpose (they both encode a transketolase). See MPEP 2144.06(II).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
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/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/CANDICE LEE SWIFT/Examiner, Art Unit 1657
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