DETAILED ACTION
Claims 1, 3, 5, 8-9, 13-16, 20, 23-24, 26-29, 31-33, and 41 are pending in the instant application.
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 .
Election/Restrictions
Applicant's election with traverse of Group I, claims 1, 3, 5, 8-9, 13-16, 20, 23-24, 26-27, and 41 and the species SEQ ID NO: 29 from Genus A, SEQ ID NO: 30 from Genus B, PDC1 from Genus C, and SEQ ID NO: 25 from Genus D in the reply filed on 3/23/2026 is acknowledged.
The traversal is on the grounds that Group II is the process of use of the product claimed in Group I and requires the same corresponding special technical feature. Applicant further argues the Office Action does not establish that Udani’s strains require an exogenous invertase of the claimed identity class and does not provide a reasoned showing that one would incorporate Jauert’s invertase engineering into Udani’s system in the manner required by claim 1. Applicant further traverses the species election requirement as premature and inconsistent with the Office’s indication of claims 1 and 28 as generic. This is not found persuasive because the technical feature of a genetically engineered yeast cell capable of producing lactate from sucrose, comprising: a polynucleotide encoding an exogenous lactate dehydrogenase enzyme; a polynucleotide encoding an exogenous invertase enzyme comprising a sequence at least 80% identical to at least one of SEQ ID NOs: 12, 33, 34, and 35; a deletion or disruption of a native pyruvate decarboxylase gene; and an exogenous polynucleotide encoding a fructose transporter, is not a special technical feature as it does not make a contribution over the prior art in view of WO2020128623 to Udani et al. (of record in IDS filed 2/15/2024) and WO2017091610 to Jauert et al. (of record in IDS filed 2/15/2024). Udani teaches a genetically engineered Kluyveromyces sp. yeast strain capable of producing lactic acid from sucrose, wherein the genetically engineered yeast comprises at least one heterologous DNA cassette that confers production of a protein functioning as a fructose importer such as FFZ1 from Zygosaccharomyces bailii or Z. rouxii and a lactate dehydrogenase gene from E. coli integrated at the PDC1 locus, in which the PDC1 gene is deleted (i.e., pyruvate decarboxylase) and further overexpressed a fructokinase or hexokinase (see Examples 2-3 and Claims 1, 3, and 6). Thus, Udani reads on a genetically engineered yeast cell capable of producing lactate from sucrose, comprising: a polynucleotide encoding an exogenous lactate dehydrogenase enzyme, a deletion of a native pyruvate decarboxylase gene, and an exogenous polynucleotide encoding a fructose transporter. Udani does not teach polynucleotide encoding an exogenous invertase enzyme comprising a sequence at least 80% identical to at least one of SEQ ID NOs: 12, 33, 34, and 35. Jauert teaches engineered yeast capable of sucrose as a fermentation substrate by encoding a functional invertase and deleting or disrupting a pyruvate decarboxylase gene (see paragraphs [0004]-[0008], [0012], [0051]-[0052], [0057]-[0058], and [0070]). Jauert further teaches sucrose-based fermentation processes would preferably use a yeast expressing the functional invertase enzyme and teaches invertase genes represented by SEQ ID NOs: 16 and 17, which are identical to SEQ ID NOs: 34 and 35 of the instant application, respectively (see paragraphs [0007], [0053] and [0058] and Appendix A for sequence alignment). Thus, it would have been obvious to further encode one of the invertases represented by SEQ ID NOs: 16 or 17, as taught by Jauert, in the genetically engineered Kluyveromyces sp. yeast strain capable of producing lactic acid from sucrose, as taught by Udani, to further utilize sucrose substrate. Therefore, the genetically engineered yeast cell capable of producing lactate from sucrose is not a special technical feature that defines a contribution over the prior art. There would have been a reasonable expectation of success modifying the yeast strain of Udani according to the disclosure of Jauert, since Jauert specifically suggests engineering yeast to encode a functional invertase with a PDC gene deleted for sucrose utilization and Udani teaches engineered yeast that can produce lactate from sucrose and that have a PDC gene deleted. With respect to the species election, Applicant has not identified a special technical feature present in all the species. Thus, the restriction and species election is maintained.
Claims 28-29 and 31-33 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. Applicant timely traversed the restriction (election) requirement in the reply filed on 3/23/2026.
The requirement is still deemed proper and is therefore made FINAL.
The examiner has withdrawn the species election requirement for Genus A, fructose transporters.
Priority
The instant application is a U.S. National Phase of PCT/US2022/074470, filed 8/3/2022, which claims Domestic Benefit to U.S. Provisional Application No. 63/234,586, filed 8/18/2021.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 2/15/2024 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Objections
Claims 1, 8-9, 24, and 41 are objected to because of the following informalities:
The genes recited in claims 1, 8-9, 24 and 41, i.e., PDC, GPD, CYB2, etc., should be italicized.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 14 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 14 recites the indefinite limitation “Issatchenkia orientalis/Pichia fermentans clade” in line 2. It is unclear what limitations are intended to be encompassed by the clade of the two yeast species. Paragraph [0042] of the instant specification provides an ambiguous definition that the clade is “the most terminal clade that contains at least the species Issatchenkia orientalis, Pichia galeiformis, Pichia sp. YB-4149 (NRRL designation), Candida ethanolica, Pichia deserticola, Pichia membranifadens, and Pichia fermentans.” However, this definition does not set forth clear metes and bounds for the recited claim limitation. Furthermore, the forward slash renders the claim indefinite because it is not clear what the relation of the two yeast species are and if the clade must overlap one or both of the yeast species. Therefore, claim 14 is indefinite.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1, 3, 5, 23-24, and 26 are rejected under 35 U.S.C. 103 as being unpatentable over Udani et al. (WO2020128623; of record in IDS filed 2/15/2024) and Jauert et al. (WO2017091610; of record in IDS filed 2/15/2024) as evidenced by Pina et al. (Microbiol. Soc., 2004, Vol. 150(7), pp.2429-2433) and GenBank Accession No. AJ515522 (retrieved from Zygosaccharomyces bailii ffz1 gene for fructose facilitator - Nucleotide - NCBI).
Regarding claim 1, Udani teaches a genetically engineered Kluyveromyces sp. yeast strain capable of producing lactate from sucrose, wherein the genetically engineered yeast comprises at least one heterologous DNA cassette that confers production of a protein functioning as a fructose importer such as FFZ1 from Zygosaccharomyces bailii or Z. rouxii and a lactate dehydrogenase gene from E. coli integrated at the PDC1 locus, in which the PDC1 gene is deleted (i.e., pyruvate decarboxylase 1) and further overexpressed a fructokinase or hexokinase (see Examples 2-3 and Claims 1, 3, and 6). Thus, Udani reads on a genetically engineered yeast cell capable of producing lactate from sucrose, comprising: a polynucleotide encoding an exogenous lactate dehydrogenase enzyme, a deletion of a native pyruvate decarboxylase gene, and an exogenous polynucleotide encoding a fructose transporter.
Udani does not teach polynucleotide encoding an exogenous invertase enzyme comprising a sequence at least 80% identical to at least one of SEQ ID NOs: 12, 33, 34, and 35.
Jauert teaches engineered yeast capable of sucrose as a fermentation substrate by encoding a functional invertase and deleting or disrupting a pyruvate decarboxylase gene (see paragraphs [0004]-[0008], [00012], [00051]-[00052], [00057]-[00058], and [00070]). Jauert further teaches sucrose-based fermentation processes would preferably use a yeast expressing the functional invertase enzyme and teaches invertase genes represented by SEQ ID NOs: 16 and 17, which are identical to SEQ ID NOs: 34 and 35 of the instant application, respectively (see paragraphs [0007], [00051]-[00053] and [00058] and Appendix A for sequence alignment; of record).
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have further encoded one of the invertases represented by SEQ ID NOs: 16 or 17, as taught by Jauert, in the genetically engineered Kluyveromyces sp. yeast strain capable of producing lactate from sucrose, as taught by Udani, to arrive at the claimed invention. One of ordinary skill in the art would have been motivated to further improve sucrose substrate utilization in the engineered Kluyveromyces sp. yeast strain capable of producing lactate from sucrose since Jauert teaches sucrose-based fermentation processes would preferably use a yeast expressing the functional invertase, yielding predictable results. The person of ordinary skill in the art would have been choosing an invertase disclosed by Jauert from a finite list of invertases with predictable effects on yeast sucrose utilization. There would have been a reasonable expectation of success since Jauert teaches their method improves sucrose utilization in yeast with a deleted pyruvate decarboxylase gene and Udani teaches their method of producing lactate from sucrose in a yeast with a pyruvate decarboxylase gene deleted.
Regarding claim 3, the yeast cell of Udani comprises the protein functioning as a fructose importer such as FFZ1 from Zygosaccharomyces bailii or Z. rouxii, and thus teaches the structural limitations of claim 3. Thus, it is expected that the peak lactic acid production rate in the engineered yeast cell is higher than the peak lactic acid production rate of an equivalent yeast cell lacking the fructose transporter.
Regarding claim 5, Udani teaches the fructose importer FFZ1 from Zygosaccharomyces bailii is expressed in the genetically engineered Kluyveromyces sp. yeast strain capable of producing lactate from sucrose in order to drive specific fructose import in the non-fructophilic yeast (see paragraphs [0042] [0090]-[0117] and Claim 3). Pina et al. and GenBank provide evidence that the fructose importer FFZ1 from Zygosaccharomyces bailii has 100% sequence identity to claimed SEQ ID NO: 28, and thus reads on the limitations of claim 5 (see Sequence Alignment in Appendix B).
Regarding claims 23-24, Udani teaches phosphorylation of fructose to produce fructose-6-phosphate by enzymes such as fructokinase or hexokinase is a potential rate limiting step and suggests expression of the native K. marxianus GLK1 hexokinase from a strong constitutive promoter such as the K. marxianus PDC1 promoter, reading on overexpressing a native hexokinase gene using the constitutive promoter PDC1 (see paragraphs [0118]-[0119] and Claim 6).
Regarding claim 26, Udani teaches that to further improve fructose utilization, an additional copy of the fructose importer FFZ1 gene was inserted into the expression cassette (see [0098]). Udani further teaches phosphorylation of fructose to produce fructose-6-phosphate by enzymes such as fructokinase or hexokinase is a potential rate limiting step and suggests expression of the native K. marxianus GLK1 hexokinase from a strong constitutive promoter such as the K. marxianus PDC1 promoter (see paragraphs [0118]-[0119] and Claim 6).
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have further included an additional copy of the native GLK1 in the expression construct inserted in the engineered Kluyveromyces sp. yeast strain capable of producing lactate from sucrose, to arrive at the claimed invention. One of ordinary skill in the art would have been motivated to further improve the phosphorylation and utilization of fructose in the modified yeast with improved fructose import, yielding predictable results.
Thus, claims 1, 3, 5, 23-24, and 26 are prima facie obvious over Udani in view of Jauert.
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Udani et al. (WO2020128623; of record in IDS filed 2/15/2024) and Jauert et al. (WO2017091610; of record in IDS filed 2/15/2024), as applied to claims 1, 3, 5, 23-24, and 26 above, and further in view of Baek et al. (Biotechnol. J., 2017, Vol. 12(10), pp.1-7).
Udani in view of Jauert teach the invention of claim 1 as outlined in the rejection above.
Regarding claim 8, Udani teaches the fructose importer FFZ1 is integrated at the ADH2 locus to simultaneously disrupt the alcohol dehydrogenase or at the ADH6 open reading frame to delete the alcohol dehydrogenase (see paragraphs [0021], [0025], [0091], and [0098]-[0104]).
Udani and Jauert do not teach wherein the engineered yeast cell comprises a deletion or disruption of a native glycerol-3-phosphate dehydrogenase (GPD) gene.
Baek discloses improvements in lactic acid production in a yeast Saccharomyces cerevisiae strain by expressing lactate dehydrogenase while deleting genes involved in ethanol production—alcohol dehydrogenase (ADH1, ADH2, ADH3, ADH4, and ADH5) and pyruvate decarboxylase (PDC1, PDC5, and PDC6)—and glycerol production—glycerol-3-phosphate dehydrogenase (GPD1 and GPD2)—as well as the degradation of lactic acid—D-lactate dehydrogenase (DLD1) (see Abstract, p.2, left column, 2nd paragraph, p.3, left column, 1st passage-last passage, and Fig. 1). Since the lactate dehydrogenase produces lactic acid from pyruvate, deleting the genes involved in ethanol production and glycerol production reduces the pyruvate flux toward ethanol production and drive the fermentative production toward lactic acid (see p.1, right col. 1st passage and 1st paragraph).
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have further deleted or disrupted all alcohol dehydrogenases, pyruvate decarboxylases, glycerol-3-phosphate dehydrogenases, and D-lactate dehydrogenases, as taught by Baek, in the engineered Kluyveromyces sp. yeast strain capable of producing lactate from sucrose, as taught by Udani in view of Jauert, to arrive at the claimed invention. One of ordinary skill in the art would have been motivated to prevent pyruvate flux toward ethanol production and to prevent lactic acid breakdown to improve fermentation production of lactic acid, yielding predictable results. Thus, claim 8 is prima facie obvious over Udani in view of Jauert and Baek. There would have been a reasonable expectation of success since each of Udani and Baek are directed to lactic acid production in yeast.
Claim 9 is rejected under 35 U.S.C. 103 as being unpatentable over Udani et al. (WO2020128623; of record in IDS filed 2/15/2024) and Jauert et al. (WO2017091610; of record in IDS filed 2/15/2024), as applied to claims 1, 3, 5, 23-24, and 26 above, and further in view of Miller et al. (US20090253189).
Udani in view of Jauert teach the invention of claim 1 as outlined in the rejection above.
Regarding claim 9, Udani teaches an L-lactate only producing yeast strain that expresses an exogenous lactate dehydrogenase from E. coli (see paragraphs [0097] and [0106]-[0119]).
Udani and Jauert do not teach wherein the engineered yeast cell comprises a deletion or disruption of an L-lactate:cytochrome c oxidoreductase (CYB2) gene.
Miller teaches disrupting or deleting L- or D-lactate:ferricytochrome c oxidoreductase (CYB2) in yeast expressing exogenous lactate dehydrogenase gene to reduce consumption of lactate and increase lactate yields in the fermentation process (see Abstract, and paragraphs [0009]-[0015], [0034], [0099]). Miller teaches in L-lactate producing yeast strains, the L-lactate:ferricytochrome c oxidoreductase gene is deleted or disrupted (see paragraphs [0010], [0012], and [0014]). Miller further teaches suitable yeast comprise Kluyveromyces (see paragraph [0039]).
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have further disrupted or deleted L-lactate:ferricytochrome c oxidoreductase (CYB2) in yeast expressing exogenous lactate dehydrogenase gene, as taught by Miller, in the engineered Kluyveromyces sp. yeast strain capable of producing lactate from sucrose, as taught by Udani in view of Jauert, to arrive at the claimed invention. One of ordinary skill in the art would have been motivated to prevent the engineered Kluyveromyces sp. yeast strain that produces L-lactate from consumption of the produced lactate, yielding predictable results. There would have been a reasonable expectation of success since Miller teaches the disruption or deletion is useful in yeast such as Kluyveromyces sp. that express an exogenous lactate dehydrogenase and Udani teaches a Kluyveromyces sp. that expresses an exogenous lactate dehydrogenase for lactate production. Thus, claim 9 is prima facie obvious over Udani in view of Jauert and Miller.
Claim 13 is rejected under 35 U.S.C. 103 as being unpatentable over Udani et al. (WO2020128623; of record in IDS filed 2/15/2024) and Jauert et al. (WO2017091610; of record in IDS filed 2/15/2024), as applied to claims 1, 3, 5, 23-24, and 26 above, and further in view of Rajgarhia et al. (US7,229,805).
Udani in view of Jauert teach the invention of claim 1 as outlined in the rejection above.
Regarding claim 13, Udani teaches a genetically engineered Kluyveromyces sp. yeast strain capable of producing lactate from sucrose that is a derivative of a Crabtree positive strain (see Examples 2-3 and Claims 1, 3, and 6).
Udani does not teach wherein the yeast cell is Crabtree negative.
Jauert teaches in some embodiments the yeast expressing the functional invertase is Crabtree-negative (see paragraphs [0007], [00037], [00051], [00053], and Claim 19).
Rajgarhia teaches methods of producing lactic acid using Crabtree-negative yeast such as of the Kluyveromyces (see Abstract, Col. 11, 1st-2nd paragraphs, and Examples 2 and 5). Crabtree-negative yeast are capable of obtaining energy via the fermentation pathway and do not require the respiratory pathway, leading to improved cell growth (see Col. 2, 1st paragraph, Col. 4, 5th paragraph, and Col. 11, 1st paragraph).
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have substituted a Crabtree-negative Kluyveromyces sp. for lactic acid production, as taught by Rajgarhia, for the Crabtree-positive Kluyveromyces sp. for lactic acid production from sucrose, as taught by Udani in view of Jauert, to arrive at the claimed invention. One of ordinary skill in the art would have been motivated to improve cell growth of the lactic acid-producing Kluyveromyces sp. yeast, yielding predictable results. Thus, claim 13 is prima facie obvious over Udani in view of Jauert and Rajgarhia.
Claims 14-15, 23, 27, and 41 are rejected under 35 U.S.C. 103 as being unpatentable over Udani et al. (WO2020128623; of record in IDS filed 2/15/2024) and Jauert et al. (WO2017091610; of record in IDS filed 2/15/2024), as applied to claims 1, 3, 5, 23-24, and 26 above, and further in view of Suominen et al. (US8,097,448).
Udani in view of Jauert teach the invention of claim 1 as outlined in the rejection above.
Regarding claims 14-15, Udani does not teach wherein the yeast cell is a yeast of the Issatchenkia orientalis/Pichia fermentans clade.
Jauert teaches yeast cells of its invention having a functional invertase could be Issatchenkia orientalis or Pichia fermentans (see paragraphs [00054]-[00056] and Claim 16).
Suominen teaches transformed Issatchenkia orientalis that encode an exogenous lactate dehydrogenase while deleting or disrupting PDC genes and efficiently produce lactic acid (see Abstract, Col. 2, 2nd-3rd paragraphs, Col. 3, 1st paragraph, Col. 7, 2nd paragraph,-Col. 8, 1st paragraph, and Examples 2A, 2B, 7-9).
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have substituted an Issatchenkia orientalis yeast for producing lactic acid, as taught by Suominen, for the engineered Kluyveromyces sp. yeast strain for producing lactic acid from sucrose, as taught by Udani in view of Jauert, to arrive at the claimed invention. One of ordinary skill in the art would have been substituting yeast strains known in the technical field to be used for lactic acid production, yielding predictable results.
Regarding claim 23, Udani teaches phosphorylation of fructose to produce fructose-6-phosphate by enzymes such as fructokinase or hexokinase is a potential rate limiting step and suggests expression of the native K. marxianus GLK1 hexokinase from a strong constitutive promoter such as the K. marxianus PDC1 promoter, reading on overexpressing a native hexokinase gene using the constitutive promoter PDC1 (see paragraphs [0118]-[0119] and Claim 6).
Regarding claim 27, SEQ ID NO: 25 corresponds to a hexokinase native to Issatchenkia orientalis.
Udani teaches phosphorylation of fructose to produce fructose-6-phosphate by enzymes such as fructokinase or hexokinase is a potential rate limiting step and suggests expression of the native K. marxianus GLK1 hexokinase from a strong constitutive promoter such as the K. marxianus PDC1 promoter, reading on overexpressing a native hexokinase gene using the constitutive promoter PDC1 (see paragraphs [0118]-[0119] and Claim 6).
Udani and Jauert do not teach wherein the native hexokinase comprises a sequence at least 80% identical to at least one of SEQ ID NOs: 24 and 25.
Suominen teaches transformed Issatchenkia orientalis that encode an exogenous lactate dehydrogenase while deleting or disrupting PDC genes and efficiently produce lactic acid (see Abstract, Col. 2, 2nd-3rd paragraphs, Col. 3, 1st paragraph, Col. 7, 2nd paragraph,-Col. 8, 1st paragraph, and Examples 2A, 2B, 7-9).
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have substituted an Issatchenkia orientalis yeast for producing lactic acid, as taught by Suominen, for the engineered Kluyveromyces sp. yeast strain for producing lactic acid from sucrose, as taught by Udani in view of Jauert, and to overexpress the native hexokinase of I. orientalis, as taught by Udani, to arrive at the claimed invention. One of ordinary skill in the art would have been substituting yeast strains known in the technical field to be used for lactic acid production, yielding predictable results. One of ordinary skill in the art would have been motivated to overexpress the native hexokinase in I. orientalis in order to ensure efficient phosphorylation of fructose and drive lactic acid fermentation, yielding predictable results.
Regarding claim 41, Udani in view of Jauert and Suominen render obvious an Issatchenkia orientalis capable of producing lactate from sucrose comprising: a polynucleotide encoding a lactate dehydrogenase from E. coli, a polynucleotide encoding the functional invertase comprising SEQ ID NO: 16 or 17, a deletion or disruption of a native pyruvate decarboxylase (PDC) gene, and an exogenous polynucleotide encoding the FFZ1 fructose transporter from Zygosaccharomyces bailii. With respect to the limitation “wherein the engineered I. orientalis cell is capable of producing lactate at a titer of at least 30 g/L,” the I. orientalis rendered obvious comprises all structural limitations recited and is expected to be capable of producing lactate at a titer of at least 30 g/L, absent evidence to the contrary.
Thus, claims 14-15, 23, 27, and 41 are prima facie obvious over Udani in view of Jauert and Suominen.
Claim 20 is rejected under 35 U.S.C. 103 as being unpatentable over Udani et al. (WO2020128623; of record in IDS filed 2/15/2024) and Jauert et al. (WO2017091610; of record in IDS filed 2/15/2024), as applied to claims 1, 3, 5, 23-24, and 26 above, and further in view of Ilmen et al. (Microb. Cell Fact., 2013, Vol. 12(53), pp.1-15) as evidenced by Savijoki et al. (Appl. Environ. Microbiol., 1997, Vol. 63(7), pp.2850-2856) and LDH_LACHE – UniProt (retrieved from ldh - L-lactate dehydrogenase - Lactobacillus helveticus (Lactobacillus suntoryeus) | UniProtKB | UniProt).
Udani in view of Jauert teach the invention of claim 1 as outlined in the rejection above.
Regarding claim 20, Udani teaches the Kluyveromyces sp. that produces lactose from sucrose expresses an exogenous lactate dehydrogenase from E. coli (see paragraphs [0087], [0088], and [0097]).
Udani and Jauert do not teach wherein the lactate dehydrogenase comprises a sequence at least 80% identical to at least one of SEQ ID NOs: 30 and 31.
Ilmen teaches a yeast Candida sonorensis that expresses a Lactobacillus helveticus L-lactate dehydrogenase, has deletions of pyruvate decarboxylase genes, and produces L-lactic acid (see Abstract, p.4, 2nd passage and paragraph bridging left and right columns, passage bridging pp.11-12, and Figures 2 and 4). The L-lactate dehydrogenase from L. helveticus transformed into C. sonorensis is disclosed from Ilmen as being the same one characterized by Savijoki, which has 99.3% sequence identity to SEQ ID NO: 30 and 100% sequence identity to SEQ ID NO: 31 (for evidence see LDH-_LACHE – UniProt and Appendix C for sequence alignments).
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have substituted the L. helveticus L-lactate dehydrogenase for L-lactic acid production, as taught by Ilmen, for the E. coli lactate dehydrogenase used for L-lactic acid production in the Kluyveromyces sp., as taught by Udani, to arrive at the claimed invention. One of ordinary skill in the art would have been substituting known lactate dehydrogenases expressed in lactate producing yeast to achieve lactate production, yielding predictable results. Thus, claim 20 is prima facie obvious over Udani in view of Jauert and Ilmen as evidenced by Savijoki and LDH_LACHE – UniProt.
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.
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Claims 1, 3, 5, 8-9, 13-16, 20, 23-24, and 26-27 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 6-9, 13-15, 17-18, 21, and 38 of copending Application No. 18/683,849 to Brady et al. in view of Udani et al. (WO2020128623; of record in IDS filed 2/15/2024).
Co-pending claim 1 of ‘849 recites a genetically engineered yeast cell capable of producing lactate from sucrose, the engineered yeast cell comprising (lines 1-2) a polynucleotide encoding an exogenous lactate dehydrogenase enzyme (line 3); a polynucleotide encoding an exogenous invertase enzyme comprising a sequence at least 80% identical to at least one of SEQ ID NOs: 12, 33, 34, and 35 (lines 4-5); a deletion or disruption of a native pyruvate decarboxylase (PDC) gene (line 6); and a genetic modification resulting in overexpression of a native hexokinase gene (line 7).
The difference between co-pending claim 1 and instant claim 1 is instant claim 1 further recites an exogenous polynucleotide encoding a fructose transporter. Udani teaches a genetically engineered Kluyveromyces sp. yeast strain capable of producing lactate from sucrose, wherein the genetically engineered yeast comprises at least one heterologous DNA cassette that confers production of a protein functioning as a fructose importer such as FFZ1 from Zygosaccharomyces bailii or Z. rouxii and a lactate dehydrogenase gene from E. coli integrated at the PDC1 locus, in which the PDC1 gene is deleted (i.e., pyruvate decarboxylase 1) and further overexpressed a fructokinase or hexokinase (see Examples 2-3 and Claims 1, 3, and 6). Udani further teaches the fructose importer FFZ1 from Zygosaccharomyces bailii is expressed in the genetically engineered Kluyveromyces sp. yeast strain capable of producing lactate from sucrose in order to drive specific fructose import in the non-fructophilic yeast (see paragraphs [0042] [0090]-[0117] and Claim 3). Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have further encoded the fructose importer FFZ1 from Zygosaccharomyces bailii, as taught by Udani, to improve fructose specific import in the I. orientalis yeast of co-pending claim 1.
Co-pending claim 2 of ‘849 recites wherein hexokinase activity in the engineered yeast cell is higher than hexokinase activity in an equivalent yeast cell lacking the genetic modification.
The difference between co-pending claim 2 and instant claim 24 is that co-pending claim 2 does not recite wherein the genetic modification comprises replacement of the native hexokinase gene promoter with a constitutive heterologous or artificial promoter selected from the group consisting of pyruvate decarboxylase (PDC1), glyceraldehyde-3-phosphate dehydrogenase (TDH3), enolase (ENO1), and 3-phosphoglycerate kinase (PGK1). Udani teaches phosphorylation of fructose to produce fructose-6-phosphate by enzymes such as fructokinase or hexokinase is a potential rate limiting step and suggests expression of the native K. marxianus GLK1 hexokinase from a strong constitutive promoter such as the K. marxianus PDC1 promoter, reading on overexpressing a native hexokinase gene using the constitutive promoter PDC1 (see paragraphs [0118]-[0119] and Claim 6). Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to encode the native hexokinase using the PDC1 constitutive promoter in order to improve phosphorylation and utilization of fructose by improving expression of the hexokinase.
Co-pending claim 3 of ‘849 recites wherein peak lactate production rate in the engineered yeast cell, when used in a fermentation process in the presence of sucrose, is higher than peak lactate production rate of an equivalent yeast cell lacking the genetic modification.
Co-pending claim 6 of ‘849 recites wherein the genetic modification comprises addition of an exogenous polynucleotide encoding the native hexokinase such that the genetically engineered yeast cell comprises at least one additional copy of a sequence encoding the native hexokinase.
Co-pending claim 7 of ‘849 recites wherein the native hexokinase comprises a sequence at least 80% identical to at least one of SEQ ID NOs:24 and 25.
Co-pending claim 8 of ‘849 recites wherein the engineered yeast cell comprises a deletion or disruption of a glycerol-3-phosphate dehydrogenase (GPD) gene.
Co-pending claim 9 of ‘849 recites wherein the engineered yeast cell comprises a deletion or disruption of an L-lactate:cytochrome c oxidoreductase (CYB2) gene.
Co-pending claim 13 of ‘849 recites wherein the yeast cell is Crabtree negative.
Co-pending claim 14 of ‘849 recites wherein the yeast is of the Issatchenkia orientalis/Pichia fermentans clade.
Co-pending claim 15 of ‘849 recites wherein the yeast cell is an Issatchenkia orientalis cell.
Co-pending claim 17 of ‘849 recites wherein the yeast cell additionally comprises an exogenous polynucleotide encoding a fructokinase.
Co-pending claim 18 of ‘849 recites wherein the fructokinase comprises a sequence at least 80% identical to SEQ ID NO: 26.
Co-pending claim 21 of ‘849 recites wherein the lactate dehydrogenase comprises a sequence at least 80% identical to at least one of SEQ ID NOs: 30 and 31.
This is a provisional nonstatutory double patenting rejection.
Claim 41 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 38 of copending Application No. 18/683,849 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because instant claim 41 is anticipated by co-pending application claim 38.
Co-pending claim 38 of ‘849 recites a genetically engineered Issatchenkia orientalis cell capable of producing lactate from sucrose, the engineered yeast cell comprising (lines 1-2) a polynucleotide encoding an exogenous lactate dehydrogenase enzyme (line 3); a polynucleotide encoding an exogenous invertase enzyme (line 4); a deletion or disruption of a native pyruvate decarboxylase (PDC) gene (line 5); and a genetic modification resulting in overexpression of a native hexokinase gene (line 6), wherein the engineered I. orientalis cell is capable of producing lactate at a titer of at least 30 g/L (lines 7-8). Therefore, patent claim 38 of ‘849 is in essence a “species” of the generic invention of application claim 41. It has been held that a generic invention is “anticipated” by a “species” within the scope of the generic invention. See In re Goodman, 29 USPQ2d 2010 (Fed. Cir. 1993).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
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/J.P.S./ Examiner, Art Unit 1651
/MELENIE L GORDON/ Supervisory Patent Examiner, Art Unit 1651
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