DETAILED ACTION
Election/Restrictions
Applicant's election with traverse of Group I, claims 1-3, 6-9, 13-15, 17-18, 21 and 38, Species A (SEQ ID NO: 12), in the reply filed on 3/25/26 is acknowledged. The traversal is on the ground(s) that the method of producing lactate from sucrose in Group II requires the cell of Group I. Applicants also argue that claim 1 requires a polynucleotide encoding an exogenous invertase activity of SEQ ID NO: 12, for example, and neither Udani or Dietrich who this claimed exogenous invertase feature.
This has been fully and carefully considered, but 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. (provided by Applicants) and newly cited WO2017091610 to Jauert et al. (provided by Applicants) and Fosmer et al (US Patent No. 10,731,184; SEQ ID NO: 6). Fosmer teaches an exogenous invertase enzyme having an amino acid sequence which is 100% identical to SEQ ID NO: 12 (see SEQ ID NO: 6 from Fosmer in sequence alignment in Public PAIR) from Klluyveromyces lactis. See 103 rejection below. 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. It has been found that 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.
The requirement is still deemed proper and is therefore made FINAL.
Claims 24, 25, 27-31 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention. Note: claim 31 was inadvertently left out of the Restriction requirement, but is the invention of Group II.
Claim Objections
Claim 7 is objected to because of the following informalities: there should be a space after the colon. Appropriate correction is required.
Claim Rejections - 35 USC § 112-2nd paragraph
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 1-3, 6-9, 13-15, 17-18, 21 and 38 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.
Claims 1-3, 6-9, 13-15, 17-18, 21 and 38, are rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of SEQ ID NOS: 12, 33, 34 and 35 is improper because the alternatives defined by the Markush grouping do not share both a single substantial structural similarity and a common use for the following reasons:
These are different invertase enzymes from different Genus/species of yeast with different amino acid sequences.
For example:
Klluyveromyces lactis (SEQ ID NO: 12); Saccharomyces cerevisiae (SEQ ID NO:33); Schizosaccharomyces pombe (SEQ ID NO:34); and Aspergillus niger (SEQ ID NO:35).
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single substantial structural similarity as well as a common use.
Claim 1 is vague and indefinite because it recites the polynucleotide encoding an exogenous lactate dehydrogenase enzyme by name only. The mere recitation of a name to describe the invention is not sufficient to satisfy the Statute's requirement of adequately describing and setting forth the inventive concept. The claim should provide any structural properties, such as the nucleic acid sequence of the polynucleotide, which would allow for one to identify polynucleotide without ambiguity. While the specification can be used to provide definitive support, the claims are not read in a vacuum. Rather, the claim must be definite and complete in and of itself. Limitations from the specification will not be read into the claims. The claims as they stand are incomplete and fail to provide adequate structural properties to allow for one to identify what is being claimed. Appropriate clarification and/or correction is required.
Claim 1 is vague and indefinite because it is unclear what gene modification would result in overexpression of a native hexokinase. The metes and bounds of the claim cannot readily be understood. The genetically engineered cell is not adequately defined without describing the modification. The claim fails to provide the technical features necessary for achieving this result. While the specification can be used to provide definitive support, the claims are not read in a vacuum. Rather, the claim must be definite and complete in and of itself. Limitations from the specification will not be read into the claims. The claims as they stand are incomplete and fail to provide adequate structural properties to allow for one to identify what is being claimed. Appropriate clarification and/or correction is required.
Claim 2 is vague and indefinite because it is unclear what is meant by an “equivalent cell lacking the gene modification.” The claimed cell contains other modifications, e.g., exogenous sequence. Is “equivalent” in reference to a wild-type cell or something else? Accordingly, the comparison required cannot be adequately made due to the vagueness of this description. Appropriate clarification and/or correction is required.
Claim 3 is vague and indefinite because it is unclear what is meant by an “equivalent cell lacking the gene modification.” The claimed cell contains other modifications, e.g., exogenous sequence. Is “equivalent” in reference to a wild-type cell or something else? Accordingly, the comparison required cannot be adequately made due to the vagueness of this description. Appropriate clarification and/or correction is required.
Claims 8 and 9 are vague and indefinite because it recites the GPD gene and CYB2 gene, respectively, by name only. The mere recitation of a name to describe the invention is not sufficient to satisfy the Statute's requirement of adequately describing and setting forth the inventive concept. The claim should provide any structural properties, such as the nucleic acid sequence of the polynucleotide, which would allow for one to identify polynucleotide without ambiguity. While the specification can be used to provide definitive support, the claims are not read in a vacuum. Rather, the claim must be definite and complete in and of itself. Limitations from the specification will not be read into the claims. The claims as they stand are incomplete and fail to provide adequate structural properties to allow for one to identify what is being claimed. Appropriate clarification and/or correction is required.
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.
Claims 17 is vague and indefinite because it recites an exogenous polynucleotide encoding a fructokinase by name only. The mere recitation of a name to describe the invention is not sufficient to satisfy the Statute's requirement of adequately describing and setting forth the inventive concept. The claim should provide any structural properties, such as the nucleic acid sequence of the polynucleotide, which would allow for one to identify polynucleotide without ambiguity. While the specification can be used to provide definitive support, the claims are not read in a vacuum. Rather, the claim must be definite and complete in and of itself. Limitations from the specification will not be read into the claims. The claims as they stand are incomplete and fail to provide adequate structural properties to allow for one to identify what is being claimed. Appropriate clarification and/or correction is required.
Claim 38 is vague and indefinite because it recites the polynucleotide encoding an exogenous lactate dehydrogenase enzyme, a polynucleotide encoding an exogenous invertase enzyme and the PDC gene by names only. The mere recitation of a name to describe the invention is not sufficient to satisfy the Statute's requirement of adequately describing and setting forth the inventive concept. The claim should provide any structural properties, such as the nucleic acid sequence of the polynucleotide, which would allow for one to identify polynucleotide without ambiguity. While the specification can be used to provide definitive support, the claims are not read in a vacuum. Rather, the claim must be definite and complete in and of itself. Limitations from the specification will not be read into the claims. The claims as they stand are incomplete and fail to provide adequate structural properties to allow for one to identify what is being claimed. Appropriate clarification and/or correction is required.
Claim 38 is also vague and indefinite because it recites a deletion or disruption of native PDC, but it is unclear what is encompassed by this. For example, is this a full gene deletion? Is this a few of several polynucleotides deleted? How is the gene disrupted and to what effect? The claims are also vague and indefinite because it is unclear what gene modification would result in overexpression of a native hexokinase. The claim fails to provide the technical features necessary for achieving this result. The metes and bounds of the claim cannot readily be understood. The genetically engineered cell is not adequately defined without describing the modification. While the specification can be used to provide definitive support, the claims are not read in a vacuum. Rather, the claim must be definite and complete in and of itself. Limitations from the specification will not be read into the claims. The claims as they stand are incomplete and fail to provide adequate structural properties to allow for one to identify what is being claimed. Appropriate clarification and/or correction is required.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-3 and 6 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 Dietrich et al (WO 2019/200079 A1; 10/17/19; provided by Applicants) and Jauert et al. (WO2017091610; of record in IDS filed 2/15/2024) and Fosmer et al (US Patent No. 10,731,184; SEQ ID NO: 6) as evidenced by Pina et al. (Microbiol. Soc., 2004, Vol. 150(7), pp.2429-2433); GenBank Accession No. AJ515522 (retrieved from Zygosaccharomyces bailii ffz1 gene for fructose facilitator - Nucleotide - NCBI).
Regarding claim 1, Udani et al discloses a genetically engineered Kluyveromyces sp. yeast strain that is capable of producing lactic acid from carbon source sucrose, wherein said genetically engineered yeast strain comprises a cassette that confers expression of gene encoding a hexokinase (see claim 6). Udani further discloses that K marxiamis, as well as many other yeasts, such as Saccharomyces cerevisiae, secretes an invertase enzyme into the fermentation medium or periplasmic space (see [0007]), meaning that many yeasts have endogenous invertase. 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. Regarding claim 1, 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). Fosmer relates to a genetically engineered yeast capable of manufacturing a fermentation product using sucrose as a fermentation substrate, and fermentation processes using such a yeast. The yeast has an exogenous invertase gene and has a deletion or disruption of the PDC activity gene (see abstract). Accordingly, the yeast is useful for manufacturing fermentation products other than ethanol from fermentation substrates containing sucrose. Fosmer teaches invertase enzyme having an amino acid sequence which is 100% identical to SEQ ID NO: 12 (see SEQ ID NO: 6 from Fosmer in sequence alignment in Public PAIR) from Klluyveromyces lactis. Paragraph 52 of Fosmer recites that exemplary invertase expression genes suitable for gene integration in a yeast strain include, but are not limited to: an invertase gene from K. lactis (KlINV); S. cerevisiae (ScSUC2); Schizosaccharomyces pombe (invl); and Aspergillus niger (invA) also identified as SEQ ID NO: 6; SEQ ID NO: 15; SEQ ID NO: 16; and SEQ ID NO: 17, respectively.
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.
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 claim 6, 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).
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.
However, Fosmer teaches invertase enzyme having an amino acid sequence which is 100% identical to SEQ ID NO: 12 (see SEQ ID NO: 6 from Fosmer in sequence alignment in Public PAIR) from Klluyveromyces lactis and 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).
Dietrich et al (WO 2019/200079 A, 10/17/19; provided by Applicants) discloses recombinant host cells and methods for the production of lactic acid, wherein sucrose can be the carbon source (see D2, abstract and [159]), wherein the recombinant cell comprises a heterologous nucleic acid encoding a lactate dehydrogenase and a genetic disruption of the gene encoding pyruvate decarboxylase (see D2, [009]-[010]).
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: 12, 16 or 17, as taught by Fosmer and 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 and Cargill 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.
Thus, claims 1-3, 5, and 6 are prima facie obvious over Udani in view of Dietrich, Fosmer and 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 Dietrich et al (WO 2019/200079 A1; 10/17/19; provided by Applicants) and Jauert et al. (WO2017091610; of record in IDS filed 2/15/2024) and Fosmer et al (US Patent No. 10,731,184; SEQ ID NO: 6), as applied to claims 1-3 and 6 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 , Fosmer 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 Fosmer 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 Claims 1-3 and 6 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 Dietrich et al (WO 2019/200079 A1; 10/17/19; provided by Applicants) and Jauert et al. (WO2017091610; of record in IDS filed 2/15/2024) and Fosmer et al (US Patent No. 10,731,184; SEQ ID NO: 6), as applied to claims 1, 3, 5 and 6 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 Fosmer Jauert and Miller.
Claim 13 is rejected under 35 U.S.C. 103 as being unpatentable over Claims 1-3 and 6 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 Dietrich et al (WO 2019/200079 A1; 10/17/19; provided by Applicants) and Jauert et al. (WO2017091610; of record in IDS filed 2/15/2024) and Fosmer et al (US Patent No. 10,731,184; SEQ ID NO: 6), as applied to claims 1, 3, 5 and 6 above, and further in view of Rajgarhia et al. (US Patent No. 7,229,805).
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 7, 14-15 and 38 are rejected under 35 U.S.C. 103 as being unpatentable over Claims 1-3 and 6 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 Dietrich et al (WO 2019/200079 A1; 10/17/19; provided by Applicants) and Fosmer et al. (WO2017091610; of record in IDS filed 2/15/2024) and Cargill et al (US Patent No. 10,731,184; SEQ ID NO: 6) ,as applied to claims 1, 3, 5 and 6 above, and further in view of Suominen et al. (US Patent No. 8,097,448).
Udani in view of Fosmer and Jauert teach the invention of claim 1 as outlined in the rejection above.
Regarding claims 7, 14-15 and 38 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 7, 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, Fosmer 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 38, 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 7, 14-15 and 38 are prima facie obvious over Udani in view of Jauert and Suominen.
Claim 21 is rejected under 35 U.S.C. 103 as being unpatentable over Claims 1-3, 5 and 6 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 Dietrich et al (WO 2019/200079 A1; 10/17/19; provided by Applicants) and Jauert et al. (WO2017091610; of record in IDS filed 2/15/2024) and Fosmer et al (US Patent No. 10,731,184; SEQ ID NO: 6), as applied to claims 1, 3, 5 and 6 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 21, 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.
Claim Rejections - 35 USC § 112-Written Description
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 1-3, 6-9, 13-15, 17-18, 21 and 38 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 1 recites:
(Currently Amended) A genetically engineered yeast cell capable of producing lactate from sucrose, the engineered yeast cell 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 (PDC) gene; and a genetic modification resulting in overexpression of a native hexokinase gene.
The instant claims are drawn to methods for alleviating any toxicity caused by any toxin which includes the use of fragments and variants of SEQ ID NO: 12. To fulfill the written description requirements set forth under 35 USC § 112, first paragraph, the specification must describe at least a substantial number of the members of the claimed genus, or alternatively describe a representative member of the claimed genus, which shares a particularly defining feature common to at least a substantial number of the members of the claimed genus, which would enable the skilled artisan to immediately recognize and distinguish its members from others, so as to reasonably convey to the skilled artisan that Applicant had possession the claimed invention at the time the application was filed.
With the written description of a genus, however, merely drawing a fence around a perceived genus is not a description of the genus. One needs to show that one has truly invented the genus, i.e., that one has conceived and described sufficient representative species encompassing the breadth of the genus. Otherwise, one has only a research plan, leaving it to others to explore the unknown contours of the claimed genus. See Ariad, 598 F.3d at 1353 (The written description requirement guards against claims that "merely recite a description of the problem to be solved while claiming all solutions to it and . . . cover any compound later actually invented and determined to fall within the claim's functional boundaries."). Abbvie Deutschland GmbH & Co. v. Janssen Biotech, Inc., 759 F.3d 1285, 1300, 111 U.S.P.Q.2d 1780, 1790, 2014 BL 183329, 12 (Fed. Cir. 2014).
The purpose of the "written description" requirement is broader than tomerely explain how to "make and use"; the applicant must convey with reasonableclarity to those skilled in the art that, as of the filing date sought, he or she was inpossession of the invention. The invention is, for purposes of the "writtendescription" inquiry, whatever is now claimed. See Vas-Cath, Inc. v. Mahurkar,935 F.2d 1555, 1563-64, 19 USPQ2d 1111, 1117 (Federal Circuit, 1991).Furthermore, the written description provision of 35 USC § 112 is severable fromits enablement provision; and adequate written description requires more than amere statement that it is part of the invention and reference to a potential methodfor isolating it. The nucleic acid [product] itself is required. See Fiers v. Revel, 25 USPQ2d 1601, 1606 (CAFC 1993) and Amgen Inc. V. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016. Possession may be shown in a variety of ways including description of an actual reduction to practice, or by showing the invention was 'ready for patenting' such as by disclosure of drawings or structural chemical formulas that show that the invention was complete, or by describing distinguishing identifying characteristics sufficient to show that the applicant was in possession of the claimed invention" (Id. at 1104). Moreover, because the claims encompass a genus of variant species, an adequate written description of the claimed invention must include sufficient description of at least a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics sufficient to show that Applicant was in possession of the claimed genus. An objective standard for determining compliance with the written description requirement is, "does the description clearly allow persons of ordinary skill in the art to recognize that he or she invented what is claimed." In re Gosteli, 872 F.2d 1008, 1012, 10 USPQ2d 1614, 1618 (Fed. Cir. 1989). To satisfy the written description requirement, an applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention, and that the invention, in that context, is whatever is now claimed. Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1563-64, 19 USPQ2d 1111, 1117 (Fed. Cir. 1991) and MPEP 2163.02.
However, factual evidence of an actual reduction to practice has not been disclosed by Applicant in the specification; nor has Applicant shown the invention was "ready for patenting" by disclosure of drawings or structural chemical formulas that show that the invention was complete; nor has Applicant described distinguishing identifying characteristics sufficient to show that Applicant were in possession of the claimed invention at the time the application was filed. For inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus'" (Id. at 1106); accordingly, it follows that an adequate written description of a genus cannot be achieved in the absence of a disclosure of at least one species within the genus. The scope of the claim includes numerous structural variants, and the genus is highly variant because a significant number of structural differences between genus members is permitted.
One of skill in the art would reasonably conclude that the disclosure fails to provide a representative number of species to describe the genus, and thus, that the applicant was not in possession of the claimed genus. The claimed subject matter is not supported by an adequate written description because a representative number of species has not been described. Devos et al., (Proteins: Structure, Function and Genetics, 2000, Vol. 41: 98-107), teach that the results obtained by analyzing a significant number of true sequence similarities, derived directly from structural alignments, point to the complexity of function prediction. Different aspects of protein function, including (i) enzymatic function classification, (ii) functional annotations in the form of key words, (iii) classes of cellular function, and conservation of binding sites can only be reliably transferred between similar sequences to a modest degree. The reason for this difficulty is a combination of the unavoidable database inaccuracies and plasticity of proteins (Abstract, page 98) and the analysis poses interesting questions about the reliability of current function prediction exercises and the intrinsic limitation of protein function prediction (Column 1, paragraph 3, page 99) and conclude that "Despite widespread use of database searching techniques followed by function inference as standard procedures in Bioinformatics, the results presented here illustrate that transfer of function between similar sequences involves more difficulties than commonly believed. Our data show that even true pair-wise sequence relations, identified by their structural similarity, correspond in many cases to different functions (column 2, paragraph 2, and page 105). Whisstock et al., (Quarterly Reviews of Biophysics 2003, Vol. 36 (3): 307-340,) also highlight the difficulties associated with "Prediction of protein function from protein sequence and structure": "To reason from sequence and structure to function is to step onto much shakier ground", closely related proteins can change function, either through divergence to a related function or by recruitment for a very different function, in such cases, assignment of function on the basis of homology, in the absence of direct experimental evidence, will give the wrong answer (page 309, paragraph 4), it is difficult to state criteria for successful prediction of function, since function is in principle a fuzzy concept. Given three sequences, it is possible to decide which of the three possible pairs is most closely related. Given three structures, methods are also available to measure and compare similarity of the pairs. However, in many cases, given three protein functions, it would be more difficult to choose the pair with most similar function, although it is possible to define metrics for quantitative comparisons of different protein sequences and structures, this is more difficult for proteins of different functions (page 312, paragraph 5), in families of closely related proteins, mutations usually conserve function but modulate specificity i.e., mutations tend to leave the backbone conformation of the pocket unchanged but to affect the shape and charge of its lining, altering specificity (page 313, paragraph 4), although the hope is that highly similar proteins will share similar functions, substitutions of a single, critically placed amino acid in an active-site residue may be sufficient to alter a protein's role fundamentally (page 323, paragraph 1). C. This finding is reinforced in the following scientific teachings for specific proteins in the art that suggest, even highly structurally homologous polypeptides do not necessarily share the same function and many functionally similar proteins will have little or no structural homology to disclosed proteins. For example, proteins having similar structure have different activities (structure does not always correlate to function).
Because the art is unpredictable, in accordance with the Written Description Guidelines, the recitation of: "a sequence at least 80% identical to oneof SEQ ID No: 12” with any changes (and any combination of changes) is not adequate. The scope of the claim includes numerous structural variants and the genus is highly variant because a significant number of structural differences between genus members is permitted. The specification does not describe any members of the claimed genus by complete structure. One of skill in the art would reasonably conclude that the disclosure fails to provide a representative number of species to describe the genus, and thus, that the applicant was not in possession of the claimed genus. The claimed subject matter is not supported by an adequate written description because a representative number of species has not been described.
There are no drawings or structural formulas disclosed of any of thesefragments or variants of the claimed polypeptides. There is no teaching in thespecification regarding which 20% of the structure can be varied and still produce a polypeptide which has the recited activity. Although the disclosure of SEQ ID NO: 12 combined with the knowledge in the art, may put one in possession of peptides that are at least 80% identical to SEQ ID NO: 12, the level of skill and knowledge in the art is such that one of ordinary skill would not be able to identify without further testing which of those peptides would have the required functional activities. Based on the lack of knowledge and predictability in the art, those of ordinaryskill in the art would not conclude that the applicant was in possession of theclaimed genus of proteins with the required activity of producing lactate from sucrose.
Applicant is referred to the revised guidelines concerning compliance with the written description requirement of U.S.C. 112, first paragraph, published in the Official Gazette and also available at www.uspto.gov
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-3, 6-9, 13-15, 17-18 and 21 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over 1, 3, 5, 8-9, 13-16, 20, 23-24, and 26-27 of copending Application No. 18/683,863 to Brady et al. in view of Udani et al. (WO2020128623; of record in IDS filed 2/15/2024).
Instant claim 1 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 instant claim 1 and co-pending claim 1 is co-pending 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.
Instant claim 2 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 instant claim 2 and co-pending claim 24 is that instant 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.
Instant claim 3 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.
Instant claim 6 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.
Instant claim 7 recites wherein the native hexokinase comprises a sequence at least 80% identical to at least one of SEQ ID NOs:24 and 25.
Instant claim 8 also recites wherein the engineered yeast cell comprises a deletion or disruption of a glycerol-3-phosphate dehydrogenase (GPD) gene.
Instant claim 9 also recites wherein the engineered yeast cell comprises a deletion or disruption of an L-lactate:cytochrome c oxidoreductase (CYB2) gene.
Instant claim 13 also recites wherein the yeast cell is Crabtree negative.
Instant claim 14 also recites wherein the yeast is of the Issatchenkia orientalis/Pichia fermentans clade.
Instant claim 15 also recites wherein the yeast cell is an Issatchenkia orientalis cell.
Instant claim 17 and co-pending claim 16 recite wherein the yeast cell additionally comprises an exogenous polynucleotide encoding a fructokinase.
Instant claim 18 recites wherein the fructokinase comprises a sequence at least 80% identical to SEQ ID NO: 26 (co-pending claim 16 recites the same).
Instant claim 21 and co-pending claim 20 recite 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 38 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 41 of copending Application No. 18/683,863 (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.
Instant claim 38 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 41 of ‘863 is in essence a “species” of the generic invention of application claim 38. 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.
Prior art, not presently relied upon:
Georis et al . Mol. Gen. Genet. 261:862-870(1999). Glucose repression of the Kluyveromyces lactis invertase gene KIIN does not require Mig1p."; 100% to SEQ 12.
Adams et al (US2009100536-A1) Kluyveromyces lactis protein, SEQ ID 9709- 100% identical to SEQ ID NO: 12.
Edgerton, M (US2005108791-A1; US Patent No. 10,732,923) Kluyveromyces lactis stress tolerance protein - SEQ ID 9709-100% identical to SEQ ID NO: 12.
100% identity to SEQ ID NO: 26 is free of the prior art. Clostridium acetobutylicum fructokinase (ScrK), SEQ 26.
Correspondence regarding this application should be directed to Group Art Unit 1645. Papers related to this application may be submitted to Group 1600 by facsimile transmission. Papers should be faxed to Group 1600 via the PTO Fax Center located in Remsen. The faxing of such papers must conform with the notice published in the Official Gazette, 1096 OG 30 (November 15,1989). The Group 1645 Fax number is 571-273-8300 which is able to receive transmissions 24 hours/day, 7 days/week.
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Any inquiry concerning this communication or earlier communications from the examiner should be directed to Jennifer E. Graser whose telephone number is (571) 272-0858. The examiner can normally be reached on Monday-Friday from 8:00 AM-4 PM.
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Any inquiry of a general nature or relating to the status of this application should be directed to the Group receptionist whose telephone number is (571) 272-0500.
/JENNIFER E GRASER/ Primary Examiner, Art Unit 1645 5/13/26
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