DETAILED ACTION
Status of claim rejections
The rejections under 35 USC 112(b) has been withdrawn in view of Applicant’s amendments/arguments in the response filed 01/08/2026.
The rejections of record under 35 USC 103 have been maintained in view of Applicant’s amendments/arguments in the response filed 01/08/2026.
Maintained 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.
First rejection
Claims 1, 3-5, 7-10, 13, 17, and 21 are rejected under 35 U.S.C. 103 as being unpatentable over Mueller Cajar et al (Biochemistry. 2007 Dec 11;46(49):14067-74; hereinafter “Mueller Cajar”; prior art of record) in view of Liang et al (Metabolic Engineering Communications 4 (2017) 29–36; hereinafter “Liang”; prior art of record), Soucaille (WO 2007141316 A2; 13 December 2007; prior art of record), and Caspar et al (US20090172832A1; 2 July 2009; hereinafter “Caspar”; prior art of record).
Mueller Cajar teaches directed evolution of Rubisco in E. coli reveals a specificity-determining hydrogen bond in the Form II enzyme (title). Mueller Cajar teaches Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the reaction responsible for virtually all global CO2 assimilation into biomass (pg. 14067, col 1, paragraph 1). The ability of Rubisco to discriminate between the substrates CO2 and O2 is given by the specificity constant Sc/o = (kccat/Kc)/(kocat/Ko), which represents the ratio of the enzyme’s carboxylation efficiency (carboxylation rate (kccat) divided by the Km for CO2 (Kc)) to oxygenation efficiency (oxygenation rate (kocat) divided by the Km for O2 (Ko)) at equal CO2 and O2 concentrations (pg. 14067, col 2, paragraph 1). Form I Rubiscos have dimers of large (L) subunits possess high Sc/o values (40-170) and are found in land plants, algae, bacteria, and cyanobacteria (pg. 14067, col 2, paragraph 2). Form II Rubiscos contain only L subunits, are found in some photosynthetic proteobacteria, chemoautotrophic bacteria, and certain dinoflagellate algae, and have high kccat values but lower Sc/o values (10-20) (pg. 14067, col 2, paragraph 2).
Mueller Cajar teaches an E. coli selection system to evolve the Form II Rubisco from Rhodospirillum rubrum toward an improved fitness and make E. coli that is metabolically engineered to be dependent on Rubisco to detoxify its substrate ribulose 1,5-bisphosphate (abstract), where plasmids containing the R. rubrum Rubisco gene (rbcM; also known as cbbM) were transformed into electrocompetent mutated MM1 E. coli cells derived from the RR1 parent E.coli strain (pg. 14068, col 1, paragraph 4) (recombinant host cell as in claim 1 in part; derived from a parent host cell as in claim 1 in part). The MM1 cells contained the MM1-pACBADPRK plasmid to co-express phosphoribulokinase from Synechococcus PCC7942 (comprises PRK activity as in claim 1) and various Rubisco mutants harboring glutamine and asparagine substitutions at histidine-44 (H44Q, H44N) (comprises Rubisco activity as in claim 1) or histidine and valine substitutions at aspartate-117 (D117H, D117V) (pg. 14068, col 2, paragraphs 1-3; Table 1; pg. 14071, Fig. 2). Using purified Rubisco enzyme, the kinetic properties of the H44N, D117V, D117H, and H44Q Rubisco variants were measured in a bid to identify the mechanism(s) by which they were selected (pg.14071, col 1, paragraph 2). Compared to the wild-type R. rubrum Rubisco showed 40% reduction in Sc/o (pg.14071, col 1, paragraph 2; Table 2). The affinity for CO2 was perturbed, as shown by a higher Michaelis constant (Km) for CO2 (Kc) for the mutant Rubiscos (pg.14071, col 1, paragraph 2). Table 2 (pg. 14072) specifically shows that the H44N Rubisco mutant shows and Sc/o = 5.5 compared to the Sc/o of 9.0 of the wildtype, an increase in Kc to 204 (decreased selectivity for CO2 over O2), and a decrease in Ko to 116 from 159 in the wildtype (an increased sensitivity for O2 as in claim 1, in part).
The difference between Mueller Cajar and the instant claims is that Mueller Cajar does not explicitly teach that the parent host cell and the recombinant host cell is a photosynthetic host cell (as in claim 1, in part).
However, Liang teaches Synechocystis PCC 6803 overexpressing Rubisco to increase growth rate and photosynthesis (title, abstract). Liang teaches that cyanobacterial and algae RuBisCO are reported to have higher efficiency compared to plant RuBisCO (pg. 30, col 1, paragraph 2). Liang teaches the engineering of Synechocystis PCC 6803 to overexpress Rubisco (recombinant photosynthetic host cell as in claim 1) in comparison with a wildtype Synechocystis (derived from a photosynthetic parent host cell as in claim 1) (pg. 30, col 1-2; pg. 31, Fig 1A-C; pg. 32 Fig. 3). Liang further teaches that the use of Synechocystis and overexpression of Rubisco may be one of the key targets to increase efficiency of carbon fixation in photoautotrophic organisms, to increase oxygen evolution rate, and increase photosynthesis and carbon fixation in cyanobacterial cells (pg. 35, col 2 paragraph 2).
Therefore, it would have been prima facie obvious to one of ordinary skill at the time of filing to modify the recombinant host cell system using Rubisco as taught by Mueller Cajar by using Synechocystis as a parent host cell to make a recombinant Synechocystis as taught by Liang to arrive at the claimed invention. As the claimed invention relies on the creation of a recombinant photosynthetic host cell with PRK and Rubisco activity, one of ordinary skill would have been motivated to perform a simple substitution of one known element (the E. coli parent and recombinant host cell of Mueller Cajar) for another (the Synechocystis parent and recombinant host cell of Liang) with a reasonable expectation of success (creating a recombinant photosynthetic host cell with PRK and Rubisco activity). One of ordinary skill would have been motivated to perform the substitution because Liang teaches successful expression of a recombinant Rubisco in Synechocystis host cell that advantageously allowed for increased oxygen evolution rate, photosynthesis capabilities, and carbon fixation.
Neither Mueller Cajar and Liang teach that the recombinant host cell produces glycolate or is substantially unable to anabolize glycolate (as in claim 1 in part).
However, Soucaille teaches a process for the conversion of glucose to glycolic acid is achieved by the use of a recombinant organism comprising a host MG1655 E. coli transformed i) to attenuate the glyoxylate consuming pathways to other compounds than glycolate ii) to use an NADPH glyoxylate reductase to convert glyoxylate to glycolate iii) to attenuate the level of all the glycolate metabolizing enzymes and iv) increase the flux in the glyoxylate pathway (abstract). By increasing NADPH availability by deactivating various genes encoding glucose-6-phosphate isomerase, 6-phosphogluconate dehydratase, and soluble transhydrogenase, a better yield of glycolate production is obtained, including 3 recombinant host cells that produce over 1 g/L (see Example 8, strains 5-7) (produce a yield of at least 1 g glycolate per liter culture medium as in claim 1; pg. 3, lines 1-13). The recombinant E. coli contains at least one gene encoding glyoxylate reductase enzyme (such as ycdW or yiaE) used to convert glyoxylate intermediate to the low toxicity final product glycolate, where the expression of the glycolate reductase enzyme is increased by using one or several copies on the genome introduced via recombination (pg. 6, lines 18-38; pg. 13, examples 1-2). The microorganism is further modified in such a way that it is unable to substantially metabolize glycolate (as in claim 1) (pg. 7, lines 9-12; pg. 13, Example 3). This result was achieved by the attenuation of at least one of the genes encoding for enzymes consuming glycolate (glcDEF encoding glycolate oxidase and aldA encoding glycolaldehyde dehydrogenase) via replacement of the natural promoter or deletion of the DNA sequence (pg. 7, lines 13-16). Soucaille further teaches the fermentative production of glycolic acid from the recombinant cell where the resulting glycolate would be concentrated in the bacteria or in the medium (pg. 8, lines 13-24; claim 20).
Therefore, it would have been prima facie obvious to one of ordinary skill at the time of filing to modify the recombinant Synechocystis expressing Rubisco and PRK as taught by Mueller Cajar and Liang, by inactivating glycolate oxidase and overexpressing glyoxylate reductase to produce glycolate in the medium as taught by Soucaille to arrive at the claimed invention. As Mueller Cajar and Liang teaches the creation of a recombinant Synechocystis cell expressing Rubisco and PRK with increased glyoxylate reductase expression, and Soucaille teaches the inactivation of glycolate oxidase and increasing glyoxylate reductase expression in a recombinant host cell for successful concentration of glycolate in the medium, one of ordinary skill would have been motivated to modify the cell of Mueller Cajar and Liang by inactivating glycolate oxidase and increase expression of glyoxylate reductase with a reasonable expectation of success. One of ordinary skill would have been motivated to inactivate glycolate dehydrogenase and increase expression of glyoxylate reductase because Soucaille teaches the successful attenuation of the glycolate consuming enzymes via replacement of the promoter or deletion of the DNA sequence, resulting in the accumulation of glycolate in fermentation medium from a recombinant host cell.
Neither Mueller Cajar, Liang, nor Soucaille explicitly teach the Rubisco has at least 95% sequence identity with SEQ ID NO: 16 (Applicant’s elected species).
However, Caspar (in the field of recombinant Rubisco enzymes) teaches the expression of Rubisco enzyme from a non-Rubisco locus (title). Caspar teaches the expression of the Rubisco from R. rubrum RRrbcM in the chloroplasts of tobacco leaf using a pTCP107 plasmid (paragraph 0147) that led to high expression of the Rubisco in the leaf tissue (paragraph 0147, paragraph 0180-0181). Caspar specifically teaches the amino acid sequence of RRrbcM (SEQ ID NO: 35) that has 98.5% identity to SEQ ID NO: 16 (a Rubisco with at least 95% sequence identity as in claim 1) (paragraph 0180-0181; see alignment below). Caspar further teaches the overexpression of RRrbcM in E. coli pRR2119 in comparison to expression of the Rubisco expression in plant 1074, and showed high expression and Rubisco activity (paragraph 0189; Table 6).
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Therefore, it would have been prima facie obvious to one of ordinary skill at the time of filing to modify the recombinant Synechocystis expressing Rubisco and PRK as taught by Mueller Cajar, Liang, and Soucaille, by using the Rubisco as taught by Caspar to arrive at the claimed invention. As Mueller Cajar, Liang, and Soucaille teach the creation of a recombinant Synechocystis cell expressing Rubisco and PRK with increased glyoxylate reductase expression, and Caspar teaches the successful use of a Rubisco amino acid sequence from R. rubrum in recombinant organisms, one of ordinary skill would have been motivated to use the Rubisco of Caspar with a reasonable expectation of success. One of ordinary skill would have been motivated to make the modification because Caspar teaches the successful use of a Rubisco amino acid sequence that is capable of causing high Rubisco expression in recombinant organisms.
Regarding claim 3 and 4, Soucaille teaches reducing or eliminating glycolate oxidase activity (see above), via gene disruption or deletion of glycolate oxidase (see above).
Regarding claim 5, Soucaille teaches the overexpression of glyoxylate reductase (see above).
Regarding claim 7, Mueller Cajar teaches decreased affinity/selectivity for CO2 using the R. rubrum Rubisco (pg.14071, col 1, paragraph 2; see Table 2).
Regarding claim 8, Mueller Cajar teaches H44N Rubisco mutant shows and Sc/o = 5.5 compared to the Sc/o of 9.0 of the wildtype (specificity constant Sc/o<55) (pg. 14072, Table 2).
Regarding claim 9, Mueller Cajar teaches using Form II Rubisco (i.e., type II Rubisco) (abstract).
Regarding claim 10, Mueller Cajar teaches using Rubisco from Rhodospirillum rubrum (abstract) with H44N mutation (pg. 14068, col 2, paragraphs 1-3; Table 1; pg. 14071, Fig. 2).
Regarding claim 17, Caspar specifically teaches the amino acid sequence of RRrbcM (SEQ ID NO: 35) that has 98.5% identity to SEQ ID NO: 16 (a Rubisco with at least 95% sequence identity as in claim 1; at least 95% sequence identity with SEQ ID NO: 16 as in claim 17).
Regarding claim 13 and 21, Liang teaches using Synechocystis, a photosynthetic cyanobacterium (see above), and Mueller Cajar, Liang, Soucaille, and Caspar teach (in combination) expression of a heterologous PRK in a photosynthetic cyanobacterial host cell.
Accordingly, the claimed invention was prima facie obvious to one of ordinary skill at the time of filing, especially in the absence of evidence to the contrary.
Second rejection
Claim 6 is rejected under 35 U.S.C. 103 as being unpatentable over Mueller Cajar, Liang, Soucaille, and Caspar as applied to claim 1, 3-5, 7-10, 13, 17 and 21 above, and further in view of Jiang et al (Proc Natl Acad Sci U S A. 2018 Jan 9;115(2):403-408; hereinafter “Jiang”).
As discussed above, claims 1, 3-5, 7-10, 13, 17, and 21 were rendered prima facie obvious by the combined teachings of Mueller Cajar, Liang, Soucaille, and Caspar.
The difference between the references and the instant claims is that none of the references explicitly teach the host cell overexpresses phosphoglycolate phosphatase in view of the parent cell (as in claim 6).
However, Jiang teaches coordinating carbon and nitrogen metabolic signaling through cyanobacterial global repressor NdhR (title). Jiang teaches the examination of the possible roles of 2-phosphoglycolate in NdhR transcriptional regulation of its target genes by constructing a recombinant BL21 E. coli strain overexpressing slr0458, that encodes phosphoglycolate phosphatase (PGPase) [“PGPase-overexpression” (POE) strain] (pg. 406, col 1, paragraph 2; pg. 407, col 2) (overexpressing phosphoglycolate phosphatase as in claim 6). This PGPase was reported to be responsible for the catabolism of intracellular 2-PG, which usually accumulates in the cell at a high level after 30 min after the shift from a high carbon level to a limiting CO2 level (pg. 406, col 1, paragraph 2; Fig. 4). The transcription level of the slr0458 gene increased by ∼25-fold in the POE strain compared with the wild type (pg. 406, col 1, paragraph 2). In the POE strain, due to the high level of PGPase that degrades the intracellular 2-PG, the transcription of NdhR target genes ndhR, ndhF3, sbtA, and bicA is significantly down-regulated, to about 20–60% of that in the wild-type strain (pg. 406, col 1, paragraph 2). This confirmed that 2-PG is an inducer that directly interacts with NdhR in vivo (pg. 406, col 1, paragraph 2). Jiang further teaches that the accumulation of the photorespiratory metabolite 2-PG is an indicator of a high N/C ratio (Fig. 5B), and an imbalanced C/N metabolism will result in the intracellular accumulation of either 2-OG or 2-PG, and their interaction with global sensors, such as NtcA, CmpR, and NdhR, switches on or off the downstream genes involved in carbon and nitrogen metabolism, eventually leading to the restoration of balance (pg. 407, col 2, paragraph 2).
Therefore, it would have been prima facie obvious to one of ordinary skill at the time of filing to modify the recombinant Synechocystis expressing Rubisco and PRK as taught by Mueller Cajar, Liang, Soucaille, and Caspar and overexpress phosphoglycolate phosphatase as taught by Jiang to arrive at the claimed invention. As Mueller Cajar, Liang, Soucaille, and Caspar teach the creation of a recombinant Synechocystis cell expressing Rubisco and PRK with increased glyoxylate reductase expression and Jiang teaches the overexpression of phosphoglycolate phosphatase in a recombinant host cell, one of ordinary skill would have been motivated to overexpress phosphoglycolate phosphatase with a reasonable expectation of success. One of ordinary skill would have been motivated to make the modification because Jiang teaches that phosphoglycolate phosphatase can be successfully overexpressed in a recombinant host cell causing a downregulation of NdhR gene to ultimately restore C/N balance in imbalanced cell metabolism.
Accordingly, the claimed invention was prima facie obvious to one of ordinary skill at the time of filing, especially in the absence of evidence to the contrary.
Response to Arguments
Applicant's arguments filed 01/08/26 have been fully considered but they are not persuasive.
On pg. 5-7 of the remarks, Applicant argues that the combination of references fail to teach a recombinant photosynthetic cyanobacterial host cell that possesses all of the claimed features. Applicant argues that the references teach non-photosynthetic organisms, not photosynthetic cyanobacteria because Mueller Cajar teaches use of chemotrophic bacterium E. coli, and Soucaille teaches E. coli modified to be unable to metabolize glycolate. Applicant also argues that Caspar teaches use of E. coli and not photosynthetic bacteria. Applicant concedes that Liang teaches use of Synechocystis cyanobacteria but does not teach the claimed features. Applicant argues that cyanobacteria have fundamentally different metabolic pathways compared to organisms like E. coli such as carbon concentrating mechanisms and carboxysomes absent in E. coli. Applicant then argues that there would be no reasonable expectation of success in combining all the claimed features in a photosynthetic cyanobacterial host cell. Applicant argues that Liang and Caspar teach away from Rubisco oxygenation, Soucaille produces glycolate via a completely different pathway, not Rubisco oxygenation, Mueller Cajar views glycolate as a waste product, and Jiang is silent as to glycolate production. Applicant further argues that while Soucaille teaches glycolate production with titers higher that 2g/L, the yield is only achieved in E. coli, not in photosynthetic bacteria, pointing to data in Table 3 of the specification as to the claimed yield of glycolate in Synechocystis.
In response, the examiner disagrees. First, the use of a photosynthetic cyanobacterial host cell was covered by the Liang reference (see above) which provides adequate teaching, suggestion, and motivation to one of ordinary skill to have utilized a photosynthetic host cell because Liang teaches successful expression of a recombinant Rubisco in Synechocystis host cell that advantageously allowed for increased oxygen evolution rate, photosynthesis capabilities, and carbon fixation. Second, In response to applicant’s argument that there is no teaching, suggestion, or motivation to combine the references, the examiner recognizes that obviousness may be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007). In this case, Mueller Cajar teaches recombinant host cell being used to express a Rubisco with increased sensitivity to O2 (as instantly claimed). Liang teaches Synechocystis PCC 6803 (a photosynthetic host cell) overexpressing Rubisco (as instantly claimed) to increase growth rate and photosynthesis as one of the key targets to increase efficiency of carbon fixation in photoautotrophic organisms, and Soucaille teaches the successful attenuation of the glycolate consuming enzymes via replacement of the promoter or deletion of the DNA sequence, resulting in the accumulation of glycolate in fermentation medium from a recombinant host cell. Finally, Caspar teaches the successful use of a Rubisco amino acid sequence that is capable of causing high Rubisco expression in recombinant organisms. One of ordinary skill would have balanced all of the teachings of the prior art to arrive at Applicant’s claimed invention with a reasonable expectation of success. Thus, the rejections are maintained as set forth above.
Conclusion
NO CLAIMS ALLOWED.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/G.C.R./Examiner, Art Unit 1651
/THOMAS J. VISONE/Supervisory Patent Examiner, Art Unit 1672