DETAILED ACTION
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 .
Claim Status
The claim set filed on 3 July 2026 contains claims 1-20, which are currently pending.
Election/Restrictions
Applicant’s election of Group I (claims 1-9) in the reply filed on 3 July 2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)). Claims 11-20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 3 July 2026.
Priority
The instant application claims priority to U.S. Provisional Application 63/502,474 (filed 16 May 2023). Therefore, the effective filing date of claims 1-9 is 16 May 2023.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 15 August 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 and 4 are objected to because of the following informalities:
In claim 1, “R. palustris” should be fully spelled out upon first use in the claims, and
In claim 4, the genes “phaR” and “phaZ” 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.
Claims 1-9 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.
Regarding claims 1 and 8 (upon which claims 2-7 and 9 depend), the claims use the terms “ΩrubI” and “ΩrubII” to refer to gene names. However, the instant specification uses the terms “ΩrubI” and “ΩrubII” to refer to refer to modified R. palustris strains, not individual genes (pg. 23, ln. 25-30). Furthermore, the terms “ΩrubI” and “ΩrubII” do not appear in the art when referring to RuBisCO genes. Thus, one of ordinary skill in the art cannot determine the scope of the claimed R. palustris strain because it is not clear what gene(s) is/are encompassed by the claim. In the interest of compact prosecution, the claim is interpreted such that any RuBisCO form I and RuBisCO form II genes may be used in the strain (see spec., pg. 21, ln. 1).
Claim 7, which depends upon claim 1, recites the limitation "the endogenous nifA deletion" in line 2. There is insufficient antecedent basis for this limitation in the claim or in the claim from which it depends. In the interest of compact prosecution, claim 7 is interpreted as being dependent upon claim 6, which recites “an endogenous nifA deletion.”
Clarification is requested.
Claim Rejections - 35 USC § 103
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.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1, 5-7, and 9 are rejected under 35 U.S.C. 103 as being unpatentable over Bai et al. (2021, Commun. Biol.; cited in IDS; herein “Bai”) as is evidenced by Lomwongsopon and Varrone (2022, Fermentation; herein “Lomwongsopon”) in view of Ha-Tran et al. (2021, PLoS ONE; herein “Ha-Tran”).
Regarding claims 1, 6-7, and 9, Bai teaches a Rhodopseudomonas palustris (R. palustris) TIE-1 strain comprising deletions of the endogenous nifA1 and nifA2 genes (pg. 3, right col., para. 1). Bai also teaches that the Nif double mutant (i.e., mutant lacking nitrogen-fixing abilities) produced the highest amount of the biofuel, n-butanol (Abstract and Fig. 2), which is a precursor in bioplastic production, as is evidenced by Lomwongsopon (section 2.3.4).
Regarding claim 5, Bai also teaches an R. palustris mutant comprising a glgA (Rpal_0386) gene deletion (pg. 3, right col., para. 1), which is a gly gene as is evidenced by the instant specification (pg. 2, ln. 33 – pg. 3, ln. 1). Bail teaches that deletion of glgA directs acetyl-CoA (i.e., a precursor in biofuel production) away from glycogen production (pg. 5, left col., para. 1).
However, Bai does not teach a R. palustris TIE-1 strain comprising exogenous RuBisCO form I and II genes, as in claim 1.
Regarding claim 1, Ha-Tran teaches a Kluyveromyces marxianus 4G5 strain which overexpresses RuBisCO form I or RuBisCO form II from R. palustris (Abstract). Ha-Tran teaches that transformed K. marxianus strains grew better and were able to produce more bioethanol (i.e., a precursor to biofuels and bioplastics) that the wild type strain (Fig. 4, A-D).
Therefore, it would have been prima facie obvious, before the effective filing date of the claimed invention, to a person of ordinary skill in the art, to modify the R. palustris TIE-1 strain taught by Bai to include deletions of nifA1, nifA2, and glgA and to overexpress RuBisCO forms I and II, as is taught by Ha-Tran, thereby arriving at the invention of claims 1, 5-7, and 9. The person of ordinary skill in the art would have been motivated to make the modification because both the gene deletions taught by Bai and the expression of RuBisCO forms I and II taught by Ha-Tran result in the increased production of precursors to bioplastic production, thereby increasing bioplastic production. Therefore, the combination is also desirable (see MPEP 2144(II)). The person of ordinary skill in the art would have had a reasonable expectation of success because overexpressing exogenous copies of native genes in bacteria is well known in the art; thus, one would predict successful overexpression of RuBisCO genes in R. palustris. Therefore, the combination leads to expected results because each element performs the same function as is does individually.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that combining prior art elements according to known methods to yield predictable results, is obvious unless its application is beyond that person's skill. KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) also discloses that the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results. In the instant case, all elements (i.e., R. palustris TIE-1, RuBisCO forms I and II, gly deletion, and nifA1 and nifA2 deletion) were known in the art. In addition, combining these elements yields a composition wherein each element merely performs the same function as it does separately; thus, the results of the combination would be recognized as predictable to one of ordinary skill in the art. Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Claims 1-2, 5-7, and 9 are rejected under 35 U.S.C. 103 as being unpatentable over Bai (2021, Commun. Biol.) as is evidenced by Lomwongsopon (2022, Fermentation) in view of Ha-Tran (2021, PLoS ONE) as applied to claims 1, 5-7, and 9 above, and further in view of Shimizu et al. (2022, Appl. Environ. Microbiol.; herein “Shimizu”) as evidenced by Kariduraganavar et al. (2014, Natural and Synthetic Biomedical Polymers; herein “Kariduraganavar”).
The combination of Bai and Ha-Tran is set forth in para. 15-20 above and incorporated by reference herein and teaches all limitations of claims 1, 5-7, and 9.
However, neither Bai nor Ha-Tran teach the deletion of an endogenous phaR gene, as in claim 2.
Regarding claim 2, Shimizu teaches a Rhodobacter sphaeroides (a purple nonsulfur phototrophic bacterium) with a deletion of phaC1 and phaR exhibits growth comparable to wild type strains and does not accumulate poly (β-hydroxybutyrate) (PHB; Abstract), which is a polymer that is of interest as a biodegradable plastic, as is evidenced by Kariduraganavar (pg. 12, section 1.4.9). Shimizu teaches that phaR encodes a transcriptional regulator capable of sensing PHB accumulation and represses expression of phaZ, phaP, and phaR, thereby reducing production of PHB (Abstract and FIG. 1).
Therefore, it would have been prima facie obvious, before the effective filing date of the claimed invention, to a person of ordinary skill in the art, to modify the R. palustris TIE-1 strain overexpressing RuBisCO forms I and II taught by the combination of Bai and Ha-Tran by deleting the phaR gene as is taught by Shimizu, thereby arriving at the invention of claims 1-2, 5-7, and 9. The person of ordinary skill in the art would have been motivated to make the modification because Shimizu teaches that the deletion of phaR allows for the continuous production of PHB, a bioplastic. Therefore, the combination is also desirable (see MPEP 2144(II)). The person of ordinary skill in the art would have had a reasonable expectation of successfully deleting the phaR gene in R. palustris TIE-1 because Shimizu teaches the deletion of the gene in R. sphaeroides, which is a purple nonsulfur phototrophic bacterium, like R. palustris, and Bai teaches the methodology for deleting genes in R. palustris TIE-1. Therefore, the combination leads to expected results because each element performs the same function as is does individually.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that combining prior art elements according to known methods to yield predictable results, is obvious unless its application is beyond that person's skill. KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) also discloses that the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results. In the instant case, all elements (i.e., R. palustris TIE-1, RuBisCO forms I and II genes, phaR gene, gly gene, nifA1 and nifA2 genes, and bioplastic production) were known in the art. In addition, combining these elements yields a composition wherein each element merely performs the same function as it does separately; thus, the results of the combination would be recognized as predictable to one of ordinary skill in the art. Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Claims 1-7, and 9 are rejected under 35 U.S.C. 103 as being unpatentable over Bai (2021, Commun. Biol.) as is evidenced by Lomwongsopon (2022, Fermentation) in view of Ha-Tran (2021, PLoS ONE) and Shimizu (2022, Appl. Environ. Microbiol.) as evidenced by Kariduraganavar (2014, Natural and Synthetic Biomedical Polymers) as applied to claims 1-2, 5-7, and 9 above, and further in view of Nangle et al. (2021, CA 3166532 A1; herein “Nangle”).
The combination of Bai, Ha-Tran, and Shimizu is as discussed above and incorporated by reference herein, set forth in para. 22-33 above and teaches all limitations of claims 1-2, 5-7, and 9.
However, none of Bai, Ha-Tran, or Shimizu teach the deletion of an endogenous phaZ gene, as in claim 3, or the deletion of both phaR and phaZ genes, as in claim 4.
The teachings of Shimizu as applied to claim 2 also apply to claim 4. Shimizu also teaches that the function of PhaZ uses PHB, thereby depleting the supply of PHB (FIG 1).
Regarding claim 3, Nangle teaches an engineered bacterium for the production of polyhydroxyalkanoates (PHA; e.g., PHB, para. 160) comprising an inactivating modification of at least one endogenous gene involved in the PHA synthesis pathway, including phaZ (para. 224). Nangle also teaches that the inactivation modification may be deletion of the entire coding sequence of the gene (para. 216).
Therefore, it would have been prima facie obvious, before the effective filing date of the claimed invention, to a person of ordinary skill in the art, to further modify the R. palustris TIE-1 strain overexpressing RuBisCO form I and form II genes and comprising a deletion of the phaR gene, as is taught by the combination of Bai, Ha-Tran, and Shimizu, by further deleting the phaZ gene, as is taught by Nangle, thereby arriving at the invention of claims 1-7 and 9. The person of ordinary skill in the art would have been motivated to make the modification because Nangle teaches that deletion of phaZ allows for increased production of PHAs (such as PHB) and Shimizu teaches that PhaZ utilizes PHB, therefore one would be motivated to delete phaZ in order to produce and collect PHB as a bioplastic. Therefore, the combination is also desirable (see MPEP 2144(II)). The person of ordinary skill in the art would have had a reasonable expectation of success because Nangle teaches the successful deletion of phaZ for bioplastic production and Bai teaches the methodological details necessary to delete endogenous genes in R. palustris TIE-1. Therefore, the combination leads to expected results because each element performs the same function as is does individually.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that combining prior art elements according to known methods to yield predictable results, is obvious unless its application is beyond that person's skill. KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) also discloses that the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results. In the instant case, all elements (i.e., R. palustris TIE-1, RuBisCO forms I and II genes, phaR gene, phaZ gene, gly gene, nifA1 and nifA2 genes, and bioplastic production) were known in the art. In addition, combining these elements yields a composition wherein each element merely performs the same function as it does separately; thus, the results of the combination would be recognized as predictable to one of ordinary skill in the art. Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Claim(s) 1 and 5-9 are rejected under 35 U.S.C. 103 as being unpatentable over Bai (2021, Commun. Biol.) as is evidenced by Lomwongsopon (2022, Fermentation) in view of Ha-Tran (2021, PLoS ONE) as applied to claims 1, 5-7, and 9 above, and further in view of Elmore et al. (2020, bioRxiv; herein “Elmore”).
The combination of Bai and Ha-Tran is as discussed above and incorporated by reference herein, set forth in para. 15-33 above and teaches all limitations of claims 1, 5-7, and 9.
However, neither Bai nor Ha-Tran teach that the exogenous RuBisCO form I and II genes are integrated into a genome of the transgenic R. palustris TIE-1 microorganism using a φC31 integrase system, as in claim 8.
Regarding claim 8, Elmore teaches an expression system using the φC31 integrase for inserting genes into the bacterial genome (Fig. 1). Elmore also teaches that this system was used in R. palustris CGA009 (pg. 3) and that φC31 is likely to work in the vast majority of organisms (pg. 2, para. 2). Elmore also teaches that their expression system is highly efficient (pg. 15, para. 2) and useful for engineering industrial bacteria (Abstract).
Therefore, it would have been prima facie obvious, before the effective filing date of the claimed invention, to a person of ordinary skill in the art, to use the φC31 integrase system taught by Elmore to integrate the RuBisCO form I and II genes taught by Ha-Tran into the genome of the R. palustris TIE-1 strain taught by Bai, thereby arriving at the invention of claims 1 and 5-9. The person of ordinary skill in the art would have been motivated to make the modification because Elmore teaches that their expression system using φC31 is highly efficient and useful for engineering industrial bacteria, such as bacteria used in production of bioplastics. Therefore, the combination is also desirable (see MPEP 2144(II)). The person of ordinary skill in the art would have had a reasonable expectation of successfully using the φC31 integrase in R. palustris TIE-1 because Elmore teaches that their expression system can be used in the vast majority of organisms, including another R. palustris strain. Therefore, the combination leads to expected results because each element performs the same function as is does individually.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that combining prior art elements according to known methods to yield predictable results, is obvious unless its application is beyond that person's skill. KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) also discloses that the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results. In the instant case, all elements (i.e., R. palustris TIE-1, RuBisCO form I and II genes, φC31 integrase system, etc.) were known in the art. In addition, combining these elements yields a composition wherein each element merely performs the same function as it does separately; thus, the results of the combination would be recognized as predictable to one of ordinary skill in the art. Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BAILEY M MORGAN whose telephone number is (703)756-5388. The examiner can normally be reached M-F 9-5 ET.
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/BAILEY M MORGAN/Examiner, Art Unit 1645
/SAMIRA J JEAN-LOUIS/Supervisory Patent Examiner, Art Unit 1642
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