Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
DETAILED ACTION
Claims 1-30 are pending. Claims 11-30 are withdrawn. Claims 1-10 are under examination on their merits.
Response to Arguments
Applicant's arguments filed 7/13/2026 have been fully considered but they are not persuasive.
Applicant argues against the written description rejection of claims under 35 U.S.C. 112(a) on the grounds that the present disclosure provides alignments showing which residues are conserved and how to substitute amino acids with minimal effect on function or activity (Arguments, paragraph bridging pages 10-11). Applicant argues that non-conserved or weakly conserved residues are likely to have no effect on function. Applicant argues further that the specification provides guidance on conservative amino acid substitution (Arguments, paragraph bridging pages 10-11).
In response, Applicant has not disclosed any species of variants of SEQ ID NO: 1, 3-6, 8, 10-12, 14, 17-18, and 20-21. Furthermore, an amino acid sequence alignment is not sufficient evidence of a structure-function correlation since amino acids distal to the active site of an enzyme can still affect catalytic activity depending on the three-dimensional structure of the enzyme. Therefore, the person of ordinary skill in the art would not have recognized that the inventors had, at the time the application was filed, possession of the claimed genus of variants of SEQ ID NO: 1, 3-6, 8, 10-12, 14, 17-18, and 20- 21.
Applicant argues against the rejection of claims under 35 U.S.C. 102(a)(1) on the grounds that each of the cited references teaches culturing bacteria in medium that is not limited to gaseous CO2 as the carbon source. For example, both Park and Yang cultures the bacteria in LB medium rather than CO2 (Arguments, pages 12-13).
In response, the claims are drawn to a bacteria capable of producing a PHA polymer from gaseous CO2 in the absence of another carbon source. The claims are not drawn to a method of culturing the bacteria to produce a PHA polymer. The wherein clause is only given weight insofar as it limits the structure of the claimed bacteria. Here, the prior art of Park teaches each of the required genes. Additionally, R. eutropha is capable of autotrophic growth on H2 and CO2 as the energy and carbon sources, respectively, as evidenced by Shimizu (Background, left column, paragraph 1). Thus, Park’s engineered R. eutropha is inherently capable of producing the PHA polymer from gaseous CO2 in the absence of another carbon source. Therefore, Park anticipates independent claim 1, as evidenced by Shimizu.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
(New Rejection Necessitated by Amendment) Claim 5 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 5 recites the limitation " the bacterium of the Pseudomonadaceae genus" in lines 1-2. There is insufficient antecedent basis for this limitation in the claim.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
(New Rejection Necessitated by the Amendment) Claims 8-9 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claims 8-9 fail to include all the limitations of the claim upon which they depend. Claims 8-9 ultimately depend from claim 1, which recites the microorganism is capable of producing a PHA polymer from gaseous CO2 in the absence of another carbon source, whereas claim 8 recites the PHA polymer comprises a carbon atom metabolized from a carbon source (not limited to gaseous CO2) and claim 9 recites carbon sources other than gaseous CO2.
Applicant may cancel the claims, amend the claims to place the claims in proper dependent form, rewrite the claims in independent form, or present a sufficient showing that the dependent claims complies with the statutory requirements.
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
(New Rejection Necessitated by Amendment) Claims 1, 4, and 6-7 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 4 recites a genus of variants of PHA synthase with at least 80% sequence identity to SEQ ID NO: 1, 3-6, 8, and 10-12.
Claim 6 recites a genus of variants of isocaprenoyl-CoA:2-hydroxyisocaproate CoA-transferase with at least 80% sequence identity to a SEQ ID NO: 14, 17-18, and 20.
Claim 7 recites a genus of variants of propionate CoA-transferase that have at least 80% sequence identity to SEQ ID NO: 21.
The specification discloses a single UniProt sequence for each protein: Q9L3F7 _CLOPR (encoded by pct), Q188l3_PEP06 (encoded by hadA) and B9WOT0_9PSEO (encoded by phaC): see [0078] of the specification. The specification also discloses a limited number of mutations in each protein: V193A for pct540 and El300, S325T, S477G, and Q481K for phaC1437 ([0078]). Thus, a limited number of species of the genus of pct genes and phaC genes is disclosed and no variants of hadA are disclosed. The majority of the phaC sequences are roughly 560 amino acids long (see SEQ ID NO: 1-13). Thus, at least 80% sequence identity corresponds to as many as 112 amino acid substitutions.
Fig. 5A-5M are sequences of additional phaC genes and Fig. 6A-6E illustrate the alignment of the amino acid sequences of PHA synthase, Fig. 7A-7G shows amino acid sequences of hydroxyl-CoA transferases (pct). However, it is unclear whether any of the other sequences have been functionally characterized or whether they are merely assigned function by sequence homology. For example, UniProt G3XCV5_PSEAE, corresponding to Fig. 5D, is a predicted protein (see G3XCV5_PSEAE website, “protein”). Likewise, PHAC1_ECTOL is a protein inferred from homology (see the PHAC1_ECTOL website, “protein”). Thus, the additional sequences and the alignment are insufficient to establish a structure-function correlation because the function has not been demonstrated for each of these proteins.
Chek et al. (Applied Microbiology and Biotechnology (2019) 103:1131–1141; cited in the Non-Final Action mailed on4/13/2026) teaches that phaC from Chromobacterium sp. USM2 and Cupriavidus necator have been crystallized (Abstract). Table 1 of Chek highlights a limited number of species of PhaC variants from Cupriavidus necator, Aeromonas caviae, Chromobacterium sp.
USM2, and Pseudomonas sp. 61–3, with possible impacts of the mutations. There are seven point mutations made individually for Pseudomonas sp. 61–3 phaC and none of the point mutations are tested in combination.
With respect to the genus of pct variants, Selmer et al. (European journal of biochemistry 269.1 (2002): 372-380; cited in the Non-Final Action mailed on4/13/2026) teaches a glutamate 324 at the active site (Abstract). Fig. 3 illustrates a sequence alignment of the active site region of various propionate CoA-transferases. However, Selmer does not generate any variants of pct and the significance of the remaining amino acids outside of the active site region is unclear. For example, amino acids outside of the active site may be involved in stabilizing the three-dimensional structure of the protein and indirectly contribute to enzyme activity.
Kim et al. (The FEBS Journal 272.2 (2005): 550-561; cited in the Non-Final Action mailed on4/13/2026) teaches hadA and its activity (Fig. 2). Kim teaches that hadA is a highly specific class III 2-hydroxyisocaproate CoA-transferase using (R)-2-hydroxyisocaproyl-CoA and (E)-isocaprenoate as well as isocaproate as substrates (page 556, left column, Discussion, bottom paragraph). Kim also teaches the nucleotide sequences around the ribosome binding site and start codons of the hadA gene (Fig. 3). However, Kim does not teach the structure-function correlation of hadA nor does Kim teach any variants of hadA that retain enzymatic activity.
Based on the limited number of species disclosed in the specification and taught by the prior art, as well as a lack of structure-function correlation for the protein encoded by each gene, the person of ordinary skill in the art would not have recognized that the inventors had possession of the claimed genera of PHA synthase variants having at least 80% sequence identity to SEQ ID NO: 1, 3-6, 8, and 10-12, isocaprenoyl-CoA:2-hydroxyisocaproate CoA-transferase variants having at least 80% sequence identity to SEQ ID NO: 14, 17-18, and 20, or propionate CoA-transferase variants having at least 80% sequence identity to SEQ ID NO: 21.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
The following rejections are necessitated by the amendment.
Claims 1-2 and 8-10 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Park et al. (Metabolic engineering 20 (2013): 20-28; cited in the Non-Final Action mailed on 4/13/2026) as evidenced by Shimizu et al. (BMC microbiology 13.1 (2013): 169; cited in the Non-Final Action mailed on4/13/2026).
Regarding claims 1-2, Park teaches a genetically engineered Ralstonia eutropha (synonym for Cupriavidus necator) comprising the Clostridium propionicum pct540 gene and Pseudomonas sp. MBEL6–19 phaC1437 gene (Abstract). The genetically engineered R. eutropha is capable of producing a PHA polymer (Abstract).
Regarding the limitation, “wherein the microorganism is capable of producing a PHA polymer from gaseous CO2 in the absence of another carbon source,” Park teaches each of the required genes for producing the PHA polymer and R. eutropha is capable of autotrophic growth on H2 and CO2 as the energy and carbon sources, respectively, as evidenced by Shimizu (Background, left column, paragraph 1). Thus, Park’s engineered R. eutropha is inherently capable of producing the PHA polymer from gaseous CO2 in the absence of another carbon source.
Regarding claims 8-9, R. eutropha is a chemoautotroph that is capable of incorporating CO2 into PHAs even when grown in heterotrophic conditions as evidenced by Shimizu (Abstract Results). Thus, the R. eutropha is necessarily capable of converting the carbon from CO2 into the PHA polymer.
Regarding claim 10, the microorganism is necessarily capable of producing the claimed polymer because the structure of the microorganism is identical to the microorganism of the instant application (i.e. the microorganism contains the required enzymes). Note that the ability of the microorganism to produce the claimed polymer is a function of the structure of the microorganism only, since the culture conditions (substrates) are not part of the claimed microorganism.
Claim 3 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Park et al. (Metabolic engineering 20 (2013): 20-28; cited in the Non-Final Action mailed on4/13/2026) as evidenced by Shimizu et al. (BMC microbiology 13.1 (2013): 169; cited in the Non-Final Action mailed on4/13/2026), as applied to claims 1-2 and 8-10 above, further evidenced by Raberg et al. (PLoS One 9.5 (2014): e95907; cited in the Non-Final Action mailed on4/13/2026).
See discussion of Park and Shimizu above, which is incorporated into this rejection as well.
Regarding claim 3, Park teaches replacing phaC with Pseudomonas
sp.6-19 phaC1437 gene (Fig. 1 caption). There are only two phaC genes in R. eutropha H16, phaC1 and phaC2, and only phaC1 is transcribed in H16 as evidenced by Raberg (page 4, left column, Results, Sequence analysis of the phaCAB operon of the PHB negative mutant R. eutropha PHB-4, paragraph 1). Therefore, Park’s genetically engineered R. eutropha is a ΔphaC1 mutant of Cupriavidus necator because the original R. eutropha phaC1 has been replaced.
Claims 4-5 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Park et al. (Metabolic engineering 20 (2013): 20-28; cited in the Non-Final Action mailed on4/13/2026) as evidenced by Shimizu et al. (BMC microbiology 13.1 (2013): 169; cited in the Non-Final Action mailed on4/13/2026), as applied to claims 1-2 and 8-10 above, further evidenced by Yang et al. (Biotechnology and bioengineering 105.1 (2010): 150-160; hereafter Yang 2010) and as by B9W0T0_9PSED (2009 website).
See discussion of Park above, which is incorporated into this rejection as well.
Regarding claims 4-5, Park teaches heterologously expressing the Pseudomonas sp. MBEL6–19 phaC1437 gene in R. eutropha (Abstract). The phaC1437 gene from Pseudomonas sp. MBEL6–19 is an evolved phaC1 with the amino acid substitutions E130D/S325T/S477G/Q481K as evidenced by Yang (Table II). The PHA synthase 1 from Pseudomonas sp. MBEL6–19 is 99.3% identical to SEQ ID NO: 1 as evidenced by B9W0T0_9PSED (OA Appendix A). Thus, the amino acid sequence of phaC1437 (the amino acid sequence of B9W0T0_9PSED with the E130D/S325T/S477G/Q481K) is identical to SEQ IDN O: 1.
Claim 7 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Park et al. (Metabolic engineering 20 (2013): 20-28; cited in the Non-Final Action mailed on4/13/2026) as evidenced by Shimizu et al. (BMC microbiology 13.1 (2013): 169; cited in the Non-Final Action mailed on4/13/2026), as applied to claims 1-2 and 8-10 above, further evidenced by Yang et al. (Biotechnology and bioengineering 105.1 (2010): 150-160; hereafter Yang 2010) and by Q9L3F7_ANAPI (2000 website).
See discussion of Park above, which is incorporated into this rejection as well.
Regarding claim 7, Park also heterologously expresses the C. propionicum pct450 gene in R. eutropha, which is an engineered pct gene with the active mutation V193A as evidenced by Yang 2010 (Table I). The C. propionicum pct gene is identical to the instant SEQ ID NO: 21 (OA Appendix C) as evidenced by Q9L3F7_ANAPI (see gene name and amino acid sequence). Therefore, Park’s pct450 is 99.8% identical to SEQ IDNO: 21 (523/524 amino acids identical).
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.
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.
The following rejection is necessitated by the amendment.
Claims 1 and 6 are rejected under 35 U.S.C. 103 as being unpatentable over Park et al. (Metabolic engineering 20 (2013): 20-28; cited in the Non-Final Action mailed on4/13/2026) in view of Yang et al. (Nature communications 9.1 (2018): 79; cited in the Non-Final Action mailed on4/13/2026) as evidenced by Shimizu et al. (BMC microbiology 13.1 (2013): 169; cited in the Non-Final Action mailed on4/13/2026) and by HADA_CLODI (2004 website).
See discussion of Park and Shimizu above, which is incorporated into this rejection as well.
Regarding claim 6, Park does not teach that the microorganism further comprises an isocaprenoyl-CoA:2-hydroxyisocaproate CoA-transferase enzyme with at least 80% identity to SEQ ID NO: 14.
Yang teaches a genetically engineered E. coli comprising Clostridium difficile isocaprenoyl-CoA:2-hydroxyisocaproate CoA-transferase (hadA) and evolved polyhydroxyalkanoate (PHA) synthase (phaC) genes (Abstract and Fig. 1). Yang teaches that the HadA from C. difficile has the potential to more efficiently produce diverse aromatic polyesters using acetyl-CoA as a CoA donor (page 4, left column, paragraph 1 and Figure 2a). Yang teaches that HadA has catalytic activity on a variety of substrates, including phenyllactate (Fig. 2a). The Clostridium difficile hadA gene encodes a protein that is identical to SEQ ID NO: 14 (OA Appendix B) as evidenced by HADA_CLODI (see gene name and amino acid sequence). The genetically engineered E. coli is capable of producing PHAs (Abstract and Introduction, left column, paragraph 1).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to heterologously express Clostridium difficile hadA into the engineered R. eutropha of Park in order to efficiently produce diverse aromatic polyesters per the suggestion of Yang. The person of ordinary skill in the art would have had a reasonable expectation of success in introducing the Clostridium difficile hadA into the engineered R. eutropha of Park.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CANDICE LEE SWIFT whose telephone number is (571)272-0177. The examiner can normally be reached M-F 8:00 AM-4:30 PM (Eastern).
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Louise Humphrey can be reached at (571)272-5543. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/CANDICE LEE SWIFT/Examiner, Art Unit 1657
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