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 .
Election/Restrictions
Applicant elected Invention I (claims 1-12) in the reply filed on 12/08/2025. 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. See MPEP § 818.01(a).
Claims 13-20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Accordingly, claims 1-12 have been examined on the merits.
Priority
The instant application claims the priority benefit of U.S. Provisional Application No. 63/338000 filed on 5/03/2022 under 35 U.S.C. 119(e).
The provisional application, however, does not disclose the limitations of claims 2-3, 7-8, and 10-12. Hence, these claims are given the effective filing date of 5/03/2023, whereas claims 1, 4-6, and 9 are granted the effective filing date of 5/03/2022.
Information Disclosure Statement
The information disclosure statement (IDS) filed on 7/31/2023 is in compliance with the provisions of 37 C.F.R. 1.97 and all references have been fully considered.
Claim Objections
Claims 2-12 are objected to because of the following informalities: a comma is missing after “phototrophic organism of claim 1” or ”claim 6” and before “wherein”. Appropriate correction is required.
Claim 5 is also objected to due to the lack of period after the abbreviation “sp”.
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim 1 is rejected under 35 U.S.C. 102(a)(1)/102(a)(2) as being anticipated by Bar-Even et al. (Pub. No. US 2015/0218528 A1).
Bar-Even et al. discloses an isolated microorganism that expresses enzymes of the reductive glycine pathway, wherein the microorganism is capable of converting formate to pyruvate or glycerate (Abstract; par. [0008]). One particular embodiment of the isolated microorganism is a formatotrophic organism that utilizes formate as its sole carbon source (par. [0078], [0128]).
In some embodiments, the isolated microorganism is genetically modified and also expresses a formate dehydrogenase (par. [0017-[0018], [0020], [0081], [0116]-[0122]). The isolated microorganisms can be phototrophic (par. [0022], [0079]) including bacteria like Chromatium and Rhodobacter (par. [0029], [0071]), as well as diatoms and cyanobacteria (par. [0073]-[0075]).
Bar-Even et al. reads on the instant application’s non-naturally occurring phototrophic organism as follows:
Regarding claim 1: the embodiment of the disclosed isolated microorganism being genetically modified and phototrophic is the same as “A non-naturally occurring phototrophic organism”.
The recombinant expression of formate dehydrogenase, which indicates that the isolated microorganism harbors a gene encoding said enzyme, meets the requirement that the phototrophic organism comprises “a non-naturally occurring gene encoding for a formate dehydrogenase enzyme”.
The isolated microorganism being capable of growing on formate as its sole carbon source satisfies “wherein the phototrophic organism can grow on formate as a sole carbon source”.
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 6-8 and 10-12 are rejected under 35 U.S.C. 102(a)(1)/102(a)(2) as being anticipated by, or in the alternative, under 35 U.S.C. 103 as obvious over Bar-Even et al. (Pub. No. US 2015/0218528 A1).
Bar-Even et al.’s teachings are set forth above and applied herein. This prior art is found to anticipate claim 1.
The disclosed microorganism is equivalent to the claims below:
Regarding claims 6-8 and 10-12: the prior art differs from the instant claims in that it does not teach “wherein the phototrophic organism exhibits increased growth in a medium comprising carbon dioxide and formate when compared to the corresponding naturally occurring phototrophic organism”, as well as the additional limitations “wherein the concentration of carbon dioxide in the medium is less than about 0.04 percent” and “wherein the concentration of formate in the medium is greater than about 5 percent”, respectively (claims 6-8). Similarly, the prior does not teach that the concentration of formate as a sole carbon source is further required to be “greater than 10 mM”, “greater than 25 mM”, and “greater than 70 mM”, respectively (claims 10-12).
Regardless, the courts have held that an inherent property does not need not be recognized at the relevant time and that discovering it does not make a known product patentable. See MPEP 2112. “[T]he discovery of a previously unappreciated property of a prior art composition, or of a scientific explanation for the prior art’s functioning, does not render the old composition patentably new to the discoverer.” Atlas Powder Co. v. Ireco Inc., 190 F.3d 1342, 1347, 51 USPQ2d 1943, 1947 (Fed. Cir. 1999). Thus the claiming of a new use, new function or unknown property which is inherently present in the prior art does not necessarily make the claim patentable. In re Best, 562 F.2d 1252, 1254, 195 USPQ 430, 433 (CCPA 1977). In this case, an embodiment of Bar-Even et al.’s isolated microorganism is a genetically modified microorganism that harbors a gene encoding a formate dehydrogenase and can grow on formate as a sole carbon source.
Furthermore, Bar-Even et al. states that transformed cells of the isolated microorganism can be cultured under effective conditions (including effective media having assimilable carbon, nitrogen, and phosphate sources) that allow for expression of high amounts of the recombinant enzymes and that such culturing conditions are within the expertise of one of ordinary skill in the art (par. [0125]). A person with ordinary skill in the art before the effective filing date of the claimed invention would have found effective concentrations of carbon dioxide and formate that would allow the isolated microorganism to grow solely on formate as the carbon source through routine experimentation and optimization.
Claims 6-8 and 10-12 are thus anticipated by, or obvious over, Bar-Even et al..
Claims 1-4 and 6-12 are rejected under 35 U.S.C. 103 as being unpatentable over Bar-Even et al. (Pub. No. US. 2015/0218528 A1) in view of Yishai et al. (Pub. No. WO 2021/116330 A1).
The teachings of Bar-Even et al. are described previously and applied herein. Bar-Even et al. anticipates claim 1. Bar-Even et al. also anticipates or renders obvious claims 6-8 and 10-12
Bar-Even et al.’s isolated microorganism is comparable to the claims below:
Regarding claim 2: the non-naturally occurring gene is further defined as having “a nucleotide sequence that is greater than 70% identical to SEQ ID NO: 29, SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, or SEQ ID NO: 17”.
Bar-Even et al. is different from the instant claim in that it does not disclose the nucleotide sequence of the formate dehydrogenase.
Nonetheless, Yishai et al. teaches a formate dehydrogenase that can be expressed by a microorganism that does not naturally express formate dehydrogenase to produce a genetically engineered microorganism capable of growing on formate (Abstract). The formate dehydrogenase is an NAD-dependent formate dehydrogenase that catalyzes the catabolism of C1 compounds like formate and carbon dioxide. One example is the formate dehydrogenase from Pseudomonas having an amino acid sequence that is at least 80% identical to the amino acid sequence of SEQ ID NO:17 or encoded by a nucleotide sequence that is at least 80% identical to SEQ ID NO: 18 (lines 25-24, page 9). When said enzyme is expressed along with formate tetrahydrofolate (THF) ligase, methenyl-THF cyclohydrolase, methyelene-THF dehydrogenase, enzyme of the glycine cleavage system, serine deaminase, and serine hyroxymethyltransferase (which are also expressed by Bar-Even et al.’s microorganism; par. [0084]) preferably in a microorganism that cannot assimilate C1 compounds natively, the resulting genetically engineered microorganism can grow on formate as the sole carbon source (lines 1-5, page 10; lines 14-15, page 16). Sequence-to-sequence alignment of Yishai et al.’s SEQ ID NO:18 with applicant’s SEQ ID NO: 3 reveals that 912 out of 1206 nucleotides match (75% identical).
Given that Bar-Even et al.’s isolated microorganism expresses formate dehydrogenase and the other enzymes expressed by Yishai et al.’s genetically engineered microorganism, one with ordinary skill in the art before the effective filing date of the claimed invention would have incorporated Yishai et al.’s gene encoding Pseudomonas formate dehydrogenase (SEQ ID NO: 18) in Bar-Even et al.’s isolated microorganism. It can be expected that having said gene in the isolated microorganism would result in its successful growth on formate as the sole carbon source.
Regarding claim 3: the non-naturally occurring gene is additionally specified to have “an amino acid sequence that is greater than 70% identical to SEQ ID NO: 30, SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, or SEQ ID NO: 18”.
Bar-Even et al. does not disclose the amino acid sequence of the formate dehydrogenase.
But as discussed above, Yishai et al. provides a NAD-dependent formate dehydrogenase from Pseudomonas having an amino acid sequence that is at least 80% identical to the amino acid sequence of SEQ ID NO:17. Sequence-to-sequence alignment of Yishai et al.’s SEQ ID NO:17 with applicant’s SEQ ID NO: 4 shows that 399 out of 401 amino acids match (99.5% identical).
Based on Yishai et al.’s teachings, a person with ordinary skill in the art before the effective filing date of the claimed invention would have used the NAD-dependent formate dehydrogenase from Pseudomonas (SEQ ID NO: 17) as the formate dehydrogenase expressed by Bar-Even et al.’s isolated microorganism with reasonable expectation that said isolated microorganism would grow on formate as the sole carbon source.
Regarding claim 4: Yishai et al. teaches expressing enzymes like formate dehydrogenase extrachromosomally from plasmids, as well as intrachromosomally by incorporating them into the genome of the genetically engineered microorganism (lines 10-14, page 12). Since Bar-Even et al.’s isolated microorganism can be algae including diatoms (par. [0073]-[0074]) which have plastids, it would have been obvious to incorporate Yishai et al.’s gene encoding for Pseudomonas formate dehydrogenase (SEQ ID NO: 18) into the plastidial genome of isolated microorganisms like diatoms.
Regarding claim 9: the NAD-dependent formate dehydrogenase uses NAD+ as a cofactor and therefore fulfills “wherein the formate dehydrogenase enzyme uses NAD+ as a cofactor”.
Regarding claims 10-12: the concentration of formate as a sole carbon source is further required to be “greater than 10 mM”, “greater than 25 mM”, and “greater than 70 mM”, respectively.
Yishai et al. demonstrates that cell density of a genetically engineered microorganism expressing a NAD-dependent formate dehydrogenase from Pseudomonas increases as the concentration of formate increases from 10 mM to about 100 mM, and growth starts to lag at concentrations of >109 mM (lines 33-37, page 30; lines 1-4, page 31; Figure 3D). Thus, one with ordinary skill in the art would have expected that growing Bar-Even et al.’s isolated microorganism having a gene encoding for said enzyme would be able to grow in a medium containing formate as the sole carbon source at concentrations of 10-100 mM.
Claims 1 and 5 are rejected under 35 U.S.C. 103 as being unpatentable over Bar-Even et al. (Pub. No. US. 2015/0218528 A1) in view of Dahlin et al. (Communications Biology 2019, Vol. 2, article 388, pages 1-9; IDS cited).
The teachings of Bar-Even et al. are discussed above and applied herein. Bar-Even et al. is found to anticipate claim 1.
The disclosed microorganism is similar to the following claim:
Regarding claim 5: the phototrophic organism is further limited to “Picochlorum renovo sp.”, which is not taught by Bar-Even et al..
Nonetheless, Dahlin et al. teaches screening, down-selecting, and developing a halophilic and thermotolerant P. renovo that exhibits rapid growth rate and high diel biomass productivity (Abstract). Through genetic engineering, this microalga is able to express multiple transgenes inserted into the nuclear or chloroplast genomes (Abstract,; third par. in left col., page 2). A person with ordinary skill in the art before the effective filing date of the claimed invention would have thus been motivated by Dahlin et al.’s teachings to use the disclosed P. renovo as the isolated microorganism in Bar-Even et al. and expect that incorporating genes for enzymes like formate dehydrogenase would allow growth in a medium with formate as the sole carbon source. Obviousness is based on some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention. See MPEP § 2143 and KSR International Co. v. Teleflex Inc., 550 U.S. 398, 82 USPQ2d 1385, 1395-97 (2007).
Hence, claim 5 is obvious over Bar-Even et al. in view of Dahlin et al..
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MICHELLE F. PAGUIO FRISING whose telephone number is (571)272-6224. The examiner can normally be reached Monday-Friday, 8:00 a.m. - 4:00 p.m..
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Melenie L. Gordon can be reached at (571) 272-8037. The fax phone number for the organization where this application is assigned is 571-273-8300.
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/Michelle F. Paguio Frising/Primary Examiner, Art Unit 1651