DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant's election without traverse of SEQ ID NOs: 3, 11, 14 in the reply filed on 11/05/2025 is acknowledged. The requirement is still deemed proper and is therefore made FINAL.
Claims 1-10 and SEQ ID NOs: 3, 11, 14 are under consideration in this Office Action.
Claim Rejections - 35 USC § 112(b) or 35 U.S.C. 112 (pre-AIA ) 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.
Claim 1-10 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 pre-AIA the applicant regards as the invention.
Claim 1 recites the phrase “selecting a synthetic enzyme with high efficiency in de novo biosynthesis of β-elemene” which renders the claim vague and indefinite since the specific identity of the enzyme and its amino acid sequence SEQ ID NO are not known and not recited in the claim.
Claim 1 recites the phrase “further increasing the production of β-elemene through RBS engineering or protein fusion technology” which renders the claim vague and indefinite since the specific steps for performing this is not known and not recited in the claim. Claim 1 recites the phrase “enhancing a precursor accumulation by rewriting a central carbon metabolism pathway” which renders the claim vague and indefinite since the specific steps for performing this is not known and not recited in the claim. Claim 1 recites the phrase “high-throughput screening of a directed evolution enzyme NS to obtain a highly active NS enzyme” which renders the claim vague and indefinite since the specific steps for performing this is not known and not recited in the claim. Claim 1 recites the phrase “increasing the production of β-elemene by adjusting metabolism to recycle accumulated pyruvic acid” which renders the claim vague and indefinite since the specific steps for performing this is not known and not recited in the claim. Claim 1 recites the phrase “adjusting an efflux pump to promote the production of β-elemene” which renders the claim vague and indefinite since the specific steps for performing this is not known and not recited in the claim.
Dependent claims 2-10 are also rejected because they do not correct the defect.
Claim Rejections - 35 USC § 112
The following is a quotation 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 35 U.S.C. 112 (pre-AIA ), first paragraph:
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 1-10 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
The claims are drawn to a broad and widely varying genus of methods for constructing a recombinant bacterium with high production of β-elemene and germacrene A, comprising: selecting a genus of synthetic enzymes with high efficiency in de novo biosynthesis of β-elemene of any amino acid sequence and structure; increasing the production of β-elemene by overexpressing a genus of enzyme ispA of any amino acid sequence and structure; further increasing the production of β-elemene through RBS engineering or protein fusion technology; enhancing a precursor accumulation by rewriting a central carbon metabolism pathway including any genus of proteins and/or enzymes of any amino acid sequence and structure; high-throughput screening of a directed evolution enzyme NS to obtain a genus of highly active NS enzyme of any amino acid sequence and structure; increasing the production of β-elemene by adjusting metabolism to recycle accumulated pyruvic acid by any genetic modifications; adjusting any genus of efflux pumps of any amino acid sequence and structure to promote the production of β-elemene; and constructing the recombinant bacterium with high yield of β-elemene and germacrene A. According to MPEP 2163:
“For each claim drawn to a genus: The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice (see i)(A), above), reduction to drawings (see i)(B), above), or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus (see i)(C), above). See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406.
A "representative number of species" means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus. See AbbVie Deutschland GmbH & Co., KG v. Janssen Biotech, Inc., 759 F.3d 1285, 1300, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014)…”
According to MPEP 2163.02:
“The courts have described the essential question to be addressed in a description requirement issue in a variety of ways. 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). Under Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1563-64, 19 USPQ2d 1111, 1117 (Fed. Cir. 1991), 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. The test for sufficiency of support in a parent application is whether the disclosure of the application relied upon "reasonably conveys to the artisan that the inventor had possession at that time of the later claimed subject matter." Ralston Purina Co. v. Far-Mar-Co., Inc., 772 F.2d 1570, 1575, 227 USPQ 177, 179 (Fed. Cir. 1985) (quoting In re Kaslow, 707 F.2d 1366, 1375, 217 USPQ 1089, 1096 (Fed. Cir. 1983)).”
The specification as originally filed does not disclose a representative number of species encompassed by the claimed genus by actual reduction to practice. The specification as originally filed does not provide a correlation between function and structure to enable one of ordinary skill in the art to predict which amino acid sequences and structures correlate with the recited synthetic enzymes with high efficiency in de novo biosynthesis of β-elemene and enzyme ispA having any enzymatic activity.
Hence, the specification does not provide sufficient written description to inform one of ordinary skill in the art that applicants were in possession at the time the application was filed of the claimed broad and widely varying genus of methods for constructing a recombinant bacterium with high production of β-elemene and germacrene A, comprising: selecting a genus of synthetic enzymes with high efficiency in de novo biosynthesis of β-elemene of any amino acid sequence and structure; increasing the production of β-elemene by overexpressing a genus of enzyme ispA of any amino acid sequence and structure; further increasing the production of β-elemene through RBS engineering or protein fusion technology; enhancing a precursor accumulation by rewriting a central carbon metabolism pathway including any genus of proteins and/or enzymes of any amino acid sequence and structure; high-throughput screening of a directed evolution enzyme NS to obtain a genus of highly active NS enzyme of any amino acid sequence and structure; increasing the production of β-elemene by adjusting metabolism to recycle accumulated pyruvic acid by any genetic modifications; adjusting any genus of efflux pumps of any amino acid sequence and structure to promote the production of β-elemene; and constructing the recombinant bacterium with high yield of β-elemene and germacrene A.
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 of this title, 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 1-10 are rejected under 35 U.S.C. 103 as being unpatentable over US20170121749 (05/04/2017; PTO 892) in view of Accession BBC01095 (24-APR-2014; PTO 892), Accession A0A066R341 (03-SEP-2014; PTO 892), Accession I3VRD9 (05-SEP-2012; PTO 892), CN113249282A (08/13/2021; PTO 892), Bornscheuer et al. (Curr Protoc Protein Sci. 2011 Nov;Chapter 26:Unit26.7; PTO 892), Yoshikuni et al. (Curr Opin Chem Biol. 2007 Apr;11(2):233-9; PTO 892).
US20170121749 teaches a recombinant Deinococcus bacterium comprising genetic modifications that increase 1-deoxyxylulose 5-phosphate synthase (DXS) activity and/or isopentenyl pyrophosphatase isomerase (IPP isomerase) activity, and method of producing a terpene or terpenoid comprising culturing said recombinant Deinococcus bacterium (see entire publication and claims especially claims 23-44). US20170121749 teaches the following in paragraphs [0008]- [0010]:
The present invention thus relates to a recombinant Deinococcus bacterium exhibiting enhanced 2-C-methyl-D-erythritol 4-phosphate/1-deoxy-D-xylulose 5-phosphate (MEP/DXP) pathway, in particular a bacterium wherein at least one enzymatic activity selected from the group consisting of DXP synthase (DXS), DXP reductoisomerase (DXR), IspD, IspE, IspF, IspG, IspH and IPP isomerase activities (IDI), is increased. Preferably, said at least one enzymatic activity is increased by overexpression of at least one gene selected from the group consisting of native, homologous or heterologous dxs, dxr, ispD, ispE, ispF, ispG, ispH and idi genes.
Preferably, the recombinant bacterium of the invention is genetically modified to increase DXS activity and/or IDI activity. In particular, said recombinant bacterium may overexpress a native, homologous or heterologous idi gene and/or overexpress a native, homologous or heterologous dxs gene.
The bacterium of the invention may further exhibit an increased FPP synthase activity. Preferably, this increase is due to the overexpression of a native, homologous or heterologous ispA gene.
US20170121749 teaches in paragraph [0022]:
In a second aspect, the present invention relates to a recombinant Deinococcus bacterium wherein the FPP synthase activity is increased. Preferably, the FPP synthase activity is increased by overexpression of a native, homologous or heterologous ispA gene.
US20170121749 teaches in paragraph [0159]:
In an embodiment, the recombinant bacterium of the invention comprises a gene encoding a heterologous (3S, 6E)-nerolidol synthase, i.e. an enzyme that converts farnesyl diphosphate to nerolidol. Examples of heterologous nerolidol synthases include, but are not limited to, nerolidol synthases from Selaginella moellendorffii (Uniprot accession number D8RNZ9), Populus trichocarpa (F8TWD1), Medicago truncatula (Q5UB06), Fragaria×ananassa (P0CV94) and Zea mays (Degenhardt and Gershenzon, 2000). Any polypeptide exhibiting a nerolidol synthase activity and having at least 70%, 80%, preferably 90%, sequence identity to any of these enzymes may be used, in particular variants of these enzymes having increased catalytic activity, specificity for the substrate, and/or stability. In a particular embodiment, the heterologous nerolidol synthase is selected from Fragaria×ananassa.
The teachings of the reference differ from the claims in that the reference does not teach the claimed method for producing a recombinant bacterium.
Accession BBC01095 teaches the beta-elemene synthesis encoded by SEQ ID NO: 3 of the instant application, a recombinant vector comprising the beta-elemene synthesis enzyme coding DNA, and method of the invention is useful for synthesizing high quality elemene in a cost effective manner (see attached record).
Accession A0A066R341 teaches the glucose-6-phosphate 1-dehydrogenase encoded by SEQ ID NO: 11 of the instant application (see attached record).
Accession I3VRD9 teaches the pyruvate:ferredoxin oxidoreductase encoded by SEQ ID NO: 14 of the instant application (see attached record).
CN113249282A teaches a β-elemene-producing recombinant strain, a construction method and application thereof, and relates to the technical fields of metabolic engineering, synthetic biology and biopharmaceuticals; the recombinant strain expresses gemene A synthase (ScGAS) from Solidago canadensis, and introduces recombinant plasmids containing atoB, idi, ispA of Escherichia coli and ERG13, tHMG1, ERG12, ERG8, MVD1 of Saccharomyces cerevisiae; the fermentation conditions are optimized and the β-elemene yield of the recombinant strain reached 156.94 mg/L. CN113249282A teaches that the recombinant bacteria constructed in the present invention has the characteristics of high yield, high purity, low cost, no pollution, and is suitable for industrial production of β-elemene. See attached English language translation of abstract and claims especially claims 1-5.
Bornscheuer et al. teach protein engineering strategies to improve or change the properties of proteins, teach concepts for protein engineering using rational design including substitution and/or deletion of amino acids, directed evolution, and combinations of them where different strategies are presented for identifying the best mutagenesis method, how to identify desired variants by screening or selection, and examples for successful applications are shown which enable researchers to choose the most promising tools to solve their protein engineering challenges (see entire publication especially pages 26.7.1- 26.7.10 and Tables 26.7.1, 26.7.2, and 26.7.3).
Yoshikuni et al. teach protein engineering methodology to redesign enzyme function which was developed on the basis of the theories of divergent molecular evolution: (i) enzymes with more active and specialized functions have evolved from ones with promiscuous functions; (ii) this process is driven by small numbers of amino acid substitutions (plasticity); and (iii) the effects of double or multiple mutations are often additive (quasi-additive assumption). Yoshikuni et al. teach the impact of multiple mutations can be calculated by first determining the effects of a mutation at a single position and subsequently summing these effects using the quasi-additive assumption where the shape of the fitness landscape of a particular enzyme function can be estimated, and the combinations of mutations predicted to yield global optima for desired functions can then be selected and introduced into the enzymes. Yoshikuni et al. teach that the methodology has been demonstrated to be very powerful to redesign enzyme function. See entire publication and abstract especially pages 234-7 and Fig. 2.
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify and/or combine the reference teachings to make the claimed invention by transforming the recombinant host of US20170121749 or CN113249282A to overexpress the beta-elemene synthesis enzyme of Accession BBC01095,
overexpress the enzyme ispA of US20170121749, overexpress a highly active nerolidol synthase obtained by using the protein engineering methods of Bornscheuer et al. and Yoshikuni et al. on the nerolidol synthase of US20170121749, overexpress the pyruvate:ferredoxin oxidoreductase of Accession I3VRD9 teaches the pyruvate:ferredoxin oxidoreductase, overexpress the genes encoding efflux pump of the recombinant host; an knocking out the gene encoding glucose-6-phosphate 1-dehydrogenase of Accession A0A066R341 to obtain the recombinant bacterium. One of ordinary skill in the art before the effective filing date of the claimed invention would have been motivated to do this in order to obtain a method for constructing a recombinant bacterium that can be sued to product high amounts of beta-elemene and/or germacrene A. It would have been obvious to overexpress and/or knock out any of the recited proteins and/or enzymes in the recited pathways using any of the recited plasmids, engineering RBS to overexpress genes for the production of beta-elemene and/or germacrene A, fusing any of the recited proteins and/or enzymes using linkers for the production of beta-elemene and/or germacrene A as routine optimization and/or as desired in order to obtain the recombinant bacterium that can be used to produce large amounts of beta-elemene and/or germacrene A by fermentation in a shaking flask at the recited concentrations. One of ordinary skill in the art at the time the invention was made would have a reasonable expectation of success because genetically modifying hosts that produce desired products including beta-elemene and/or germacrene A are known in the art as shown by the reference teachings. Hence, the claimed invention as a whole is prima facie obvious.
Conclusion
No claim is allowed.
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/CHRISTIAN L FRONDA/Primary Examiner, Art Unit 1652