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 .
Claims Status
Claims 1-20 are pending.
Claims 1, 5, and 17 have been amended.
Election/Restrictions
Applicant's election with traverse of Group II, claims 19-20, in the reply filed on 01/02/2026 is acknowledged. The traversal is on the ground(s) that the claims of Group I contain all the claim elements of claim 19 of Group II and that there is no substantial additional burden to search for prior art for Group I over Group II. This is not found persuasive as the inventions are independent or distinct from each other because Invention Group II and Invention Group I are related as product and process of use and search for prior art would require searching different classification areas and sequence databases.
The Applicant did not select a single species from each group of Species Group I, II, or III as requested by the Examiner.
The requirement is still deemed proper and is therefore made FINAL.
Claims 1-18 (Group I) are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 01/02/2026.
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.
Claims 19-20 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.
With regards to claim 19 (and claim 20 dependent from), the claim recites “one or more of the following conserved amino acid residues: N at amino acid position 160, SEQ ID NO:2 at amino acid residue positions 160-165, QH at amino acid residue positions 181- 182, H at amino acid position 182, E at amino acid position 224, and/or E at amino acid position 273” without clearly providing a reference sequence to which these positions are relative to. Therefore, the claim is indefinite.
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.
Claims 19-20 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 19 (and claim 20 dependent from) is directed to all possible “host cells capable of producing a 4-vinylphenol (4VP) and/or 4-vinylguaiacol (4VG) comprising polypeptides having a phenolic acid decarboxylase (PAD) enzymatic activity wherein the polypeptide is capable of converting p-coumaric (CA) and/or ferulic acid (FA) into 4-vinylphenol (4VP) and/or 4-vinylguaiacol (4VG) comprising: (i) an amino acid sequence having at least about 70% amino acid sequence identity with SEQ ID NO:1; and, (ii) one or more of the following conserved amino acid residues: N at amino acid position 160, SEQ ID NO:2 at amino acid residue positions 160-165, QH at amino acid residue positions 181-182, H at amino acid position 182, E at amino acid position 224, and/or E at amino acid position 273”. The specification, however, only provides the representative species of the “host cell capable of producing a 4-vinylphenol (4VP) and/or 4-vinylguaiacol (4VG) comprising a polypeptide having a phenolic acid decarboxylase (PAD) enzymatic activity wherein the polypeptide is capable of converting p-coumaric (CA) and/or ferulic acid (FA) into 4-vinylphenol (4VP) and/or 4-vinylguaiacol (4VG)”, having the amino acid sequence of SEQ ID NO:1 encompassed by these claims. There is no disclosure of any particular structure to function/activity relationship in the disclosed species. The molecular mechanism of phenolic acid decarboxylases (PADs) is not fully understood (see Sheng et al., FEBS Journal, Vol. 24, pg. 4703-13, 2015). The specification also fails to describe additional representative species of polypeptides with PAD activity by any identifying structural characteristics or properties, for which no predictability of structure is apparent.
Regarding the level of skill and knowledge of the art of amino acid mutation, the reference of Singh et al. (Curr. Protein Pept. Sci. 18:1-11, 2017, cited on the attached Form PTO-892) reviews various protein engineering methods and discloses that despite the availability of an ever-growing database of protein structures and highly sophisticated computational algorithms, protein engineering is still limited by the incomplete understanding of protein functions, folding, flexibility, and conformational changes (see column 1, top, pg. 7). Also, the unpredictability associated with amino acid mutations is exemplified by the reference of Zhang et al. (Structure 26:1474-1485, 2018, cited on the attached Form PTO-892) which discloses that even a mutation of a surface residue that was predicted to be benign caused significant structural changes and unexpected effects on the function of a polypeptide (column 1, pg. 1475).
Given this lack of additional representative species as encompassed by the claims, Applicants have failed to sufficiently describe the claimed invention, in such full, clear, concise, and exact terms that a skilled artisan would recognize Applicants were in possession of the claimed invention.
Applicant is referred to the revised guidelines concerning compliance with the written description requirement of U.S.C. 112, first paragraph, published in the Official Gazette and also available at www.uspto.gov.
Claims 19-20 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for “a host cell capable of producing a 4-vinylphenol (4VP) and/or 4-vinylguaiacol (4VG) comprising a polypeptide having a phenolic acid decarboxylase (PAD) enzymatic activity wherein the polypeptide is capable of converting p-coumaric (CA) and/or ferulic acid (FA) into 4-vinylphenol (4VP) and/or 4-vinylguaiacol (4VG) and having the amino acid sequence of SEQ ID NO: 1, does not reasonably provide enablement for all possible “host cells capable of producing a 4-vinylphenol (4VP) and/or 4-vinylguaiacol (4VG) comprising polypeptides having a phenolic acid decarboxylase (PAD) enzymatic activity and having an amino acid sequence of at least 70% amino acid sequence identity of SEQ ID NO: 1 and one or more of the following conserved amino acid residues: N at amino acid position 160, SEQ ID NO:2 at amino acid residue positions 160-165, QH at amino acid residue positions 181-182, H at amino acid position 182, E at amino acid position 224, and/or E at amino acid position 273”. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
Factors to be considered in determining whether undue experimentation is required, are summarized in In re Wands (858 F.2d 731, 8 USPQ 2nd 1400 (Fed. Cir. 1988)) as follows: (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claim(s).
Claims 19-20 are so broad as to encompass all possible “host cells capable of producing a 4-vinylphenol (4VP) and/or 4-vinylguaiacol (4VG) comprising polypeptides having a phenolic acid decarboxylase (PAD) enzymatic activity and having at least 70% sequence identity of SEQ ID NO: 1 and one or more of the following conserved amino acid residues: N at amino acid position 160, SEQ ID NO:2 at amino acid residue positions 160-165, QH at amino acid residue positions 181-182, H at amino acid position 182, E at amino acid position 224, and/or E at amino acid position 273”. The scope of the claims is not commensurate with the enablement provided by the disclosure with regard to the extremely large number of “host cells capable of producing a 4-vinylphenol (4VP) and/or 4-vinylguaiacol (4VG) comprising the required recombinant enzymes of the phenolic acid decarboxylase (PAD) group and variants broadly encompassed by the claims. The claims rejected under this section of U.S.C. 112, first paragraph, place minimal structural limits on the required variant polypeptides having phenolic acid decarboxylase (PAD) enzymatic activity encompassed by the claims. Since the amino acid sequence of a protein determines its structural and functional properties, predictability of which changes can be tolerated in a protein's amino acid sequence and obtain the desired activity requires a knowledge of and guidance with regard to which amino acids in the protein's sequence, if any, are tolerant of modification and which are conserved (i.e. expectedly intolerant to modification), and detailed knowledge of the ways in which the proteins' structure relates to its function. However, in this case the disclosure is limited to that “host cell capable of producing a 4-vinylphenol (4VP) and/or 4-vinylguaiacol (4VG) comprising a polypeptide having a phenolic acid decarboxylase (PAD) enzymatic activity having the amino acid sequence of SEQ ID NO: 1.
While recombinant and mutagenesis techniques are known, it is not routine in the art to screen for multiple substitutions or multiple modifications, as encompassed by the instant claims, and the positions within a protein's sequence where amino acid modifications can be made with a reasonable expectation of success in obtaining the desired activity/utility are limited in any protein and the result of such modifications is unpredictable. In addition, one skilled in the art would expect any tolerance to modification for a given protein to diminish with each further and additional modification, e.g. multiple substitutions.
The specification does not support the broad scope of the claims which encompass any possible “host cells capable of producing a 4-vinylphenol (4VP) and/or 4-vinylguaiacol (4VG) comprising polypeptide having a phenolic acid decarboxylase (PAD) enzymatic activity having at least 70% amino acid sequence identity of SEQ ID NO: 1 and one or more of the following conserved amino acid residues: N at amino acid position 160, SEQ ID NO:2 at amino acid residue positions 160-165, QH at amino acid residue positions 181-182, H at amino acid position 182, E at amino acid position 224, and/or E at amino acid position 273” because the specification does not establish: (A) regions of the polypeptide which may be modified effecting the phenolic acid decarboxylase (PAD) activity; (B) the general tolerance of enzymes of the phenolic acid decarboxylase (PAD) group to modification and extent of such tolerance; (C) a rational and predictable scheme for modifying any amino acid residue of an enzyme of the phenolic acid decarboxylase (PAD) group with an expectation of obtaining the desired biological function; and (D) the specification provides insufficient guidance as to which of the essentially infinite possible choices is likely to be successful. Because of this lack of guidance, the extended experimentation that would be required to determine which substitutions would be acceptable to retain the required phenolic acid decarboxylase (PAD) activities and the fact that the relationship between the sequence of a peptide and its tertiary structure (i.e. its activity) are not well understood and are not predictable (e.g., see Sheng et al, FEBS J., Vol. 24, pg. 4703-13, 2015, Ngo et al. in The Protein Folding Problem and Tertiary Structure Prediction, 1994, Merz et al. (ed.), Birkhauser, Boston, MA, pp. 433 and 492-495; Franceus et al., J. Ind. Microbiol. Biotechnol. Vol 44, pp 687-695, 2017), it would require undue experimentation for one skilled in the art to arrive at the majority of polypeptides having phenolic acid decarboxylase (PAD) enzymatic activity of the claimed genus.
Thus, applicants have not provided sufficient guidance to enable one of ordinary skill in the art to make and use the claimed invention in a manner reasonably correlated with the scope of the claims broadly including any “host cells capable of producing a 4-vinylphenol (4VP) and/or 4-vinylguaiacol (4VG) comprising a polypeptide having a phenolic acid decarboxylase enzymatic activity having at least 70% amino acid sequence identity of SEQ ID NO: 1 and one or more of the following conserved amino acid residues: N at amino acid position 160, SEQ ID NO:2 at amino acid residue positions 160-165, QH at amino acid residue positions 181-182, H at amino acid position 182, E at amino acid position 224, and/or E at amino acid position 273”. The scope of the claims must bear a reasonable correlation with the scope of enablement (In re Fisher, 166 USPQ 19 24 (CCPA 1970)). Without sufficient guidance, determination of “host cells capable of producing a 4-vinylphenol (4VP) and/or 4-vinylguaiacol (4VG) comprising polypeptides having phenolic acid decarboxylase (PAD) enzymatic activity and having the desired biological characteristics” is unpredictable and the experimentation left to those skilled in the art is unnecessarily, and improperly, extensive and undue. See In re Wands 858 F.2d 731, 8 USPQ2nd 1400 (Fed. Cir, 1988).
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.
Claim 19 is rejected under 35 U.S.C. 103 as being unpatentable over Salgado et al. (Bioresource Technology, Vol. 117, pg. 274-285; August 2012; Epub: April 21, 2012), hereinafter referred to as Salgado et al., in view of NCBI Reference Sequence: (WP_125122041.1, first accession date: December 11, 2018), hereinafter referred to as S1, as evidenced by Parada-Fabián et al. (Journal of Plant Biochemistry and Biotechnology, Vol. 28, pg. 91-104; published August 09, 2018), hereinafter referred to as Parada-Fabián et al., and further in view of Xu et al. (PLoS One, Vol. 12:e0179240; published June 16, 2017), hereinafter referred to as Xu et al..
Salgado et al. teaches a recombinant Escherichia coli (E.coli) cells (genetically modified host cell) that overproduce a phenolic acid decarboxylase (PAD) from Lactobacillus plantarum CECT 48 that decarboxylates some cinnamic acids, namely p-coumaric acid (p-CA), caffeic acid, and ferulic acid (FA), into their corresponding 4-vinyl derivatives: 4-vinyl phenol (4-VP), 4-vinyl catechol, and 4-vinyl guaiacol (4-VG), respectively (see abstract, pg. 274). Salgado et al. also teaches that sterilized liquors obtained after alkaline hydrolysis of corn cob or alkaline hydrolysis of the solid residue coming from acid hydrolysis of corn cob (carbon source, pretreated lignocellulosic hydrolysate) were employed as growth media in fermentations performed in a shaker (see abstract, pg. 274).
Salgado et al. do not teach that the PAD polypeptide from Lactobacillus plantarum CECT 48 has at least 70% amino acid sequence identity with SEQ ID NO:1 of the current instant application nor that the PAD has one or more of the following conserved amino acid residues: N at amino acid position 160, SEQ ID NO:2 at amino acid residue positions 160-165, QH at amino acid residue positions 181-182, H at amino acid position 182, E at amino acid position 224, and/or E at amino acid position 273.
However, S1 teaches a phenolic acid decarboxylase BsdC from Bacillus amyloliquefaciens polypeptide that shares 100% amino acid sequence identity with the SEQ ID NO: 1 (organism: Bacillus amyloliquefaciens) polypeptide of the current instant application and that contains one or more of the following conserved amino acid residues: N at amino acid position 160, SEQ ID NO:2 at amino acid residue positions 160-165, QH at amino acid residue positions 181-182, H at amino acid position 182, E at amino acid position 224, and E at amino acid position 273. The ability of the phenolic acid decarboxylase, as taught by S1 to decarboxylate phenolic acids such as p-coumaric and ferulic acids, is evidenced by Parada-Fabián et al. who teach that some bacteria have developed a detoxification system which consists of the synthesis of enzymes that decarboxylate phenolic acids such as p-coumaric and ferulic acids and that produce less toxic compounds named vinyl-derivatives (see Introduction, pg. 91). Parada-Fabián et al. further teach that the reaction is mediated by a group of enzymes named phenolic acid decarboxylases (PAD) and that there are more than 100 bacterial genera where these enzymes are present and have been sequenced (see Introduction, pg. 91-92).
Salgado et al. do not teach that the host cell is deleted or knocked out for expression of endogenous pta, poxB, and/or ackA genes. However, Xu et al. teach that acetate accumulation during E. coli fermentation is a major problem because of its inhibition of cell growth and that the conversion of acetyl-CoA through phosphotransacetylase (pta) and acetate kinase (ackA) is the major pathway for acetate synthesis in E. coli and the second pathway is the conversion of pyruvate directly into acetate via pyruvate oxidase B (poxB). The application of metabolic engineering to reduce carbon flow to the acetate biosynthesis pathway are direct strategies to attenuate acetate accumulation (see middle paragraph, pg. 2). Xu et al. teach that the elimination of pta, ackA, and poxB activities has been found to result in a significant reduction in acetate accumulation (see middle paragraph, pg.2). Xu et al. further teach the construction of mutant E. coli strains with single and multigene knockout mutants targeting pta, ackA, and poxB (see materials and methods, pg.4).
It would therefore have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to modify the E. coli host cell taught Salgado et al. by substituting the phenolic acid decarboxylase taught by S1 for the phenolic acid decarboxylase (PAD) from Lactobacillus plantarum CECT 48 taught by Salgado et al. to produce a 4-vinylphenol and/or 4-vinylguaiacol via the enzymatic conversion of p-coumaric acid and/or ferulic acid, respectively.
One of ordinary skill in the art would also be further motivated by the teachings of Xu et al. to modify the above E. coli host cell made obvious by Salgado et al. and S1, as evidenced by Parada-Fabián et al., by deleting the pta, poxB, and/or ackA genes as taught by Xu et al. as a metabolic engineering strategy to reduce acetate accumulation during fermentation in order to reduce the harmful effects of acetate accumulation on cell growth.
The expectation of success would be high based on the high level of skill in the art in the area of recombinant protein engineering as exemplified by Salgado et al., S1, Parada-Fabián et al. and Xu et al. who teach all the methods and components that are necessary to produce the genetically modified host cell.
Thus, claim 19 is rejected under 35 U.S.C. 103 as being unpatentable over Salgado et al. (Bioresource Technology, Vol. 117, pg. 274-285; August 2012; Epub: April 21, 2012) in view of NCBI Reference Sequence: (WP_125122041.1, first accession date: December 11, 2018) as evidenced by Parada-Fabián et al. (Journal of Plant Biochemistry and Biotechnology, Vol. 28, pg. 91-104; published August 09, 2018) and further in view of Xu et al. (PLoS One, Vol. 12:e0179240; published June 16, 2017).
Claim 20 is rejected under 35 U.S.C. 103 as being unpatentable over Salgado et al. (Bioresource Technology, Vol. 117, pg. 274-285; published August 2012; Epub: April 21, 2012), hereinafter referred to as Salgado et al., in view of NCBI Reference Sequence: (WP_125122041.1, first accession date: December 11, 2018,) hereinafter referred to as S1, as evidenced by Parada-Fabián et al. (Journal of Plant Biochemistry and Biotechnology, Vol. 28, pg. 91-104; published August 09, 2018), hereinafter referred to as Parada-Fabián et al., and further in view of Xu et al. (PLoS One, Vol. 12:e0179240; published June 16, 2017) as applied to claim 19 above, and further in view of Lin et al. (Applied Genetics and Molecular Biotechnology, Vol. 71, pg. 870-874; published online February 22, 2006), hereinafter referred to as Lin et al.
With regards to claim 20, the genetically modified host cell made obvious over the above references here is discussed above. Salgado et al. teach recombinant Escherichia coli (E.coli) cells (genetically modified host cell) that overproduce a phenolic acid decarboxylase (PAD) from Lactobacillus plantarum CECT 48 that decarboxylates some cinnamic acids namely p-coumaric acid (p-CA), caffeic acid, and ferulic acid (FA) into their corresponding 4-vinyl derivatives: 4-vinyl phenol (4-VP), 4-vinyl catechol, and 4-vinyl guaiacol (4-VG), respectively but does not teach that the host cell is modified to have an increased expression of an acetyl-CoA synthetase (ACS). S1, Parada-Fabián et al., and Xu et al. also do not specifically teach a host cell that is modified to have an increased expression of an acetyl-coA synthetase (ACS).
Lin et al. teach that Escherichia coli is known to produce significant amounts of acetate in high cell density cultures and that high acetate accumulation is harmful to cell growth (see Introduction, paragraph 1, pg. 870). Lin et al. further teach that enhancing the capability of E. coli to assimilate acetate would reduce harmful effects of acetate, recycle wasted carbon, and increase carbon flux toward desired pathways and that this would provide a potentially useful tool in metabolic engineering. Lin et al. teach the overexpression of acetyl-Coenzyme A (CoA) synthetase (ACS) in E. coli to enhance the assimilation of acetate and the activation to acetyl-CoA (see Introduction, paragraph 2, pg.870). Lin et al. teach the use of an expression vector to overexpress acetyl-CoA synthetase in E. coli MG1655 (genetically modified host cell) (see materials and methods section, strains and plasmids, pg. 871).
It would therefore have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to incorporate an expression vector to overexpress acetyl-CoA synthetase (ACS) as taught by Lin et al. in the E. coli host cell made obvious by Salgado et al. and S1 (as evidenced by Parada-Fabián et al.) and Xu et al. in order to increase the expression of acetyl-CoA synthetase (ACS). One of ordinary skill in the art would be motivated to do so as a means to provide a potentially useful metabolic engineering tool to enhance the expression of acetyl-CoA synthetase in order to assimilate acetate and reduce harmful effects of acetate, recycle wasted carbon, and increase carbon flux toward desired pathways. The expectation would be high based upon the high level of skill in the art in the area of recombinant protein engineering as exemplified by Salgado et al, S1, Parada-Fabián et al, Xu et al. and Lin et al. who teach all the methods and components that are necessary to produce the genetically modified host cell.
Thus, claim 20 is rejected under 35 U.S.C. 103 as being unpatentable over Salgado et al. (Bioresource Technology, Vol. 117, pg. 274-285; published August 2012; Epub: April 21, 2012) in view of NCBI Reference Sequence: (WP_125122041.1, first accession date: December 11, 2018) as evidenced by Parada-Fabián et al. (Journal of Plant Biochemistry and Biotechnology, Vol. 28, pg. 91-104; published August 09, 2018) and further in view of Xu et al. (PLoS One, Vol. 12:e0179240; published June 16, 2017) as applied to claim 19 above, and further in view of Lin et al. (Applied Genetics and Molecular Biotechnology, Vol. 71, pg. 870-874; published online February 22, 2006).
Conclusion
No claims are allowed.
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/GEORGE THEMISTOCLIS LOUNTOS/ Examiner, Art Unit 1652
/RICHARD G HUTSON/ Primary Examiner, Art Unit 1652