DETAILED ACTION
Claims 1-23 are pending.
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’s election without traverse of Group I, claims 1-18 in the reply filed on 06/26/2026 is acknowledged. Claims 19-23 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention there being no allowable generic or linking claim.
Information Disclosure Statement
The information disclosure statements (IDS) filed on 02/23/2024 and 03/22/2024 are acknowledged and have been considered.
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter “Legal Framework”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation by reference statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - The incorporation by reference paragraph required by 37 CFR 1.834(c)(1), 1.835(a)(2), or 1.835(b)(2) should recite the size of the file in bytes (19121 bytes).
Required response - Applicant must:
• Provide a substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required incorporation by reference paragraph, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
Specification
The disclosure is objected to because of the following informalities: “Figure” on pages 7-14, 16, 22, 29-31, 34, 42-48, and 51-55 should be replaced with “FIG.” to be consistent with the terminology in the drawings.
Appropriate correction is required.
Claim Objections
Claims 5 and 18 are objected to because of the following informalities:
In claim 5, line 2, “bacterium” should not be italicized.
In claim 18, Applicant may consider replacing “nh-pSer” with “nhpSer” in order to be consistent with the terminology of claim 1.
Appropriate correction is required.
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 1-18 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.
Claim 1 recites in line 3 “a genetically modified host cell comprising” and recites in line 16 “the genetically modified host cell comprises”. The claim is indefinite because it is not clear if the host cell requires all the recited nucleic acids. Applicant may consider amending the claim to recite in line 16 “wherein the genetically modified host cell further comprises” in order to obviate the rejection.
Claim 1 recites in lines 3-4 “genetically modified host cell comprising at least one expression vector that can express the protein of interest” and also recites in line 21 “the genetically modified host cell comprises…at least one heterologous nucleic acid encoding the protein of interest”. The claim is indefinite because it is not clear if the expression vector that can express the protein of interest and the at least one heterologous nucleic acid encoding the protein of interest are the same or two separate constructs.
Claim 1 recites in lines 24-26 “culturing the genetically modified host cell under conditions such that the nucleic acids encoding the enzymes of the pathway are translated and the non-hydrolyzable-phosphoserine is inserted into the protein of interest and the nucleic acid encoding the protein of interest is translated”. The claim is indefinite because the order of the steps is incorrect. The step of inserting the non-hydrolyzable-phosphoserine happens during the translation of the nucleic acid encoding the protein of interest. Applicant may consider amending the claim to recite “the nucleic acids encoding the enzymes of the pathway and the protein of interest are translated and the non-hydrolyzable-phosphoserine is inserted into the protein of interest”.
Claim 6 recites “wherein at least two of phosphoenolpyruvate mutase (EC 5.4.2.9), 2-phosphonomethylmalate synthase (EC 2.3.3.19), aconitate hydratase (EC 4.2.1.3), isocitrate dehydrogenase NAD+ (EC 1.1.1.41), isocitrate dehydrogenase NADP+ (EC 1.1.1.42), an isozyme of isocitrate dehydrogenase NAD+ (EC 1.1.1.41), an isozyme of isocitrate dehydrogenase NADP+ (EC 1.1.1.42), and a transaminase are operatively associated to comprise the biosynthetic pathway”. The claim is indefinite because it is not clear if the claim requires two enzymes from each species to be operatively associated, for example, 2 phosphoenolpyruvate mutases, or if it requires that two enzymes from the list of different species to be operatively associated, for example, a phosphoenolpyruvate mutase and a 2-phosphonomethylmalate synthase.
Claims 2-5 and 7-18 which depend from claims 1 and 6 do not cure the indefiniteness and are also rejected.
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.
Claims 6 and 11 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.
Claim 6 recites “a transaminase”, “an isozyme of isocitrate dehydrogenase NAD+”, and “an isozyme of isocitrate dehydrogenase NADP+” in lines 4-5. Claim 6 depends from 5, which depends from claim 1. Claim 6 is not a proper dependent claim because it fails to include all the limitations of the base claim from which it ultimately depends. Claim 1 does not recite a transaminase or any isozymes.
Claim 11 recites “the biosynthetic pathway requires the isocitrate dehydrogenase NAD+ (EC 1.1.1.41) and the isocitrate dehydrogenase NADP+ (EC1.1.1.42)”. Claim 11 depends from 6, which depends from claim 5, which depends from claim 1. Claim 11 does not further limit the subject matter of the base claim from which it ultimately depends because claim 1 already requires the host cell to comprise a nucleic acid encoding an isocitrate dehydrogenase NAD+ (EC 1.1.1.41) and isocitrate dehydrogenase NADP+ (EC 1.1.1.42).
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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.
Claims 1-2, 5-9, 11-14, and 17-18 are rejected under 35 U.S.C. 103 as being unpatentable over Eliot (Chemistry & biology 15.8 (2008): 765-770, of record in IDS) in view of Rogerson (Nature chemical biology 11.7 (2015): 496-503, of record in IDS), and as evidenced by DQ267750.1 (GenBank: DQ267750.1 Streptomyces rubellomurinus FR900098 biosynthetic gene cluster, complete sequence; and dxrB (dxrB) gene, complete cds, 2008, of record in IDS) and Appendix A (sequence alignment, 2026).
Regarding claim 1, Eliot teaches a pathway to produce 2-amino-4-phosphonobutyrate (Figure 3B compound VI) and E. coli and S. lividans 4G7 host cells transformed with a vector comprising nucleic acid encoding the enzymes FrbD, FrbC, FrbA, and FrbB and/or FrbE (page 768 “Cloning of the FR900098 Gene Cluster from S. rubellomurinus”, Figure 3 A). Eliot teaches culturing S. lividans 4G7 comprising the nucleic acids encoding the enzymes of the pathway (page 768 para. “Heterologous Expression of the FR900098 Gene Cluster in S. lividans”)
2-amino-4-phosphonobutyrate is a non-hydrolyzable phosphoserine (see instant specification page 14 last para., Fig. 2A). FrbD is phosphoenolpyruvate mutase (EC 5.4.2.9), FrbC is 2-phosphonomethylmalate synthase (EC 2.3.3.19), FrbA is aconitate hydratase (EC 4.2.1.3), and FrbB is isocitrate dehydrogenase (NAD+) and isocitrate dehydrogenase (NADP+) (EC 1.1.1.41 and EC 1.1.1.42) (see instant specification page 21).
Eliot does not teach the cell to produce non-functional releasing factor 1 (RF1), at least one heterologous nucleic acid that encodes an aminoacyl tRNA synthetase (aaRS), at least one heterologous nucleic acid that encodes a tRNA which decodes the UAG amber codon, or at least one heterologous nucleic acid encoding the protein of interest wherein the amber codon is inserted at a selected position where the non-hydrolyzable phosphoserine is to be inserted.
However, Rogerson teaches a method for site-specifically installing a non-hydrolysable analog of phosphoserine into recombinant proteins (page 2 first para.). Rogerson teaches culturing an engineered E. coli capable of site-specific incorporation of a non-hydrolysable analog of phosphoserine into a protein (Abstract). Rogerson teaches that the cell has an RF1 deletion (page 7 last para.) and an aminoacyl-tRNA synthetase/tRNACUA pair (Abstract). Rogerson teaches that the cell also comprises myo(127TAG)-His6 (i.e., nucleic acid encoding the protein of interest wherein the amber codon is inserted at a selected position) and gene for SepRS(2)/tRNA(B4)CUA pair, and teaches adding the non-hydrolyzable amino acid 2-amino-4-phosphonobutyric acid (i.e., nhpSer) which is an efficient substrate for the SepRS(2)/tRNA(B4)CUA pair (i.e., an aminoacyl tRNA synthetase can charge a tRNA with the nhpSer and tRNA can decode the UAG amber codon) (page 9 para. 4 and page 10 second para., Figure 6). Rogerson teaches that myo(127TAG)-His6 is translated and incorporated 2-amino-4-phosphonobutyric acid at a specific position (Figure 6C and 6f).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to further modify Eliot’s E. coli to delete RF1 protein and express SepRS(2)/tRNA(B4)CUA pair and myo(127TAG)-His6, as suggested by Rogerson. One of ordinary skill in the art would be motivated to do so in order to do a one-pot reaction for the synthesis of a protein comprising 2-amino-4-phosphonobutyrate and simplify the process. Since Eliot teaches a method to produce 2-amino-4-phosphonobutyrate in vivo and since Rogerson teaches 2-amino-4-phosphonobutyrate is a substrate used to express protein comprising 2-amino-4-phosphonobutyrate in vivo, there is a reasonable expectation of success.
Regarding claim 2, Eliot teaches that the sequences of the genes have been deposited in GenBank with accession number DQ267750. An alignment with the DQ267750 translated FrbE sequence shows 100% identity to the instant SEQ ID NO: 5 (See Appendix A page 1 for alignment).
Regarding claim 5, Eliot teaches that the genes involved in the pathway are derived from Streptomyces rubellomurinus (Title).
Regarding claim 6, Eliot teaches that the enzymes FrbD (i.e., phosphoenolpyruvate mutase (EC 5.4.2.9)), FrbC (i.e., 2-phosphonomethylmalate synthase (EC 2.3.3.19)), FrbA (i.e, aconitate hydratase (EC 4.2.1.3)), and FrbB (i.e., isocitrate dehydrogenase NAD+ (EC 1.1.1.41) and isocitrate dehydrogenase NADP+ (EC 1.1.1.42)) and FrbE (i.e., isozyme of isocitrate dehydrogenase NAD+ (EC 1.1.1.41) and isozyme isocitrate dehydrogenase NADP+ (EC 1.1.1.42)) are operatively associated to comprise the biosynthetic pathway (Figure 3).
Regarding claim 7, an alignment with DQ267750 shows that the translated polypeptide sequence of FrbD is 100% identical to the instant SEQ ID NO: 1 (See Appendix A page 2 for alignment), and the polypeptide sequence of FrbC is 100% identical to SEQ ID NO: 2 (See Appendix A page 3 for alignment). Eliot teaches that FrbD and FrbC convert phosphoenolpyruvate (compound I) to 2-phosphonomethylmalate (compound III) (Figure 3).
Regarding claim 8, an alignment with DQ267750 shows that the translated polypeptide sequence of FrbA is 100% identical to the instant SEQ ID NO: 3 (See Appendix A pages 4-5 for alignment). Eliot teaches that FrbA converts 2-phosphonomethylmalate (compound III) to 3-phosphonomethylmalate (compound IV) (Figure 3).
Regarding claim 9, an alignment with DQ267750 shows that the translated polypeptide sequence of FrbB is 100% identical to the instant SEQ ID NO: 4 (See Appendix A page 6 for alignment). Eliot teaches that FrbB converts 3-phosphonomethylmalate (compound IV) to 2-oxo-4-phosphonobutyrate (compound V) (Figure 3).
Regarding claims 11-12, Eliot teaches that the pathway comprises FrbB (i.e., isocitrate dehydrogenase NAD+ (EC 1.1.1.41) and isocitrate dehydrogenase NADP+ (EC 1.1.1.42)) and FrbE (i.e., isozyme of isocitrate dehydrogenase NAD+ (EC 1.1.1.41) and isozyme isocitrate dehydrogenase NADP+ (EC 1.1.1.42)) (Figure 3).
Regarding claims 13-14, Eliot teaches that the genes are inserted into recombinant plasmids with promoter and inserted into E. coli and S. lividans 4G7 (i.e., prokaryotic cell) (page 768 para. “Cloning of the FR900098 Gene Cluster from S. rubellomurinus” and “Heterologous Expression of the FR900098 Gene Cluster in S. lividans”).
Regarding claim 17, Rogerson teaches that the tRNA is an orthogonal tRNACUA (i.e., recognizes the UAG amber codon) (Abstract).
Regarding claim 18, Rogerson teaches that the tRNA synthetase is an orthogonal aminoacyl-tRNA synthetase (Abstract), and that the non-hydrolyzable amino acid 2-amino-4-phosphonobutyric acid (i.e., nhpSer) is an efficient substrate for the SepRS(2)/tRNA(B4)CUA pair and the cell produces myo(127TAG)-His6 containing at least one 2-amino-4-phosphonobutyric acid (i.e., nhpSer) (page 9 para. 4 and page 10 second para., Figure 6).
Claims 3 and 10 are rejected under 35 U.S.C. 103 as being unpatentable over Eliot and Rogerson as applied to claims 1 and 6 above, and further in view of DeSieno (Microbial synthesis of antimalarial compound FR-900098: pathway characterization and engineering. Diss. University of Illinois at Urbana-Champaign, 2012).
Regarding claims 3 and 10, Eliot and Rogerson do not teach that the recombinant biosynthetic pathway further comprises at least one heterologous nucleic acid encoding a transaminase.
However, DeSieno teaches the reaction of transforming 2-oxo-4-phosphonobutryate (i.e., compound V in Eliot’s Figure 3) to 2-amino-4 phosphonobutyrate (i.e., compound VI in Eliot’s Figure 3) is catalyzed by an aminoethylphosphonate (AEP) transaminase (page 34 para. “2.2.5 Transaminase Reaction”, Figure 2.9). The limitation “wherein the addition of the transaminase to the recombinant biosynthetic pathway improves the efficiency of nhpSer biosynthesis” recites the result of the recited step and does not require additional steps. Thus, this limitation does not limit the claim. See MPEP 2111.04.
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to further modify Eliot’s E coli cell by additional transformation with a nucleic acid encoding an aminoethylphosphonate (AEP) transaminase as suggested by DeSieno. One of ordinary skill in the art would be motivated to do so in order to catalyze the transformation of 2-oxo-4-phosphonobutryate into 2-amino-4 phosphonobutyrate. Since Eliot and DeSieno both teach a desire to form 2-amino-4 phosphonobutyrate, there is a reasonable expectation of success.
Claim 4 is rejected under 35 U.S.C. 103 as being unpatentable over Eliot, Rogerson, and DeSieno as applied to claim 3 above, and further in view of P96060 (Uniprot P96060, 2-aminoethylphosphonate--pyruvate transaminase, May 2022) as evidenced by Appendix A.
Regarding claim 4, Eliot, Rogerson, and DeSieno do not teach aminoethylphosphonate transaminase with SEQ ID NO: 8.
However, P96060 teaches AEP transaminase EC 2.6.1.37 from Salmonella typhimurium with an amino acid sequence 100% identical to instant SEQ ID NO: 8. (page 1 RecName, Alt Name) (See Appendix A page 7 for alignment).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to further modify Eliot’s E coli cell by substituting P96060’s aminoethylphosphonate (AEP) transaminase for DeSieno’s AEP transaminase. One of ordinary skill in the art would be motivated to do so in order to catalyze the transformation of 2-oxo-4-phosphonobutryate into 2-amino-4 phosphonobutyrate. MPEP 2144.06 II states it is obvious to substitute equivalents know for the same purpose. Since DeSieno teaches the reaction requires the action of an AEP transaminase, and since P96060 teaches an isolated and sequenced AEP transaminase, there is a reasonable expectation of success.
Claims 15 and 16 are rejected under 35 U.S.C. 103 as being unpatentable over Eliot and Rogerson as applied to claim 1 above, and further in view of Woodcock (US 2013/0231305, of record in IDS) as evidenced by Appendix A.
Regarding claims 15 and 16, Eliot and Rogerson do not teach the protein of interest is 14-3-3ζ comprises nhpSer at amino acid position 58 (Ser58) in the sequence as set forth in SEQ ID NO: 12.
However, Woodcock teaches a method of modulating protein 14-3-3 or variant by phosphorylating Ser58 residues ([0011], [0014]). Woodcock teaches 14-3-3ζ with SEQ ID NO: 11 which is 100% identical to instant SEQ ID NO: 12 (See Appendix A page 8 for alignment).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to further modify Eliot’s E coli cell by additional transformation with a nucleic acid encoding for 14-3-3ζ with SEQ ID NO: 11 comprising an UAG amber codon at position Ser58, as suggested by Woodcock. One of ordinary skill in the art would be motivated to do so in order to phosphorylate 14-3-3ζ at position Ser58. Since Eliot and Rogerson teach a method of phosphorylating a specific residue in vivo and since Woodcock teaches a desire to phosphorylate 14-3-3ζ at position Ser58, there is a reasonable expectation of success.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARY A CRUM whose telephone number is (571)272-1661. The examiner can normally be reached M-F 8:00-5:00 CT with alternate Fridays off.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, LOUISE W 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.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/MARY A CRUM/Examiner, Art Unit 1657
Prosecution Insights