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's election with traverse of Group I, claims 1-11 and species “genus of Escherichia” in claim 8 and “Accession NO. DSM 34297 (claim 11) in the reply filed on 08/25/2025 is acknowledged. The traversal is on the ground(s) that: “Group I (claims 1-11) and Group II (claims 12-17) are both directed to a recombinant microorganism with a specific combination of genes, and thus involve a single, searchable, and unifying aspect that links all the pending claims.” and “these two strains are distinct embodiments, they share a single inventive concept: a unique gene combination designed to enhance the efficiency of itaconic acid production.” This is not found persuasive because the restriction/election requirement was made under 35 U.S.C. 121 and was not based on the special technical feature covered by the prior art and the lack of unity of invention. Inventions were shown to be independent and distinct as described in the restriction based on MPEP 806.05(h).
The requirement is still deemed proper and is therefore made FINAL.
Claims 12-17 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 08/25/2025.
The election of species of the recombinant organisms with Accession NO. DSM 34296 (claim 10) and Accession NO. DSM 34297 (claim 11) is withdrawn.
Claims 1-11 (claim set filed 08/25/2025) are examined on the merits herein.
Priority
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d) based on application TAIWAN 111140468 filed 10/25/2022. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
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 4-7 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 4 recites the limitation for the gene encoding cis-aconitic decarboxylase to comprises “a nucleotide sequence having at least 80% identity to SEQ ID NO: 1 and an activity identical to SEQ ID NO:1”. It is not clear what is meant by the “identical activity”, whether the recitation refers to the activity of the gene to encode cis-aconitic decarboxylase or to encode cis-aconitic decarboxylase with identical enzymatic activity which is questionable since 20% of the sequence can be variable. The scope and boundaries of claim 4 are not certain making claim 4 indefinite.
Claims 5-7 have similar issues with the limitations for the genes encoding aconitase (claims 5 and 6) and the gene encoding GroELS (claim 7). The scope and boundaries of claims 5-7 are not certain making claims 5-7 indefinite.
For examination claims are interpreted as directed to nucleotide sequences of the genes encoding the corresponding proteins and wherein sequences encode proteins with corresponding functional activities, for instance, claim 4 is interpreted to be directed to the gene encoding cis-aconitic decarboxylase comprising a nucleotide sequence having at least 80% identity to SEQ ID NO: 1 and encoding functionally active cis-aconitic decarboxylase.
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 4-7 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 the limitation for the gene encoding cis-aconitic decarboxylase to comprises a nucleotide sequence having at least 80% identity to SEQ ID NO: 1 and an activity identical to SEQ ID NO: 1. Claim 4 is interpreted as the recombinant microorganism wherein 20% or less of the sequence encoding cis-aconitic decarboxylase vary from SEQ ID NO: 1 and cis-aconitic decarboxylase is functionally active (see claim interpretation in 112(b) rejection). Claims 5 recites the limitation for the gene encoding aconitase to comprises a nucleotide sequence having at least 80% identity to SEQ ID NO: 2 and an activity identical to SEQ ID NO: 2. Claim 5 is interpreted as the recombinant microorganism wherein 20% or less of the sequence encoding aconitase vary from SEQ ID NO: 2 and aconitase is functionally active (see claim interpretation in 112(b) rejection). Claims 6 recites the limitation for the gene encoding aconitase to comprises a nucleotide sequence having at least 60% identity to SEQ ID NO: 3 and an activity identical to SEQ ID NO: 3. Claim 6 is interpreted as the recombinant microorganism wherein 40% or less of the sequence encoding aconitase vary from SEQ ID NO: 3 and aconitase is functionally active (see claim interpretation in 112(b) rejection). Claims 7 recites the limitation for the gene encoding GroELS to comprises a nucleotide sequence having at least 80% identity to SEQ ID NO: 5 and an activity identical to SEQ ID NO: 5. Claim 7 is interpreted as the recombinant microorganism wherein 20% or less of the sequence encoding GroELS vary from SEQ ID NO: 5 and GroELS is functionally active (see claim interpretation in 112(b) rejection).
Thus, claims 4-7 broadly encompass a genus of cis-aconitic decarboxylase genes having 80% or more sequence identity to SEQ ID NO:1, a genus of aconitase genes having 80% or more sequence identity to SEQ ID NO: 2, a genus of aconitase genes having 60% or more sequence identity to SEQ ID NO:3 and a genus of GroELS genes having 80% or more sequence identity to SEQ ID NO: 5. This would represent a large pools of variant nucleotide sequences encoding the respective proteins which are functional. At the same time cis-aconitic decarboxylase genes can have 20% or less of sequences that can differ from SEQ ID NO:1, aconitase genes can have 20% or less of sequences that can differ from SEQ ID NO:2 or 40% or less of sequences that can differ from SEQ ID NO:3 and GroELS genes can have 20% or less of sequences that can differ from SEQ ID NO:5. The Specification does not provide structure function correlation for cis-aconitic decarboxylase, aconitase and GroELS and does not describe domains and/or amino acid residues essential for cis-aconitic decarboxylase, aconitase and GroELS functions and domain and/or amino acid residues which can be modified without loss of cis-aconitic decarboxylase, aconitase or GroELS functions. Further, applicants have not shown possession of a representative number of species for cis-aconitic decarboxylase, aconitase and GroELS gene sequences as Specification provides only examples of introduction of the corresponding genes with 100% sequence identity to SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3 and SEQ ID NO:5 and evaluation of the function of the encoded by them proteins in production of itaconic acid (Examples 2, 4 and 5).
Thus, one of ordinary skill in the art would not be able to identify which nucleotide sequences that have at least 80% identity to SEQ ID NO:1 encode for functional cis-aconitic decarboxylase, which nucleotide sequences that have at least 80% identity to SEQ ID NO:2 or 60% identity to SEQ ID NO:3 encode for functional aconitase and which nucleotide sequences that have at least 80% identity to SEQ ID NO:5 encode for functional GroELS. One of ordinary skill in the art would conclude based on the lack of representative number of species and the lack of describing the domains or amino acid residues of SEQ ID NO: 1 critical for the function of cis-aconitic decarboxylase, of SEQ ID NO:2 and SEQ ID NO:3 critical for function of aconitase and of SEQ ID NO:5 critical for function of GroELS, that the Applicant was not is possession of the claimed genera and that the specification fails to satisfy the requirements of written description under 35 U.S.C. 112 (a).
Claims 10 and 11 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 enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Claims 10 and 11 are directed to the recombinant microorganisms deposited under the Accession NO. DSM 34296 and DSM 34297, respectively. It is apparent that microorganisms DSM 34296 and DSM 34297 are required to practice the claimed invention. As such the biological material must be readily available or obtainable by a repeatable method set forth in the specification, or otherwise readily available to the public. If it is not so obtainable or available, the requirements of 35 USC 112, first paragraph, may be satisfied by a deposit of the strain.
The process disclosed in the specification does not appear to be repeatable, it is not clear that the invention will work with commonly available material and it is not apparent if the biological materials considered necessary to make and use the invention is both known and readily available to the public. The prior art of Yang (KR 20190027631 A) teaches Escherichia coli BL-21 (DE3) with a recombinant vector comprising genes for cis-aconitate decarboxylase and aconitase (paragraphs 0022, 0036 and 0076), however the described E. coli strain does not have GroELS integrated in the genome. Thus, a person skilled in the art could not make or use the invention defined without access to the specific biological material.
It is noted that the novel strains were deposited: “the novel integrated strain provided in the present disclosure, AtCg/BD::7G, was deposited at the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) GmbH (InhoffenstraJ3e 7B,38124 Braunschweig, Germany) under Accession No. DSM 34296 on Jun 17, 2022. And, the other novel integrated strain provided in the present disclosure, AtEcN/BD::7G, was deposited at the Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) GmbH (InhoffenstraJ3e 7B, 38124 Braunschweig, Germany) under Accession No. DSM 34297 on Jun 17, 2022 “ (specification, paragraph 0013). The depositary information and the viability statement filed 03/23/2023 are acknowledged, however, there is no indication as to public availability statement.
If the deposit is made under the terms of the Budapest Treaty, then a statement, affidavit or declaration by Applicants, or by an attorney of record over his or her signature and registration number, or by someone in a position to corroborate the facts of the deposit, that the instant invention will be irrevocably and without restriction released to the public upon the issuance of a patent, would satisfy the deposit requirement made herein.
If the deposit is a non-Budapest Treaty deposit, then in order to certify that the deposit meets the requirements set forth in 37 CFR 1.801-1.809 and MPEP 2402-2411.05, a statement, affidavit or declaration Applicant, by an attorney of record over his or her signature and registration number, or by someone in a position to corroborate the facts of the deposit would satisfy the requirements herein by stating and providing that:
(a) During the pendency of the application, access to the invention will be afforded to the Commissioner upon request;
(b) All restrictions upon availability to the public will be irrevocably removed upon granting of the patent;
(c) The deposit will be maintained in a public depositary for a period of 30 years, or 5 years after the last request or for the enforceable life of the patent, whichever is longer; and
(d) Provide evidence of the test of the viability of the biological material at the time of deposit (see 37 CFR 1.807).
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.
Claims 1-5, 8 and 9 are rejected under 35 U.S.C. 103 as being unpatentable over Yang (KR 20190027631 A) in view of Chen (CN 113481136 A) and Hao (Hao et al. ACS Synth. Biol., 2021, 10, 1633-1639).
Regarding claim 1, Yang teaches method for production of itaconic acid by culturing Escherichia coli containing recombinant vector comprising an aconitase (acn) gene and cis-aconitate decarboxylase (cadA) gene derived from Aspergillus terreus (paragraph 0022). Yang mentions that itaconic acid is produced by the whole-cell bioconversion (paragraph 0022). Yang discloses that E.coli is used for the whole-cell reactions with the bioconversion providing the rate significantly higher than in the conventional method of itaconic acid production by fermentation (paragraph 0036).
Yang does not teach the genome of the recombinant microorganism to comprise a gene for molecular chaperone protein GroELS.
Chen teaches recombinant Halomonas microorganism producing itaconic acid by catalyzing citric acid (Abstract). The microorganism contains a high-copy expression vector carrying gene encoding cis-aconitic acid decarboxylase from Aspergillus terreus and gene encoding aconitase from Corynebacterium glutamicum (p. 3, paragraphs 16 and 17). Chen discloses that the recombinant microorganism contains additional expression vector carrying GroESL chaperone gene from Halomonas sp. (p. 3, paragraph 19). Chen mentions that overexpression of GroESL enhanced the soluble expression of protein (p. 4, paragraph 16).
Hao teaches method and tools for inserting DNA into the bacterial chromosome based on site-specific recombination reactions (Abstract). Hao mentions that integration of DNA into genome minimizes the metabolic burden on host cells, reduces cell-to-cell variation and eliminates the need for continuous selection with antibiotics (p. 1633, left column, 1st paragraph). Hao describes development of “a set of independently inducible expression modules with tight control and high dynamic range which can be inserted at specific chromosomal locations” (Abstract).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to add expression of GroELS described in Chen teaching to itaconic acid production by whole-cell bioconversion of E. coli taught by Yang. One would have been motivated to do so since expression of GroELS will increase production of soluble proteins including cis-aconitic acid decarboxylase and aconitase necessary for production of itaconic acid. A skilled artisan would have reasonably expected success in that because Yang and Chen teach production of itaconic acid and recombinant vector carrying cis-aconitic acid decarboxylase and aconitase genes.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to follow guidance of Hao and integrate the GroELS genes described in Chen teaching into genome of E.coli carrying recombinant vector for production of itaconic acid taught by Yang and Chen. One would have been motivated to do so since integration will minimizes the metabolic burden on host cells, reduce cell-to-cell variation and eliminate the need for separate antibiotic selection for plasmid carrying GroELS genes. A skilled artisan would have reasonably expected success in that because Yang described method of itaconic acid production by bio-conversion in E.coli, Chen pointed to advantage of GroELS expression to increase solubility of expressed proteins and Hao provided method to optimize GroELS expression by integration into bacterial genome. Thus, Yang, Chen and Hao teachings render claim 1 obvious.
Regarding claims 2 and 3, Yang teaches plasmids for preparation of recombinant vector comprising inducible T7 promoter (paragraph 0077). Thus, Yang, Chen and Hao teachings render claims 2 and 3 obvious.
Regarding claim 4, Yang teaches the gene encoding cis-aconitic acid decarboxylase derived from Aspergillus itaconicus containing the nucleotide sequence with SEQ ID NO:1 codon optimized for Escherichia coli expression (paragraph 0038). The sequence with SEQ ID NO: 1 of Yang teaching has 81.7% identity to instant nucleotide sequence with SEQ ID NO:1. Thus, Yang, Chen and Hao teachings render claim 4 obvious.
Regarding claim 8 and 9, Yang teaches Escherichia coli as a preferrable host and BL21 (DE3) strain carrying recombinant vectors (paragraphs 0036 and 0076). Thus, Yang, Chen and Hao teachings render claims 8 and 9 obvious.
Regarding claim 5, Yang teaches aconitase gene derived from Corynebacterium glutamicum (paragraph 0010), however, does not provide its sequence. Chen teaches the gene encoding aconitase derived from Corynebacterium glutamicum having the nucleotide sequence with SEQ ID NO: 6. The sequence with SEQ ID NO: 6 of Chen teaching is 100% % identical to instant nucleotide sequence with SEQ ID NO:2.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to follow Chen teaching and use the nucleotide sequence with SEQ ID NO: 6 from Chen teaching (which is 100% identical to instant SEQ ID NO:2 ) for aconitase gene in the expression vector of Yang teaching used for production of itaconic acid. One would have been motivated to do so with reasonably expected success since Yang and Chen teach aconitase gene derived from Corynebacterium glutamicum used in itaconic acid production. Thus, Yang, Chen and Hao teachings render claim 5 obvious.
Claim 6 is rejected under 35 U.S.C. 103 as being unpatentable over Yang (KR 20190027631 A) in view of Chen (CN 113481136 A) and Hao (Hao et al. ACS Synth. Biol., 2021, 10, 1633-1639) as applied to claim 1 above, and further in view of Lee (US 20150267230 A1).
The teachings of Yang, Chen and Hao have been set forth above.
Yang, Chen and Hao do not teach the gene encoding aconitase comprising nucleotide sequence having at least 60% identity to SEQ ID NO:3 and activity of SEQ ID NO:3.
Lee teaches recombinant microorganism expressing fusion polypeptide containing aconitase and cis-aconitate decarboxylase and producing itaconic acid (Abstract). Lee discloses that the recombinant microorganism can be E.coli and the nucleic acid encoding fusion polypeptide can have inducible promoter (paragraph 0006). Lee describes that cells expressing the fusion protein possessed both aconitase and cis-aconitate decarboxylase activities (paragraph 0045). Lee discloses that the aconitase gene derived from E.coli has the nucleotide sequence with SEQ ID NO:3 (paragraph 0025). The sequence with SEQ ID NO:3 of Lee teaching has 97.8% identity to instant nucleotide sequence with SEQ ID NO:3.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to use the nucleotide sequence with SEQ ID NO: 3 from Lee teaching having 97.8% identity to instant SEQ ID NO:3 for aconitase gene for production of itaconic acid based on Yang, Chen and Hao teachings. One would have been motivated to do so since aconitase gene taught by Lee is derived from E. coli and was shown by Lee to possess aconitase activity when expressed in E. coli and hence can be included in the expression vector of Yang to be used in E.coli. A skilled artisan would have reasonably expected success in that because Yang, Chen and Lee teach production of itaconic acid in microorganisms and with expression vector carrying acn and cadA genes. Thus, Yang, Chen, Hao and Lee teachings render claim 6 obvious.
Claim 7 is rejected under 35 U.S.C. 103 as being unpatentable over Yang (KR 20190027631 A) in view of Chen (CN 113481136 A) and Hao (Hao et al. ACS Synth. Biol., 2021, 10, 1633-1639) as applied to claim 1 above, and further in view of Sogo (US 6197547 B1).
The teachings of Yang, Chen and Hao have been set forth above.
Yang, Chen and Hao do not teach the gene encoding chaperone protein GroELS comprising nucleotide sequence having at least 80% identity to SEQ ID NO:5 and activity of SEQ ID NO:5.
Sogo teaches an expression plasmid comprising operon carrying genes encoding trigger factor, GroEL and GroES that can be cotransformed with the expression vector for foreign protein for production of foreign protein in a solubilized form and correct conformation (Abstract). Sogo describes E. coli strains as a host (column 6, lines 33-34). Sogo provides example of expression of murine endostatin protein and described that when coexpressed with GroEL and GroES the majority of endostatin was detected in soluble fraction (column 10, lines 22-26). Sogo discloses the nucleotide sequences for genes encoding E. coli GroEL and GroES and the resulting operon sequence with SEQ ID NO:7 (column 5, lines 1-3, column 21-25) which comprises a nucleotide sequence having 99.6% identity to instant SEQ ID NO:5.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to use the nucleotide sequence for GroELS from Sogo teaching with SEQ ID NO: 7 comprising sequence having 99.6% identity to instant SEQ ID NO:5 for production of itaconic acid based on Yang, Chen and Hao teachings. One would have been motivated to do so since GroELS gene taught by Sogo are derived from E. coli and was shown by Sogo to improve solubility of foreign protein expressed in E. coli and hence can be used for integration into genome of E. coli based as described by Hao to improve expression of cadA and acn genes for production of itaconic acid. A skilled artisan would have reasonably expected success in that because Yang, Chen and Lee teach production of itaconic acid in microorganisms by expression of aconitase and cis-aconitic decarboxylase and Chen and Sogo teach GroELS to improve folding and solubility of expressed proteins. Thus, Yang, Chen, Hao and Sogo teachings render claim 7 obvious.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to LIOUBOV G KOROTCHKINA whose telephone number is (571)270-0911. The examiner can normally be reached Monday-Friday: 8:00-5:30.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Sharmila G Landau can be reached at (571)272-0614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/L.G.K./Examiner, Art Unit 1653
/SHARMILA G LANDAU/Supervisory Patent Examiner, Art Unit 1653