DETAILED ACTION
Status of the Application
Claims 1, 4-6, 9-12, 15-21 are pending.
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 amendment of claims 1, 4-6, 9, 11-12, 15, addition of claims 16-21, cancellation of claims 2-3, 7-8, 13-14, and amendments to the specification as submitted in a communication filed on 10/15/2025 is acknowledged.
Applicant elected with traverse Group I, claims 1-8, 11-14, drawn in part to a genetically modified microorganism that expresses a YeeX protein, in a communication filed on 6/23/2025.
New claims 16-19 are drawn to the elected invention. New claims 20-21 are directed to a non-elected invention. Claims 9-10, 15, 20-21 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 6/23/2025.
Claims 1, 4-6, 11-12, 16-19 are at issue and are being examined herein.
Specification
The specification was objected to due to lack of clarity with regard to Tables 1 and 2. In view of Applicant’s submission of legible copies of Tables 1 and 2, this objection is hereby withdrawn.
Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA )
Claims 1, 4-6, 11-12 remain rejected and new claims 16-19 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. New grounds of rejection are necessitated by amendment.
Claim 1 (claims 4-6 dependent thereon) is indefinite in the recitation of “comprising a gene capable of expressing a mutated YeeX protein having an amino acid sequence with a sequence identity of 90% or more to the amino acid sequence of SEQ ID NO: 1, wherein said mutated YeeX protein has a substitution of alanine corresponding to the amino acid at position 84 in the amino acid sequence of SEQ ID NO: 1 to another amino acid, wherein said gene has a function to increase productivity of …adipic acid when said gene is introduced into a microorganism belonging to the genus Escherichia having an ability to produce…..compared to the microorganism before the introduction of said gene, wherein a gene encoding CoA transferase was introduced into said microorganism” for the following reasons.
The term “YeeX” appears to be generic and not limited to a specific organism. While the nomenclature used may be appropriate for a E. coli protein encoded by the E. coli yeeX gene, the use of this nomenclature for proteins of identical function from other organisms may not be accurate. As known in the art, genes encoding proteins of identical function in two different organisms may use different designations. For example, the ARO4 gene of Candida albicans encodes a DAHP synthase whereas the E. coli counterpart is the aroF gene. See the abstract of Sousa et al. (Microbiology 148(Pt5):1291-1303, 2002). As such, the use of gene terminology which is applicable to some organisms and not to others is confusing because one cannot determine if the claim intends to limit the proteins to those from organisms that use that nomenclature and exclude those that have the same activity but are from organisms that do not use this nomenclature. Please note that the term “YeeX” is not a recognized term that conveys a particular function.
In addition, the term “having an amino acid sequence with a sequence identity of 90% or more…” is unclear because one cannot determine if the limitation is associated to the mutated YeeX protein or the YeeX protein prior the mutation. Moreover, it is unclear if the term “wherein said mutated YeeX protein has a substitution of alanine corresponding to the amino acid at position 84 in the amino acid sequence of SEQ ID NO: 1 to another amino acid” intends to limit the mutated YeeX protein to one that comprises a substitution at the position corresponding to position 84 of the polypeptide of SEQ ID NO: 1. Furthermore, while a protein can have the ability to alter the production of an organic acid, it is unclear as to how a gene when introduced into a microorganism can increase the productivity of an organic acid. If the intended subject matter is a genetically modified Escherichia microorganism, wherein said genetically modified Escherichia microorganism comprises a gene encoding a protein having at least 90% sequence identity to the polypeptide of SEQ ID NO: 1, wherein said protein has a substitution at the position corresponding to position 84 of the polypeptide of SEQ ID NO: 1, wherein said genetically modified Escherichia microorganism further comprises a gene encoding a CoA transferase, the claim should be amended accordingly. Correction is required.
Claim 5 is indefinite in the recitation of “…microorganism according to claim 4, which results from mutation of a gene capable of expressing YeeX protein in the genome or replacement of the gene capable of expressing the YeeX gene with said gene capable of expressing the mutated YeeX protein” for the following reasons. Claim 1, from which claim 5 ultimately depends, does not indicate that the microorganism results from mutation of a gene capable of expressing YeeX protein or replacement of the gene capable of expressing the YeeX gene. Claim 1 only refers to that the microorganism that comprises a gene that expresses a mutated YeeX protein. Please note that any reference to introducing a gene is in reference to an effect in the productivity of several organic acids. Therefore, claim 5 appears to be of different scope compared to claim 1. For examination purposes, it will be assumed that claim 5 is a duplicate of claim 1. Correction is required.
Claim 11 (claim 12 dependent thereon) is indefinite in the recitation of “comprising a gene capable of expressing a mutated YeeX protein having an amino acid sequence with a sequence identity of 90% or more to the amino acid sequence of SEQ ID NO: 1, wherein said mutated YeeX protein has a substitution of alanine corresponding to the amino acid at position 84 in the amino acid sequence of SEQ ID NO: 1 to another amino acid, wherein said gene has a function to increase productivity of …adipic acid when said gene is introduced into a microorganism belonging to the genus Escherichia having an ability to produce…..compared to the microorganism before the introduction of said gene” for the following reasons.
The term “YeeX” appears to be generic and not limited to a specific organism. While the nomenclature used may be appropriate for a E. coli protein encoded by the E. coli yeeX gene, the use of this nomenclature for proteins of identical function from other organisms may not be accurate. As known in the art, genes encoding proteins of identical function in two different organisms may use different designations. For example, the ARO4 gene of Candida albicans encodes a DAHP synthase whereas the E. coli counterpart is the aroF gene. See the abstract of Sousa et al. As such, the use of gene terminology which is applicable to some organisms and not to others is confusing because one cannot determine if the claim intends to limit the proteins to those from organisms that use that nomenclature and exclude those that have the same activity but are from organisms that do not use this nomenclature. Please note that the term “YeeX” is not a recognized term that conveys a particular function.
In addition, the term “having an amino acid sequence with a sequence identity of 90% or more…” is unclear because one cannot determine if the limitation is associated to the mutated YeeX protein or the YeeX protein prior the mutation. Moreover, it is unclear if the term “wherein said mutated YeeX protein has a substitution of alanine corresponding to the amino acid at position 84 in the amino acid sequence of SEQ ID NO: 1 to another amino acid” intends to limit the mutated YeeX protein to one that comprises a substitution at the position corresponding to position 84 of the polypeptide of SEQ ID NO: 1. Furthermore, while a protein can have the ability to alter the production of an organic acid, it is unclear as to how a gene when introduced into a microorganism can increase the productivity of an organic acid. If the intended subject matter is a genetically modified Escherichia microorganism, wherein said genetically modified Escherichia microorganism comprises a gene encoding a protein having at least 90% sequence identity to the polypeptide of SEQ ID NO: 1, wherein said protein has a substitution at the position corresponding to position 84 of the polypeptide of SEQ ID NO: 1, the claim should be amended accordingly. Correction is required.
Claim 12 is indefinite in the recitation of “or the homolog thereof” because there is no antecedent basis for “the homolog thereof”. For examination purposes, no patentable weight will be given to this term. Correction is required.
Claim 16 (claim 17 dependent thereon) is indefinite in the recitation of “..microorganism belonging to the genus Serratia comprising a gene capable of expressing a mutated YeeX protein having an amino acid sequence that is the same as that amino acid sequence of SEQ ID NO: 2 except that said mutated YeeX protein has a substitution of alanine corresponding to the amino acid at position 87 in the amino acid sequence of SEQ ID NO: 2 to another amino acid, wherein said gene has a function to increase productivity of …adipic acid when said gene is introduced into a microorganism….compared to the microorganism before the introduction of said gene, wherein a gene encoding CoA transferase was introduced into said microorganism” for the following reasons.
The term “YeeX” appears to be generic and not limited to a specific organism. While the nomenclature used may be appropriate for a E. coli protein encoded by the E. coli yeeX gene, the use of this nomenclature for proteins of identical function from other organisms may not be accurate. As known in the art, genes encoding proteins of identical function in two different organisms may use different designations. For example, the ARO4 gene of Candida albicans encodes a DAHP synthase whereas the E. coli counterpart is the aroF gene. See the abstract of Sousa et al. As such, the use of gene terminology which is applicable to some organisms and not to others is confusing because one cannot determine if the claim intends to limit the proteins to those from organisms that use that nomenclature and exclude those that have the same activity but are from organisms that do not use this nomenclature. Please note that the term “YeeX” is not a recognized term that conveys a particular function.
Moreover, it is unclear if the term “wherein said mutated YeeX protein has a substitution of alanine corresponding to the amino acid at position 87 in the amino acid sequence of SEQ ID NO: 2 to another amino acid” intends to limit the mutated YeeX protein to one that comprises a substitution at the position corresponding to position 87 of the polypeptide of SEQ ID NO: 2. Furthermore, while a protein can have the ability to alter the production of an organic acid, it is unclear as to how a gene when introduced into a microorganism can increase the productivity of an organic acid. If the intended subject matter is a genetically modified Serratia microorganism, wherein said genetically modified Serratia microorganism comprises a gene encoding a protein that comprises all of SEQ ID NO: 2 except for a substitution at the position corresponding to position 87 of the polypeptide of SEQ ID NO: 2, wherein said genetically modified Serratia microorganism further comprises a gene encoding a CoA transferase, the claim should be amended accordingly. Correction is required.
Claim 17 is indefinite in the recitation of “which is a substitution of the alanine corresponding to the amino acid at position 84 in the amino acid sequence of SEQ ID NO: 2 to valine….” for the following reasons. Upon a cursory review of SEQ ID NO: 2, it was noted that there is no alanine at position 84 of SEQ ID NO: 2 but rather an isoleucine residue. Therefore, it is unclear as to which is the mutation referred to in the preamble. For examination purposes, it will be assumed that claim 17 is a duplicate of claim 16 as interpreted above. Correction is required.
Claim 18 is indefinite in the recitation of “..microorganism belonging to the genus Serratia comprising a gene capable of expressing a mutated YeeX protein having an amino acid sequence that is the same as that amino acid sequence of SEQ ID NO: 2 except that said mutated YeeX protein has a substitution of alanine corresponding to the amino acid at position 87 in the amino acid sequence of SEQ ID NO: 2 to another amino acid, wherein said gene has a function to increase productivity of …adipic acid when said gene is introduced into a microorganism….compared to the microorganism before the introduction of said gene” for the following reasons.
The term “YeeX” appears to be generic and not limited to a specific organism. While the nomenclature used may be appropriate for a E. coli protein encoded by the E. coli yeeX gene, the use of this nomenclature for proteins of identical function from other organisms may not be accurate. As known in the art, genes encoding proteins of identical function in two different organisms may use different designations. For example, the ARO4 gene of Candida albicans encodes a DAHP synthase whereas the E. coli counterpart is the aroF gene. See the abstract of Sousa et al. As such, the use of gene terminology which is applicable to some organisms and not to others is confusing because one cannot determine if the claim intends to limit the proteins to those from organisms that use that nomenclature and exclude those that have the same activity but are from organisms that do not use this nomenclature. Please note that the term “YeeX” is not a recognized term that conveys a particular function.
Moreover, it is unclear if the term “wherein said mutated YeeX protein has a substitution of alanine corresponding to the amino acid at position 87 in the amino acid sequence of SEQ ID NO: 2 to another amino acid” intends to limit the mutated YeeX protein to one that comprises a substitution at the position corresponding to position 87 of the polypeptide of SEQ ID NO: 2. Furthermore, while a protein can have the ability to alter the production of an organic acid, it is unclear as to how a gene when introduced into a microorganism can increase the productivity of an organic acid. If the intended subject matter is a genetically modified Serratia microorganism, wherein said genetically modified Serratia microorganism comprises a gene encoding a protein that comprises all of SEQ ID NO: 2 except for a substitution at the position corresponding to position 87 of the polypeptide of SEQ ID NO: 2, the claim should be amended accordingly. Correction is required.
Claim 19 is indefinite in the recitation of “which is a substitution of the alanine corresponding to the amino acid at position 84 in the amino acid sequence of SEQ ID NO: 2 to valine….” for the following reasons. Upon a cursory review of SEQ ID NO: 2, it was noted that there is no alanine at position 84 of SEQ ID NO: 2 but rather an isoleucine residue. Therefore, it is unclear as to which is the mutation referred to in the preamble. For examination purposes, it will be assumed that claim 19 is a duplicate of claim 18 as interpreted above. Correction is required.
When amending the claims, applicant is advised to carefully review all examined claims and make the necessary changes to ensure proper antecedent basis and dependency.
Claim Rejections - 35 USC § 112(a) or First Paragraph (pre-AIA )
Claims 1, 4-6, 11-12 remain rejected and new claims 16-19 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.
Claims 1, 4-6, 11-12 remain rejected and new claims 16-19 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 microorganism that comprises a nucleic acid encoding a protein that (i) comprises SEQ ID NO: 44, or (ii) comprises SEQ ID NO: 12, wherein said microorganism has been transformed with the P. putida pcaF gene of SEQ ID NO: 13, the S. marcescens gene encoding a 3-oxoadipyl-CoA reductase of SEQ ID NO: 14, the P. putida paaF gene of SEQ ID NO: 15, the A. baylyi dcaA gene of SEQ ID NO: 16, the P. putida pcaI gene of SEQ ID NO: 17 and the P. putida pcaJ gene of SEQ ID NO: 18, does not reasonably provide enablement for a microorganism that comprises (i) a nucleic acid encoding any variant of the polypeptide of SEQ ID NO: 1 having at least 90% sequence identity to the polypeptide of SEQ ID NO: 1, wherein said variant has a substitution at the position corresponding to position 84 of the polypeptide of SEQ ID NO: 1 and optionally a nucleic acid encoding any transferase, or (ii) a nucleic acid encoding a variant of the polypeptide of SEQ ID NO: 2 that comprises all of SEQ ID NO: 2 except for a substitution at the position corresponding to position 87 of the polypeptide of SEQ ID NO: 2 and optionally a nucleic acid encoding any transferase, wherein said microorganism has been genetically modified by any means to produce succinic acid, acetic acid, 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid. 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/or use the invention commensurate in scope with these claims.
These rejections have been discussed at length in the prior Office action. It is maintained and further applied to new claims 16-19 for the reasons of record and those set forth below.
Applicant argues that the claims as amended comply with the enablement and written description requirements of 35 USC § 112(a).
Applicant’s arguments have been fully considered but not deemed persuasive to overcome the instant rejections or avoid the rejection of new claims 16-19. The Examiner acknowledges the amendments made to the claims. However, the Examiner disagrees with Applicant’s contention that the claims as amended comply with the written description and enablement requirements.
As indicated above, the claims as amended, including new claims 16-19 require Escherichia or Serratia microorganisms that comprise a genus of genes encoding a genus of proteins which are variants of the polypeptide of SEQ ID NO: 1 or 2 having any function or the ability to increase the production of succinic acid, acetic acid, 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid, wherein said Escherichia or Serratia microorganisms have been modified by any means to produce succinic acid, acetic acid, 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid. See Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA ) for claim interpretation.
While the specification in the instant application discloses the structure of a limited number of species of the genus of proteins encoded by the nucleic acids of the claims, it provides no clue as to the structural elements required in any protein having the same biological activity as that of the polypeptide of SEQ ID NO: 1 or any protein having CoA transferase activity, nor does it teach which structural elements within the polypeptide of SEQ ID NO: 1 are required in any variant having the ability to increase the production of succinic acid, acetic acid, 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid. No disclosure of a structure/function correlation has been provided which would allow one of skill in the art to recognize which proteins encoded by the recited genus of nucleic acids have the ability to increase the production of succinic acid, acetic acid, 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid, or which proteins have transferase activity. The specification is silent with regard to the structural features in the polypeptide of SEQ ID NO: 1 which are essential for increasing the production of succinic acid, acetic acid, 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid in any Escherichia or Serratia microorganism.
In addition, the claims require a genetically engineered Escherichia or Serratia microorganism that can produce succinic acid, acetic acid, 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid. As such, the claims require a genus of enzymes having any structure and function such that when expressed in any Escherichia or Serratia microorganism, said microorganism can produce succinic acid, acetic acid, 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid, as well as unknown genetic modifications in the microorganism to allow the synthesis of succinic acid, acetic acid, 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid. While the specification discloses the production of a limited number of organic acids and discloses a limited number of the enzymes that would allow the synthesis of these organic acids, it provides no clue as to the structural elements required in any enzyme that can be expressed in any microorganism to produce succinic acid, acetic acid, 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid. No disclosure of a structure/function correlation has been provided which would allow one of skill in the art to recognize which enzymes can be expressed in any microorganism to produce succinic acid, acetic acid, 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid as required by the claims. Nothing is known with regard to the genetic modifications required in any Escherichia or Serratia microorganism such that it can produce succinic acid, acetic acid, 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid.
A polypeptide having 90% sequence identity with the polypeptide of SEQ ID NO: 1 allows for any combination of 11 amino acid modifications within SEQ ID NO: 1 (11 = 0.1x109; SEQ ID NO: 1 has 109 amino acids). The total number of variants of a polypeptide having a specific number of amino acid substitutions can be calculated from the formula N!x19A/(N-A)!/A!, where N is the length in amino acids of the reference polypeptide and A is the number of allowed substitutions. Thus, the total number of variants having at least 90% sequence identity to the polypeptide of SEQ ID NO: 1 that result from amino acid substitutions is 109!x1911/(109-11)!/11! or 4.46x1028 variants.
While the argument can be made that the structure/identity of those enzymes and proteins and their corresponding genes can be obtained by structural homology, the art clearly teaches that (i) there is a high level of unpredictability associated with accurate functional annotation of proteins based solely on structural homology, and (ii) modification of a protein’s amino acid sequence to obtain the desired activity without any guidance/knowledge as to which amino acids in a protein are tolerant of modification and which ones are conserved is highly unpredictable. See teachings of Singh et al., Sadowski et al., Witkowski et al., Seffernick et al. and Tang et al. previously discussed.
While methods of generating or isolating variants of a polynucleotide or polypeptide were known in the art, and enzymatic assays were also known in the art at the time of the invention, it was not routine in the art to screen by a trial and error process for an essentially infinite number of proteins and polynucleotides to find those that can increase the production of succinic acid, acetic acid, 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid by an Escherichia or Serratia microorganism that expresses them, and the genetic modifications and enzymes required in any Escherichia or Serratia microorganism to synthesize succinic acid, acetic acid, 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid. In the absence of (i) a rational and predictable scheme for selecting those nucleic acids encoding proteins most likely to have the desired functional features, (ii) a rational and predicable scheme for selecting those genetic modifications most likely to have the desired effect in any microorganism, and/or (iii) a correlation between structure and the desired activity, one of skill in the art would have to test any number of nucleic acids, proteins and genetic modifications to determine which ones have the desired functional characteristics and effects.
Therefore, for the reasons of record and those set forth above, one cannot reasonably conclude that the entire scope of the claims is adequately described or enabled by the teachings of the specification and/or the prior art.
Claim Rejections - 35 USC § 102 (AIA )
Claims 1-8, 11-14 were rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Isobe et al. (WO 2019/107516 published 6/6/2019; publication of PCT/JP2018/044080 which entered the US National stage as application No. 16/766,979, which was published as U.S. Publication No. 2020/0291435) as evidenced by Lucas et al. (GenBank accession No. ACT28708, 12/24/2013) and Parales et al. (Journal of Bacteriology 176(14):4657-4666, 1992).
In view of Applicant’s cancellation of claims 2-3, 7-8, 13-14 and amendments of claims 1, 4-6, 11-12. which now require a gene encoding a protein having at least 90% sequence identity to the polypeptide of SEQ ID NO: 1, wherein said protein has a substitution at the position corresponding to position 84 of the polypeptide of SEQ ID NO: 1, and the fact that the cell of Isobe et al. does not have such gene, this rejection is hereby withdrawn.
Claims 1-18 and 11-14 were rejected under 35 U.S.C. 102(a)(1) as being anticipated by Parales et al. (Journal of Bacteriology 176(14):4657-4666, 1992) as evidenced by Ferenci et al. (Journal of Bacteriology 191(12):4025-4029, 2009).
In view of Applicant’s cancellation of claims 2-3, 7-8, 13-14 and amendments of claims 1, 4-6, 11-12. which now require a gene encoding a protein having at least 90% sequence identity to the polypeptide of SEQ ID NO: 1, wherein said protein has a substitution at the position corresponding to position 84 of the polypeptide of SEQ ID NO: 1, and the fact that the cell of Parales et al. does not have such gene, this rejection is hereby withdrawn.
Conclusion
No claim is in condition for allowance.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a). A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension fee pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the date of this final action.
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Any inquiry concerning this communication or earlier communications from the examiner should be directed to DELIA M RAMIREZ, Ph.D., whose telephone number is (571) 272-0938. The examiner can normally be reached on Monday-Friday from 8:30 AM to 5:00 PM. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Robert B. Mondesi, can be reached at (408) 918-7584. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
/DELIA M RAMIREZ/Primary Examiner, Art Unit 1652
DR
January 16, 2026