DETAILED ACTION
Status of the Application
Claims 1, 4, 8-9, 11-14, 17, 19-20, 22-23, 25-26, 28-31 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, 8-9, 11-14, 17, 19-20, 22-23, 25-26, 28-29, cancellation of claims 2, 15-16, 18, 21, amendments to the specification and a declaration under 37 CFR § 1.132 by inventor Jan Marienhagen (hereinafter the “Marienhagen declaration”), as submitted in a communication filed on 12/2/2026 are acknowledged.
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 12/2/2025 has been entered.
Applicant elected without traverse Group I, drawn in part to coryneform bacteria that comprises modifications in one or more genes, wherein said genes are selected from the group consisting of fasB, gltA, accBC and accD1, the combination of genes fasB, gltA, accBC and accD1, the combination of all the modifications listed as a-f in previously presented claim 2, the deletion of phdBCDE, cat, ben, pca, pobA, and qsuB, the combination of genes 4cl, sts, chs, chi, and pcs, C. glutamicum and the polypeptide of SEQ ID NO: 2, in a communication filed on 8/22/2024.
Claims 28-31 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 8/22/2024. Claims 1, 4, 8-9, 11-14, 17, 19-20, 22-23, 25-26 are at issue and will be examined to the extent they encompass the elected invention.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Rejections and/or objections not reiterated from previous office actions are hereby withdrawn.
Specification
The previous objection to the disclosure due to the presence of an embedded hyperlink and/or other form of browser-executable code is hereby withdrawn by virtue of Applicant’s amendment.
Claim Objections
Claim 1 is objected to due to the recitation of “..Corynebacterium glutamicum bacterium fatty acid synthase encoding gene fastB”. To enhance clarity and to be consistent with commonly used claim language, the term should be amended to recite “mutation or partial deletion of the Corynebacterium glutamicum fasB gene”. Appropriate correction is required.
Claim 1 is objected to due to the recitation of “…..deletions of the Corynebacterium glutamicum bacteria gene clusters cg0344-47 (phdBCDE operon), cg2625-40 (cat, ben, and pca), cg1226 (pobA) and cg0502 (qsuB)”. To enhance clarity and to be consistent with commonly used claim language, the term should be amended to recite “wherein the cell comprises deletions in the endogenous Corynebacterium glutamicum gene clusters cg0344-cg0347 (phdBCDE operon), cg2625-cg2640 (cat gene, ben gene, and pca gene), cg1226 (pobA gene) and cg0502 (qsuB gene)”. Appropriate correction is required.
Claim 26 is objected to due to the recitation of “group comprising…”. To be consistent with commonly used claim language, the term should be amended to recite “selected from the group consisting of”. Appropriate correction is required.
Claim 26 is objected to due to the recitation of “a Corynebacterium glutamicum bacterium aroF1 gene and a Corynebacterium glutamicum bacterium tal gene”. To be consistent with commonly used claim language, the term should be amended to recite “a Corynebacterium glutamicum aroF1 gene and a Corynebacterium glutamicum tal gene”. Appropriate correction is required.
Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA )
Claims 1, 4, 8-9, 11-14, 17, 19-20, 22, 23, 25-26 remain 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, 8-9, 11-14, 17, 19-20, 22, 23, 25-26 dependent thereon) is indefinite in the recitation of “…bacteria cell with an increased intracellular amount of malonyl-CoA compared to its wildtype….reduced or eliminated synthase functionality of a Corynebacterium glutamicum bacterium fatty acid synthase FasB compared to its synthase functionality in the wildtype..” for the following reasons. The terms “its wildtype” and “the wildtype” are unclear and confusing because one cannot determine what the wildtype is. In addition, the term “reduced or eliminated synthase functionality of a Corynebacterium glutamicum bacterium fatty acid synthase FasB..” is indefinite because the term “a Corynebacterium glutamicum bacterium fatty acid synthase FasB” implies that the reduction/elimination of synthase function is made in any FasB of any Corynebacterium glutamicum and not necessarily the FasB of the Corynebacterium glutamicum of the preamble. If the intended modification is one that reduces or eliminates the synthase activity of the C. glutamicum FasB protein compared to the corresponding C. glutamicum cell lacking the modification, the claim should be amended accordingly. Correction is required.
Claim 1 (claims 4, 8-9, 11-14, 17, 19-20, 22, 23, 25-26 dependent thereon) is indefinite in the recitation of “..reduced or eliminated functionality of the operator binding sites (fasO) for a Corynebacterium glutamicum bacterium regulator FasR in the promoter regions of the Coryneform glutamicum bacterium accBC and accD1 genes coding for acetyl-CoA carboxylase subunits compared to its functionality in the wildtype” for the following reasons. The term “the wildtype” is unclear and confusing because one cannot determine what the wildtype is. In addition, it is unclear as to which is the functionality of the operator binding sites that is being reduced or eliminated. Furthermore, it is unclear if the term in parentheses “fasO” is limiting the operator binding sites. If the intended modification is a mutation of the motif fasO in the binding site for the C. glutamicum FasR transcriptional regulator in the C. glutamicum accD and accD1 genes, the claim should be amended accordingly. Correction is required.
Claim 1 (claims 4, 8-9, 11-14, 17, 19-20, 22, 23, 25-26 dependent thereon) is indefinite in the recitation of “derepressed expression of the Corynebacterium glutamicum bacterium accBC and accD1 genes coding for the acetyl-CoA carboxylase subunits compared with their expression in the wildtype” for the following reasons. The term “the wildtype” is unclear and confusing because one cannot determine what the wildtype is. If the intended modification is one that results in the expression of the C. glutamicum accBC and accD1 genes not to be repressed, the claim should be amended accordingly. Correction is required.
Claim 1 (claims 4, 8-9, 11-14, 17, 19-20, 22, 23, 25-26 dependent thereon) is indefinite in the recitation of “…reduced functionality of a promoter operatively linked to the C. glutamicum bacterium nitrate synthase gltA gene thereby reducing expression of the gltA gene coding for the citrate synthase CS compared to its expression in the wildtype” for the following reasons. The term “the wildtype” is unclear and confusing because one cannot determine what the wildtype is. In addition, it is unclear as to which is the functionality of the promoter that is being reduced. If the intended modification is a mutation to the endogenous promoter of the C. glutamicum gltA gene to reduce the expression of said gene compared to the corresponding C. glutamicum lacking the modification, the claim should be amended accordingly. Correction is required.
Claim 1 (claims 4, 8-9, 11-14, 17, 19-20, 22, 23, 25-26 dependent thereon) is indefinite in the recitation of “wherein the cell further comprises enzymes derived from plants or the genes encoding them for polyphenol or polyketide synthesis, wherein the cell comprises one or more genes derived from plants …selected from the group consisting of a …4cl gene, an Arachis…sts gene, a Petunia x…chs gene, a Petunia….chi gene and an Aloe…pcs gene” for the following reasons. While the term appears to imply that the cell can comprise enzymes or genes that encode them, the term also appears to require the cell to comprise genes encoding the enzymes due to the recitation of “wherein the cell comprises or more genes..”. Also, as written, it is unclear if the enzymes from the term “wherein the cell further comprises enzymes…” are those encoded by the P. crispum 4cl gene, the A. phyposea sts gene, the Peturnia x hybrida chs gene, the Petunia x hybrida chi gene or the Aloe arborescens pcs gene. If the intended limitation is “wherein the cell further comprises enzymes or genes encoding said enzymes, wherein said enzymes are associated with polyphenol or polyketide synthesis”, the claim should be amended according. For examination purposes it will be assumed that the cell further comprises enzymes or genes encoding said enzymes, wherein said enzymes are associated with the synthesis of polyphenols or polyketides. Correction is required.
Claim 4 is indefinite in the recitation of “…reduced compared to the expression in the wildtype by mutation of the operatively linked promoter” for the following reasons. The term “the wildtype” is unclear and confusing because one cannot determine what the wildtype is. In addition, it is unclear if the operably linked promoter is the endogenous promoter of the gltA gene. If the intended limitation is “wherein the C. glutamicum cell comprises a mutation in the endogenous promoter of the C. glutamicum gltA gene”, the claim should be amended accordingly. Correction is required.
Claim 8 is indefinite in the recitation of “..wherein the cell comprises the Corynebacterium…fatty acid synthase FasB whose functionality is reduced or turned off compared to the functionality in the wildtype…” for the following reasons. The term is unclear because one cannot determine which is the functionality that has to be reduced or turned off. A protein can have more than one function simultaneously. In addition, the term “the wildtype” is unclear and confusing because one cannot determine what the wildtype is. As written, it is unclear if the FasB amino acid sequence having at least 95% identity to SEQ ID NO: 2 refers to the endogenous FasB protein or the FasB protein modified to reduce or eliminate its “functionality”. For examination purposes, it will be assumed that claim 8 is a duplicate of claim 1 as interpreted above. Correction is required.
Claim 9 is indefinite in the recitation of”…polynucleotide comprising a nucleic acid sequence coding for a fatty acid synthase FasB…selected from the group consisting of: a nucleic acid sequence containing at least 95% identity to…SEQ ID NO: 1… a nucleic acid sequence which, in a polynucleotide, under stringent conditions hybridizes with a polynucleotide comprising a complementary nucleic acid sequence selected from the group…SEQ ID NO: 1…, a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1…, a nucleic acid sequence coding for a Corynebacterium glutamicum bacterium fatty acid synthase FasB …but which differs from these nucleic acids ..by the degeneracy of the genetic code” for the following reasons. As written, it is unclear if the nucleic acid sequences listed in parts a-d refer to the nucleic acid sequence of an endogenous gene in the Corynebacterium glutamicum bacterium or if the nucleic acid sequence listed in parts a-d refer to the nucleic acid sequence of an endogenous gene that has been modified so that the protein encoded by said gene has its “functionality” reduced or turned off. In addition, the term “a nucleic acid sequence which in a polynucleotide under stringent conditions hybridizes with a polynucleotide comprising a complementary sequence selected from.. SEQ ID NO: 1” is completely unclear because one cannot determine if the nucleic acid sequence is that of a polynucleotide that hybridizes under stringent conditions with the full length complement of the polynucleotide of SEQ ID NO: 1. Moreover, as previously indicated, the term “stringent conditions” is a relative term which encompasses diverse hybridization conditions that do not result in the hybridization of the same nucleic acids. Nucleic acids which will hybridize under some hybridization conditions will not necessarily hybridize under different conditions. The art does not recognize a single set of experimental conditions as “stringent”. Therefore, it is unclear which nucleic acid is recited absent a statement of the experimental conditions under which the hybridization reaction is performed. For examination purposes, claim 9 will be interpreted as a duplicate of claim 1 as interpreted. Correction is required.
Claim 11 is indefinite in the recitation of “…reduced or eliminated functionality of a Corynebacterium glutamicum bacterium fatty acid synthase…compared with its functionality in the wildtype, wherein the FasB amino acid sequence has at least 95% identity to the…SEQ ID NO: 2…mutation or partial deletion of the fatty acid synthase…wherein the fasB nucleic acid sequence has at least 95% identity to…SEQ ID NO: 1.., reduced functionality of the promoter operably linked to the citrate synthase gltA gene… compared with its functionality in the wildtype, wherein the promoter nucleic acid sequence comprises SEQ ID NO: 11;… …reduced or eliminated functionality of the operator binding sites for the regulator….compared with their functionality in the wildtype, wherein the nucleic acid sequences of the accBC and accD1 promoter regions respectively comprise SEQ ID NO: 13 and 15;… …” for the following reasons.
The term “the wildtype” is unclear and confusing because one cannot determine what the wildtype is. In addition, the term “functionality” is unclear in the absence of a definition of the function to be compared. FasB can have, for example, enzymatic activity, binding activity, or antibody eliciting activity. Therefore, one would require the recitation of the actual function so that the comparison can be properly made. Moreover, it is noted that while the modifications recited in parts a, b, c, and d are all required in claim 1, claim 11 refers to them in the alternative due to the recitation of “one or more modifications selected from the group consisting of”. As such, the scope of claim 11 is broader than that of claim 1, from which it depends, thus being an improper dependent claim. As written, it is unclear if (i) the FasB amino acid sequence having at least 95% identity to SEQ ID NO: 2 refers to the endogenous FasB protein or the FasB protein modified to reduce or eliminate its “functionality”, (ii) the fasB nucleic acid sequence having at least 95% identity to SEQ ID NO: 1 refers to the endogenous fasB gene or a mutated fasB gene, (iii) the promoter nucleic acid sequence refers to the endogenous promoter of the C. glutamicum gltA gene in the C. glutamicum bacterium, or if the promoter nucleic acid sequence refers to the nucleic acid sequence of a modified promoter with reduced “functionality”, (iv) the nucleic acid sequences of the accBC and accD1 promoters are those of the promoters of endogenous accBC and accD1 genes, or if the nucleic acid sequences of SEQ ID NO: 13 and SEQ ID NO: 15 are the nucleic acid sequences of modified promoters in the accBC and accD1 genes to reduce or eliminate “functionality” of the operator binding sites for the FasR regulator in the promoter regions of the accBC and accD1 genes. For examination purposes, claim 11 will be interpreted as a duplicate of claim 1 as interpreted. Correction is required.
Claim 12 is indefinite in the recitation of “wherein the modifications are to nucleic acid sequences of chromosomally encoded genes” for the following reasons. As written, it is unclear as to which are the chromosomally encoded genes being referred to. For examination purposes, it will be assumed that claim 12 is a duplicate of claim 1 as interpreted. Correction is required.
Claim 13 remains indefinite in the recitation of “wherein the cell is non-recombinantly altered” for the following reasons. It is unclear as to how this term further limits the cell. Does it refer to a naturally occurring cell that has the recited mutations? Does it refer to a particular method by which the cell has been modified? For examination purposes, claim 13 will be interpreted as a duplicate of claim 1 as interpreted. Correction is required.
Claim 20 is indefinite in the recitation of “wherein the cell comprises a polynucleotide comprising a nucleic acid sequence selected from the group consisting of: a. a nucleic acid sequence containing at least 95% identity to the nucleic acid sequence according to SEQ ID NO. 19, b. a nucleic acid sequence which, under stringent conditions, hybridizes with a complementary sequence of a nucleic acid sequence according to SEQ ID NO. 19, c. a nucleic acid sequence according to SEQ. ID NO. 19, d. a nucleic acid sequence coding for a 5,7-dihydroxy-2-methylchromone synthase corresponding to each of the nucleic acids in accordance with a)-c) which is adapted to the codon usage of coryneform bacteria, and e. that differs from these nucleic acid sequences in accordance with a)-d) by the degeneracy of the genetic code” for the following reasons.
The term “sequence selected from the group consisting of ..e. that differs from these nucleic acid sequences..” is completely unclear and confusing because the term “that differs from…” is not a sequence. In addition, the term “a nucleic acid sequence which, under stringent conditions, hybridizes with a complementary sequence of a nucleic acid sequence” is unclear because as known in the art, nucleotide sequences are graphical representations of the order in which nucleotides are arranged in a nucleic acid molecule. Hybridization occurs between nucleic acid molecules. Therefore, it is unclear as to how a graphical representation can hybridize to another graphical representation. Furthermore, the term “stringent conditions” is a relative term which encompasses diverse hybridization conditions that do not result in the hybridization of the same nucleic acids. Nucleic acids which will hybridize under some hybridization conditions will not necessarily hybridize under different conditions. The art does not recognize a single set of experimental conditions as “stringent”. Therefore, it is unclear which nucleic acid is recited absent a statement of the experimental conditions under which the hybridization reaction is performed. For examination purposes, it will be assumed that the term “stringent conditions” reads “any hybridization conditions”. For examination purposes, it will be assumed that the claim requires a nucleic acid having at least 95% sequence identity to the polynucleotide of SEQ ID NO: 19, or a nucleic acid that can hybridize under any conditions to the full-length complement of the polynucleotide of SEQ ID NO: 19. Correction is required.
Claim 22 is indefinite in the recitation of “wherein the plant genes are present under the expression…” for the following reasons. There is no antecedent basis for the plant genes in claim 1. Please note that claim 1 refers to genes derived from plants, which encompasses variants of plant genes which are not necessarily plant genes. For examination purposes, claim 22 will be interpreted as a duplicate of claim 1 as interpreted above. Correction is required.
Claim 23 is indefinite in the recitation of “wherein the cell comprises a Petroselinum crispum 4clPc gene as chromosomal coding under the expression control of an inducible promoter” for the following reasons. The term “4clPc” does not convey a specific gene structure/identity. Therefore, it is unclear as to which Petroselinum crispum gene is encompassed by the term “4clPc”. In addition, the term “chromosomal coding” is unclear because one cannot determine how it further limits the gene. Does the term refer to a gene that is present in the chromosome? If the intended gene, or the protein that it encodes, is one that has a sequence identifier provided in the specification as originally filed, the claim could be amended to refer to the specific gene, or protein encoded by said gene, using a sequence identifier. For examination purposes, it will be assumed that the claim requires the cell to comprise a Petroselinum crispum gene encoding a 4-coumarate-CoA ligase, wherein said gene is under the control of an inducible promoter. Correction is required.
Claim 25 is indefinite in the recitation of “wherein the cell comprises genes selected from the group consist of …pcsshort” for the following reasons. The term “pcsshort” is unclear because it fails to convey a particular gene structure/identity, and whether it represents a genus of genes or a single gene. If the intended gene, or the protein that it encodes, is one that has a sequence identifier provided in the specification as originally filed, the claim could be amended to refer to the specific gene, or protein encoded by said gene, using a sequence identifier. For examination purposes, no patentable weight has been given to the term “pcsshort”. Correction is required.
Claim 26 is indefinite in the recitation of “..wherein the cell further comprises genes selected form the group Aloe arborescens-derived pcsshort coding for a protein with an increased 5,7-dihydroxy-2-methylchromone synthase activity (PCSshort) for the synthesis of polyketides, and b. a Corynebacterium glutamicum bacterium aroF1 gene and a Corynebacterium glutamicum bacterium tal gene” for the following reasons. The term “Aloe arborescens-derived gene pcsshort coding for a protein with an increased 5,7-dihydroxy-2-methylchromone synthase activity (PCSshort)” is unclear because one cannot determine what an Aloe arborescens-derived gene pcsshort is. Moreover, the term “increased” is a relative term and the claim fails to provide the reference for comparison (i.e., increased compared to what?). If the intended gene, or the protein that it encodes, is one that has a sequence identifier provided in the specification as originally filed, the claim could be amended to refer to the specific gene, or protein encoded by said gene, using a sequence identifier. For examination purposes, it will be assumed that the claim requires the C. glutamicum cell of claim 1 to have a gene encoding a protein having 5,7-dihydroxy-2-methylchromone synthase activity. 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, 8-9, 11-14, 17, 19-20, 22, 23, 25-26 remain 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.
This rejection has been discussed at length in the prior Office action. It is maintained for the reasons of record and those set forth below.
Applicant argues that the claims as amended now recite a specific Corynebacterium glutamicum bacteria cell comprising modifications to specific C. glutamicum genes and proteins, such that there is no doubt that the claims as amended comply with the written description requirement. Applicant states that the elements of claim 2, particularly the modifications previously recited in items a and b of claim 2 have been incorporated into claim 1. Applicant states that the subject matter of claims 14-16, 18 and 21 has been incorporated into claim 1.
Applicant’s arguments have been fully considered but not deemed persuasive to overcome the instant rejection. The Examiner acknowledges the amendments made to the claims. However, the Examiner disagrees with Applicant’s contention that the entire scope of the claims is adequately described by the teachings of the specification and/or the prior art. The claims as interpreted still require any plant enzyme associated with the production of any polyphenol or polyketide, including any 4-coumarate-CoA ligase, any stilbene synthase, any chalcone synthase, any chalcone isomerase, or any 5,7-dihydroxy-2-methylchromone synthase. See Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA ) for claim interpretation. It should also be noted that claims 19 and 20 require variants of the polypeptide of SEQ ID NO: 22 having any function, and variants of the nucleic acid of SEQ ID NO: 19 encoding proteins having any function. It is reiterated herein that no structure/function correlation has been provided that would allow one of skill in the art to recognize which proteins have the desired functional characteristics.
In addition, while the claims require any method to obtain reduction or elimination of the synthase activity of an endogenous C. glutamicum FasB protein, any method to obtain reduction or elimination of the function of a region of a promoter of an endogenous C. glutamicum gene encoding an acetyl-CoA carboxylase, any method to derepress an endogenous C. glutamicum accBC gene and accD1 gene, and any method to reduce the function of an endogenous promoter of a C. glutamicum gltA gene,
it is noted that the specification and the prior art are silent as to additional methods to obtain the desired reduction, elimination or derepression beyond deletions in the desired genes, or specific modifications to the promoter region of the C. glutamicum gltA. accBC and accD1 genes. These methods can encompass the use of unknown chemical inhibitors of enzymatic activity, unknown modifications to the FasB protein or its gene to reduce or eliminate enzymatic activity activity, expression of antisense molecules to block expression of the desired genes, or the expression of unknown repressors of the expression of the desired genes. The claims also encompass unknown methods to reduce or eliminate the recited operator binding site, such as expressing unknown nucleic acids or unknown proteins that compete with FasR for binding. The claims require derepression of the accBC and accD1 genes by means of, for example, the expression of antisense molecules of unknown structure that would block the expression of a repressor of these unknown genes, or the expression of proteins that can block the repressors of the expression of these C. glutamicum genes. The specification and the prior art are silent regarding these repressors, chemical compounds, or antisense molecules. Therefore, contrary to Applicant’s assertions, one of skill in the art cannot reasonably conclude that the entire scope of the claims is adequately described by the teachings of the specification and/or the prior art.
Claims 1-2, 4, 8-9, 11-23, 25-26 remain 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 C. glutamicum cell that comprises (i) a disruption in the endogenous fasB gene and/or the endogenous gltA gene, (ii) a disruption in the endogenous phdBCDE operon, endogenous cat gene, endogenous ben gene, endogenous pca gene, endogenous pobA gene, and/or endogenous qsuB gene, (iii) the C. glutamicum accBC and accD1 genes under the control of an inducible promoter, (iv) an E. coli gene encoding a feedback resistant DAHP synthase and an E. coli gene encoding a tyrosine ammonium lyase, (v) a nucleic acid encoding the P. crispum 4-coumarate-CoA ligase of SEQ ID NO: 22, and a nucleic acid encoding the A. hypogea stilbene synthase of SEQ ID NO: 24, (vi) nucleic acids encoding the P. hybrida chalcone synthase of SEQ ID NO: 26, and the P. hybrida chalcone isomerase of SEQ ID NO: 28, does not reasonably provide enablement for a C. glutamicum cell that has been modified by any means to (a) reduce the synthase activity of the endogenous C. glutamicum FasB protein, including any genetic modification to reduce the expression of the endogenous C. glutamicum fasB gene, (b) reduce the expression of the endogenous C. glutamicum gltA gene, (c) derepress the endogenous C. glutamicum accBC and accD1 genes, or (d) alter the ability of the endogenous promoter of the C. glutamicum gltA gene to initiate expression of said gene, wherein said C. glutamicum cell further expresses any gene encoding an enzyme associated with the synthesis of polyphenols or polyketides, wherein said C. glutamicum cell comprises variants of the polypeptide of SEQ ID NO: 22 having any function, and wherein said C. glutamicum cell comprises variants of the polynucleotide of SEQ ID NO: 19 encoding proteins having any function.. 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.
This rejection has been discussed at length in the prior Office action. It is maintained for the reasons of record and those set forth below.
Applicant submits that the claims as amended recite both structure of the proteins and genes by name and by organism, such that the claims are not directed towards any protein or any gene encoding said protein. Applicant submits that one of skill in the art could make and use the subject matter of the amended claims, Applicant argues that the claims have been amended to recite both the structure of the proteins and genes by name and by organism, such that the claims are not directed towards any protein or any gene encoding the same but rather specific proteins encoded by specific genes. Applicant states that one of skill in the art could make and use the subject matter of the amended claims. Applicant further argues that the claims 15 and 16 have been cancelled and claim 26 has been amended to remove references to an inactivated catabolic pathway.
Applicant’s arguments have been fully considered but not deemed persuasive to overcome the instant rejection. The Examiner acknowledges the amendments made to the claims. However, the Examiner disagrees with Applicant’s contention that the entire scope of the claims is fully enabled.
As explained above, the claims as interpreted still require any plant enzyme associated with the production of any polyphenol or polyketide, including any 4-coumarate-CoA ligase, any stilbene synthase, any chalcone synthase, any chalcone isomerase, or any 5,7-dihydroxy-2-methylchromone synthase. See Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA ) for claim interpretation. Moreover, claims 19 and 20 require variants of the polypeptide of SEQ ID NO: 22 having any function, and variants of the nucleic acid of SEQ ID NO: 19 encoding proteins having any function. While the specification in the instant application discloses the structure of a limited number of species of the recited genus of genes and proteins, it provides no clue as to the structural elements required in any plant enzyme associated with the production of any polyphenol or polyketide, 4-coumarate-CoA ligase, stilbene synthase, chalcone synthase, chalcone isomerase, or 5,7-dihydroxy-2-methylchromone synthase required by the claims. Similarly, the specification fails to disclose if any variant of the polypeptide of SEQ ID NO: 22 having the recited % sequence identity has 4-coumarate-CoA ligase activity or if any variant of the nucleic acid of SEQ ID NO: 19 encodes a protein with 5,7-dihydroxy-2-methylchromone synthase activity. No structure/function correlation has been provided that would allow one of skill in the art to recognize which proteins have the desired functional characteristics.
As previously discussed, while the claims require any method to obtain reduction or elimination of the synthase activity of an endogenous C. glutamicum FasB protein, any method to obtain reduction or elimination of the function of a region of a promoter of an endogenous C. glutamicum gene encoding an acetyl-CoA carboxylase, any method to derepress an endogenous C. glutamicum accBC gene and accD1 gene, and any method to reduce the function of an endogenous promoter of a C. glutamicum gltA gene,
the specification and the prior art are silent as to additional methods to obtain the desired reduction, elimination or derepression beyond deletions in the desired genes, or specific modifications to the promoter region of the C. glutamicum gltA, accBC and accD1 genes. These methods can encompass the use of unknown chemical inhibitors of enzymatic activity, unknown modifications to the FasB protein or its gene to reduce or eliminate enzymatic activity, expression of unknown antisense molecules to block expression of the desired genes, or the expression of unknown repressors of the expression of the desired genes. The claims also encompass unknown methods to reduce or eliminate the recited operator binding site, such as expressing unknown nucleic acids or unknown proteins that compete with FasR for binding. The claims require derepression of the accBC and accD1 genes by means of, for example, the expression of antisense molecules of unknown structure that would block the expression of a repressor of these genes, or the expression of proteins that block the repressors of these C. glutamicum genes. The specification and the prior art are silent regarding these repressors, chemical compounds, or antisense molecules.
In the absence of a rational and predictable scheme for selecting those genetic modifications, chemicals, proteins or nucleic acids that would result in the increase/decrease of expression of the desired gene or enzymatic activity, one of skill in the art would have to test an essentially infinite number of genes, proteins, genetic modifications and compounds to enable the entire scope of the claimed invention. Therefore, contrary to Applicant’s assertions, the entire scope of the claims is not fully enabled by the teachings of the specification and/or the prior art.
Claim Rejections - 35 USC § 103 (AIA )
Claims 1, 4, 8-9, 11-14, 17, 19, 22, 25 remain rejected under 35 U.S.C. 103 as being unpatentable over Kallscheuer et al. (Metabolic engineering 38:47-55, 2016; cited in the IDS) in view of Radmacher et al. (Microbiology 151:2421-2427, 2005; cited in the IDS), van Ooyen et al. (Journal of Biotechnology 154:140-148, 2011), Eikmanns et al. (Microbiology 140:1817-1828, 1994), Nickel et al. (Molecular Microbiology 78(1):253-265, 2010), and Yoon et al. (Biotechnology and Bioengineering 115:2067-2074, August 2018).
This rejection has been discussed at length in the prior Office action. It is maintained for the reasons of record and those set forth below.
Applicant states that for the reasons stated in the response of 5/2/2025, none of the references previously cited, either alone or in combination, disclose or suggest the features of independent claim 1. Applicant states that none of the references disclose or suggest a C. glutamicum bacteria cell with the recited modifications and an increased provision of malonyl-CoA compared to its wildtype. Applicant states that given that fasB mutants are not essential and do not appreciably affect growth, a person of ordinary skill in the art would instead conclude that fasB has little effect at all, particularly in the absence of any data or discussion on malonyl-CoA levels. Applicant states that the Examiner has failed to address Applicant’s argument that in view of the teachings of Radmacher et al. one of skill in the art would have assumed that FasA would take over the FasB function upon loss of FasB activity. Applicant argues that there is no showing that a person of ordinary skill in the art would have had a reasonable expectation that a C. glutamicum bacteria cell with the modifications recited in amended claim 1 would have an increased intracellular amount of malonyl-CoA and that it is only with the benefit of impermissible hindsight that such expectation could be made out based on the disclosures of the cited references. Applicant states that the Office relies on six references to conclude that all elements of the pending claims are disclosed or suggested.
Applicant states that there is no showing that one of skill in the art would reasonably conclude that reduced functionality of the promoter operably linked to the C. glutamicum gltA gene would not have any deleterious effects on cell growth, which would prevent an increase in intracellular amounts of malonyl-CoA. Applicant states that there is no suggestion in any of the six references cited of unexpected high yields. Applicant refers to sections of the specification, such as Figure 24 and paragraph [204] of the specification in support of the argument that the subject matter of the pending claims elicit unexpected high yields of malonyl-CoA as well as high yields of polyphenols and polyketides. Applicant refers to the Marienhagen declaration as disclosing a Figure (Figure 1) that shows the levels of resveratrol obtained with strains having different modifications and how the levels of resveratrol are the highest with a strain that comprises the features according to claim 1 as amended. Applicant states that the Marienhagen declaration shows that the inventive strain yielded 125% the amount of resveratrol as the nearest strain and over 300% of the other two tested strains. Applicant reiterates the argument that none of the cited references disclose or suggest that the subject matter of the claims would produce such unexpected high yields.
Applicant’s arguments have been fully considered but not deemed persuasive to overcome the instant rejection. The Examiner acknowledges the amendments made to the claims. The Examiner has also fully considered the Marienhagen declaration. However, the Examiner disagrees with Applicant’s contention that the cited prior art does not render the claimed invention obvious.
Contrary to Applicant’s assertions, the cited references clearly suggest that a C. glutamicum cell with the recited modifications could produce higher levels of malonyl-CoA compared to the corresponding C. glutamicum cell lacking the recited modifications. As taught by Kallscheuer et al., malonyl-CoA can be increased by increasing the expression of the genes that encode acetyl-CoA carboxylase. Another method to improve the production of acetyl-CoA carboxylase is suggested by Nickel et al. who teach that mutations in the promoter region of the accD1 and accBC genes that would inhibit the binding of the negative regulator FasR would allow the deregulated expression of the genes encoding acetyl-CoA carboxylase. Moreover, as evidenced by Yoon et al., since acetyl-CoA is a precursor of malonyl-CoA, one of skill in the art would have been highly motivated to increase the intracellular pool of acetyl-CoA so that more malonyl-CoA could be synthesized. Therefore, mutations that would reduce or eliminate the expression of genes encoding enzymes that catalyze the conversion of acetyl-CoA into other metabolites, such as the C. glutamicum gltA gene, would be highly desirable. Please note that the prior art, as evidenced by Eikmanns et al. teach that citrate synthase uses acetyl-CoA as a substrate. While it is agreed that neither Eikmanns et al. nor van Ooyen et al. specifically teach the effect of mutations to the gltA gene on malonyl-CoA levels, one of skill in the art would have understood that mutations to the gltA gene would increase the levels of acetyl-CoA, a precursor of malonyl-CoA by virtue of the fact that an enzyme that consumes acetyl-CoA as a substrate is no longer able to consume it.
With regard to the argument that the Examiner has failed to address Applicant’s argument that in view of the teachings of Radmacher et al. one of skill in the art would have assumed that FasA would take over the FasB function upon loss of FasB activity, it is noted that the Examiner provided a reasoned statement as to why one of skill in the art would have reasonably conclude that the inactivation of the fasB gene could lead to an increase in malonyl-CoA. The Examiner acknowledges that Radmacher et al. disclose the possibility of FasA being able to functionally replace FasB. However, there is no evidence to suggest that the level of biosynthesis of fatty acids from malonyl-CoA with only FasA present is absolutely unchanged, such that the consumption of malonyl-CoA is exactly the same as if FasB were to be present. Since Kallscheuer et al. teach that blocking the biosynthesis of fatty acids from malonyl-CoA allows for an increase in the intracellular malonyl-CoA pool, inactivating mutations in genes encoding fatty acid synthases is desirable. As known in the art and also taught by Radmacher et al., FAS-I enzymes such as FasB use malonyl-CoA as a substrate (page 151, right column, last three lines). While Applicant argues that one of skill in the art would have not been motivated to delete the fasB gene because fasB was found to be non-essential, it is noted that, on the contrary, one of skill in the art would have been highly motivated to delete the fasB gene because by doing so, an enzyme that consumes the desired precursor, malonyl-CoA, is no longer active, and growth is not affected. Please note that the fact that growth is not affected by a deletion in the fasB gene is an advantage. While it is agreed that Radmacher et al. do not specifically teach the effect of the fasB deletion on malonyl-CoA levels, one of skill in the art would have understood that the level of malonyl-CoA would increase by virtue of the fact that an enzyme that uses malonyl-CoA (FasB) is no longer active to consume it.
With regard to the argument that there is no showing that a person of ordinary skill in the art would have had a reasonable expectation that a C. glutamicum bacteria cell with the modifications recited in amended claim 1 would have an increased intracellular amount of malonyl-CoA and that it is only with the benefit of impermissible hindsight that such expectation could be made out based on the disclosures of the cited references, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971).
With regard to the argument that the Office relies on six references to conclude that all elements of the pending claims are disclosed or suggested, it is noted that reliance on a large number of references in a rejection does not, without more, weigh against the obviousness of the claimed invention. See In re Gorman, 933 F.2d 982, 18 USPQ2d 1885 (Fed. Cir. 1991).
With regard to the argument that there is no showing that one of skill in the art would reasonably conclude that reduced functionality of the promoter operably linked to the C. glutamicum gltA gene would not have any deleterious effects on cell growth, which would prevent an increase in intracellular amounts of malonyl-CoA, it is noted that the C. glutamicum mutants having reduced citrate synthase activity disclosed by van Ooyen et al. show growth in media comprising glucose and/or acetate (Table 3).
With regard to the unexpected levels of malonyl-CoA disclosed in the specification and the unexpected levels of resveratrol disclosed in the Marienhagen declaration, it is noted that these “unexpected” results are found in a C. glutamicum cell modified to have specific structural modifications and to express specific enzymes associated with the synthesis of resveratrol. See page 2 of the Marienhagen declaration that describes the specific modifications made to the C. glutamicum cell that produces the results shown in Figure 1. It should be noted that the claims are currently generic with regard to some of the modifications and genes required. Also, while it is agreed that the cited prior art does not teach or suggest the specific amounts of malonyl-CoA of Figure 24/paragraph [204] of the specification, or the specific amounts of resveratrol shown in Figure 1 of the Marienhagen declaration, one of skill in the art did not need to know these specific amounts to be motivated to combine the teachings of the prior art to reasonably expect some increase in malonyl-CoA. For the reasons extensively discussed above and in prior Office actions, the teachings of the prior art as evidenced by Radmacher et al., van Ooyen et al., Eikmanns et al., Nickel et al. and Yoon et al. clearly suggest the modifications that could lead to an increase in malonyl-CoA and Kallscheuer et al. clearly provide the motivation to increase intracellular malonyl-CoA. Therefore, for the reasons of record and those set forth above, one of skill in the art would conclude that the claimed invention is obvious over the cited prior art.
Conclusion
No claim is in condition for allowance.
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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
March 25, 2026
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