DETAILED ACTION
Claims 1-9 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 .
Claim Objections
Claims 6, 6-7, and 9 are objected to because of the following informalities:
In claim 4, line 1, “a” before “ketol” should be replaced with --the--.
In claim 6, “Corynebacterium glutamicum” should be italicized.
In claims 7 and 9, line 1, “a” before “ketol” should be replaced with --the--.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claim 9 is rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon without significantly more. The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception.
The claim recites a medium in which a microorganism is cultured. This judicial exception is not integrated into a practical application because such media include soils, water, and organisms in nature; the claim does not require that the medium comprising the microorganism comprising the variant of claim 1. Thus, this claim is not directed to significantly more than a product of nature.
Claim Rejections - 35 USC § 112
The following is a quotation 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 35 U.S.C. 112 (pre-AIA ), first paragraph:
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 1-9 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.
Claim 1 requires any ketol-acid reductoisomerase variant as long as it has a V or D at the amino acid corresponding to amino acid 87 of SEQ ID NO:1. Claim 1 is drawn to a broad genus of variants encompassing ketol-acid reductoisomerases from any source with any number of variations relative to the original protein.
Dependent claim 2 requires a ketol-acid reductoisomerase variant with 80% identity to SEQ ID NO:3 or 25. Proteins with 80% identity to 338 amino acid long SEQ ID NO:3 or 25 would have 67 amino acid substitutions relative to SEQ ID NO:3 or 25.
The specification fails to describe the full scope of ketol-acid reductoisomerases and fails to describe the full scope of ketol-acid reductoisomerases with 80% identity to 338 amino acid long SEQ ID NO:3 or 25.
The prior art does not describe ketol-acid reductoisomerases with 80% to 92% identity to SEQ ID NO:1, 3, or 25. A ketol-acid reductoisomerase with 92% identity to SEQ ID NO:1was known in the prior art (GenBank ILVC_COREF, 2003, www.ncbi.nlm.nih.gov/protein/Q8FPX1; alignment shown below), but ones 80% to 92% identity to SEQ ID NO:1, 3, or 25 were not.
ILVC_COREF
ID ILVC_COREF Reviewed; 337 AA.
AC Q8FPX1;
DT 06-JUN-2003, integrated into UniProtKB/Swiss-Prot.
DT 06-JUN-2003, sequence version 2.
DT 18-JUN-2025, entry version 127.
DE RecName: Full=Ketol-acid reductoisomerase (NADP(+)) {ECO:0000255|HAMAP-Rule:MF_00435};
DE Short=KARI {ECO:0000255|HAMAP-Rule:MF_00435};
DE EC=1.1.1.86 {ECO:0000255|HAMAP-Rule:MF_00435};
DE AltName: Full=Acetohydroxy-acid isomeroreductase {ECO:0000255|HAMAP-Rule:MF_00435};
DE Short=AHIR {ECO:0000255|HAMAP-Rule:MF_00435};
DE AltName: Full=Alpha-keto-beta-hydroxylacyl reductoisomerase {ECO:0000255|HAMAP-Rule:MF_00435};
DE AltName: Full=Ketol-acid reductoisomerase type 1 {ECO:0000255|HAMAP-Rule:MF_00435};
DE AltName: Full=Ketol-acid reductoisomerase type I {ECO:0000255|HAMAP-Rule:MF_00435};
GN Name=ilvC {ECO:0000255|HAMAP-Rule:MF_00435}; OrderedLocusNames=CE1367;
OS Corynebacterium efficiens (strain DSM 44549 / YS-314 / AJ 12310 / JCM 11189
OS / NBRC 100395).
OC Bacteria; Bacillati; Actinomycetota; Actinomycetes; Mycobacteriales;
OC Corynebacteriaceae; Corynebacterium.
OX NCBI_TaxID=196164;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 44549 / YS-314 / AJ 12310 / JCM 11189 / NBRC 100395;
RX PubMed=12840036; DOI=10.1101/gr.1285603;
RA Nishio Y., Nakamura Y., Kawarabayasi Y., Usuda Y., Kimura E., Sugimoto S.,
RA Matsui K., Yamagishi A., Kikuchi H., Ikeo K., Gojobori T.;
RT "Comparative complete genome sequence analysis of the amino acid
RT replacements responsible for the thermostability of Corynebacterium
RT efficiens.";
RL Genome Res. 13:1572-1579(2003).
CC -!- FUNCTION: Involved in the biosynthesis of branched-chain amino acids
CC (BCAA). Catalyzes an alkyl-migration followed by a ketol-acid reduction
CC of (S)-2-acetolactate (S2AL) to yield (R)-2,3-dihydroxy-isovalerate. In
CC the isomerase reaction, S2AL is rearranged via a Mg-dependent methyl
CC migration to produce 3-hydroxy-3-methyl-2-ketobutyrate (HMKB). In the
CC reductase reaction, this 2-ketoacid undergoes a metal-dependent
CC reduction by NADPH to yield (R)-2,3-dihydroxy-isovalerate.
CC {ECO:0000255|HAMAP-Rule:MF_00435}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R)-2,3-dihydroxy-3-methylbutanoate + NADP(+) = (2S)-2-
CC acetolactate + NADPH + H(+); Xref=Rhea:RHEA:22068, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:49072, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349,
CC ChEBI:CHEBI:58476; EC=1.1.1.86; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00435};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R,3R)-2,3-dihydroxy-3-methylpentanoate + NADP(+) = (S)-2-
CC ethyl-2-hydroxy-3-oxobutanoate + NADPH + H(+); Xref=Rhea:RHEA:13493,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:49256, ChEBI:CHEBI:49258,
CC ChEBI:CHEBI:57783, ChEBI:CHEBI:58349; EC=1.1.1.86;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00435};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00435};
CC Note=Binds 2 magnesium ions per subunit. {ECO:0000255|HAMAP-
CC Rule:MF_00435};
CC -!- PATHWAY: Amino-acid biosynthesis; L-isoleucine biosynthesis; L-
CC isoleucine from 2-oxobutanoate: step 2/4. {ECO:0000255|HAMAP-
CC Rule:MF_00435}.
CC -!- PATHWAY: Amino-acid biosynthesis; L-valine biosynthesis; L-valine from
CC pyruvate: step 2/4. {ECO:0000255|HAMAP-Rule:MF_00435}.
CC -!- SIMILARITY: Belongs to the ketol-acid reductoisomerase family.
CC {ECO:0000255|HAMAP-Rule:MF_00435}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAC18177.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; BA000035; BAC18177.1; ALT_INIT; Genomic_DNA.
DR RefSeq; WP_006769331.1; NC_004369.1.
DR AlphaFoldDB; Q8FPX1; -.
DR SMR; Q8FPX1; -.
DR STRING; 196164.gene:10741776; -.
DR KEGG; cef:CE1367; -.
DR eggNOG; COG0059; Bacteria.
DR HOGENOM; CLU_033821_0_1_11; -.
DR OrthoDB; 9804088at2; -.
DR UniPathway; UPA00047; UER00056.
DR UniPathway; UPA00049; UER00060.
DR Proteomes; UP000001409; Chromosome.
DR GO; GO:0005829; C:cytosol; IEA:TreeGrafter.
DR GO; GO:0004455; F:ketol-acid reductoisomerase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0050661; F:NADP binding; IEA:InterPro.
DR GO; GO:0009097; P:isoleucine biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0009099; P:L-valine biosynthetic process; IEA:UniProtKB-UniRule.
DR FunFam; 3.40.50.720:FF:000023; Ketol-acid reductoisomerase (NADP(+)); 1.
DR Gene3D; 6.10.240.10; -; 1.
DR Gene3D; 3.40.50.720; NAD(P)-binding Rossmann-like Domain; 1.
DR HAMAP; MF_00435; IlvC; 1.
DR InterPro; IPR008927; 6-PGluconate_DH-like_C_sf.
DR InterPro; IPR013023; KARI.
DR InterPro; IPR000506; KARI_C.
DR InterPro; IPR013116; KARI_N.
DR InterPro; IPR014359; KARI_prok.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR NCBIfam; TIGR00465; ilvC; 1.
DR NCBIfam; NF004017; PRK05479.1; 1.
DR NCBIfam; NF009940; PRK13403.1; 1.
DR PANTHER; PTHR21371; KETOL-ACID REDUCTOISOMERASE, MITOCHONDRIAL; 1.
DR PANTHER; PTHR21371:SF1; KETOL-ACID REDUCTOISOMERASE, MITOCHONDRIAL; 1.
DR Pfam; PF01450; KARI_C; 1.
DR Pfam; PF07991; KARI_N; 1.
DR PIRSF; PIRSF000116; IlvC_gammaproteo; 1.
DR SUPFAM; SSF48179; 6-phosphogluconate dehydrogenase C-terminal domain-like; 1.
DR SUPFAM; SSF51735; NAD(P)-binding Rossmann-fold domains; 1.
DR PROSITE; PS51851; KARI_C; 1.
DR PROSITE; PS51850; KARI_N; 1.
PE 3: Inferred from homology;
KW Amino-acid biosynthesis; Branched-chain amino acid biosynthesis; Magnesium;
KW Metal-binding; NADP; Oxidoreductase; Reference proteome.
FT CHAIN 1..337
FT /note="Ketol-acid reductoisomerase (NADP(+))"
FT /id="PRO_0000151305"
FT DOMAIN 3..183
FT /note="KARI N-terminal Rossmann"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01197"
FT DOMAIN 184..329
FT /note="KARI C-terminal knotted"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01198"
FT ACT_SITE 109
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00435"
FT BINDING 26..29
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00435"
FT BINDING 49
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00435"
FT BINDING 52
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00435"
FT BINDING 54
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00435"
FT BINDING 84..87
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00435"
FT BINDING 135
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00435"
FT BINDING 192
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00435"
FT BINDING 192
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00435"
FT BINDING 196
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00435"
FT BINDING 228
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00435"
FT BINDING 232
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00435"
FT BINDING 253
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00435"
SQ SEQUENCE 337 AA; 36236 MW; D955FECFCE32C498 CRC64;
Query Match 92.5%; Score 1588.5; Length 337;
Best Local Similarity 91.1%;
Matches 308; Conservative 14; Mismatches 15; Indels 1; Gaps 1;
Qy 1 MAIELLYDADADLSLIQGRKVAIVGYGSQGHAHSQNLRDSGVEVVIGLREGSKSAEKAKE 60
||||| ||||||||:||||||||:|||||||||:||||||||||||||||||||||||||
Db 1 MAIELFYDADADLSIIQGRKVAIIGYGSQGHAHAQNLRDSGVEVVIGLREGSKSAEKAKE 60
Qy 61 AGFEVKTTAEAAAWADVIMLLAPDTSQAEIFTNDIEPNLNAGDALLFGHGLNIHFDLIKP 120
|||||||||||||||::||:|||||||| |||||:||||| |||| ||||||||||||||
Db 61 AGFEVKTTAEAAAWANLIMILAPDTSQASIFTNDVEPNLNEGDALFFGHGLNIHFDLIKP 120
Qy 121 ADDIIVGMVAPKGPGHLVRRQFVDGKGVPCLIAVDQDPTGTAQALTLSYAAAIGGARAGV 180
||:||||||||||||||||||||||||||||||:|||||| |||| ||||:|||| |||:
Db 121 ADNIIVGMVAPKGPGHLVRRQFVDGKGVPCLIAIDQDPTGDAQALALSYASAIGGGRAGI 180
Qy 181 IPTTFEAETVTDLFGEQAVLCGGTEELVKVGFEVLTEAGYEPEMAYFEVLHELKLIVDLM 240
||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||
Db 181 IPTTFEAETVTDLFGEQAVLCGGTEELVKTGFEVLTEAGYEPEMAYFEVLHELKLIVDLM 240
Qy 241 FEGGISNMNYSVSDTAEFGGYLSGPRVIDADTKSRMKDILTDIQDGTFTKRLIANVENGN 300
|||||:||||||||||||||||||||||:|||| ||||||||||||||||||||||||||
Db 241 FEGGITNMNYSVSDTAEFGGYLSGPRVINADTKERMKDILTDIQDGTFTKRLIANVENGN 300
Qy 301 TELEGLRASYNNHPIEETGAKLRDLMSWVKVDARAETA 338
|||||||| | |||||||||||||||||| : |||
Db 301 TELEGLRAKYAEHPIEETGAKLRDLMSWVK-NPLTETA 337
The specification fails to make up for the lack of knowledge on the art. The specification also fails to describe the full scope of ketol-acid reductoisomerases.
The only species described in the specification is SEQ ID NO:1 and single amino acid variants thereof. One of skill in the art would not recognize that Applicant was in possession of the necessary common attributes or features of the genus in view of the disclosed species.
Hence, Applicant has not, in fact, described variant ketol-acid reductoisomerases over the full scope of the claims, and the specification fails to provide an adequate written description of the claimed invention.
Therefore, given the lack of written description in the specification with regard to the structural and functional characteristics of the claimed compositions, Applicant does not appear to have been in possession of the claimed genus at the time this application was filed.
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 the second paragraph of 35 U.S.C. 112:
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 2 and 9 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 that the inventor or a joint inventor, or for pre-AIA the applicant, regards as the invention. Dependent claims are included in all rejections.
Claim 2 is indefinite in its recitation of “amino acid sequence having sequence identity of 80% or more thereto”. It is not clear if this refers to a variant with 80% or more identity to SEQ ID NO:3 or SEQ ID NO:25 because it is not clear to what “thereto” refers.
Claim 9 is indefinite in its recitation of “a combination of two or more thereof”. The options for the claimed composition are a microorganism or a medium. For there to be a combination of or more than two thereof, there would need to be at least a third option. It is not clear what that might be.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), fourth paragraph:
Subject to the [fifth paragraph of 35 U.S.C. 112 (pre-AIA )], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 4-9 are rejected under 35 U.S.C. 112(d) or 35 U.S.C. 112(pre-AIA ), fourth paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 4 is drawn to a microorganism comprising the ketol acid reductoisomerase variant of claim 1 or a polynucleotide encoding the variant, claim 7 is drawn to a method of using such a microorganism, and claim 9 is drawn to a composition comprising such a microorganism. A microorganism comprising a polynucleotide encoding the variant does not necessarily comprise the variant itself. Thus, the claims fail to include all the limitations of the claim upon which they depend.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention.
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 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.
Claim 9 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Li et al (2016, US 9,512,408).
Li et al teach a medium for growing a microorganism and 48-well plates comprising it (column 60, lines 22-45); these plates are a composition comprising a medium for growing the microorganism.
The prior art does not teach a ketol-acid reductoisomerase variant with a V or D at the amino acid corresponding to amino acid 87 of SEQ ID NO:1. For example, while Li et al (2016, US 9,512,408) teach numerous ketol-acid reductoisomerase variant (see columns 2-4), none have a V or D at the amino acid corresponding to amino acid 87 of SEQ ID NO:1 (amino acid 87 of SEQ ID NO:1 corresponds to amino acid 86 of their proteins).
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Anne R. Kubelik, Ph.D., whose telephone number is (571) 272-0801. The examiner can normally be reached Monday through Friday, 9:00 am - 5:00 pm Eastern.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Amjad Abraham, can be reached at (571) 270-7058. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Anne Kubelik/Primary Examiner, Art Unit 1663
