DETAILED ACTION
Claims 1-10 are pending.
The non-final rejection mailed 3 September 2026 is withdrawn and replaced with the instant non-final rejection.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
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.
Section 33(a) of the America Invents Act reads as follows:
Notwithstanding any other provision of law, no patent may issue on a claim directed to or encompassing a human organism.
Claims 3, 5-7 and 9-10 are rejected under 35 U.S.C. 101 and section 33(a) of the America Invents Act as being directed to or encompassing a human organism. See also Animals - Patentability, 1077 Off. Gaz. Pat. Office 24 (April 21, 1987) (indicating that human organisms are excluded from the scope of patentable subject matter under 35 U.S.C. 101).
Claim 3 is drawn to a transformant comprising the variant of SEQ ID NO:1 or a nucleic acid encoding it. Such transformants include humans. Dependent claim 5 recites that the transformant has the ability to produce L-glutamic acid, which humans can do. Claim 6 is drawn to a method of isolating L-glutamic acid from the transformant.
As all these encompass humans, these claims are excluded from the scope of patentable subject matter under 35 U.S.C. 101).
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 1-10 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter that was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
The claims are broadly drawn to a deoxyribose-phosphate aldolase variant consisting of SEQ ID NO: 2, a nucleic acid encoding it, a transformant comprising either, and a method of using the transformant to make L-glutamic acid.
Applicant did not delete the cysteine at position 225 of the deoxyribose-phosphate aldolase of SEQ ID NO:4
Example 1 of the specification proports to describe the construction of a vector expressing a deoxyribose-phosphate aldolase variant that has a deletion of cysteine at position 225 of the deoxyribose-phosphate aldolase of SEQ ID NO:4 (¶63).
However, this is not what was actually done.
SEQ ID NO:4 is only 224 amino acids long:
PNG
media_image1.png
466
592
media_image1.png
Greyscale
Thus, SEQ ID NO:4 has no cysteine at position 225 to remove, and Applicant could not have constructed a vector expressing a deoxyribose-phosphate aldolase variant that has a deletion of cysteine at position 225 of the deoxyribose-phosphate aldolase of SEQ ID NO:4.
SEQ ID NO:2 is not a deoxyribose-phosphate aldolase and expressing SEQ ID NO:2 in a transformant will not produce L-glutamic acid
Second, while SEQ ID NO:2 is 214 amino acids long, it only has 75 amino acids of SEQ ID NO:4.
US-18-993-134-4
Sequence 4, US/18993134
GENERAL INFORMATION
APPLICANT: DAESANG CORPORATION (en)
TITLE OF INVENTION: Mutant microorganism of Corynebacterium genus producing L-glutamic acid and method for producing L-glutamic acid using the same (en)
FILE REFERENCE: BPX230022PCT
CURRENT APPLICATION NUMBER: US/18/993,134
CURRENT FILING DATE: 2025-01-10
NUMBER OF SEQ ID NOS: 9
SEQ ID NO 4
LENGTH: 224
TYPE: PRT
FEATURE:
NAME/KEY: source
LOCATION: 1..224
QUALIFIERS: mol_type = protein
organism = Corynebacterium sp.
Query Match 33.5%; Score 374; Length 224;
Best Local Similarity 100.0%;
Matches 75; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MDMTISRATMAQILDYTLLGPEVTNSELAAFIDSAIELGVGTICVPNSMVNLTAKAQEAG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MDMTISRATMAQILDYTLLGPEVTNSELAAFIDSAIELGVGTICVPNSMVNLTAKAQEAG 60
Qy 61 IRVATVAGFPHGKTP 75
|||||||||||||||
Db 61 IRVATVAGFPHGKTP 75
As SEQ ID NO:2 only comprises one-third of a deoxyribose-phosphate aldolase, it does not have any deoxyribose-phosphate aldolase activity. The specification does not teach how to use a protein comprising only one-third of a deoxyribose-phosphate aldolase; the protein itself will not have any activity in any biochemical reaction. Transformants comprising a nucleic acid encoding it would not produce L-glutamic acid.
As SEQ ID NO:2 is not a deoxyribose-phosphate aldolase or a variant of one and does not have any function, an organism transformed with it will not produce L-glutamic acid in excess of what the organism does naturally. The specification does not teach any other way to use such a transformant.
SEQ ID NO:1 does not encode SEQ ID NO:2
The specification implies that SEQ ID NO:1 encodes SEQ ID NO:2 (¶25-26).
SEQ ID NO:1 does not encode SEQ ID NO:2:
US-18-993-134-1
Sequence 1, US/18993134
GENERAL INFORMATION
APPLICANT: DAESANG CORPORATION (en)
TITLE OF INVENTION: Mutant microorganism of Corynebacterium genus producing L-glutamic acid and method for producing L-glutamic acid using the same (en)
FILE REFERENCE: BPX230022PCT
CURRENT APPLICATION NUMBER: US/18/993,134
CURRENT FILING DATE: 2025-01-10
NUMBER OF SEQ ID NOS: 9
SEQ ID NO 1
LENGTH: 674
TYPE: DNA
FEATURE:
NAME/KEY: source
LOCATION: 1..674
QUALIFIERS: mol_type = other DNA
organism = synthetic construct
Alignment Scores:
Length: 674
Score: 1023.00 Matches: 214
Percent Similarity: 95.5% Conservative: 0
Best Local Similarity: 95.5% Mismatches: 0
Query Match: 91.5% Indels: 10
Gaps: 9
US-18-993-134-2 (1-214) x US-18-993-134-1 (1-674)
Qy 1 MetAspMetThrIleSerArgAlaThrMetAlaGlnIleLeuAspTyrThrLeuLeuGly 20
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 ATGGATATGACGATCTCCCGCGCCACCATGGCCCAAATCCTTGACTACACCCTCCTCGGA 60
Qy 21 ProGluValThrAsnSerGluLeuAlaAlaPheIleAspSerAlaIleGluLeuGlyVal 40
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 CCAGAAGTAACCAACTCCGAACTGGCCGCATTTATAGATTCCGCAATTGAGCTGGGAGTC 120
Qy 41 GlyThrIleCysValProAsnSerMetValAsnLeuThrAlaLysAlaGlnGluAlaGly 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 GGAACGATCTGTGTCCCCAATAGCATGGTCAACTTAACTGCAAAAGCCCAAGAAGCTGGA 180
Qy 61 IleArgValAlaThrValAlaGlyPheProHisGlyLysThrProArgTrp---LysPro 79
||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||
Db 181 ATTCGCGTGGCCACCGTCGCAGGATTCCCGCACGGCAAAACCCCGCGTTGGTGAAAGCCG 240
Qy 80 ProLysLeuAlaLeuProTyrSerProGluLeuProLys---MetLeuPheTrpIleLeu 98
||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Db 241 CCGAAGCTCGCCTTGCCGTACAGTCCGGAGCTTCCGAAGTAGATGTTGTTTTGGATATTG 300
Qy 99 Arg------LysArgGluMetProIleGlyCysCysArgLysLeuTrpGlnSerGlyArg 116
||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 CGGTAGTGAAAGAGGGAGATGCCAATAGGTTGCTGCAGGAAATTGTGGCAATCAGGGAGG 360
Qy 117 LeuPheHisLeuLeuTrpCys---AsnSerSerSerArgArgLeuSerTrpValMetMet 135
||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Db 361 CTGTTCCATCTCCTGTGGTGCTGAAATTCATCCTCGAGACGGCTGTCGTGGGTGATGATG 420
Qy 136 GlnLeu---LeuGln---MetHis---LeuLeuGlnValLeuThrSerLeuLysLeuPro 152
|||||| |||||| |||||| |||||||||||||||||||||||||||||||||
Db 421 CAATTGTGACTGCAGTGAATGCATTGATTGCTGCAGGTGCTGACTTCGCTAAAACTTCCA 480
Qy 153 ArgAspSerThrGlnArgGluGluGlnLeuLeuArgLeuPheGly---TrpLeuArgLeu 171
||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||
Db 481 CGGGATTCCACCCAGCGGGAGGAGCAACTGTTGAGGCTGTTCGGGTGATGGCTTCGGCTT 540
Qy 172 LeuGlyGluGlyLeuGluLeuArgLeuProValGly---ThrLeuGlyLysMetArgTrp 190
|||||||||||||||||||||||||||||||||||| |||||||||||||||||||||
Db 541 CTCGGGGAAGGGTTGGAATTAAGGCTGCCGGTGGGGTGAACACTTGGGAAGATGCGGTGG 600
Qy 191 ArgLeuLeuLysGlnGlyLeuLeuAlaLeuGluLeuLeuMetArgGluProPheTrpArg 210
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 CGTTTGTTGAAGCAGGGGCTACTCGCATTGGAACTTCTAATGCGGGAGCCATTTTGGAGG 660
Qy 211 ValArgArgSer 214
||||||||||||
Db 661 GTGCGCCGGAGT 672
SEQ ID NO:1 has a stop codon at bases 242-244, as well as having other in-frame stop codons (all such stop codons are in bold above).
Instead, SEQ ID NO:1 is a one-base deletion of SEQ ID NO:3 at base 220:
US-18-993-134-3
Sequence 3, US/18993134
GENERAL INFORMATION
APPLICANT: DAESANG CORPORATION (en)
TITLE OF INVENTION: Mutant microorganism of Corynebacterium genus producing L-glutamic acid and method for producing L-glutamic acid using the same (en)
FILE REFERENCE: BPX230022PCT
CURRENT APPLICATION NUMBER: US/18/993,134
CURRENT FILING DATE: 2025-01-10
NUMBER OF SEQ ID NOS: 9
SEQ ID NO 3
LENGTH: 675
TYPE: DNA
FEATURE:
NAME/KEY: source
LOCATION: 1..675
QUALIFIERS: mol_type = genomic DNA
organism = Corynebacterium sp.
Query Match 98.4%; Score 663; Length 675;
Best Local Similarity 99.9%;
Matches 674; Conservative 0; Mismatches 0; Indels 1; Gaps 1;
Qy 1 ATGGATATGACGATCTCCCGCGCCACCATGGCCCAAATCCTTGACTACACCCTCCTCGGA 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 ATGGATATGACGATCTCCCGCGCCACCATGGCCCAAATCCTTGACTACACCCTCCTCGGA 60
Qy 61 CCAGAAGTAACCAACTCCGAACTGGCCGCATTTATAGATTCCGCAATTGAGCTGGGAGTC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 CCAGAAGTAACCAACTCCGAACTGGCCGCATTTATAGATTCCGCAATTGAGCTGGGAGTC 120
Qy 121 GGAACGATCTGTGTCCCCAATAGCATGGTCAACTTAACTGCAAAAGCCCAAGAAGCTGGA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 GGAACGATCTGTGTCCCCAATAGCATGGTCAACTTAACTGCAAAAGCCCAAGAAGCTGGA 180
Qy 181 ATTCGCGTGGCCACCGTCGCAGGATTCCCGCACGGCAAAA-CCCCGCGTTGGTGAAAGCC 239
|||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||
Db 181 ATTCGCGTGGCCACCGTCGCAGGATTCCCGCACGGCAAAACCCCCGCGTTGGTGAAAGCC 240
Qy 240 GCCGAAGCTCGCCTTGCCGTACAGTCCGGAGCTTCCGAAGTAGATGTTGTTTTGGATATT 299
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 GCCGAAGCTCGCCTTGCCGTACAGTCCGGAGCTTCCGAAGTAGATGTTGTTTTGGATATT 300
Qy 300 GCGGTAGTGAAAGAGGGAGATGCCAATAGGTTGCTGCAGGAAATTGTGGCAATCAGGGAG 359
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 GCGGTAGTGAAAGAGGGAGATGCCAATAGGTTGCTGCAGGAAATTGTGGCAATCAGGGAG 360
Qy 360 GCTGTTCCATCTCCTGTGGTGCTGAAATTCATCCTCGAGACGGCTGTCGTGGGTGATGAT 419
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 GCTGTTCCATCTCCTGTGGTGCTGAAATTCATCCTCGAGACGGCTGTCGTGGGTGATGAT 420
Qy 420 GCAATTGTGACTGCAGTGAATGCATTGATTGCTGCAGGTGCTGACTTCGCTAAAACTTCC 479
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 GCAATTGTGACTGCAGTGAATGCATTGATTGCTGCAGGTGCTGACTTCGCTAAAACTTCC 480
Qy 480 ACGGGATTCCACCCAGCGGGAGGAGCAACTGTTGAGGCTGTTCGGGTGATGGCTTCGGCT 539
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 ACGGGATTCCACCCAGCGGGAGGAGCAACTGTTGAGGCTGTTCGGGTGATGGCTTCGGCT 540
Qy 540 TCTCGGGGAAGGGTTGGAATTAAGGCTGCCGGTGGGGTGAACACTTGGGAAGATGCGGTG 599
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 TCTCGGGGAAGGGTTGGAATTAAGGCTGCCGGTGGGGTGAACACTTGGGAAGATGCGGTG 600
Qy 600 GCGTTTGTTGAAGCAGGGGCTACTCGCATTGGAACTTCTAATGCGGGAGCCATTTTGGAG 659
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 GCGTTTGTTGAAGCAGGGGCTACTCGCATTGGAACTTCTAATGCGGGAGCCATTTTGGAG 660
Qy 660 GGTGCGCCGGAGTAG 674
|||||||||||||||
Db 661 GGTGCGCCGGAGTAG 675
Applicant produced L-glutamic acid by replacing SEQ ID NO:3 with SEQ ID NO:1 in a Corynebacterium glutamicum strain, not by expressing SEQ ID NO:2, per se.
SEQ ID NO:3 encodes SEQ ID NO:4:
US-18-993-134-3
Sequence 3, US/18993134
GENERAL INFORMATION
APPLICANT: DAESANG CORPORATION (en)
TITLE OF INVENTION: Mutant microorganism of Corynebacterium genus producing L-glutamic acid and method for producing L-glutamic acid using the same (en)
FILE REFERENCE: BPX230022PCT
CURRENT APPLICATION NUMBER: US/18/993,134
CURRENT FILING DATE: 2025-01-10
NUMBER OF SEQ ID NOS: 9
SEQ ID NO 3
LENGTH: 675
TYPE: DNA
FEATURE:
NAME/KEY: source
LOCATION: 1..675
QUALIFIERS: mol_type = genomic DNA
organism = Corynebacterium sp.
Alignment Scores:
Length: 675
Score: 1087.00 Matches: 224
Percent Similarity: 100.0% Conservative: 0
Best Local Similarity: 100.0% Mismatches: 0
Query Match: 100.0% Indels: 0
Gaps: 0
US-18-993-134-4 (1-224) x US-18-993-134-3 (1-675)
Qy 1 MetAspMetThrIleSerArgAlaThrMetAlaGlnIleLeuAspTyrThrLeuLeuGly 20
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 ATGGATATGACGATCTCCCGCGCCACCATGGCCCAAATCCTTGACTACACCCTCCTCGGA 60
Qy 21 ProGluValThrAsnSerGluLeuAlaAlaPheIleAspSerAlaIleGluLeuGlyVal 40
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 CCAGAAGTAACCAACTCCGAACTGGCCGCATTTATAGATTCCGCAATTGAGCTGGGAGTC 120
Qy 41 GlyThrIleCysValProAsnSerMetValAsnLeuThrAlaLysAlaGlnGluAlaGly 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 GGAACGATCTGTGTCCCCAATAGCATGGTCAACTTAACTGCAAAAGCCCAAGAAGCTGGA 180
Qy 61 IleArgValAlaThrValAlaGlyPheProHisGlyLysThrProAlaLeuValLysAla 80
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 ATTCGCGTGGCCACCGTCGCAGGATTCCCGCACGGCAAAACCCCCGCGTTGGTGAAAGCC 240
Qy 81 AlaGluAlaArgLeuAlaValGlnSerGlyAlaSerGluValAspValValLeuAspIle 100
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 GCCGAAGCTCGCCTTGCCGTACAGTCCGGAGCTTCCGAAGTAGATGTTGTTTTGGATATT 300
Qy 101 AlaValValLysGluGlyAspAlaAsnArgLeuLeuGlnGluIleValAlaIleArgGlu 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 GCGGTAGTGAAAGAGGGAGATGCCAATAGGTTGCTGCAGGAAATTGTGGCAATCAGGGAG 360
Qy 121 AlaValProSerProValValLeuLysPheIleLeuGluThrAlaValValGlyAspAsp 140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 GCTGTTCCATCTCCTGTGGTGCTGAAATTCATCCTCGAGACGGCTGTCGTGGGTGATGAT 420
Qy 141 AlaIleValThrAlaValAsnAlaLeuIleAlaAlaGlyAlaAspPheAlaLysThrSer 160
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 GCAATTGTGACTGCAGTGAATGCATTGATTGCTGCAGGTGCTGACTTCGCTAAAACTTCC 480
Qy 161 ThrGlyPheHisProAlaGlyGlyAlaThrValGluAlaValArgValMetAlaSerAla 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 ACGGGATTCCACCCAGCGGGAGGAGCAACTGTTGAGGCTGTTCGGGTGATGGCTTCGGCT 540
Qy 181 SerArgGlyArgValGlyIleLysAlaAlaGlyGlyValAsnThrTrpGluAspAlaVal 200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 TCTCGGGGAAGGGTTGGAATTAAGGCTGCCGGTGGGGTGAACACTTGGGAAGATGCGGTG 600
Qy 201 AlaPheValGluAlaGlyAlaThrArgIleGlyThrSerAsnAlaGlyAlaIleLeuGlu 220
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 GCGTTTGTTGAAGCAGGGGCTACTCGCATTGGAACTTCTAATGCGGGAGCCATTTTGGAG 660
Qy 221 GlyAlaProGlu 224
||||||||||||
Db 661 GGTGCGCCGGAG 672
For background, SEQ ID NO:4 differs from the closest deoxyribose-phosphate aldolase in the art (GenBank AKF26444, 2015, www.ncbi.nlm.nih.gov/protein/AKF26444) by a few amino acids:
A0A0F6SQM0_9CORY
ID A0A0F6SQM0_9CORY Unreviewed; 224 AA.
AC A0A0F6SQM0;
DT 22-JUL-2015, integrated into UniProtKB/TrEMBL.
DT 22-JUL-2015, sequence version 1.
DT 08-OCT-2025, entry version 43.
DE RecName: Full=Deoxyribose-phosphate aldolase {ECO:0000256|HAMAP-Rule:MF_00114};
DE Short=DERA {ECO:0000256|HAMAP-Rule:MF_00114};
DE EC=4.1.2.4 {ECO:0000256|HAMAP-Rule:MF_00114};
DE AltName: Full=2-deoxy-D-ribose 5-phosphate aldolase {ECO:0000256|HAMAP-Rule:MF_00114};
DE AltName: Full=Phosphodeoxyriboaldolase {ECO:0000256|HAMAP-Rule:MF_00114};
DE Short=Deoxyriboaldolase {ECO:0000256|HAMAP-Rule:MF_00114};
GN Name=deoC {ECO:0000256|HAMAP-Rule:MF_00114};
GN ORFNames=YH66_02185 {ECO:0000313|EMBL:AKF26444.1};
OS [Brevibacterium] flavum.
OC Bacteria; Bacillati; Actinomycetota; Actinomycetes; Mycobacteriales;
OC Corynebacteriaceae; Corynebacterium.
OX NCBI_TaxID=92706 {ECO:0000313|EMBL:AKF26444.1, ECO:0000313|Proteomes:UP000034037};
RN [1] {ECO:0000313|EMBL:AKF26444.1, ECO:0000313|Proteomes:UP000034037}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 15168 {ECO:0000313|EMBL:AKF26444.1,
RC ECO:0000313|Proteomes:UP000034037};
RA Ahn J., Park G., Jeon W., Jang Y., Jang M., Lee H., Lee H.;
RT "Complete Genome Sequence of Brevibacterium flavum ATCC 15168.";
RL Submitted (APR-2015) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes a reversible aldol reaction between acetaldehyde
CC and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-
CC phosphate. {ECO:0000256|HAMAP-Rule:MF_00114}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate +
CC acetaldehyde; Xref=Rhea:RHEA:12821, ChEBI:CHEBI:15343,
CC ChEBI:CHEBI:59776, ChEBI:CHEBI:62877; EC=4.1.2.4;
CC Evidence={ECO:0000256|ARBA:ARBA00048791, ECO:0000256|HAMAP-
CC Rule:MF_00114};
CC -!- PATHWAY: Carbohydrate degradation; 2-deoxy-D-ribose 1-phosphate
CC degradation; D-glyceraldehyde 3-phosphate and acetaldehyde from 2-
CC deoxy-alpha-D-ribose 1-phosphate: step 2/2. {ECO:0000256|HAMAP-
CC Rule:MF_00114}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00114}.
CC -!- SIMILARITY: Belongs to the DeoC/FbaB aldolase family. DeoC type 1
CC subfamily. {ECO:0000256|ARBA:ARBA00010936, ECO:0000256|HAMAP-
CC Rule:MF_00114}.
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DR EMBL; CP011309; AKF26444.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A0F6SQM0; -.
DR PATRIC; fig|92706.3.peg.455; -.
DR HOGENOM; CLU_053595_0_0_11; -.
DR UniPathway; UPA00002; UER00468.
DR Proteomes; UP000034037; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004139; F:deoxyribose-phosphate aldolase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006018; P:2-deoxyribose 1-phosphate catabolic process; IEA:UniProtKB-UniRule.
DR GO; GO:0016052; P:carbohydrate catabolic process; IEA:TreeGrafter.
DR GO; GO:0009264; P:deoxyribonucleotide catabolic process; IEA:UniProtKB-UniRule.
DR CDD; cd00959; DeoC; 1.
DR Gene3D; 3.20.20.70; Aldolase class I; 1.
DR HAMAP; MF_00114; DeoC_type1; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR011343; DeoC.
DR InterPro; IPR002915; DeoC/FbaB/LacD_aldolase.
DR InterPro; IPR028581; DeoC_typeI.
DR NCBIfam; TIGR00126; deoC; 1.
DR PANTHER; PTHR10889; DEOXYRIBOSE-PHOSPHATE ALDOLASE; 1.
DR PANTHER; PTHR10889:SF1; DEOXYRIBOSE-PHOSPHATE ALDOLASE; 1.
DR Pfam; PF01791; DeoC; 1.
DR PIRSF; PIRSF001357; DeoC; 1.
DR SMART; SM01133; DeoC; 1.
DR SUPFAM; SSF51569; Aldolase; 1.
PE 3: Inferred from homology;
KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_00114};
KW Lyase {ECO:0000256|ARBA:ARBA00023239, ECO:0000256|HAMAP-Rule:MF_00114};
KW Reference proteome {ECO:0000313|Proteomes:UP000034037};
KW Schiff base {ECO:0000256|ARBA:ARBA00023270, ECO:0000256|HAMAP-
KW Rule:MF_00114}.
FT ACT_SITE 95
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00114"
FT ACT_SITE 158
FT /note="Schiff-base intermediate with acetaldehyde"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00114"
FT ACT_SITE 188
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00114"
SQ SEQUENCE 224 AA; 22768 MW; 3635F963AF0B87BD CRC64;
Query Match 98.6%; Score 1072; Length 224;
Best Local Similarity 98.7%;
Matches 221; Conservative 1; Mismatches 2; Indels 0; Gaps 0;
Qy 1 MDMTISRATMAQILDYTLLGPEVTNSELAAFIDSAIELGVGTICVPNSMVNLTAKAQEAG 60
||| |||:||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MDMMISRSTMAQILDYTLLGPEVTNSELAAFIDSAIELGVGTICVPNSMVNLTAKAQEAG 60
Qy 61 IRVATVAGFPHGKTPALVKAAEARLAVQSGASEVDVVLDIAVVKEGDANRLLQEIVAIRE 120
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Db 61 IRVATVAGFPHGKTPALVKAAEARLAVQSGASEVDVVLDIAVVKEGDANRLLQEIVAIRE 120
Qy 121 AVPSPVVLKFILETAVVGDDAIVTAVNALIAAGADFAKTSTGFHPAGGATVEAVRVMASA 180
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Db 121 AVPSPVVLKFILETAVVSDDAIVTAVNALIAAGADFAKTSTGFHPAGGATVEAVRVMASA 180
Qy 181 SRGRVGIKAAGGVNTWEDAVAFVEAGATRIGTSNAGAILEGAPE 224
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Db 181 SRGRVGIKAAGGVNTWEDAVAFVEAGATRIGTSNAGAILEGAPE 224
Applicant amplified DNA from wild-type C. glutamicum strain ATCC 13869 using the primers of SEQ ID NOs:6-9 (¶64-66). SEQ ID NOs:7 and 8 are complementary and span bases 216-235 of SEQ ID NO:3. However, over bases 221-225 of SEQ ID NO:3, they have only 4 Cs or Gs instead of the 5 present in SEQ ID NO:3. When the amplification product produced from SEQ ID NO:6 and 7 was joined with the one produced from SEQ ID NO:8 and 9, the resulting DNA had a deletion of a cytosine at base 220 of SEQ ID NO:3; i.e., it produced SEQ ID NO:1.
Applicant then transformed this into C. glutamicum strain U3 to produce strain DDC1 (¶69-70). Strain DDC1 had about 10% increased L-glutamic acid production over strain U3 (¶78; Table 1).
As SEQ ID NO:1 does not encode a deoxyribose-phosphate aldolase, what appears to have happened in strain U3 is that the functional deoxyribose-phosphate aldolase gene of SEQ ID NO:3 was replaced with the non-functional gene of SEQ ID NO:1. Strain U3 appears to be a deoxyribose-phosphate aldolase gene null mutant.
The only polynucleotides encoding SEQ ID NO:2 that have use are those that can replace an endogenous deoxyribose-phosphate aldolase in a transformant. The only such polynucleotide taught in the specification is SEQ ID NO:1 and the only such transformant taught in the specification is a C. glutamicum strain. The specification is not enabled for other such polynucleotides or transformants. No claim is drawn to SEQ ID NO:1 or a C. glutamicum transformant in which it replaced the endogenous deoxyribose-phosphate aldolase gene.
Given the claim breath, nature of the invention, and lack of guidance in the specification as discussed above, the instantly claimed invention is not enabled.
Claims 1-10 are free of the art, given the failure of the prior art to teach or suggest a protein of SEQ ID NO:2.
Conclusion
No claim is allowed.
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/Anne Kubelik/Primary Examiner, Art Unit 1663
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