DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Restrictions Requirements
Applicant’s amendment of claims submitted on 11/20/25 is acknowledged.
The election of species was made without traverse in the reply filed on 06/17/2025.
Claims 1, 3-6, 9, 11, 16-17, 20, 58, 60, 64, 69-71, 78, 89, 92 are pending, the claims along with elected species of SEQ ID NO:77 as the nucleotide sequence from claims 1 and 58; SEQ ID NO:129 as the mutant nucleotide sequence and SEQ ID NO:130 as the corresponding encoded protein; SEQ ID NO:77 as the nucleotide sequence from claim 78 and SEQ ID NO:107 as the one corresponding spacer nucleotide sequence are examined in this office action.
Rejections that are withdrawn
Claim Rejection under 35 USC § 112 as indefinite rejection is withdrawn in light of applicant’s amendment of claims by reciting the plant to be corn plant, by deleting indefinite term “about” from claim 17 and by deleting claim 8.
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.
Claims 1, 3-6, 16, 17 and 20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter. The claim does not fall within at least one of the four categories of patent eligible subject matter because the claimed invention is directed to judicial exception (i.e., a law of nature, natural phenomenon, or an abstract idea) without significantly more.
Claims are drawn to a plant comprising at least one mutation in an Elongated Hypocotyl5 (HY5) gene encoding a HY5 transcription factor having at least 80% sequence identity to the amino acid sequence of SEQ ID N0:74.
Since there is no limit of mutations (i.e. deletion and/or substitutions) and no limit on structure of mutant Elongated Hypocotyl5 (HY5) gene (that could be deletion, insertions, substitutions etc.) encoding a HY5 transcription factor, any mutated gene in any corn plant anticipates the claim. However following analysis is based on the interpretation that the mutant plant would require to maintain at least 80% sequence identity to the nucleotide and protein of HY5 gene.
The claim is interpreted as “product by process claim” wherein [E]ven though product by process claims are limited by and defined by the process, determination of patentability is based on the product itself. If the product in the product by process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process."
Regarding claim 1, alignment of SEQ ID NO: 74 to the Uniprot database showed the locus has 98.1% sequence identity to the locus A0A1D6H3I5 of maize inbred line B73 (see alignment below) which showed an insertion of amino acid sequence “KLATTSGMAPR” at about position 30 in the SEQ ID NO: 74 as compared to the maize locus A0A1D6H3I5.
The Uniport database showed the locus is from maize inbred lines B73 (see below). Bornowski et al. (Published: 2021, Journal: Plant Genome. 2021;14:e20114. https://doi.org/10.1002/tpg2.20114) teaches maize inbred line B73 was developed by recurrent selection program from Iowa Stiff Stalk Synthetic (BSSS) population (page 4, Table 1). Therefore, the locus A0A1D6H3I5 has structure of the gene which would be a naturally occurring mutation as compared to the applicant’s SEQ ID NO: 74 with 98.1% sequence identity.
Regarding claim 3, since the N-terminal region of the endogenous HY5 transcription factor has not been described the insertion of “KLATTSGMAPR” at about position 30 in the SEQ ID NO: 74 amino acid sequences in the locus A0A1D6H3I5 is in the N-terminal region of the endogenous HY5 transcription factor.
Regarding claims 4-5, Gangappa et al. (Published: 2015, Journal: Molecular Plant 9: 1353–1365) teaches ACGT is a COP1 binding sequence for HY5 gene (page 1354, Table 1). The alignment of SEQ ID NO: 73 aligns with EU975706 from maize (see alignments below) which has the mutation in “ACGT” which is the COP1 binding site (see alignment below between positions 121-180 of the SEQ ID NO:73. Therefore the sequence is lack of COP1 binding site. Therefore, the mutant is naturally occurring sequence in B73 genome. Furthermore, reduced COP1 binding would be inherent to the structure of the mutation in any COP1 binding site in SEQ ID NO:73.
Regarding claim 6, the mutation is in the region of endogenous HY5 of locus A0A1D6H3I5 which has 91.6% sequence identity to SEQ ID NO: 106 (see alignment below).
Regarding claim 9 and 11, locus A0A1D6H3I5 as compared to SEQ ID NO:73 would be in frame or out frame deletion as compared to one another which are within the limit of at least 80% identity to SEQ ID NO:73.
Since there is no limit on in frame deletions the deletion of nucleotides encoding the 11 missing amino acids would be the nucleotides with in-frame deletions with truncated protein (see alignment below). Furthermore, the SEQ ID NO:73 is itself is a locus from B73 corn line as BT063353 (see alignment below). Therefore, locus BT063353 from B73 corn line would have in frame deletions with truncated protein compared to the A0A1D6H3I5 from line B73 line.
Regarding claims 16 and 17, the claims recite inherent property of the recited plants.
Alignment of SEQ ID NO: 74 to the Uniprot database:
RESULT 2
A0A1D6H3I5_MAIZE
ID A0A1D6H3I5_MAIZE Unreviewed; 181 AA.
AC A0A1D6H3I5;
DT 30-NOV-2016, integrated into UniProtKB/TrEMBL.
DT 30-NOV-2016, sequence version 1.
DT 05-FEB-2025, entry version 38.
DE SubName: Full=Transcription factor HY5 {ECO:0000313|EMBL:AQK69394.1};
GN ORFNames=ZEAMMB73_Zm00001d015743 {ECO:0000313|EMBL:AQK69394.1};
OS Zea mays (Maize).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; PACMAD clade;
OC Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea.
OX NCBI_TaxID=4577 {ECO:0000313|EMBL:AQK69394.1};
RN [1] {ECO:0000313|EMBL:AQK69394.1}
RP NUCLEOTIDE SEQUENCE.
RC TISSUE=Seedling {ECO:0000313|EMBL:AQK69394.1};
RG Maize Genome Sequencing Project;
RA Ware D.;
RT "Update maize B73 reference genome by single molecule sequencing
RT technologies.";
RL Submitted (DEC-2015) to the EMBL/GenBank/DDBJ databases.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000256|ARBA:ARBA00004123}.
CC -!- SIMILARITY: Belongs to the bZIP family.
CC {ECO:0000256|ARBA:ARBA00007163}.
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DR EMBL; CM000781; AQK69394.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A1D6H3I5; -.
DR SMR; A0A1D6H3I5; -.
DR STRING; 4577.A0A1D6H3I5; -.
DR InParanoid; A0A1D6H3I5; -.
DR ExpressionAtlas; A0A1D6H3I5; baseline and differential.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IEA:InterPro.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IEA:InterPro.
DR GO; GO:0010017; P:red or far-red light signaling pathway; IBA:GO_Central.
DR GO; GO:0010099; P:regulation of photomorphogenesis; IBA:GO_Central.
DR GO; GO:0010218; P:response to far red light; IBA:GO_Central.
DR GO; GO:0010114; P:response to red light; IBA:GO_Central.
DR CDD; cd14704; bZIP_HY5-like; 1.
DR FunFam; 1.20.5.490:FF:000004; Transcription factor HY5; 1.
DR Gene3D; 1.20.5.490; Single helix bin; 1.
DR InterPro; IPR004827; bZIP.
DR InterPro; IPR046347; bZIP_sf.
DR InterPro; IPR044280; Hac1/HY5.
DR PANTHER; PTHR46714; TRANSCRIPTIONAL ACTIVATOR HAC1; 1.
DR PANTHER; PTHR46714:SF6; TRANSCRIPTIONAL ACTIVATOR HAC1; 1.
DR Pfam; PF00170; bZIP_1; 1.
DR SMART; SM00338; BRLZ; 1.
DR SUPFAM; SSF57959; Leucine zipper domain; 1.
DR PROSITE; PS50217; BZIP; 1.
DR PROSITE; PS00036; BZIP_BASIC; 1.
PE 3: Inferred from homology;
KW Coiled coil {ECO:0000256|SAM:Coils};
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125};
KW Transcription {ECO:0000256|ARBA:ARBA00023163};
KW Transcription regulation {ECO:0000256|ARBA:ARBA00023015}.
FT REGION 1..103
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 118..159
FT /evidence="ECO:0000256|SAM:Coils"
FT COMPBIAS 21..31
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 181 AA; 19830 MW; 50C45B0C01239AA0 CRC64;
Query Match 98.1%; Score 821.5; Length 181;
Best Local Similarity 93.9%;
Matches 170; Conservative 0; Mismatches 0; Indels 11; Gaps 1;
Qy 1 MQEQAASSRPSSSERSSSSGHHVDMEVKEG-----------MESDDEIRRVPELGLELPG 49
|||||||||||||||||||||||||||||| |||||||||||||||||||
Db 1 MQEQAASSRPSSSERSSSSGHHVDMEVKEGKLATTSGMAPRMESDDEIRRVPELGLELPG 60
Qy 50 ASTSGREAGPGAAGADRALAQSSTAQASARRRVRSHADKEHKRLKRLLRNRVSAQQARER 109
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 ASTSGREAGPGAAGADRALAQSSTAQASARRRVRSHADKEHKRLKRLLRNRVSAQQARER 120
Qy 110 KKAYLTDLEVKVRDLEKKNSEMEERLSTLQNENQMLRQILKNTAVNRRGSGSTASGEGHG 169
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 KKAYLTDLEVKVRDLEKKNSEMEERLSTLQNENQMLRQILKNTAVNRRGSGSTASGEGHG 180
Qy 170 Q 170
|
Db 181 Q 181
Alignment of SEQ ID NO: 73 to the GenEmbl database:
EU975706
LOCUS EU975706 819 bp mRNA linear PLN 10-DEC-2008
DEFINITION Zea mays clone 497680 transcription factor HY5 mRNA, complete cds.
ACCESSION EU975706
VERSION EU975706.1
KEYWORDS FLI_CDNA.
SOURCE Zea mays
ORGANISM Zea mays
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; PACMAD
clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae;
Zea.
REFERENCE 1 (bases 1 to 819)
AUTHORS Alexandrov,N.N., Brover,V.V., Freidin,S., Troukhan,M.E.,
Tatarinova,T.V., Zhang,H., Swaller,T.J., Lu,Y.P., Bouck,J.,
Flavell,R.B. and Feldmann,K.A.
TITLE Insights into corn genes derived from large-scale cDNA sequencing
JOURNAL Plant Mol. Biol. 69 (1-2), 179-194 (2009)
PUBMED 18937034
REFERENCE 2 (bases 1 to 819)
AUTHORS Alexandrov,N.N., Brover,V.V., Freidin,S., Troukhan,M.E.,
Tatarinova,T.V., Zhang,H., Swaller,T.J., Lu,Y.-P., Bouck,J.,
Flavell,R.B. and Feldmann,K.A.
TITLE Direct Submission
JOURNAL Submitted (04-AUG-2008) Ceres, Inc., 1535 Rancho Conejo Blvd.,
Thousand Oaks, CA 91320, USA
FEATURES Location/Qualifiers
source 1..819
/organism="Zea mays"
/mol_type="mRNA"
/db_xref="taxon:4577"
/clone="497680"
CDS 107..619
/note="similar to NP_001046236.1"
/codon_start=1
/product="transcription factor HY5"
/protein_id="ACG47824.1"
/translation="MQEQAASSRPSSSERSSSSGHHVDMEVKEGMESDDEIRRVPELG
LELPGASTSGREAGPGAAGADRALAQSSTAQASARRRVRSHADKEHKRLKRLLRNRVS
AQQARERKKAYLTDLEVKVRDLEKKNSEMEERLSTLQNENQMLRQILKNTAVNRRGSG
STASGEGHGQ
Query Match 99.7%; Score 511.4; Length 819;
Best Local Similarity 99.8%;
Matches 512; Conservative 0; Mismatches 1; Indels 0; Gaps 0;
Qy 1 ATGCAGGAGCAGGCGGCGAGCTCGCGGCCTTCCAGCAGCGAGAGGTCGTCCAGCTCCGGG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 107 ATGCAGGAGCAGGCGGCGAGCTCGCGGCCTTCCAGCAGCGAGAGGTCGTCCAGCTCCGGG 166
Qy 61 CACCACGTGGACATGGAGGTCAAGGAAGGGATGGAGAGCGACGATGAGATAAGGAGAGTG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 167 CACCACGTGGACATGGAGGTCAAGGAAGGGATGGAGAGCGACGATGAGATAAGGAGAGTG 226
Qy 121 CCGGAGCTGGGCCTGGAGTTGCCGGGAGCCTCCACGTCGGGCAGGGAGGCTGGCCCTGGC 180
||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||
Db 227 CCGGAGCTGGGCCTGGAGTTGCCGGGAGCCTCCACATCGGGCAGGGAGGCTGGCCCTGGC 286
Qy 181 GCTGCGGGCGCAGACCGCGCCCTTGCCCAGTCGTCCACGGCGCAGGCCAGCGCGCGCCGC 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 287 GCTGCGGGCGCAGACCGCGCCCTTGCCCAGTCGTCCACGGCGCAGGCCAGCGCGCGCCGC 346
Qy 241 CGCGTCCGCAGCCACGCCGACAAGGAGCACAAGCGCCTCAAAAGGTTACTGAGGAACAGG 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 347 CGCGTCCGCAGCCACGCCGACAAGGAGCACAAGCGCCTCAAAAGGTTACTGAGGAACAGG 406
Qy 301 GTGTCAGCTCAACAGGCTAGAGAGAGGAAGAAGGCTTATTTAACTGATCTGGAGGTGAAG 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 407 GTGTCAGCTCAACAGGCTAGAGAGAGGAAGAAGGCTTATTTAACTGATCTGGAGGTGAAG 466
Qy 361 GTGAGAGATCTGGAGAAGAAGAACTCGGAGATGGAAGAGAGGCTCTCCACCCTCCAGAAC 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 467 GTGAGAGATCTGGAGAAGAAGAACTCGGAGATGGAAGAGAGGCTCTCCACCCTCCAGAAC 526
Qy 421 GAGAACCAGATGCTCCGACAGATACTGAAGAACACCGCTGTAAACAGAAGAGGTTCAGGA 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 527 GAGAACCAGATGCTCCGACAGATACTGAAGAACACCGCTGTAAACAGAAGAGGTTCAGGA 586
Qy 481 AGCACTGCTAGTGGAGAGGGCCACGGCCAATAG 513
|||||||||||||||||||||||||||||||||
Db 587 AGCACTGCTAGTGGAGAGGGCCACGGCCAATAG 619
Alignment of SEQ ID NO:73 to GenEmbl database:
RESULT 1
BT063353
LOCUS BT063353 792 bp mRNA linear PLN 21-FEB-2009
DEFINITION Zea mays full-length cDNA clone ZM_BFc0055M22 mRNA, complete cds.
ACCESSION BT063353
VERSION BT063353.1
KEYWORDS FLI_CDNA.
SOURCE Zea mays
ORGANISM Zea mays
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; PACMAD
clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae;
Zea.
REFERENCE 1 (bases 1 to 792)
AUTHORS Soderlund,C., Descour,A., Kudrna,D., Bomhoff,M., Boyd,L.,
Currie,J., Angelova,A., Collura,K., Wissotski,M., Ashley,E.,
Morrow,D., Fernandes,J., Walbot,V. and Yu,Y.
TITLE Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs
JOURNAL PLoS Genet. 5 (11), E1000740 (2009)
PUBMED 19936069
REMARK Publication Status: Online-Only
REFERENCE 2 (bases 1 to 792)
AUTHORS Yu,Y., Currie,J., Lomeli,R., Angelova,A., Collura,K., Wissotski,M.,
Campos,D., Kudrna,D., Golser,W., Ashely,E., Haller,K., Descour,A.,
Fernandes,J., Soderlund,C. and Walbot,V.
TITLE Direct Submission
JOURNAL Submitted (21-FEB-2009) Plant Sciences, Arizona Genomics Institute,
1657 E. Helen Street, Thomas Keating Building, Tucson, AZ 85721,
USA
FEATURES Location/Qualifiers
source 1..792
/organism="Zea mays"
/mol_type="mRNA"
/strain="B73"
/db_xref="taxon:4577"
/clone="ZM_BFc0055M22"
CDS 71..583
/codon_start=1
/product="unknown"
/protein_id="ACN28050.1"
/translation="MQEQAASSRPSSSERSSSSGHHVDMEVKEGMESDDEIRRVPELG
LELPGASTSGREAGPGAAGADRALAQSSTAQASARRRVRSHADKEHKRLKRLLRNRVS
AQQARERKKAYLTDLEVKVRDLEKKNSEMEERLSTLQNENQMLRQILKNTAVNRRGSG
STASGEGHGQ
Query Match 100.0%; Score 513; Length 792;
Best Local Similarity 100.0%;
Matches 513; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 ATGCAGGAGCAGGCGGCGAGCTCGCGGCCTTCCAGCAGCGAGAGGTCGTCCAGCTCCGGG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 71 ATGCAGGAGCAGGCGGCGAGCTCGCGGCCTTCCAGCAGCGAGAGGTCGTCCAGCTCCGGG 130
Qy 61 CACCACGTGGACATGGAGGTCAAGGAAGGGATGGAGAGCGACGATGAGATAAGGAGAGTG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 131 CACCACGTGGACATGGAGGTCAAGGAAGGGATGGAGAGCGACGATGAGATAAGGAGAGTG 190
Qy 121 CCGGAGCTGGGCCTGGAGTTGCCGGGAGCCTCCACGTCGGGCAGGGAGGCTGGCCCTGGC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 191 CCGGAGCTGGGCCTGGAGTTGCCGGGAGCCTCCACGTCGGGCAGGGAGGCTGGCCCTGGC 250
Qy 181 GCTGCGGGCGCAGACCGCGCCCTTGCCCAGTCGTCCACGGCGCAGGCCAGCGCGCGCCGC 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 251 GCTGCGGGCGCAGACCGCGCCCTTGCCCAGTCGTCCACGGCGCAGGCCAGCGCGCGCCGC 310
Qy 241 CGCGTCCGCAGCCACGCCGACAAGGAGCACAAGCGCCTCAAAAGGTTACTGAGGAACAGG 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 311 CGCGTCCGCAGCCACGCCGACAAGGAGCACAAGCGCCTCAAAAGGTTACTGAGGAACAGG 370
Qy 301 GTGTCAGCTCAACAGGCTAGAGAGAGGAAGAAGGCTTATTTAACTGATCTGGAGGTGAAG 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 371 GTGTCAGCTCAACAGGCTAGAGAGAGGAAGAAGGCTTATTTAACTGATCTGGAGGTGAAG 430
Qy 361 GTGAGAGATCTGGAGAAGAAGAACTCGGAGATGGAAGAGAGGCTCTCCACCCTCCAGAAC 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 431 GTGAGAGATCTGGAGAAGAAGAACTCGGAGATGGAAGAGAGGCTCTCCACCCTCCAGAAC 490
Qy 421 GAGAACCAGATGCTCCGACAGATACTGAAGAACACCGCTGTAAACAGAAGAGGTTCAGGA 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 491 GAGAACCAGATGCTCCGACAGATACTGAAGAACACCGCTGTAAACAGAAGAGGTTCAGGA 550
Qy 481 AGCACTGCTAGTGGAGAGGGCCACGGCCAATAG 513
|||||||||||||||||||||||||||||||||
Db 551 AGCACTGCTAGTGGAGAGGGCCACGGCCAATAG 583
Alignment of SEQ ID NO: 106 to NCBI protein database:
RESULT 8
A0A1D6H3I5_MAIZE
ID A0A1D6H3I5_MAIZE Unreviewed; 181 AA.
AC A0A1D6H3I5;
DT 30-NOV-2016, integrated into UniProtKB/TrEMBL.
DT 30-NOV-2016, sequence version 1.
DT 05-FEB-2025, entry version 38.
DE SubName: Full=Transcription factor HY5 {ECO:0000313|EMBL:AQK69394.1};
GN ORFNames=ZEAMMB73_Zm00001d015743 {ECO:0000313|EMBL:AQK69394.1};
OS Zea mays (Maize).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; PACMAD clade;
OC Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea.
OX NCBI_TaxID=4577 {ECO:0000313|EMBL:AQK69394.1};
RN [1] {ECO:0000313|EMBL:AQK69394.1}
RP NUCLEOTIDE SEQUENCE.
RC TISSUE=Seedling {ECO:0000313|EMBL:AQK69394.1};
RG Maize Genome Sequencing Project;
RA Ware D.;
RT "Update maize B73 reference genome by single molecule sequencing
RT technologies.";
RL Submitted (DEC-2015) to the EMBL/GenBank/DDBJ databases.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000256|ARBA:ARBA00004123}.
CC -!- SIMILARITY: Belongs to the bZIP family.
CC {ECO:0000256|ARBA:ARBA00007163}.
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DR EMBL; CM000781; AQK69394.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A1D6H3I5; -.
DR SMR; A0A1D6H3I5; -.
DR STRING; 4577.A0A1D6H3I5; -.
DR InParanoid; A0A1D6H3I5; -.
DR ExpressionAtlas; A0A1D6H3I5; baseline and differential.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IEA:InterPro.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IEA:InterPro.
DR GO; GO:0010017; P:red or far-red light signaling pathway; IBA:GO_Central.
DR GO; GO:0010099; P:regulation of photomorphogenesis; IBA:GO_Central.
DR GO; GO:0010218; P:response to far red light; IBA:GO_Central.
DR GO; GO:0010114; P:response to red light; IBA:GO_Central.
DR CDD; cd14704; bZIP_HY5-like; 1.
DR FunFam; 1.20.5.490:FF:000004; Transcription factor HY5; 1.
DR Gene3D; 1.20.5.490; Single helix bin; 1.
DR InterPro; IPR004827; bZIP.
DR InterPro; IPR046347; bZIP_sf.
DR InterPro; IPR044280; Hac1/HY5.
DR PANTHER; PTHR46714; TRANSCRIPTIONAL ACTIVATOR HAC1; 1.
DR PANTHER; PTHR46714:SF6; TRANSCRIPTIONAL ACTIVATOR HAC1; 1.
DR Pfam; PF00170; bZIP_1; 1.
DR SMART; SM00338; BRLZ; 1.
DR SUPFAM; SSF57959; Leucine zipper domain; 1.
DR PROSITE; PS50217; BZIP; 1.
DR PROSITE; PS00036; BZIP_BASIC; 1.
PE 3: Inferred from homology;
KW Coiled coil {ECO:0000256|SAM:Coils};
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125};
KW Transcription {ECO:0000256|ARBA:ARBA00023163};
KW Transcription regulation {ECO:0000256|ARBA:ARBA00023015}.
FT REGION 1..103
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 118..159
FT /evidence="ECO:0000256|SAM:Coils"
FT COMPBIAS 21..31
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 181 AA; 19830 MW; 50C45B0C01239AA0 CRC64;
Query Match 91.6%; Score 168.5; Length 181;
Best Local Similarity 77.1%;
Matches 37; Conservative 0; Mismatches 0; Indels 11; Gaps 1;
Qy 1 SSSERSSSSGHHVDMEVKEG-----------MESDDEIRRVPELGLEL 37
|||||||||||||||||||| |||||||||||||||||
Db 11 SSSERSSSSGHHVDMEVKEGKLATTSGMAPRMESDDEIRRVPELGLEL 58
Response to Arguments
Applicant's arguments filed 11/20/2025 have been fully considered but they are not persuasive.
Applicant argues claim 1 is amended herein to recite that "the at least one mutation is a deletion and/or substitution." Applicant argues as shown in the amino acid sequence comparison at page 6 of the Office Action, the comparator sequence under Accession No. A0A1D6H3I5 has an insertion at position 30 relative to SEQ ID N0:74. Applicant respectfully submits that the corn plant or plant part thereof as claimed possesses markedly different characteristics from a naturally occurring plant or plant part (response to rejection, pages 8 and 9, last and first paragraphs).
Applicant argues at page 4, the Office Action cites Gangappa et al. (Molecular Plant 9: 1353-1365; hereinafter "Gangappa") as teaching that "ACGT is a COP1 binding sequence for HY5 gene (page 1354, Table l)." Applicant argues the Office Action further asserts that Accession No. EU975706 from maize has a mutation in "ACGT" and is therefore a naturally occurring mutant sequence in the B73 genome. See Office Action, page 4. Applicant argues Table 1 of Gangappa shows "Key genes targeted by HY5," wherein COP1 is a target gene of HY5. Applicant argues in addition, Table 1 shows that COP1 has the binding sequence "ACGT." Gangappa further explains:
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See Gangappa, page 1355, col. 1.
Applicant argues contrary to the assertions in the Office Action, Gangappa teaches that the sequence "ACGT" is present in the promoter of the COP1 gene. Applicant argues the Office Action's assertions regarding Gangappa are not relevant to the claims because the "ACGT" sequence being referred to in this reference is in a different gene, namely COP1 (response to rejection, page 9, paragraphs 2-3).
Applicant argues with respect to claims 9 and 11, the Office Action further contends that "locus A0A1D6H3I5 as compared to SEQ ID NO:73 would be either in frame insertion or in frame deletion as compared to one another." Applicant argues the amino acid sequence comparison at page 6 of the Office Action shows that the polypeptide under Accession No. A0A1D6H3I5 has an insertion of the amino acid sequence "KLATTSGMAPR" at about position 30 of SEQ ID NO:74. Applicant argues contrary to the assertions in the Office Action, this does not constitute an in-frame deletion. Applicant argues indeed none of the comparators cited in the Office Action have a deletion (response to rejection, page 9, second to last paragraph).
Applicant argues regarding claims 16, 17, and 92, the Office Action states that "the claims recite inherent property of the recited plants." See Office Action, page 4. Applicant argues the Office Action provides no basis for concluding that the recited phenotypes would be inherent to any one of the comparators cited in the Office Action (response to rejection, page 9 and 10, last and first paragraphs).
Applicant argues with respect to claims 20 and 89, the Office Action contends that "A0A1D6H3I5 _ MAIZE of the B73 has 96.1% sequence identity to the Applicant's SEQ ID NO:130." See Office Action, page 5. Applicant argues as amended herein, claims 20 and 89 recite that sequence identity is over the entire length of the referenced sequence. Applicant argues on this basis, the sequence of A0A1D6H3I5 only shares 81 % identity with SEQ ID NO:130. Applicant argues therefore, the corn plant or plant part thereof of claim 20 and nucleic acid of claim 89 are markedly different from the sequence of A0A1D6H3I5.
Applicant's arguments have been fully considered but they are not persuasive since:
Regarding argument on claim now reciting deletion and/or substitution limit in the claim, it is not found persuasive since the combination of any number of deletions and substitutions would produce the recited sequences since there is no limit of nucleotide or amino acids deleting and substituting in any of the recited sequences. Since the genomic structure 0f the claimed corn plant is same as the referenced plants, the recited broad characteristics would be inherent in the plants.
Regarding argument on "ACGT" sequence is in a different gene, namely COP1, it was not found persuasive since the evidence was about a Constitutive Photomorphogenic 1 (COP1) binding site that claim 4 recite and that is also found in the gene of corn line B73. For example, claim 4 require any deletion and substitution in COP1 binding site which is ACGT and found in the sequence of B73 and furthermore there is no limit of genomic structure of the corn plant since the mutation would be any numbers of deletion and substitutions.
Regarding argument on claims 9 and 11, that the claim is amended to not include in frame insertion or an out of frame insertions, it is not found persuasive since locus A0A1D6H3I5 as compared to SEQ ID NO:73 would be in frame deletion or out frame deletion as compared to one another which are within the limit of at least 80% identity to SEQ ID NO:73. Since there is no limit on in frame deletions the deletion of nucleotides encoding the 11 missing amino acids would be the nucleotides with in-frame deletions with truncated protein (see alignment below). Furthermore, the SEQ ID NO:73 is itself is a locus from B73 corn line as BT063353 (see alignment above). Therefore, the naturally occurring locus BT063353 from B73 corn line would have in frame deletions with truncated protein compared to the A0A1D6H3I5 from line B73 line.
Regarding augment on inherent property. The claim is directed to corn plant with specific genomic structure after any mutation of deletion and substitution that is found in nature and the plant would have inherent property recited in claims 16, 17 and 92. Claims are broad to encompass increased density tolerance without any control plant therefore the increase encompass any increase. Furthermore, claim 93 merely recite a corn plant and any characteristics of the plants are optional components.
Regarding argument on amendment of claims 20 and 89 now require identity is over the entire length, it is found persuasive therefore the 101 rejection over claims 20 and 89 has been withdrawn.
Claim Rejections - 35 USC § 112 – Written Description Requirements
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1, 3-6, 8-9, 11, 16-17, 20, 58, 60, 64, 69-71, 78, 89 and 92 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Following analysis is modified necessitated by amendment of claims not reciting the plant is a corn plant and the mutation is deletion and/or substitution and furthermore the amendment of claims 20 and 89 to recite the “sequence identity over the entire length”.
Analysis of Breadth of Claims
The COP1 binding sites would have any structure in any plant (claims 4, 5 and 60).
The variants of polynucleotides having at least 80% sequence identity to the nucleotide sequence of SEQ ID N0: 72, 73, 77 would encompass large number of molecules (claims 1, 4-5, 58).
The variants of polypeptides having at least 80% sequence identity to the nucleotide sequence of SEQ ID N0: 74 and 106 would encompass large number of molecules (claims 1, 6, 69).
N-Terminal region of SEQ ID NO: 74 would encompass any combination of the nucleotides on N-terminal.
Increased density of plant would encompass any increase in any plant.
A mutant of HY5 gene and encoded protein having at least 90% sequence identity over the entire length to any one of SEQ ID NOs: 129 and 130 respectively would encompass large number of molecules (claims 20, 70, 89).
A mutation as a deletion and/or substitution mutation which is any number of deletions and substitutions in any sequence encoding a protein having 80% sequence identity to SEQ ID NO:70 would encompass large number of mutation in any of the sequence in SEQ ID NO:70 (claim 1).
What is Described in the Specification
Applicant describes the following:
A CRISPR guide nucleic acids comprising spacers (SEQ ID NOs: 107-113)(see Table 1) having complementarity to targets within the HY5 gene from maize (e.g. Zm00001d015743) (SEQ ID NO:72) were designed and placed into a construct for generating a deletion at the N-terminus of the HY5 polypeptide (page 104, lines 21-23).
Edited alleles of the HY5 gene Zm00001 d015743 were generated wherein there were deletion from 3bp to upto 36 bp as alleles A-H (page 106, Table 5), allele I (page 108, Table 8), alleles J-N (page 109, Table 9) in position 2148 to position 2519 of the SEQ ID NO:72.
Tables 6-7 and 10-11 showed increase in sheath height in the different mutated alleles.
Difference Between What was described and What is Claimed
Applicant has not described a sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID N0:72 or SEQ ID N0:73 (claims 1, 4-5, 58).
Applicant has not described a region having at least 80% sequence identity to any one of the nucleotide 77.
Applicant has not described a polypeptide comprising a sequence having at least 80% sequence identity to the amino acid sequence of SEQ ID N0:74.
Applicant has not described a region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO: 106 (claims 1, 6, 69).
Applicant has not described mutant HY5 genes and encoded proteins having at least 90% sequence identity over the entire length to any one of SEQ ID NOs: 129 and 130 respectively (claims 20, 70, 89).
Applicant has not described use of a nucleic acid and encoded protein having at least 90% sequence identity over the entire length to any one of SEQ ID NOs: 129 and 130 respectively without the nuclei acid being in a plant cell (claim 89).
Applicant has not described COP1 binding sites (claims 4 and 5).
Applicant has not described the structure of N-Terminal region of SEQ ID NO: 74.
Applicant has not described increased density of plant as compared to what control standard of the plant density (claims 16-17).
Applicant has not described reduced Shade Avoidance Response comprises increased yield, increased upright growth, decreased reduced lodging rate, delayed senescence, substantially no change in flowering time, increased photosynthesis efficiency and grain filling, and/or enhanced defense responses against pathogens and herbivores when planted in close proximity with one or more plants comprising a reduced Shade Avoidance Response (claims 71 and 92).
Applicant has not described any sequence having at least 90% sequence identity over the entire length of SEQ ID NO:129 encodes a mutated HY5 polypeptide having at least 90% sequence identity over the entire length to any one of SEQ ID NO:130 (claims 20, 89).
Applicant has not described any corn plant wherein the at least one mutation is a deletion and/or substitution mutation which is any number of deletions and substitutions in any sequence encoding a protein having 80% sequence identity to SEQ ID NO:70 to have any use.
Analysis
The purpose of the written description is to ensure that the inventor had possession at the time the invention was made, of the specific subject claimed. For a broad generic claim, the specification must provide adequate written description to identify the genus of the claim.
Applicant has not described variants of polynucleotides having at least 80% sequence identity to the nucleotide sequence of SEQ ID N0: 72, 73, 77 (claims 1, 4-5, 58). For example, SEQ ID NO: 72 is 9107 nucleotides long wherein a variant of SEQ ID NO:72 having at least 90% identity would have 911 nucleic acid (NA) changes (i.e., substitutions, deletions, insertions, or additions) relative to SEQ ID NO:72, and this encompasses a genus of nucleic acid sequence that includes at least ~4911 different molecules. For this reason, the genus of nucleic acid molecules having at least 90% identity to SEQ ID NO: 72 is a very large genus of molecules.
Applicant has not described variants of polypeptides having at least 80% sequence identity to the nucleotide sequence of SEQ ID N0: 74 and 106 (claims 1, 6, 69). For example, SEQ ID NO: 74 is 170 amino acids (AA) long wherein a variant of SEQ ID NO: 74 having at least 90% identity would have ~17 AA changes (i.e., substitutions, deletions, insertions, or additions) relative to SEQ ID NO: 74, and this encompasses a genus of nucleic acid sequence that includes at least ~2017 different molecules. For this reason, the genus of nucleic acid molecules having at least 80% identity to SEQ ID NO: 74 is a very large genus of molecules.
Furthermore, similarly Applicant has not described mutant HY5 genes and encoded proteins having at least 90% sequence identity to any one of SEQ ID NOs: 129 and 130 respectively (claims 20, 70, 89).
Furthermore, the state of the art at the time of the instant invention was that it is impossible to predict such a broad sequence variation will have any required function. For example, Guo et al. (Published Year: 2004, Journal: Proceedings of the National Academy of Sciences, Vol. 101(25), pages: 9205-9210) teaches that while proteins are fairly tolerant to mutations resulting in single amino acid changes, increasing the number of substitutions additively increases the probability that the protein will be inactivated (page 9209, right. col., paragraph 2).
Furthermore, HY5 has been found in various function in plants. For example, Xiao et al. (Published: 2022, Journal: Frontiers in Plant Science, 12:1-11, doi: 10.3389/fpls.2021.800989) teaches HY5 is originally identified as a positive regulator of photomorphogenesis, root gravitropic response, and lateral root development wherein HY5 gene encodes a bZIP-type transcription factor that controls approximately one-third of the expression of genes throughout the whole genome (page2, left paragraph 1).
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Xiao et al. teaches extensive studies have revealed that HY5 regulates a variety of developmental processes, responsiveness of various hormonal and environmental signals through divergent but overlapping signaling networks in plants (page2, left paragraph 1). Xiao et al. teaches HY5 acts as a transcription factor that predominantly binds to the ACGT- containing cis-element (e.g., G-box and T/G-box) and controls the expression of numerous target genes in response to light signals, which in turn serves to modulate distinct light-regulated physiological and developmental processes in plants (page2, left paragraph 1). Xiao et al. teaches HY5 directly or indirectly regulates the expression of over 3,000 genes, thereby controlling diverse physiological growth and responses to various hormonal and environmental signals (page 2, right paragraph 1).
Gangappa et al. (Published: 2015, Journal: Molecular Plant 9: 1353–1365) teaches HY5 regulates the transcription of a large number of genes by directly binding to cis-regulatory elements and activate its own expression under both visible and UV-B light.
Therefore, there is dearth of description of the polynucleotide variants having at least 80% sequence identity to the nucleotide sequence of SEQ ID N0: 72, 73, 77; polypeptide variants having at least 80% sequence identity to the nucleotide sequence of SEQ ID N0: 74 and 106 and mutant HY5 genes and encoded proteins having at least 90% sequence identity to any one of SEQ ID NOs: 129 and 130 respectively.
Applicant has not described COP1 binding sites (claims 4, 5 and 60). Lee et al. (Published: 2007, Journal: The Plant Cell, Vol. 19: 731–749) teaches when known consensus binding sites of HY5 were searched in the promoter regions of HY5 target genes, the frequency of the G box (CACGTG) was highest, and it was ;1.6 times higher in the target genes compared with the whole genome. Lee et al. teaches in addition G box, CG hybrid (GACGTG) and CA hybrid (GACGTA), that are also known as HY5 binding consensus sequences (page 734, right paragraph 2, see figure below). Furthermore, applicant has only showed SEQ ID NO:125 has a 34bp deletion comprising “ACGT” motif (page 106, Table). Since many of the variants of the sequences are found in different regions of any of the COP1 gene, there is dearth of description of COP1 binding sites of claims 4, 5 and 60 that would require to have mutation and the mutation would require to reduce COP1 binding.
Applicant has not described the structure of N-Terminal region of SEQ ID NO: 74 that is required to have mutation (claim 3). A N-terminal region would mean a region comprising initial amino acid sequences which does not described the specific region of the N-terminal to be mutated. For example Creative Proteomics defines “The N-terminus also referred to as the amino-terminus, NH₂-terminus, or N-terminal end, initiates the polypeptide chain. It is characterized by a free amine group (-NH₂) and represents the initial amino acid in the sequence.” (see enclosed PDF, accessed, https://www.creative-proteomics.com/, on 08/20/2025). Therefore, the region has not been described by applicant of which combination of the nucleotides of the region comprise the N-terminal region of SEQ ID NO: 74.
Applicant has not described increased density of plant as compared to what control standard of the plant density (claims 16-17). Applicant has not described that the mutation would cause density tolerance in the plants. For example, Assefa et al. (Published: 2018, Journal: Scientific Reports, 8(1), 4937) teaches for example for the modern maize hybrid the higher planting density of more than 100,000 plant ha-1 decreases the grain yield (Assefa, page 4, figure 3), which furthermore varies with yield environment where in very high yielding environment (VHY) the maize grain yield is maintained wherein in low environment (LY) it shows significantly reduced grain yield (Assefa, page5, figure5). Furthermore, Assefa et al. teaches change in maize management practices and nitrogen use efficiency, and genotype x environment and management factors interactions (page 1, second paragraph, page 2, second paragraph, page 8, Figure 8). Therefore, there is dearth of description of mutation would cause density tolerance in any plants.
Claim 1 recite the phrase “at least one mutation in an endogenous Elongated Hypocotyl5 (HY5) gene encoding a HY5 transcription factor” in any corn plant, “wherein the at least one mutation is a deletion and/or substitution”. The combination of any number of deletions and substitutions would produce large number of variants of sequences that does not require to have any functions except broad functions described in claims 16, 17, 71 and 92. There is no limit of nucleotide or amino acids deleting and substituting in any of the recited sequences. Therefore there is dearth of description of mutation which is any number of deletions and substitutions in any sequence encoding a protein having 80% sequence identity to SEQ ID NO:74 to have any desirable functions to be used for. Instead applicant has not described any other protein with mutated sequence SEQ ID NOs: NOs:115, 117, 120, 122, 124, 126, 128, 130, 132, 134, 136, or 138 that has some advantages for shade avoidance as showed in Tables 6-7 and 10-11. Applicant has not described any sequence that has 90% identity to SEQ ID NO: 130 would have any increase in shade avoidance other than SEQ ID NO: 140 itself.
Furthermore, Applicant has not described use of a nucleic acid and encoded protein having at least 90% sequence identity over the entire length to any one of SEQ ID NOs: 129 and 130 respectively without the nuclei acid being in a plant cell (claim 89). The mutated nucleic acid at specific places has been described to disrupts binding of COP1 to HY5 transcription in a corn plant cell. So there is dearth of description for a nucleic acid and encoded protein having at least 90% sequence identity over the entire length to any one of SEQ ID NOs: 129 and 130 respectively without the nuclei acid being in a plant cell (claim 89).
Applicant has not described any sequence having at least 90% sequence identity over the entire length of SEQ ID NO:129 encodes any mutated HY5 polypeptide having at least 90% sequence identity over the entire length to any one of SEQ ID NO:130 (claims 20, 89). SEQ ID NO:129 is 4750 nucleotides long and SEQ ID NO:130 is 146 amino acids long. Any sequence having 90% of SEQ ID NO: 129 would have at least 4275 which would lead to a amino acid sequence having at least 1425 amino acids. Therefore there is dearth of description of any sequence having at least 90% sequence identity over the entire length of SEQ ID NO:129 encodes any mutated HY5 polypeptide having at least 90% sequence identity over the entire length to any one of SEQ ID NO:130 (claims 20, 89). Applicant are advised to claim such that the amino acid and protein sequence claims would be dependent but would be separate or claim such that it would only claim either protein or nucleotides by using term ‘or” and not “and/or”
Given the large structural variable associated with these embodiments, the claims read on an extremely broad and highly diverse structures that produces a mutated plant comprising mutation in an endogenous Elongated Hypocotyl5 (HY5) gene encoding a HY5 transcription factor. Furthermore, claims 16-17 require the mutation would cause plant density tolerance. Thus, in view of the analysis presented above, a skilled artisan would appreciate that the claims are directed to extremely broad and highly diverge genus of sequence variants that are required to have the specific function of producing stink bug pheromone synthesis system.
Given the large size and structural diversity associated with the claimed genus, Applicant’s disclosure is not representative of the claimed genus as a whole. This point is particularly relevant because, as discussed above, the prior art speaks to the disconnection between the structure of the broadly claimed variants in any plants and the recited specific function.
"The test for sufficiency is whether the disclosure of the application relied upon reasonably conveys to one skilled in the art that the inventor had possession of the claimed subject matter as of the filing date." Ariad Pharm, Inc, v EH Lilly & Co., 598 F.3d 1336, 1351 (Fed. Cir. 2010). To satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. Lockwood v. Amer. Airlines, ina, 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966 (Fed. Cir. 1997). "An applicant shows possession of the claimed invention by describing the claimed invention with all of its limitations. Lockwood, 107 F.3d at 1572, 41 USPG2d at 1966". While the written description requirement does not demand either examples or an actual reduction, actual "possession" or reduction to practice outside of the specification is not enough. Ariad Pharm, Inc. v. Eli Lilly & Co., 598 F,3d 1336,1352 (Fed. Cir. 2010). Rather, it is the specification itself that must demonstrate possession. Id.
The Federal Circuit has clarified the application of the written description requirement to inventions in the field of biotechnology. The court stated that, “A description of a genus of cDNAs may be achieved by means of a recitation of a representative number of cDNAs, defined by nucleotide sequence, falling within the scope of the genus or of a recitation of structural features common to members of the genus, which features constitute a substantial portion of the genus.” See University of California v. Eli Lilly and Co., 119 F. 3d 1559; 43 USPQ2d 1398, 1406 (Fed. Cir. 1997).
Thus, based on the analysis above, Applicant has not met either of the two elements of the written description requirement as set forth in the court's decision in Eli Lilly. As a result, it is not clear that Applicant was has described the structure of claimed genus to have application as recited function at the time this application was filed.
Response to Arguments
Applicant's arguments filed 11/20/2025 have been fully considered but they are not persuasive.
Applicant argues as filed specification provides the genomic and coding sequence of the HY5 gene (SEQ ID NOs:72 and 73), as well as the amino acid sequence of the HY5 transcription factor (SEQ ID N0:74) and COP1 binding site (SEQ ID N0:106) from corn. See at least page 8, lines 6-8 and page 64, lines 8-12. Applicant argues in addition, as filed specification describes nucleotide sequences having 80% sequence identity to the HY5 gene as including, e.g., homologs, that may be identified by methods such as computer-based alignments and hybridization under stringent conditions. See at least pages 32-37 of the specification. Applicant argues in addition, at page 37, lines 23-26, the specification states: "Nucleotide sequences that do not hybridize to each other under stringent conditions are still substantially identical if the proteins that they encode are substantially identical. Applicant argues this can occur, for example, when a copy of a nucleotide sequence is created using the maximum codon degeneracy permitted by the genetic code." Applicant argues indeed, at the time of filing of the specification, one of ordinary skill in the art would have appreciated that two nucleotide sequences sharing 80% sequence identity may still encode the same protein. Applicant argues accordingly, not only does the specification describe sequences having at least 80% sequence identity to those recited in the claims, the specification provides specific guidance for identifying such sequences (response to rejection, page 11, last paragraph).
Applicant agues the teachings of Guo et al. are of no relevance to the nucleotide or amino acid sequences of corn HY5 as this reference describes a different gene (AAG) from a different species (human). Applicant argues thus, Guo et al. do not provide a basis for concluding a lack of written support for corn HY5 sequences as claimed (response to rejection, page 12, first paragraph).
Applicant argues the extensive studies described in Xiao and Gangappa show that one of ordinary skill in the art would have been well aware of HY5 genes in plants and the function of the same. Applicant argues in this context, using the sequences and guidance disclosed in the specification, one of skill in the art could readily 'visualize or recognize' the members of the genus of sequences claimed. Ariad, 598 F.3d at 1350 (response to rejection, page 12, paragraph 2).
Applicant argues contrary to the assertions in the Office Action, the COP1 binding site not a consensus nucleotide sequence of a COP1 gene that HY5 binds to. Applicant argues claims 4, 5, and 60 are clearly directed to a COP1 binding site located within the HY5 transcription factor amino acid sequence. Applicant argues in this respect, page 64, lines 8-12, of the as filed specification states that "a mutation may be located in the region of the HY5 gene that encodes the COP1 binding site, optionally wherein the region may encode a sequence having at least 80% sequence identity (optionally the sequence identity may be at least 90% or it may be at least 95%, optionally the sequence identity may be at least 100%) to the amino acid sequence of SEQ ID N0:106." Applicant argues further, page 2, lines 7-9 of the specification specifies that the mutation in the claimed plant or plant part thereof "disrupts the binding of the HY5 transcription factor by a Constitutive Photomorphogenic 1 (COP1) polypeptide (i.e., disrupts binding of COP1 to HY5 transcription) in the plant or part thereof." Therefore, the claims and specification make it clear that the COP1 binding site is an amino acid sequence within the HY5 polypeptide sequence and further provides an adequate description of the COP1 binding site as claimed (response to rejection, page 13, paragraph 1).
Applicant argues Applicant describes the structure of N Terminal region of SEQ ID NO: 74 that is required to have mutation:
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Applicant submits that one of ordinary skill in the art would recognize that Applicant's specification provides a description of the sequence of the HY5 gene of SEQ ID N0:72 that encodes the HY5 transcription factor (SEQ ID N0:74), as well as the sequence being targeted for mutation (i.e., the region being targeted by the guide nucleic acids comprising the spacers of SEQ ID NOs:107-113), which generates a deletion at the N-terminus of the HY5 polypeptide (response to rejection, page 13 and 14, last and first paragraphs).
Regarding argument on applicant has described structure of N Terminal region to be mutated in the amino acid sequence having 80% sequence identity to the amino acid sequence of SEQ ID N0:74. For example Tables 5, 8, and 9 showed for example mutation in position ranging from 11-47, therefore it since an amino acid would have N-terminal and C-terminal region, it is not clear what constitute the N-terminal region and which sequence when mutated would have any useful function? Therefore applicant has not described the specific limit of N-terminal region of any amino acid sequence having 80% sequence identity SEQ ID NO:74.
Regarding the analysis on increased density in OA applicant argues high-density planting induces the shade avoidance response (SAR), which causes tall plant stature. Applicant argues as shown in the Tables 6, 7, I 0, and 11 of the specification, plants with edited alleles of HY5 exhibited reduced sheath height in the shade as compared to controls. Applicant argues for example, whereas wild-type control plants exhibited a 5.07 mm increase in V1 sheath height and 4.88 mm increase in V2 sheath height in the shade compared to normal light conditions, Allele I only exhibited 3.70 mm increase in VI sheath height and 0.93 mm increase in V2 sheath height in the shade compared to normal light conditions. See Specification, Table 11. Applicant agues as such, Applicant's specification provides exemplary plants that exhibit reduced SAR, thereby allowing for increased planting density, as claimed.
Applicant's arguments have been fully considered but they are not persuasive since:
Regarding argument nucleotide sequences having on 80% sequence identity to the HY5 gene as including, e.g., homolog shas been described in specification was not found persuasive since sequence having 80% identity to SEQ ID NOs:72-75 are large number of variants that has diverse functions, see analysis above. Applicant has not described the representative number of amino acids and nucleotide sequences falling within the scope of the genus or of a recitation of structural features common to members of the genus which features constitute a substantial portion of the genus. Hy5 genes constitute various domains or motifs to interact with other proteins leading to their various function, see analysis above. Applicant has not described which domains or motifs are conserved in the recited sequence variants with 80% identity to SEQ ID NOs:72-75 that when conserved would have any function when creating any of the deletion or substitution in the large genus of sequences.
Regarding argument on Guo et al. teaches about human gene was not found persuasive since Guo teaches that while proteins are fairly tolerant to mutations resulting in single amino acid changes, increasing the number of substitutions additively increases the probability that the protein will be inactivated with the large number of mutations (page 9209, right. col., paragraph 2) with 105 diversity, this constitute a large study to see the effect of random amino acids changes which applicant is claiming of large number of variants of SEQ ID NOs:72-75 that will be further mutated to produce the recited plants. Therefore, the art is relevant to show the evidence that large number of variants such as with 80% identity to SEQ ID NOs:72-75 is a large genus that applicant does not have the representative number of amino acids and nucleotide sequences falling within the scope of the genus that has been described in specification or any existing arts. The diversity was further showed by Gangappa et al. and Xiao et al. that certain domain or motif would vary and certain are conserved to have various function of the genes. Applicant has not described which of the sequence which domain or motif structure are the applicant is claiming in the nucleotide with 80% sequence identity t0 SEQ ID NOs:72-75.
Regarding argument on 80% identity to SEQ ID NO:106 is not found persuasive since it is 37 amino acids long. Any nucleotide sequence encoding amino acids with 80% identity to SEQ ID NO:106 is large genus of molecules that would require when mutated to disrupts the binding of the HY5 transcription factor by a Constitutive Photomorphogenic 1 (COP1) polypeptide. Regarding description of, page 2, lines 7-9, the statement is a mere option showed by term “optionally” so it does not clearly show the sequence or any sequence with 80% identity to SEQ ID NO:106 constitute the COP1 binding site and found in any other sequence other than SEQ ID NO:74.
Regarding argument on applicant has described increased density tolerance, the argument was not found persuasive since Applicant has not described increased density of plant as compared to what control standard of the plant density (claims 16-17). Given diversity and various factor leading to density tolerance without comparing to any control standard of a plant, it is not clear what does an increase in density tolerance would mean. Applicant are advised to claim that the increase was increase as compared to a control plant not comprising the mutation.
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.
Anticipated maize plant B73
Claims 1, 3-6, 8, 9, 11, 16, and 17 are rejected under 35 U.S.C. 102 (a) (1) as being anticipated by maize inbred line B73 disclosed in Bornowski et al. (Published: 2021, Journal: Plant Genome. 2021;14:e20114. https://doi.org/10.1002/tpg2.20114) and as evidence by Gangappa et al. (Published: 2015, Journal: Molecular Plant 9: 1353–1365).
Claims are drawn to a plant comprising at least one mutation in an Elongated Hypocotyl5 (HY5) gene encoding a HY5 transcription factor having at least 80% sequence identity to the amino acid sequence of SEQ ID N0:74. The claims are drawn to wherein the plant exhibits reduced shade avoidance response.
Since there is no limit of mutations (i.e. insertions, deletion or substitutions) and no limit on structure of mutant Elongated Hypocotyl5 (HY5) gene (that could be deletion, insertions, substitutions etc.) encoding a HY5 transcription factor, any mutated gene in any plant anticipates the claim. However, following analysis is based on the interpretation that the mutant plant would require to maintain at least 80% sequence identity to the nucleotide and protein of HY5 gene.
The claim is interpreted as “product by process claim” wherein [E]ven though product by process claims are limited by and defined by the process, determination of patentability is based on the product itself. If the product in the product by process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process."
Regarding claim 1, alignment of SEQ ID NO: 74 to the Uniprot database showed the locus has 98.1% sequence identity to the locus A0A1D6H3I5 of maize inbred line B73 (see alignment above) which showed a insertions of amino acid sequence “KLATTSGMAPR” of about position 30 in the SEQ ID NO: 74 as compared to the maize locus A0A1D6H3I5.
The Uniport database showed the locus is from maize inbred lines B73 (see above). Bornowski et al. discloses maize inbred line B73 was developed by recurrent selection program from Iowa Stiff Stalk Synthetic (BSSS) population (page 4, Table 1). Therefore, the locus A0A1D6H3I5 has structure of the gene which would have a naturally occurring mutation as compared to the applicant’s SEQ ID NO: 74 with 98.1% sequence identity.
Regarding claim 3, since the N-terminal region of the endogenous HY5 transcription factor has not been described the insertion of “KLATTSGMAPR” of about position 30 in the SEQ ID NO: 74 amino acid sequences in the locus A0A1D6H3I5 is in the N-terminal region of the endogenous HY5 transcription factor.
Regarding claims 4-5, Ganappa et al. showed the evidence that the ACGT is a COP1 binding sequence for HY5 gene (page 1354, Table 1). The alignment of SEQ ID NO: 73 aligns with EU975706 from maize (see alignments above) which has the mutation in “ACGT” which is the COP1 binding site (see alignment above between positions 121-180 of the SEQ ID NO:73). Therefore, the sequence has a lack of COP1 binding site. Therefore, the mutant is naturally occurring sequence in B73 genome. Furthermore, reduced COP1 binding would be inherent to the structure of the mutation in any COP1 binding site in SEQ ID NO:73.
Regarding claim 6, the mutation is in the region of endogenous HY5 of locus A0A1D6H3I5 which has 91.6% sequence identity to SEQ ID NO: 106 (see alignment above).
Regarding claim 8, mutation would be insertion.
Regarding claim 9 and 11, locus A0A1D6H3I5 as compared to SEQ ID NO:73 would be either in frame insertion or in frame deletion as compared to one another which are with the limit of at least 80% identity to SEQ ID NO:73.
Regarding claims 16 and 17 the claims recite inherent property of the recited plants.
Therefore, line B73 anticipates the claim.
Response to Arguments
Applicant's arguments filed 11/20/2025 have been fully considered but they are not persuasive.
Applicant argues as amended herein, claim 1 recites a corn plant or plant part thereof comprising at least one mutation in an endogenous HY5 gene encoding a HY5 transcription factor, wherein the at least one mutation is a deletion and/or substitution. Applicant argues Bornowski fails to teach a corn plant or plant part thereof comprising a deletion and/or substitution in an endogenous HY5 gene as claimed. Applicant argues the cited teachings of Gangappa are of no relevance to the claims because the "ACGT" sequence being referred to in Gangappa is with regard to a sequence present in the COP I gene (response to rejection, page 15, paragraphs 2 and 3).
Applicant argues Office Action provides no basis for concluding that the recited phenotypes would be inherent to the B73 plant of Bornowski. Applicant agues As amended herein, claims 20 and 89 recite that sequence identity is over the entire length of the referenced sequence. Applicant agues on this basis, the sequence of A0A1D6H3l5 only shares 81 % identity with SEQ ID NO:130. Applicant argues therefore, Bornowski fails to teach the corn plant or plant part thereof of claim 20 or the nucleic acid of claim 89 as claimed.
Applicant's arguments have been fully considered but they are not persuasive since:
Regarding argument on claim 1 now reciting deletion and/or substitution limit in the claim, it is not found persuasive since the combination of any number of deletions and any substitutions would produce the recited sequences since there is no limit of nucleotide or amino acids deleting and substituting in any of the recited sequences in the claim. Since the genomic structure 0f the claimed corn plant is same as the referenced plants, the recited broad characteristics would be inherent in the plants.
Regarding argument on Bornowski fails to teach a corn plant or plant part thereof comprising a deletion and/or substitution in an endogenous HY5 gene as claimed, the argument was not found persuasive since the structure of the genome recited in the claims 1, 3-6, 8, 9, 11, 16, 17, and 92 is found in the B73 which was evidenced by the nucleotide and protein database, see analysis above.
Regarding argument on Gangappa is of no relevance to the claims because the "ACGT" sequence being referred to in Gangappa is with regard to a sequence present in the COP I gene, it was not found persuasive since the Table 1 showed the sequence “ACGT” is binding sequence between HY5 and COP1.
Regarding argument on, Bornowski fails to teach the corn plant or plant part thereof of claim 20 or the nucleic acid of claim 89 as claimed, it was found persuasive given the amendment of claims to require “over the entire length”, therefore the rejection over the claims 20 and 89 is withdrawn.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Obvious over Huai et al. and further in view of Binkert et al., Ang et al., and Char et al.
Claims 58, 60, 64, 69-71 and 78 are rejected under 35 U.S.C. 103 as being unpatentable over Huai et al. (Published: 2020, Journal: Physiologia Plantarum 169: 369–379), and further in view of Binkert et al. (Published: 2014, Journal: The Plant Cell, Vol. 26: 4200–4213), and further in view of Ang et al. (Published:1998, Journal: Molecular Cell, Vol. 1, 213–222) and further in view of Char et al. ( Published: 2017, Journal: Plant Biotechnology Journal 15: 257–268).
The claims are drawn to a method for producing a plant or plant part thereof comprising at least one cell having a mutation in an endogenous Elongated Hypocotyl5 (HY5) gene using a nuclease and comprising a cleavage domain and a nucleic acid binding domain. The claims are drawn to wherein the method produces a plant that exhibits reduced shade avoidance response.
Regarding claim 58, Huai et al. teaches ZmHY5 from B73 as
NP_001152483.1 (see supplementary Figure S2) which has 100% sequence identity to SEQ ID NO:74 (see sequence alignment below). Huai et al. teaches ZmCOP1 and ZmHY5 have high similarity and conserved domains with COP1 and HY5 proteins in Arabidopsis and other plant species (Figs S1 and S2) (page 375, right last paragraph). Huai et al. teaches overexpression of ZmHY5 complements the hy5-215 mutant phenotypes (Fig. 4) wherein ZmCOP1 and ZmHY5 perform similar functions in regulating photomorphogenesis in maize and Arabidopsis (page 376, left paragraph 1). Huai et al. teaches generation of loss-of-function of ZmCOP1 and/or ZmHY5 in maize will help resolve their functions and regulatory mechanism (page 377, left last paragraph).
Binkert et al. teaches T/G-box (290-CACGTT-85), in the HY5 promoter that is required for its UV-B responsiveness and it modulates the activity and UV-B induction of HY5 (see Figure 5 below showing effect of deletion of different regions of the promoter of HY5) in Arabidopsis (page 4200, Abstract, page 4205, left paragraph 1) wherein the deletion of different regions of HY5 promoter causes various effect to the activity and UV-B induction of HY5.
Furthermore, Ang et al. teaches in Arabidopsis COP1 acts as a light-in activable repressor of photomorphogenic development wherein COP1 negatively regulates HY5, a bZIP protein and a positive wherein the deletion of the N-terminal 77 amino acids of HY5, leaving the bZIP domain of HY5 intact, completely abolished its ability to interact with COP1 ((page 213, abstract, page 214, Figure 1 see figure blow). Therefore, someone skilled in the art would produce such mutation to remove light inactivable repressor of photomorphogenic development to induce the growth and development of the plant in dark (i.e. reduced shade avoidance).
Huai et al. and Binkert et al. and Ang et al. do not teach the mutation is carried out by contacting a target site within the endogenous HY5 gene in plant with a nuclease comprising a cleavage domain and a nucleic acid binding domain (i.e. CRISPR/Cas9 with guide RNA).
However, creating any mutation using CRISPR/Cas9 with guide RNA was known to a skilled in the art. Char et al. teaches targeted mutagenesis in maize lines Hi-II and B104 using CRISPR/Cas9 and guide RNAs leading to over 70% rate of targeted mutants per transgenic events in both Hi-II and B104 genotypes (page 257, Abstract). It would have been obvious to find a target region from the ZmHY5 gene taught by Huai et al. Char et al. teaches designing two gRNAs to target two sites within each allele, endogenous Argonaute 18 and dihydroflavonol 4-reductase in maize (page 258, left last paragraph, page 259, left last paragraph).
Thus it would have been obvious before the effective date of filing of the invention from Some teaching, suggestion, or motivation in the Huai et al. to create mutation in ZmHY5 for modifying shade avoidance or UV-B responsiveness in maize plant that would led one of skilled in the art to modify the ZmHY5 as Applicant’s SEQ ID NO: 74 as taught by Ang et al. and Brinkert et al. and modify by targeting specific target sequence as taught by Char et al. to arrive at the claimed invention of method of producing a plant comprising at least one cell having a mutation in an endogenous Elongated Hypocotyl5 (HY5) gene of maize encoding SEQ ID NO: 74 using a nuclease and comprising a cleavage domain and a nucleic acid binding domain.
Regarding claim 60, Hui et al.’s ZmHY5 is an endogenous HY5 gene from cultivar B73 (see alignment below). Furthermore, Char et al. teaches targeting the endogenous maize genes to produce the mutants.
Furthermore, Ang et al. teaches in Arabidopsis COP1 acts as a light-in activable repressor of photomorphogenic development wherein COP1 negatively regulates HY5, a bZIP protein and a positive wherein the deletion of the N-terminal 77 amino acids of HY5, leaving the bZIP domain of HY5 intact, completely abolished its ability to interact with COP1 ((page 213, abstract, page 214, Figure 1 see figure blow). Therefore, someone skilled in the art would target N-terminal amino acids of the HY5 gene to remove light inactivable repressor of photomorphogenic development to induce the growth and development of the plant in dark (i.e. reduced shade avoidance).
Regarding claim 64, the targeted mutation would produce either in-frame or out-of-frame insertions or deletions.
Regarding claim 69, Since the SEQ ID NO: 106 is a part of the SEQ ID NO:74 (see alignment above) and it is within the N-terminal 77 amino acids of ZmHY5, someone skilled in the art obviously try to have deletion at this region that would lead to inactivate the repressor COP1 that would lead to reduced shade avoidance in the mutated maize plants.
Regarding claim 71, the method would lead to reduced shade avoidance response as inherent property of the mutation.
Regarding claim 78, developing any guide nucleic acid of a known gene taught by Hui et al. is within the reach of skilled in the art as taught by Char et al. for developing guide RNA (page 266, left last paragraph). Furthermore, Hui et al. teaches primers in supplementary table S1 in page 2, where it shows fragments of the ZmHY5 gene which would be target regions for the guide RNA.
Regarding claim 70, Since the mutation in SEQ ID NO: 130 is within the N-terminal 77 amino acids of ZmHY5 (see alignment above), someone skilled in the art obviously try to have deletion at this region that would lead to inactivate the repressor COP1 that would lead to reduced shade avoidance in the mutated maize plants. Furthermore, Spec, page 108, Table 8 teaches the SEQ ID NO: 130 comprises deletion that removes the first 40 amino acids of SEQ ID N0:74 and replaces them with the amino acids "MQEQAASSRPSSSERS". The naturally occurring alternate allele A0A1D6H3I5_MAIZE is found in the B73 (see alignment above) someone skilled in the art would produce the mutant mimicking the naturally occurring A0A1D6H3I5_MAIZE that has 96.1% sequence identity to the Applicant’s SEQ ID NO: 130 (see alignment above).
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Alignment of SEQ ID NO: 74 to the Uniprot database:
RESULT 1
B6UEP1_MAIZE
ID B6UEP1_MAIZE Unreviewed; 170 AA.
AC B6UEP1;
DT 16-DEC-2008, integrated into UniProtKB/TrEMBL.
DT 16-DEC-2008, sequence version 1.
DT 05-FEB-2025, entry version 103.
DE SubName: Full=BZIP transcription factor {ECO:0000313|EMBL:AIB04436.1};
DE SubName: Full=Transcription factor HY5 {ECO:0000313|EMBL:ACG47824.1};
GN Name=LOC100286123 {ECO:0000313|EnsemblPlants:Zm00001eb235510_P001};
GN Synonyms=bZIP61 {ECO:0000313|EMBL:AIB04436.1};
GN ORFNames=ZEAMMB73_Zm00001d015743 {ECO:0000313|EMBL:AQK69393.1};
OS Zea mays (Maize).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; PACMAD clade;
OC Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea.
OX NCBI_TaxID=4577 {ECO:0000313|EMBL:ACG47824.1};
RN [1] {ECO:0000313|EMBL:ACG47824.1}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=18937034; DOI=10.1007/s11103-008-9415-4;
RA Alexandrov N.N., Brover V.V., Freidin S., Troukhan M.E., Tatarinova T.V.,
RA Zhang H., Swaller T.J., Lu Y.P., Bouck J., Flavell R.B., Feldmann K.A.;
RT "Insights into corn genes derived from large-scale cDNA sequencing.";
RL Plant Mol. Biol. 69:179-194(2009).
RN [2] {ECO:0000313|EMBL:ACN28050.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=B73 {ECO:0000313|EMBL:ACN28050.1};
RX PubMed=19936069; DOI=10.1371/journal.pgen.1000740;
RA Soderlund C., Descour A., Kudrna D., Bomhoff M., Boyd L., Currie J.,
RA Angelova A., Collura K., Wissotski M., Ashley E., Morrow D., Fernandes J.,
RA Walbot V., Yu Y.;
RT "Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.";
RL PLoS Genet. 5:E1000740-E1000740(2009).
RN [3] {ECO:0000313|Proteomes:UP000007305}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. B73 {ECO:0000313|Proteomes:UP000007305};
RX PubMed=19965430; DOI=10.1126/science.1178534;
RA Schnable P.S., Ware D., Fulton R.S., Stein J.C., Wei F., Pasternak S.,
RA Liang C., Zhang J., Fulton L., Graves T.A., Minx P., Reily A.D.,
RA Courtney L., Kruchowski S.S., Tomlinson C., Strong C., Delehaunty K.,
RA Fronick C., Courtney B., Rock S.M., Belter E., Du F., Kim K., Abbott R.M.,
RA Cotton M., Levy A., Marchetto P., Ochoa K., Jackson S.M., Gillam B.,
RA Chen W., Yan L., Higginbotham J., Cardenas M., Waligorski J., Applebaum E.,
RA Phelps L., Falcone J., Kanchi K., Thane T., Scimone A., Thane N., Henke J.,
RA Wang T., Ruppert J., Shah N., Rotter K., Hodges J., Ingenthron E.,
RA Cordes M., Kohlberg S., Sgro J., Delgado B., Mead K., Chinwalla A.,
RA Leonard S., Crouse K., Collura K., Kudrna D., Currie J., He R.,
RA Angelova A., Rajasekar S., Mueller T., Lomeli R., Scara G., Ko A.,
RA Delaney K., Wissotski M., Lopez G., Campos D., Braidotti M., Ashley E.,
RA Golser W., Kim H., Lee S., Lin J., Dujmic Z., Kim W., Talag J., Zuccolo A.,
RA Fan C., Sebastian A., Kramer M., Spiegel L., Nascimento L., Zutavern T.,
RA Miller B., Ambroise C., Muller S., Spooner W., Narechania A., Ren L.,
RA Wei S., Kumari S., Faga B., Levy M.J., McMahan L., Van Buren P.,
RA Vaughn M.W., Ying K., Yeh C.-T., Emrich S.J., Jia Y., Kalyanaraman A.,
RA Hsia A.-P., Barbazuk W.B., Baucom R.S., Brutnell T.P., Carpita N.C.,
RA Chaparro C., Chia J.-M., Deragon J.-M., Estill J.C., Fu Y., Jeddeloh J.A.,
RA Han Y., Lee H., Li P., Lisch D.R., Liu S., Liu Z., Nagel D.H., McCann M.C.,
RA SanMiguel P., Myers A.M., Nettleton D., Nguyen J., Penning B.W.,
RA Ponnala L., Schneider K.L., Schwartz D.C., Sharma A., Soderlund C.,
RA Springer N.M., Sun Q., Wang H., Waterman M., Westerman R., Wolfgruber T.K.,
RA Yang L., Yu Y., Zhang L., Zhou S., Zhu Q., Bennetzen J.L., Dawe R.K.,
RA Jiang J., Jiang N., Presting G.G., Wessler S.R., Aluru S.,
RA Martienssen R.A., Clifton S.W., McCombie W.R., Wing R.A., Wilson R.K.;
RT "The B73 maize genome: complexity, diversity, and dynamics.";
RL Science 326:1112-1115(2009).
RN [4] {ECO:0000313|EMBL:AIB04436.1}
RP NUCLEOTIDE SEQUENCE.
RA Burdo B., Gray J., Goetting-Minesky M.P., Wittler B., Hunt M., Li T.,
RA Velliquette D., Thomas J., Gentzel I., Dos Santos Brito M.,
RA Mejia-Guerra M.K., Connolly L.N., Qaisi D., Li W., Casas M.I., Doseff A.I.,
RA Grotewold E.;
RT "The Maize TFome - Development of a transcription factor open reading frame
RT collection for functional genomics.";
RL Submitted (APR-2014) to the EMBL/GenBank/DDBJ databases.
RN [5] {ECO:0000313|EMBL:AQK69393.1}
RP NUCLEOTIDE SEQUENCE.
RC TISSUE=Seedling {ECO:0000313|EMBL:AQK69393.1};
RG Maize Genome Sequencing Project;
RA Ware D.;
RT "Update maize B73 reference genome by single molecule sequencing
RT technologies.";
RL Submitted (DEC-2015) to the EMBL/GenBank/DDBJ databases.
RN [6] {ECO:0000313|EnsemblPlants:Zm00001eb235510_P001}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. B73 {ECO:0000313|EnsemblPlants:Zm00001eb235510_P001};
RA Seetharam A., Woodhouse M., Cannon E.;
RL Submitted (JUL-2019) to the EMBL/GenBank/DDBJ databases.
RN [7] {ECO:0000313|EnsemblPlants:Zm00001eb235510_P001}
RP IDENTIFICATION.
RC STRAIN=cv. B73 {ECO:0000313|EnsemblPlants:Zm00001eb235510_P001};
RG EnsemblPlants;
RL Submitted (MAY-2021) to UniProtKB.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000256|ARBA:ARBA00004123}.
CC -!- SIMILARITY: Belongs to the bZIP family.
CC {ECO:0000256|ARBA:ARBA00007163}.
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DR EMBL; EU975706; ACG47824.1; -; mRNA.
DR EMBL; BT063353; ACN28050.1; -; mRNA.
DR EMBL; KJ726945; AIB04436.1; -; mRNA.
DR EMBL; CM000781; AQK69393.1; -; Genomic_DNA.
DR RefSeq; NP_001152483.1; NM_001159011.2.
DR PaxDb; 4577-GRMZM2G137046_P01; -.
DR EnsemblPlants; Zm00001eb235510_T001; Zm00001eb235510_P001; Zm00001eb235510.
DR GeneID; 100286123; -.
DR Gramene; Zm00001eb235510_T001; Zm00001eb235510_P001; Zm00001eb235510.
DR KEGG; zma:100286123; -.
DR eggNOG; KOG1414; Eukaryota.
DR HOGENOM; CLU_068771_1_0_1; -.
DR OMA; SAHHMEM; -.
DR OrthoDB; 674948at2759; -.
DR Proteomes; UP000007305; Chromosome 5.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IEA:InterPro.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IEA:InterPro.
DR CDD; cd14704; bZIP_HY5-like; 1.
DR FunFam; 1.20.5.490:FF:000004; Transcription factor HY5; 1.
DR Gene3D; 1.20.5.490; Single helix bin; 1.
DR InterPro; IPR004827; bZIP.
DR InterPro; IPR046347; bZIP_sf.
DR InterPro; IPR044280; Hac1/HY5.
DR PANTHER; PTHR46714; TRANSCRIPTIONAL ACTIVATOR HAC1; 1.
DR PANTHER; PTHR46714:SF6; TRANSCRIPTIONAL ACTIVATOR HAC1; 1.
DR Pfam; PF00170; bZIP_1; 1.
DR SMART; SM00338; BRLZ; 1.
DR SUPFAM; SSF57959; Leucine zipper domain; 1.
DR PROSITE; PS50217; BZIP; 1.
DR PROSITE; PS00036; BZIP_BASIC; 1.
PE 1: Evidence at protein level;
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125};
KW Proteomics identification {ECO:0007829|PeptideAtlas:B6UEP1};
KW Reference proteome {ECO:0000313|Proteomes:UP000007305};
KW Transcription {ECO:0000256|ARBA:ARBA00023163};
KW Transcription regulation {ECO:0000256|ARBA:ARBA00023015}.
FT DOMAIN 89..152
FT /note="BZIP"
FT /evidence="ECO:0000259|PROSITE:PS50217"
FT REGION 1..109
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 151..170
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 21..41
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 151..164
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 170 AA; 18716 MW; 7E3D376A909F8212 CRC64;
Query Match 100.0%; Score 837; Length 170;
Best Local Similarity 100.0%;
Matches 170; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MQEQAASSRPSSSERSSSSGHHVDMEVKEGMESDDEIRRVPELGLELPGASTSGREAGPG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MQEQAASSRPSSSERSSSSGHHVDMEVKEGMESDDEIRRVPELGLELPGASTSGREAGPG 60
Qy 61 AAGADRALAQSSTAQASARRRVRSHADKEHKRLKRLLRNRVSAQQARERKKAYLTDLEVK 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 AAGADRALAQSSTAQASARRRVRSHADKEHKRLKRLLRNRVSAQQARERKKAYLTDLEVK 120
Qy 121 VRDLEKKNSEMEERLSTLQNENQMLRQILKNTAVNRRGSGSTASGEGHGQ 170
||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 VRDLEKKNSEMEERLSTLQNENQMLRQILKNTAVNRRGSGSTASGEGHGQ 170
Alignment of SEQ ID NO: 73 to the EST database:
EE010671
LOCUS EE010671 762 bp mRNA linear EST 26-JUL-2007
DEFINITION ZM_BFc0055M22.r ZM_BFc Zea mays cDNA clone ZM_BFc0055M22 5', mRNA
sequence.
ACCESSION EE010671
VERSION EE010671.2
DBLINK BioSample: SAMN00150567
KEYWORDS EST.
SOURCE Zea mays
ORGANISM Zea mays
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; PACMAD
clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae;
Zea.
REFERENCE 1 (bases 1 to 762)
AUTHORS Collura,K., Wissotski,M., Campos,D., Kudrna,D., Golser,W.,
Ashely,E., Haller,K., Wing,R., Soderlund,C., Walbot,V. and Yu,Y.
TITLE Maize Full-length cDNA Project
JOURNAL Unpublished
COMMENT On Jul 18, 2006 this sequence version replaced EE010671.1.
Contact: Yeisoo Yu
Arizona Genomics Institute
The University of Arizona
Forbes Building Room 303, Tucson, AZ 85721-0036, USA
Tel: 520 626 9585
Fax: 520 621 1259
Email: yeisoo\@genome.arizona.edu
Plate: 0055 row: M column: 22.
FEATURES Location/Qualifiers
source 1..762
/organism="Zea mays"
/mol_type="mRNA"
/cultivar="B73"
/db_xref="taxon:4577"
/clone="ZM_BFc0055M22"
/tissue_type="mixed"
/clone_lib="SAMN00150567 ZM_BFc"
/dev_stage="mixed"
/lab_host="DH10B T1 phage resistant"
/note="Vector: pCMV.SPORT-6.1; Site_1: EcoRI; Site_2:
NotI; Maize Full length cDNA library constructed by
Invitrogen from multiple tissues: 7 day seedling, 7 day
seedling with 2 day salt treatment, 4 hour 45 C heat
shock, 24 hour 10 C treatment, 4 hour UV-B treatment, 2
day osmotic stress, 7 day etiolated seedling and Juvenile
leaf. Vector: pCMV-SPORT 6.1; Site_1: EcoRV; Site_2: NotI;
This is a Gateway compatible vector, permitting clone
movement to new vector backbones for expression in diverse
host cells using recombination rather than restriction
enzymes. poly(A)+ mRNA was prepared by Invitrogen, and
equimolar amounts of RNA from each tissue samples were
mixed together for selection of mRNA with a 5' cap. After
synthesis of cDNA, a normalization step was conducted
against the mixture of RNA sources.
Query Match 100.0%; Score 513; Length 762;
Best Local Similarity 100.0%;
Matches 513; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 ATGCAGGAGCAGGCGGCGAGCTCGCGGCCTTCCAGCAGCGAGAGGTCGTCCAGCTCCGGG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 71 ATGCAGGAGCAGGCGGCGAGCTCGCGGCCTTCCAGCAGCGAGAGGTCGTCCAGCTCCGGG 130
Qy 61 CACCACGTGGACATGGAGGTCAAGGAAGGGATGGAGAGCGACGATGAGATAAGGAGAGTG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 131 CACCACGTGGACATGGAGGTCAAGGAAGGGATGGAGAGCGACGATGAGATAAGGAGAGTG 190
Qy 121 CCGGAGCTGGGCCTGGAGTTGCCGGGAGCCTCCACGTCGGGCAGGGAGGCTGGCCCTGGC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 191 CCGGAGCTGGGCCTGGAGTTGCCGGGAGCCTCCACGTCGGGCAGGGAGGCTGGCCCTGGC 250
Qy 181 GCTGCGGGCGCAGACCGCGCCCTTGCCCAGTCGTCCACGGCGCAGGCCAGCGCGCGCCGC 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 251 GCTGCGGGCGCAGACCGCGCCCTTGCCCAGTCGTCCACGGCGCAGGCCAGCGCGCGCCGC 310
Qy 241 CGCGTCCGCAGCCACGCCGACAAGGAGCACAAGCGCCTCAAAAGGTTACTGAGGAACAGG 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 311 CGCGTCCGCAGCCACGCCGACAAGGAGCACAAGCGCCTCAAAAGGTTACTGAGGAACAGG 370
Qy 301 GTGTCAGCTCAACAGGCTAGAGAGAGGAAGAAGGCTTATTTAACTGATCTGGAGGTGAAG 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 371 GTGTCAGCTCAACAGGCTAGAGAGAGGAAGAAGGCTTATTTAACTGATCTGGAGGTGAAG 430
Qy 361 GTGAGAGATCTGGAGAAGAAGAACTCGGAGATGGAAGAGAGGCTCTCCACCCTCCAGAAC 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 431 GTGAGAGATCTGGAGAAGAAGAACTCGGAGATGGAAGAGAGGCTCTCCACCCTCCAGAAC 490
Qy 421 GAGAACCAGATGCTCCGACAGATACTGAAGAACACCGCTGTAAACAGAAGAGGTTCAGGA 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 491 GAGAACCAGATGCTCCGACAGATACTGAAGAACACCGCTGTAAACAGAAGAGGTTCAGGA 550
Qy 481 AGCACTGCTAGTGGAGAGGGCCACGGCCAATAG 513
|||||||||||||||||||||||||||||||||
Db 551 AGCACTGCTAGTGGAGAGGGCCACGGCCAATAG 583
Response to Arguments
Applicant's arguments filed 11/20/2025 have been fully considered but they are not persuasive.
Applicant argues each of Huai, Binkert and Ang describes the activity of HY5 in Arabidopsis. Applicant argues in particular, Huai teaches that the introduction of a 35S: :ZmHY5-GFP construct in an Arabidopsis hy5-2 J 5 null mutant complements the hy5 mutation as evidenced by hypocotyl lengths indistinguishable from wild-type seedlings. See Huai, page 373-374 (response to rejection, page 16, last paragraph). Applicant argues Binkert teaches that the association of HY5 with target genes is regulated by UV-B and identifies cis-regulatory elements that mediated transcription of HY5 in Arabidopsis. See Binkert, abstract. Applicant argues Ang shows that COP1 and HY5 in Arabidopsis interact and role of the same in light-regulated seedling development. See Ang, e.g., page 214. Applicant argues thus, the combination of Huai, Binkert and Ang fails to teach or suggest a method for producing a corn plant or plant part thereof comprising at least one cell having a mutation in an endogenous HY5 gene as claimed. Applicant argues in addition, the combination of Huai, Binkert, and Ang fails to teach or suggest a guide nucleic acid that binds to a target site within an endogenous HY5 gene as claimed or provide a target sequence encoding a polypeptide of SEQ ID N0:106 (response to rejection, page 17 first paragraph).
Applicant argues Char describes the use of the CRISPR-Cas9 system for targeted mutagenesis of ZmAgo18a ZmAgol8b, which have been implicated in 24-nt phasiRNA biogenesis (See Chen, page 259, col. 1, last paragraph) and maize anthocyanin biosynthesis genes al and a4. Applicant argues these are completely different genes with completely different functions than that of HY5. Applicant argues in this regard, Char fails to provide any guidance such that one of ordinary skill would have had any reasonable expectation of successfully targeting a HY5 gene of corn as claimed. Applicant argues moreover, because Char describes a mutation in a different gene in a different plant than that of Huai, Binkert, and Ang, there would have been no motivation or rationale to combine Huai, Binkert, and Ang with Char as the Office Action asserts (response to rejection, page 17, second paragraph).
Applicant's arguments have been fully considered but they are not persuasive since:
Regarding argument on Huai, Binkert are in Arabidopsis and combination of Char fails to teach claimed corn plant, it was not found persuasive since it would have been obvious before the effective date of filing of the invention from Some teaching, suggestion, or motivation in the Huai et al. to create mutation in ZmHY5 for modifying shade avoidance or UV-B responsiveness in maize plant that would led one of ordinary skill to modify the ZmHY5 as Applicant’s SEQ ID NO: 74 as taught by Ang et al. and Brinkert et al. and modify by targeting specific target sequence as taught by Char et al. to arrive at the claimed invention of method of producing a plant comprising at least one cell having a mutation in an endogenous Elongated Hypocotyl5 (HY5) gene of maize encoding SEQ ID NO: 74 using a nuclease and comprising a cleavage domain and a nucleic acid binding domain.
Regarding argument on Huai, Binkert, and Ang fails to teach or suggest a guide nucleic acid that binds to a target site was not found persuasive since applicant has not claimed any guide nucleic acid sequence except the spacer of claim 78 which is optional limitation not required by claim. Furthermore, developing any guide nucleic acid of a known gene taught by Hui et al. is within the reach of skilled in the art as taught by Char et al. for developing guide RNA (page 266, left last paragraph). Furthermore, Hui et al. teaches primers in supplementary table S1 in page 2, where it shows fragments of the ZmHY5 gene which would be target regions for the guide RNA.
Furthermore, where a rejection of a claim is based on two or more references, a reply that is limited to what a subset of the applied references teaches or fails to teach, or that fails to address the combined teaching of the applied references may be considered to be an argument that attacks the reference(s) individually. Where an applicant’s reply establishes that each of the applied references fails to teach a limitation and addresses the combined teachings and/or suggestions of the applied prior art, the reply as a whole does not attack the references individually as the phrase is used in Keller and reliance on Keller would not be appropriate. This is because the test for obviousness is what the combined teachings of the references would have suggested to a person having ordinary skill in the art (PHOSITA).”
Conclusion
No claim is allowed.
Claims 20, 89 and 92 are free of prior art. The closest prior art is Bornowski et al. which disclose the maize line B73, the B73 does not comprise mutated endogenous HY5 gene having at least 90% sequence identity over the entire length of SEQ ID NO: 129 encoding a protein having at least 90% sequence identity over the entire length of SEQ ID NO:30. Furthermore the other closest prior art Huai et al. teaches hy5 mutant in Arabidopsis. Hua et al. teaches function and regulatory mechanism of the COP1-HY5 signaling pathway in maize and Arabidopsis (page 369, Abstract). Huai et al. teaches their disclosed ZM-HY5 is Applicant’s SEQ ID NO:74 (see sequence alignment above). The patentable distinction is Huai et al. specifically does not teach making specific mutation in SEQ ID NO:74 that would lead to polypeptide of SEQ ID NO:130 which deletes first 40 amino acids of SEQ ID N0:74 and replaces them with the amino acids "MQEQAASSRPSSSERS" (Spec, page 108, Table 8, Notes).
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 nonprovisional extension fee (37 CFR 1.17(a)) 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 mailing date of this final action.
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/SANTOSH SHARMA/Examiner, Art Unit 1663
/DAVID H KRUSE/Primary Examiner, Art Unit 1663