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 .
Status of Claims
Claims 1, 10-13 & 16-26 are under examination on the merits.
Claims 2, 27-29, 46-48 & 53-55 were withdrawn without traverse in the election filed 4/29/2025.
The objection to the specification is withdrawn in light of Applicant’s amendments.
The objections to claims 1, 3, 5, 9, 11, 12, 22, 23 & 26 are withdrawn in light of Applicant’s amendments or cancelation of claims.
The rejection of claim 9 under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, is withdrawn in light of Applicant’s cancelation of the claim.
The rejection of claims 1, 3, 5, 9-13, & 16-22 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112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement is withdrawn in light of Applicant’s amendments.
The rejection of claims 1, 3, 5, 9-13 & 16-26 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to provide enablement for the full scope of the claims is withdrawn in light of Applicant’s amendments.
The rejection of claims 1 & 9 under 35 U.S.C. 102(a)(1) as being anticipated by Innes et al US 2019/0256864 A1 taken with the evidence of Chen et al (2014) Molecular Plant Pathology. 15(5), 433–446 is withdrawn in light of Applicant’s amendments.
The rejection of claims 1, 9, 11, 16 & 18-22 under 35 U.S.C. 103 as being unpatentable over Innes et al US 2019/0256864 A1 taken with the evidence of Chen et al (2014) Molecular Plant Pathology. 15(5), 433–446 and Goellner et al (2010) Molecular Plant Pathology. 11(2), 169–177 is withdrawn in light of Applicant’s amendments.
The rejection of claims 1, 9, 10, 11, 13 & 16-22 under 35 U.S.C. 103 over Innes and Innes et al US 9,816,102 B2, taken with the evidence of Chen, Goellner, and GenBank Accession NM_001198041.1 is withdrawn in light of Applicant’s amendments.
The rejection of claims 1, 9, 11, 12, 16 & 18-22 under 35 U.S.C. 103 over Innes, taken with the evidence of Chen and Goellner, further in view of Goellner is withdrawn in light of Applicant’s amendments.
Information Disclosure Statement
The information disclosure statement filed 11/11/2025 fails to comply with 37 CFR 1.98(a)(2),
which requires a legible copy of each non-patent literature publication or that portion which caused it to be listed. It has been placed in the application file, but the information referred to therein has not been considered. No copy of Periyannan et al (2017) was provided with the IDS submitted 11/11/2025.
Claim Objections
Claims 1, 13 & 23 are objected to because of the following informalities:
Claim 1 (line 7) and claim 23 (line 13 & 15) recite a PBS1 polypeptide. Claim 13 (line 3) recites an RPS5 resistance protein. Gene names should be written out in full before using an abbreviation in at least each independent claim.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
Indefiniteness
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 13 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Due to Applicant’s amendment of the claims, this rejection is modified from the rejection set forth in the Office action mailed 6/16/2025, as applied to claims 5, 11-13 & 17. Applicant' s arguments filed 9/15/2025 have been fully considered, however they are not persuasive as they do not address the new rejection based on amendment of claim 13.
Claim 13 recites the limitation "the RPS5 resistance protein" in lines 3-4. There is insufficient antecedent basis for this limitation in the claim.
Written Description
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.
A. Claims 1, 10-13, & 16-26 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.
This is a new rejection. Applicant' s arguments filed 9/15/2025 in response to the rejection of claims 1, 3, 5, 9-13, & 16-22 under 35 U.S.C. 112(a) have been fully considered below as they apply to the new rejection but they are not persuasive.
Claims 1, 10-13, & 16-26 require a nucleotide sequence that encodes a protein comprising a PBS1 polypeptide comprising an amino acid sequence having at least 90% identity to SEQ ID NO: 1 and retaining PBS1 activity and a heterologous Basidiomycete-specific protease cleavage site comprising a cleavage sequence with at least 90% identity to SEQ ID NO: 9, 17, 21, 24, 26, 27, 29, 29, or 52, or the recombinant protein encoded by the nucleic acid molecule, or a plant comprising the nucleic acid molecule. Claims 1,10-13, & 16-22 require SEQ ID NO: 9, 17, 21, 24, 26, 27, 29, 29, or 52. Claim 10 further requires that the cleavage site is located between about amino acid position 238 to about amino acid position 248 in reference to SEQ ID NOs: 1 and 53-97. Claim 11 further requires that the protein comprises a protease cleavage site for a protease from a Phakopsora plant pathogen species and claim 23 requires that the protein is cleaved by a protease of Phakopsora pachyrhizi.
Thus, the claims broadly require a nucleotide sequence encoding a polypeptide with 90% identity to SEQ ID NO: 1 comprising a cleavage sequence of SEQ ID NOs: 9, 17, 21, 24, 26, 27, 29, 29, or 52, or with 90% sequence identity to the recited cleavage sites, with PBS1 activity and/or the protein encoded by such a sequence.
Polypeptide sequences with 90% identity to SEQ ID NO: 1 encompass sequences with 45 substitutions relative to the 456 amino acid-long SEQ ID NO: 1. Polypeptide sequences with 90% identity to SEQ ID NO: 52 encompass sequences with 1 substitutions relative to the 12 amino acid-long SEQ ID NO: 52.
The specification provides an amino acid sequence (SEQ ID NO: 1) and a nucleic acid sequence (SEQ ID NO: 2) of PBS1 in Arabidopsis thaliana as well as amino acid sequences (SEQ ID NOs: 150-152) described as Glycine homologs of the A. thaliana PBS1. No other PBS1 polypeptides in other species are provided. SEQ ID NOs: 53-97 are modified from SEQ ID NO: 1 by replacing the endogenous cleavage site (SEQ ID NO: 7) with a heterologous cleavage site (one of SEQ ID NOs: 8-52). The specification does not teach polypeptides wherein the cleavage site is located at a different position between about amino acid 238 to about amino acid 248 as in claim 10.
The specification describes that recognition of a pathogen specific protease requires interaction between a substrate protein such as PBS1 and resistance proteins such as RPS5 (page 4 line 30-page 5 line 1). The only structural motif taught by the instant specification for the substrate protein is the cleavage site (page 27, lines 3-6).
The instant specification provides examples of Basidiomycete-specific cleavage sites: SEQ ID NOs: 8-29 & 52 (page 31, lines 16-24; page 34, lines 5-11). These sequences are highly diverse; SEQ ID NOs: 17, 21, 24, 26-29 or 52 have no significant sequence similarity to SEQ ID NO: 9 in a blastp alignment. The instant specification describes a degenerate six amino acid motif that can be included in the cleavage site (page 30, lines 26-page 31, line 2). The specification teaches only Basidiomycete-specific cleavage sequences of 6 amino acids, or in the case of SEQ ID NO: 52, a 12 amino acid sequence that is a combination of SEQ ID NOs: 21 & 24.
Beyond the degenerate cleavage sequence motifs, the instant specification does not describe the features of the cleavage sequences that make them Basidiomycete-specific and not generally recognized by another pathogen or endogenous protease. In fact, the specification describes Basidiomycete-specific cleavage site peptide sequences, inserted in PBS1 variants and introduced into N. benthamiana, leading to cell death or a hypersensitive response with all PBS1 variants regardless of whether plant pathogen specific proteases were present or not. The specification proposes that N. benthamiana may contain a protease with similar substrate specificity as the pathogen specific proteases (page 51, lines 12-30). Furthermore, the instant specification describes that pathogen specific cleavage was enhanced in N. tabacum (page 52, lines 1-8) and describes "several" of the variants as inducing pathogen-specific protease cell death (table 1). The instant specification does not describe what differentiates these variants from the other Basidiomycete-specific protease cleavage sites provided that makes them Basidiomycete specific.
PBS1 proteins with high sequence identity to SEQ ID NO: 1 are known in the art. UniProtKB entry A0A9W3D583_RAPSA (available 11/8/2023, after the filing of the instant application) describes a protein in Raphanus sativus with as little as 90.1% identity to SEQ ID NO: 1 and a PANTHER annotation of PBS1. See first alignment below. In addition, Innes et al (WO2020219879 published 10/29/2020) teaches a PBS1 protease cleavage fusion protein from Brassica rapa with as little as 91% sequence identity to SEQ ID NO: 1. See second alignment below. PBS1 proteins with 90% sequence identity to SEQ ID NO: 1 from species outside the Brassicaceae are not described in the art nor with variation across the full sequence of SEQ ID NO: 1.
A0A9W3D583_RAPSA
ID A0A9W3D583_RAPSA Unreviewed; 485 AA.
AC A0A9W3D583;
DT 08-NOV-2023, integrated into UniProtKB/TrEMBL.
DT 08-NOV-2023, sequence version 1.
DT 08-OCT-2025, entry version 11.
DE RecName: Full=non-specific serine/threonine protein kinase {ECO:0000256|ARBA:ARBA00012513};
DE EC=2.7.11.1 {ECO:0000256|ARBA:ARBA00012513};
GN Name=LOC108836105 {ECO:0000313|RefSeq:XP_056858849.1};
OS Raphanus sativus (Radish) (Raphanus raphanistrum var. sativus).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus.
OX NCBI_TaxID=3726 {ECO:0000313|Proteomes:UP000504610, ECO:0000313|RefSeq:XP_056858849.1};
RN [1] {ECO:0000313|Proteomes:UP000504610}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. WK10039 {ECO:0000313|Proteomes:UP000504610};
RX PubMed=30722041;
RA Yu H.J., Baek S., Lee Y.J., Cho A., Mun J.H.;
RT "The radish genome database (RadishGD): an integrated information resource
RT for radish genomics.";
RL Database 2019:5306501-5306501(2019).
RN [2] {ECO:0000313|RefSeq:XP_056858849.1}
RP IDENTIFICATION.
RC TISSUE=Leaf {ECO:0000313|RefSeq:XP_056858849.1};
RG RefSeq;
RL Submitted (APR-2025) to UniProtKB.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP +
CC H(+); Xref=Rhea:RHEA:17989, Rhea:RHEA-COMP:9863, Rhea:RHEA-
CC COMP:11604, ChEBI:CHEBI:15378, ChEBI:CHEBI:29999, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:83421, ChEBI:CHEBI:456216; EC=2.7.11.1;
CC Evidence={ECO:0000256|ARBA:ARBA00048679};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] +
CC ADP + H(+); Xref=Rhea:RHEA:46608, Rhea:RHEA-COMP:11060, Rhea:RHEA-
CC COMP:11605, ChEBI:CHEBI:15378, ChEBI:CHEBI:30013, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:61977, ChEBI:CHEBI:456216; EC=2.7.11.1;
CC Evidence={ECO:0000256|ARBA:ARBA00047899};
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000256|ARBA:ARBA00004193};
CC Lipid-anchor {ECO:0000256|ARBA:ARBA00004193}.
CC -!- SIMILARITY: Belongs to the protein kinase superfamily. Ser/Thr protein
CC kinase family. {ECO:0000256|ARBA:ARBA00008684}.
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DR RefSeq; XP_056858849.1; XM_057002869.1.
DR GeneID; 108836105; -.
DR OrthoDB; 4062651at2759; -.
DR Proteomes; UP000504610; Chromosome 2.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004674; F:protein serine/threonine kinase activity; IEA:UniProtKB-KW.
DR GO; GO:0045087; P:innate immune response; IEA:UniProtKB-ARBA.
DR GO; GO:0031349; P:positive regulation of defense response; IEA:UniProtKB-ARBA.
DR GO; GO:0045088; P:regulation of innate immune response; IEA:UniProtKB-ARBA.
DR CDD; cd14066; STKc_IRAK; 1.
DR FunFam; 1.10.510.10:FF:000032; Serine/threonine-protein kinase PBS1; 1.
DR FunFam; 3.30.200.20:FF:000248; Serine/threonine-protein kinase PBS1; 1.
DR Gene3D; 3.30.200.20; Phosphorylase Kinase, domain 1; 1.
DR Gene3D; 1.10.510.10; Transferase(Phosphotransferase) domain 1; 1.
DR InterPro; IPR011009; Kinase-like_dom_sf.
DR InterPro; IPR000719; Prot_kinase_dom.
DR InterPro; IPR017441; Protein_kinase_ATP_BS.
DR InterPro; IPR008271; Ser/Thr_kinase_AS.
DR PANTHER; PTHR47985; OS07G0668900 PROTEIN; 1.
DR PANTHER; PTHR47985:SF44; SERINE_THREONINE-PROTEIN KINASE PBS1; 1.
DR Pfam; PF00069; Pkinase; 1.
DR SUPFAM; SSF56112; Protein kinase-like (PK-like); 1.
DR PROSITE; PS00107; PROTEIN_KINASE_ATP; 1.
DR PROSITE; PS50011; PROTEIN_KINASE_DOM; 1.
DR PROSITE; PS00108; PROTEIN_KINASE_ST; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|PROSITE-
KW ProRule:PRU10141}; Cell membrane {ECO:0000256|ARBA:ARBA00022475};
KW Kinase {ECO:0000256|ARBA:ARBA00022777, ECO:0000313|RefSeq:XP_056858849.1};
KW Lipoprotein {ECO:0000256|ARBA:ARBA00023288};
KW Membrane {ECO:0000256|ARBA:ARBA00023136};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|PROSITE-
KW ProRule:PRU10141}; Palmitate {ECO:0000256|ARBA:ARBA00023139};
KW Phosphoprotein {ECO:0000256|ARBA:ARBA00022553};
KW Plant defense {ECO:0000256|ARBA:ARBA00022821};
KW Reference proteome {ECO:0000313|Proteomes:UP000504610};
KW Serine/threonine-protein kinase {ECO:0000256|ARBA:ARBA00022527,
KW ECO:0000256|RuleBase:RU000304};
KW Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT DOMAIN 122..399
FT /note="Protein kinase"
FT /evidence="ECO:0000259|PROSITE:PS50011"
FT REGION 1..33
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 425..485
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 429..458
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 475..485
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 151
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU10141"
SQ SEQUENCE 485 AA; 53424 MW; F8CD5D5B807CB479 CRC64;
Query Match 90.5%; Score 2149.5; Length 485;
Best Local Similarity 85.4%;
Matches 422; Conservative 14; Mismatches 11; Indels 47; Gaps 3;
Qy 1 MGCFSCFDSSDDEKLNPVDESNHGQKKQSQPTVSNNISGLPS------------------ 42
||||||||||||| ||| :|| :|||||||||::|||||
Db 1 MGCFSCFDSSDDETLNPAEESK--AQKQSQPTVSNSLSGLPSGLLIIQSPILYGHTLSQD 58
Qy 43 --------------------GGEKLSSKTNGGSKRELLLPRDGLGQIAAHTFAFRELAAA 82
||||||||:|| || ||||||||| |||||||||||||||
Db 59 LILIRPNVVWSGHNNLVAVLGGEKLSSKSNGVSKTELLLPRDGLAQIAAHTFAFRELAAA 118
Qy 83 TMNFHPDTFLGEGGFGRVYKGRLDSTGQVVAVKQLDRNGLQGNREFLVEVLMLSLLHHPN 142
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 119 TMNFHPDTFLGEGGFGRVYKGRLDSTGQVVAVKQLDRNGLQGNREFLVEVLMLSLLHHPN 178
Qy 143 LVNLIGYCADGDQRLLVYEFMPLGSLEDHLHDLPPDKEALDWNMRMKIAAGAAKGLEFLH 202
||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Db 179 LVNLIGYCADGDQRLLVYEFMSLGSLEDHLHDLPPDKEALDWNMRMKIAAGAAKGLEFLH 238
Qy 203 DKANPPVIYRDFKSSNILLDEGFHPKLSDFGLAKLGPTGDKSHVSTRVMGTYGYCAPEYA 262
||||||||||||||||||||:|||||||||||||||||||||||||||||||||||||||
Db 239 DKANPPVIYRDFKSSNILLDDGFHPKLSDFGLAKLGPTGDKSHVSTRVMGTYGYCAPEYA 298
Qy 263 MTGQLTVKSDVYSFGVVFLELITGRKAIDSEMPHGEQNLVAWARPLFNDRRKFIKLADPR 322
|||||||||||||||||||||||||||||::||||||||||||||||||||||||||||:
Db 299 MTGQLTVKSDVYSFGVVFLELITGRKAIDTDMPHGEQNLVAWARPLFNDRRKFIKLADPK 358
Qy 323 LKGRFPTRALYQALAVASMCIQEQAATRPLIADVVTALSYLANQAYDPSKDDSRRNRDER 382
|||||||||||||||||||||||||||||||||||||||||||| ||| |::||
Db 359 LKGRFPTRALYQALAVASMCIQEQAATRPLIADVVTALSYLANQGYDP-------NKNER 411
Qy 383 GARLITRNDDGGGSGSKFDLEGSEKEDSPRETARILNRDINRERAVAEAKMWGESLREKR 442
||||:||||:| |||||||||||||||||||||:|||||||||||||||||||||||||
Db 412 GARLMTRNDEGCVSGSKFDLEGSEKEDSPRETARMLNRDINRERAVAEAKMWGESLREKR 471
Qy 443 RQSEQGTSESNSTG 456
||||||||||||||
Db 472 RQSEQGTSESNSTG 485
BIN32025
ID BIN32025 standard; protein; 451 AA.
XX
AC BIN32025;
XX
DT 24-DEC-2020 (first entry)
XX
DE PBS1-protease cleavage fusion protein, SEQ 61.
XX
KW PBS1 protein; Protease; chimeric protein; crop improvement;
KW disease resistance; fusion protein; plant; protein production; serine;
KW substrate; threonine-protein kinase PBS1; transgenic plant.
XX
OS Brassica rapa.
OS Turnip mosaic virus.
OS Chimeric.
XX
CC PN WO2020219879-A1.
XX
CC PD 29-OCT-2020.
XX
CC PF 24-APR-2020; 2020WO-US029815.
XX
PR 25-APR-2019; 2019US-0838786P.
PR 07-MAY-2019; 2019US-0844310P.
XX
CC PA (INDV ) UNIV INDIANA RES & TECHNOLOGY CORP.
XX
CC PI Innes RW, Helm MD;
XX
DR WPI; 2020-A5938M/094.
XX
CC PT Activating disease resistance in a plant involves modifying a gene in the
CC PT plant to produce a modified PBS1 protein, incorporating pathogen protease
CC PT cleavage site, and cleaving the modified protein with pathogen protease.
XX
CC PS Example 3; SEQ ID NO 61; 83pp; English.
XX
CC The present invention relates to a method for activating disease
CC resistance in a plant. The method involves: (a) modifying a gene in the
CC plant to produce a modified serine/threonine-protein kinase PBS1 (PBS1)
CC protein of SEQ ID NO: 10, 12 and 14 (see BIN31974, BIN31976 and
CC BIN31978), where the modification involves incorporating a pathogen
CC protease cleavage site; and (b) cleaving the modified protein with the
CC pathogen protease to activate disease resistance in the plant. The
CC invention further claims: (1) a monocot plant with a gene encoding the
CC modified PBS1 protein; (2) a modified PBS1 protein having an amino acid
CC sequence of SEQ ID NO: 24, 27, 30, 33 and 36 (see BIN31988, BIN31991,
CC BIN31994, BIN31997 and BIN32000); (3) a gene with a DNA sequence encoding
CC the PBS1 protein; (4) a synthetic PBS1 decoy protein with a protease
CC cleavage motif of SEQ ID NO: 37-39 (see BIN32001-BIN32003); and (5) a
CC method for generating the PBS1 decoy protein. The method is useful for:
CC activating disease resistance in plants; and engineering novel pathogen
CC disease resistance traits into crops (such as soybeans, barley, wheat,
CC rice, sorghum, corn, tomato, canola and citrus). The present sequence is
CC a fusion protein containing rapeseed PBS1 protein and turnip mosaic virus
CC (TuMV) protease cleavage motif, which is useful in the method for
CC activating disease resistance in plants.
XX
SQ Sequence 451 AA;
Query Match 91.0%; Score 2160.5; Length 451;
Best Local Similarity 91.3%;
Matches 418; Conservative 15; Mismatches 16; Indels 9; Gaps 2;
Qy 1 MGCFSCFDSSDDEKLNPVDESNHGQKKQSQPTVSNNISGLPSGGEKL--SSKTNGGSKRE 58
||||||||||||| ||| | : :|||||||||::| |||||||| :||:|||:| |
Db 1 MGCFSCFDSSDDETLNPAAEESSKTQKQSQPTVSNSLSALPSGGEKLNSNSKSNGGAKTE 60
Qy 59 LLLPRDGLGQIAAHTFAFRELAAATMNFHPDTFLGEGGFGRVYKGRLDSTGQVVAVKQLD 118
|||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||
Db 61 LLLPRDGLGQIAAHTFTFRELAAATMNFHPDTFLGEGGFGRVYKGRLDSTGQVVAVKQLD 120
Qy 119 RNGLQGNREFLVEVLMLSLLHHPNLVNLIGYCADGDQRLLVYEFMPLGSLEDHLHDLPPD 178
||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||
Db 121 RNGLQGNREFLVEVLMLSLLHHPNLVNLIGYCADGDQRLLVYEFMSLGSLEDHLHDLPPD 180
Qy 179 KEALDWNMRMKIAAGAAKGLEFLHDKANPPVIYRDFKSSNILLDEGFHPKLSDFGLAKLG 238
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 KEALDWNMRMKIAAGAAKGLEFLHDKANPPVIYRDFKSSNILLDEGFHPKLSDFGLAKLG 240
Qy 239 PTGDKSHVSTRVMGTYGYCAPEYAMTGQLTVKSDVYSFGVVFLELITGRKAIDSEMPHGE 298
||| || |||||||||||||||||||||||||||||||||||||||||||||::|||||
Db 241 PTGGCSHQSTRVMGTYGYCAPEYAMTGQLTVKSDVYSFGVVFLELITGRKAIDTDMPHGE 300
Qy 299 QNLVAWARPLFNDRRKFIKLADPRLKGRFPTRALYQALAVASMCIQEQAATRPLIADVVT 358
|||||||||||||||||||||||:|||||||||||||||||||||| :||||||||||||
Db 301 QNLVAWARPLFNDRRKFIKLADPKLKGRFPTRALYQALAVASMCIQGEAATRPLIADVVT 360
Qy 359 ALSYLANQAYDPSKDDSRRNRDERGARLITRNDDGGGSGSKFDLEGSEKEDSPRETARIL 418
|||||||| ||| |::|||||||||||:||||||||||||||||||||||||:|
Db 361 ALSYLANQGYDP-------NKNERGARLITRNDEGGGSGSKFDLEGSEKEDSPRETARML 413
Qy 419 NRDINRERAVAEAKMWGESLREKRRQSEQGTSESNSTG 456
||||||||||||||||||||||||||||||||||||||
Db 414 NRDINRERAVAEAKMWGESLREKRRQSEQGTSESNSTG 451
Similarly, PBS1 proteins with modified pathogen-specific recognition sites are known in the art. Kim et al (2016) Science. 351(6274): 684-687 (published 2/12/2016, hereafter Kim) describes NLR proteins as highly specific with regard to pathogen effectors detected (page 684, column 3, paragraph 1). Kim describes a modified protein in which the normal PBS1 proteolytic target site/cleavage site (Gly-Asp-Lys-Ser-His-Val-Ser) is switched with Val-Pro-Lys-Phe-Gly-Asp-Trp (page 685, first column, paragraph 3), leading to a hypersensitive response-associated phenotype to the Pseudomonas syringae virulence factor AvrRpt2 instead of AvrPphB. Kim suggests that the system should be usable to engineer resistance to any pathogen that uses a protease as part of infection process where the protease targets a defined recognition sequence of seven or fewer amino acids, but does not describe longer effective recognition sequences and does not describe PBS1 polypeptides that vary at locations other than the cleavage site or in which the cleavage recognition site is moved to another location in the sequence (page 687, column 2 paragraph 3; figure 1).
The structural features that distinguish polypeptides with PBS1 activity with only 90% amino acid identity to SEQ ID NO: 1 and Basidiomycete-specific protease cleavage sites are not described in the specification. One of skill in the art would not recognize that Applicant was in possession of the necessary common attributes or features of the full genus of polypeptides with PBS1 activity comprising a Basidiomycete-specific protease cleavage site in view of the disclosed species.
Since the specification fails to sufficiently describe the genus of nucleotide sequences encoding PBS1 polypeptides with 90% sequence identity to SEQ ID NO: 1 comprising a Basidiomycete-specific protease cleavage site of SEQ ID NOs: 9, 17, 21, 24, 26, 27, 29, 29, or 52, recombinant nucleic acid molecules, vectors, plants, plant parts, plant cells, seeds comprising said nucleotide sequences and methods of using nucleotide sequences are similarly not described.
Given the lack of written description in the specification with regard to the structural and functional characteristics of the claimed compositions, Applicant does not appear to have been in possession of the full scope of the claimed genus at the time this application was filed.
Applicant urges that amended claims require a polypeptide having at least 90% sequence identity to SEQ ID NO: 1 and a cleavage site of SEQ ID NOs: 9, 17, 21, 24, 26-29 or 52, rendering the rejection moot (Remarks, page 2, paragraph 6).
This argument is unpersuasive to the current rejection, because the amended claims require a polypeptide with as little as 90% identity to SEQ ID NO: 1. Based on the examples and description of such proteins in the specification and the state of the prior art, Applicant does not appear to have been in possession of the full scope of the claimed genus of PBS1 proteins with 90% sequence identity to SEQ ID NO: 1 comprising the recited cleavage sites at the recited positions at the time this application was filed.
B. Claims 1, 10-13, & 16-22 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.
This is a new rejection.
Claim 13 requires a RPS5 resistance protein comprising an amino acid sequence having at least 90% identity to SEQ ID NO: 3 that retains RPS5 activity.
A protein comprising 90% sequence identity to SEQ ID NO: 3 encompasses proteins with 88 amino acid substitutions relative to the 889 amino acid-long SEQ ID NO: 3.
The instant specification describes RPS5 as an R gene which confers resistance to plant pathogens through the specific recognition of pathogen specific proteases (page 4, lines 27-30). The specification provides an amino acid sequence (SEQ ID NO: 3) and a nucleic acid sequence (SEQ ID NO: 4) of RPS5 from Arabidopsis thaliana. The instant specification describes that R-genes may comprise motifs such as a Toll/Interleukin-1 receptor, a nucleotide-binding site and a leucine rich-repeat, although the specification does not describe that the RPS5 gene of claim 13 requires these motifs (page 20, lines 18-25). No additional structural features or examples of RPS5 proteins are provided by the instant specification
RESISTANCE TO PSEUDOMONAS SYRINGAE5 (RPS5) proteins are known in the art. The Arabidopsis RPS5, in particular, is known to comprise an LRR domain that promotes RPS5 activation in the presence of PBS1 cleavage and suppresses activation in the absence of PBS1 cleavage (Qi et al (2012) Plant Physiology. 158:1819-1832, published April 2012, hereafter Qi; abstract, page 1825, right column, paragraph 3). The LRR domain in plant R proteins is under diversifying selection and possibly coevolving with pathogen effectors (Qi page 1820, left column, paragraph 3). Swapping LRR domains of closely related paralogs can result in constitutive activation of the proteins (Qi page 1820, left column, paragraph 3-right column, paragraph 1 & page 1826, let column, paragraph 1).
Sequences of resistance proteins with as little as 93.5% sequence identity to instant SEQ ID NO: 3 are known in plants of the Arabidopsis genus. See alignment below of UniProtKB entry Q38JY9_ARALY from Arabidopsis lyrate (available 11/22/2005). RPS5 protein sequences with as little as 90% sequence identity to RPS5 or in other genera are not described in the art.
Q38JY9_ARALY
ID Q38JY9_ARALY Unreviewed; 891 AA.
AC Q38JY9;
DT 22-NOV-2005, integrated into UniProtKB/TrEMBL.
DT 22-NOV-2005, sequence version 1.
DT 05-FEB-2025, entry version 76.
DE SubName: Full=Disease resistance protein {ECO:0000313|EMBL:ABB00216.1};
DE Flags: Fragment;
GN Name=RPS5 {ECO:0000313|EMBL:ABB00216.1};
GN ORFNames=At1g12220 {ECO:0000313|EMBL:ABB00216.1};
OS Arabidopsis lyrata (Lyre-leaved rock-cress) (Arabis lyrata).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=59689 {ECO:0000313|EMBL:ABB00216.1};
RN [1] {ECO:0000313|EMBL:ABB00216.1}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=16452149; DOI=10.1534/genetics.105.047290;
RA Shen J., Araki H., Chen L., Chen J.Q., Tian D.;
RT "Unique evolutionary mechanism in R-genes under the presence/absence
RT polymorphism in Arabidopsis thaliana.";
RL Genetics 172:1243-1250(2006).
CC -!- SIMILARITY: Belongs to the disease resistance NB-LRR family.
CC {ECO:0000256|ARBA:ARBA00008894}.
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DR EMBL; DQ220640; ABB00216.1; -; Genomic_DNA.
DR AlphaFoldDB; Q38JY9; -.
DR ExpressionAtlas; Q38JY9; baseline.
DR GO; GO:0043531; F:ADP binding; IEA:InterPro.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0006952; P:defense response; IEA:UniProtKB-KW.
DR FunFam; 3.40.50.300:FF:001091; Probable disease resistance protein At1g61300; 1.
DR FunFam; 1.10.10.10:FF:000322; Probable disease resistance protein At1g63360; 1.
DR FunFam; 3.80.10.10:FF:000799; Probable disease resistance protein At5g63020; 1.
DR FunFam; 1.10.8.430:FF:000003; Probable disease resistance protein At5g66910; 1.
DR Gene3D; 1.10.8.430; Helical domain of apoptotic protease-activating factors; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1.
DR Gene3D; 3.80.10.10; Ribonuclease Inhibitor; 2.
DR InterPro; IPR042197; Apaf_helical.
DR InterPro; IPR001611; Leu-rich_rpt.
DR InterPro; IPR032675; LRR_dom_sf.
DR InterPro; IPR002182; NB-ARC.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR050905; Plant_NBS-LRR.
DR PANTHER; PTHR33463:SF220; NB-ARC DOMAIN-CONTAINING PROTEIN; 1.
DR PANTHER; PTHR33463; NB-ARC DOMAIN-CONTAINING PROTEIN-RELATED; 1.
DR Pfam; PF13855; LRR_8; 1.
DR Pfam; PF00931; NB-ARC; 1.
DR PRINTS; PR00364; DISEASERSIST.
DR SUPFAM; SSF52058; L domain-like; 1.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
PE 3: Inferred from homology;
KW Plant defense {ECO:0000256|ARBA:ARBA00022821}.
FT DOMAIN 161..402
FT /note="NB-ARC"
FT /evidence="ECO:0000259|Pfam:PF00931"
FT NON_TER 891
FT /evidence="ECO:0000313|EMBL:ABB00216.1"
SQ SEQUENCE 891 AA; 101518 MW; BFCCFAC5B0E99B99 CRC64;
Query Match 93.5%; Score 4309.5; Length 891;
Best Local Similarity 93.6%;
Matches 833; Conservative 24; Mismatches 32; Indels 1; Gaps 1;
Qy 1 MGGCFSVSLPCDQVVSQFSQLLCVRGSYIHNLSKNLASLQKAMRMLKARQYDVIRRLETE 60
|||||||||||||||||||||||||||||||||:|||||:||| :|: |||||||||| |
Db 1 MGGCFSVSLPCDQVVSQFSQLLCVRGSYIHNLSENLASLEKAMGVLQGRQYDVIRRLERE 60
Qy 61 EFTGRQQRLSQVQVWLTSVLIIQNQFNDLLRSNEVELQRLCLCGFCSKDLKLSYRYGKRV 120
||||||||||||||||||||:|||||:||||| |||||||||||||||||||||||||:|
Db 61 EFTGRQQRLSQVQVWLTSVLLIQNQFDDLLRSKEVELQRLCLCGFCSKDLKLSYRYGKKV 120
Qy 121 IMMLKEVESLSSQGFFDVVSEATPFADVDEIPFQPTIVGQEIMLEKAWNRLMEDGSGILG 180
|||:|||||||:||||||:||||||:|||||||||||||:|||||||||||||||||||
Db 121 NMMLREVESLSSRGFFDVVAEATPFAEVDEIPFQPTIVGQKIMLEKAWNRLMEDGSGILG 180
Qy 181 LYGMGGVGKTTLLTKINNKFSKIDDRFDVVIWVVVSRSSTVRKIQRDIAEKVGLGGMEWS 240
||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||
Db 181 LYGMGGVGKTTLLTKINNKFSKIGDRFDVVIWVVVSRSSTVRKIQRDIAEKVGLGGMEWG 240
Qy 241 EKNDNQIAVDIHNVLRRRKFVLLLDDIWEKVNLKAVGVPYPSKDNGCKVAFTTRSRDVCG 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 EKNDNQIAVDIHNVLRRRKFVLLLDDIWEKVNLKAVGVPYPSKDNGCKVAFTTRSRDVCG 300
Qy 301 RMGVDDPMEVSCLQPEESWDLFQMKVGKNTLGSHPDIPGLARKVARKCRGLPLALNVIGE 360
|||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||
Db 301 RMGVDDPMEVSCLQPEESWDLFQMTVGKNTLGSHPDIPGLARKVARKCRGLPLALNVIGE 360
Qy 361 AMACKRTVHEWCHAIDVLTSSAIDFSGMEDEILHVLKYSYDNLNGELMKSCFLYCSLFPE 420
||||||||||| ||| |||||| |||||||||||||||| ||||||||||| ||||||||
Db 361 AMACKRTVHEWSHAIYVLTSSATDFSGMEDEILHVLKYSSDNLNGELMKSCSLYCSLFPE 420
Qy 421 DYLIDKEGLVDYWISEGFINEKEGRERNINQGYEIIGTLVRACLLLEEERNKSNVKMHDV 480
|||||||| ||| | |||||||||||| :||||||||||||||||:||||||||||||||
Db 421 DYLIDKEGWVDYGICEGFINEKEGRERTLNQGYEIIGTLVRACLLMEEERNKSNVKMHDV 480
Qy 481 VREMALWISSDLGKQKEKCIVRAGVGLREVPKVKDWNTVRKISLMNNEIEEIFDSHECAA 540
||||||||||||||||||||||||||| |||||||||||||:||||||||||||||:|||
Db 481 VREMALWISSDLGKQKEKCIVRAGVGLCEVPKVKDWNTVRKMSLMNNEIEEIFDSHKCAA 540
Qy 541 LTTLFLQKNDVVKISAEFFRCMPHLVVLDLSENQSLNELPEEISELASLRYFNLSYTCIH 600
||||||||||:|||||||||||||||||||||| |||||||||||| |||||||||||||
Db 541 LTTLFLQKNDMVKISAEFFRCMPHLVVLDLSENHSLNELPEEISELVSLRYFNLSYTCIH 600
Qy 601 QLPVGLWTLKKLIHLNLEHMSSLGSILGISNLWNLRTLGLRDSRLLLDMSLVKELQLLEH 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 QLPVGLWTLKKLIHLNLEHMSSLGSILGISNLWNLRTLGLRDSRLLLDMSLVKELQLLEH 660
Qy 661 LEVITLDISSSLVAEPLLCSQRLVECIKEVDFKYLKEESVRVLTLPTMGNLRKLGIKRCG 720
|||:|||||||||||||||| |||||||||| ||||||:|||||||||||||:|||| ||
Db 661 LEVVTLDISSSLVAEPLLCSHRLVECIKEVDIKYLKEEAVRVLTLPTMGNLRRLGIKMCG 720
Qy 721 MREIKIERTTSSSSRNKSPTTPCFSNLSRVFIAKCHGLKDLTWLLFAPNLTFLEVGFSKE 780
||||||| |||||||| ||||| ||||| |||||||||||||||||||||||||||||||
Db 721 MREIKIESTTSSSSRNISPTTPFFSNLSSVFIAKCHGLKDLTWLLFAPNLTFLEVGFSKE 780
Qy 781 VEDIISEEKAEEH-SATIVPFRKLETLHLFELRGLKRIYAKALHFPCLKVIHVEKCEKLR 839
||||||||||:|| ||||||||||||||| ||||||||||| | |||||||||:||||||
Db 781 VEDIISEEKADEHSSATIVPFRKLETLHLLELRGLKRIYAKTLPFPCLKVIHVQKCEKLR 840
Qy 840 KLPLDSKSGIAGEELVIYYGEREWIERVEWEDQATQLRFLPSSRWRWRET 889
|||||||||| ||||:|||||||||||||||||||:||||||||||| ||
Db 841 KLPLDSKSGITGEELIIYYGEREWIERVEWEDQATKLRFLPSSRWRWIET 890
One of skill in the art would not recognize that Applicant was in possession of the necessary common attributes or features of the full genus of amino acid sequences with 90% sequence identity to SEQ ID NO: 3 with RPS5 activity in view of the disclosed species.
Since the specification fails to sufficiently describe the genus of amino acid sequences with 90% sequence identity to SEQ ID NO: 3 with RPS5 activity, recombinant nucleic acid molecules, vectors, plants, plant parts, plant cells, seeds comprising said sequences are not described. Given the lack of written description in the specification with regard to the structural and functional characteristics of the claimed compositions, Applicant does not appear to have been in possession of the full scope of the claimed genus at the time this application was filed.
Scope of Enablement
Claims 1, 10-13, & 16-26 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first
paragraph, because the specification, while being enabling for a PBS1 polypeptide of SEQ ID NO: 1 comprising a Basidiomycete-specific protease cleavage site of SEQ ID NO: 9, 17, 21, 24, 26, 27, 28, 29 or 52 and method of enhancing pathogen resistance in a plant of Nicotiana tabacum or soybean, does not reasonably provide enablement for all PBS1 proteins with 90% identity to SEQ ID NO: 1 comprising Basidiomycete-specific proteases cleavage sites of SEQ ID NOs: 9, 17, 21, 24, 26, 27, 28, 29 or 52 in all species of plant. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
This is a new rejection. Applicant' s arguments filed 9/15/2025 in response to the rejection of claims 1, 3, 5, 9-13 & 16-26 under 35 U.S.C. 112(a) have been fully considered below as they apply to the new rejection but they are not persuasive.
The claims broadly require a nucleotide sequence encoding a substrate protein comprising 90% identity to SEQ ID NO:1 comprising a Basidiomycete-specific protease cleavage site or the protein encoded by such a nucleotide sequence. Claim 10 further requires that the cleavage site is located between about amino acid position 238 to about amino acid position 248 in reference to SEQ ID NOs: 1 and 53-97. Claim 11 further requires that the protein comprises a protease cleavage site for a protease from a Phakopsora plant pathogen species and claim 23 requires that the protein is cleaved by a protease of Phakopsora pachyrhizi. Claims 23-26 merely require that the cleavage site comprises a cleavage sequence have at least 90% sequence identity to SEQ ID NOs: 9, 17, 21, 24, 26-29 or 52.
The instant specification teaches Basidiomycete-specific cleavage sites: SEQ ID NOs: 8-29 & 52 (page 31, lines 16-24; page 34, lines 5-11). SEQ ID NOs: 17, 21, 24, 26-29 or 52 have no significant sequence similarity to SEQ ID NO: 9 in a blastp alignment. The instant specification describes a degenerate six amino acid motif that can be included in the cleavage site (page 30, lines 26-page 31, line 2).
The specification teaches an amino acid sequence (SEQ ID NO: 1) and a nucleic acid sequence (SEQ ID NO: 2) of PBS1 in Arabidopsis thaliana as well as amino acid sequences (SEQ ID NOs: 150-152) described as Glycine homologs of the A. thaliana PBS1. No other PBS1 polypeptides in other species are provided. SEQ ID NOs: 53-97 are modified from SEQ ID NO: 1 by replacing the endogenous cleavage site (SEQ ID NO: 7) with a heterologous cleavage site (one of SEQ ID NOs: 8-52). The specification does not teach polypeptides wherein the cleavage site is located at a different position between about amino acid 238 to about amino acid 248 as in claim 10.
The specification teaches that recognition of a pathogen specific protease requires interaction between a substrate protein such as PBS1 and resistance proteins such as RPS5 (page 4 line 30-page 5 line 1). The only structural motif taught by the instant specification for the substrate protein is the cleavage site (page 27, lines 3-6).
Although the specification teaches successful methods wherein Basidiomycete-specific cleavage site peptide sequences are inserted in PBS1 variants and introduced into N. tabacum to enhance pathogen-specific cleavage (page 52, lines 1-8) and describes several of the variants as inducing pathogen-specific protease cell death (table 1), the specification also teaches methods wherein modified PBS1 proteins are introduced into N. benthamiana leading to cell death or a hypersensitive response variants regardless of whether plant pathogen specific proteases are present or not, suggesting N. benthamiana may contain a protease with similar substrate specificity as the “pathogen specific” proteases (page 51, lines 12-30).
PBS1 homologs are known in the art, including homologs in other Brassicaceae species with 90.1% sequence identity to instant SEQ ID NO: 1 (UniProtKB entry A0A9W3D583_RAPSA, available 11/8/2023, after the filing of the instant application). See alignment above.
However, PBS1 homologs in other species, such as wheat, have more sequence divergence. Triticum aestivum PBS1 has only 75% sequence similarity to Arabidopsis thaliana PBS1 (Sun et al (2017) Scientific Reports. 7: 5487. Published 7/14/2017, hereafter Sun; page 2, paragraph 4). Cleavage of wheat PBS1 is not sufficient to trigger Arabidopsis RPS5-mediated HR response (Sun page 2, paragraph 5-6), because wheat PBS1 lacks the SEMPH motif found in PBS1 of mustard species related to Arabidopsis (Sun page 4, paragraph 5). However, adding a SEMPH motif to wheat PBS1 and co-expressing with Arabidopsis RPS5 still generates a weaker HR response than Arabidopsis PBS1 in N. benthamiana (Sun page 5, paragraph 1). Thus, the ability of PBS1 proteins to trigger RPS5-mediated hypersensitive response is unpredictable across species with different PBS1 sequences.
Kim et al (2016) Science. 351(6274): 684-687 (published 2/12/2016, hereafter Kim) teaches NLR proteins as highly specific with regard to pathogen effectors detected (page 684, column 3, paragraph 1). Kim teaches a modified protein in which the normal PBS1 proteolytic target site/cleavage site (Gly-Asp-Lys-Ser-His-Val-Ser) is switched with Val-Pro-Lys-Phe-Gly-Asp-Trp (page 685, first column, paragraph 3), leading to a hypersensitive response-associated phenotype to the Pseudomonas syringae virulence factor AvrRpt2 instead of AvrPphB. Kim suggests that the system should be usable to engineer resistance to any pathogen that uses a protease as part of infection process where the protease targets a defined recognition sequence of seven or fewer amino acids, but does not teach longer effective recognition sequences and does not describe PBS1 polypeptides that vary at locations other than the cleavage site or in which the cleavage recognition site is moved to another location in the sequence (page 687, column 2 paragraph 3; figure 1). In addition, Kim teaches that the specific pathogen protease should localize to the host cell cytoplasm early in the infection cycle (page 687, column 2 paragraph 3), because proteases that do not may activate the resistance gene response after the infection has already spread (page 687, column 1, paragraph 2-column 2, paragraph 2).
Given the diversity of pathogen proteases, protease localization, and protease cleavage sites, the unpredictability that the cleavage sites will be specific to a Basidiomycete-specific protease and
not recognized by a host protease, and the unpredictability that a PBS1 homolog would associate effectively with an RPS5 homolog to trigger a hypersensitive response, one of ordinary skill in the art would be required to conduct undue trial and error experimentation to figure out which cleavage site sequences with 90% identity to SEQ ID NO: 52 are Basidiomycete-specific and which PBS1 polypeptide sequences with 90% identity to SEQ ID NO: 1 would effectively enhance pathogen resistance in a given host.
Thus, claims 1, 10-13, & 16-26, while being enabled for a nucleotide encoding a PBS1 polypeptide of SEQ ID NO: 1 comprising a Basidiomycete-specific protease cleavage site of SEQ ID NOs: 9, 17, 21, 24, 26-29 or 52 in N. tabacum or soybean, are not enabled for any PBS1 polypeptide with 90% sequence identity to SEQ ID NO: 1 comprising a Basidiomycete-specific protease cleavage site in any plant species.
Applicant urges that the amended claims recite nucleotide sequences encoding the cleavage sites of SEQ ID NOs: 9, 17, 21, 24, 26-29 and 52 (Remarks, page 2, paragraph 7-page 3, paragraph 1).
This argument is unpersuasive to the current rejection, because the amended claims require a polypeptide with as little as 90% identity to SEQ ID NO: 1. Based on the examples and description of such proteins in the specification and teaching in the prior art of variation in PBS1 proteins, one of ordinary skill in the art would have been required to conduct undue experimentation to make and use the claimed PBS1 proteins over the full scope of the claimed genus of PBS1 proteins with 90% sequence identity to SEQ ID NO: 1 comprising the recited cleavage sites at the recited positions across different species of plants.
Conclusion
No claims are allowed.
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/VICTORIA L DELEO/Examiner, Art Unit 1662
/Anne Kubelik/Primary Examiner, Art Unit 1663