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 .
Claim Status
Claims 1-33 and 35-38 are pending and being examined.
All the claims will be examined to the extent of the elected species, as described in previous Office action, dated 8/18/2025.
All previous objections and rejections not set forth below have been withdrawn in view of applicant’s amendments to the claims. However, the amendments in claims 1, 16, 23 and 37 by the Applicant by adding new issues, which was not present before, necessitated new grounds of rejections, as discussed below.
Claim Rejections - 35 USC § 112(a)
Scope of Enablement
Claims 1, 3-15, 18-19 and 23-38 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 transgenic plants overexpressing CIPK15 polypeptide comprising 100% sequence identity to SEQ ID NO: 1 which contains an isoleucine at position 48, does not reasonably provide enablement for transgenic or gene-edited plants that do not overexpress a CIPK15 polypeptide comprising 100% sequence identity to SEQ ID NO: 1 which contains an isoleucine at position 48. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
The invention is related to a method of overexpressing a calcineurin B- like (CBL) interacting protein kinase15 (CIPK15) having an isoleucine (Ile) residue at position 48 in plants which can promote growth of the plants (Spec, page 1, para 0003). The native or endogenous rice CIPK15 polypeptide comprising SEQ ID NO: 1 contains an isoleucine (Ile) residue at position 48. The Applicant describes expressing full-length CIPK15 cDNA under the control of i) inducible promoter (spec, page 26, para 000136, line 1-2), ii) a 2 kb CIPK15 promoter region plus 1.4 kb 5’ untranslated region (UTR) including the first intron (spec, page 26, para 000136, line 4-5), and iii) a constitutive ubiquitin promoter (spec, page 26, para 000138).
Rice and green foxtail (S. vridis) plants were transformed with a construct containing the rice CIPK15 cDNA under the control of rice CIPK15 promoter (OsCIPK15:OsCIPK15) (page 27, para 000150). The Applicant describes that overexpression of CIPK15 cDNA under the control of strong constitutive ubiquitin (Ubi) promoter severely inhibits the growth of transgenic rice plants (spec, page 30, para 000174, line 5-6). On the other hand, inducible overexpression under the control of a 3-estradiol-inducible XVE promoter increased aerenchyma and root development (root elongation and increased root radius) (spec, page 30, para 000174, line 7-9). The rice plants overexpressing CIPK15 under the control of its native promoter (as described) carrying CIPK15:CIPK15 showed normal growth but having increased yield by 26-46% (spec, page 32, para 000183).
Oryza genus (rice) is unique where the native CIPK15 polypeptide has an isoleucine at position 48 while other orthologues contain Val-48 or Ala-48 (page 36, para 000200, line 1-4). Instant description implies that rice CIPK15 exert unique functions different from those of other CIPK15s (page 38, para 000207, line 2-3). However, the Applicant does not provide any experimental evidence or reference in that regard.
The Applicant does not describe any transgenic plant, other than rice (Oryza spp.) expressing or overexpressing the endogenous CIPK15 gene or a non-rice CIPK15 protein containing only one substitution of isoleucine (I) at a position corresponding to position 48 of SEQ ID NO: 1.
The CIPK15 protein in green foxtail (SEQ ID NO: 7), as recited in claim 3, has 35 amino acid mismatches as compared to the OsCIPK15 polypeptide (SEQ ID NO: 1), as shown below. The amino acid residues at position 48 is highlighted in grey.
Title: US-18-645-166-1
Perfect score: 2224
Sequence: 1 MESRGKILMERYELGRLLGK..........EYRQLLEEGIRPALKDIVLA 434
Scoring table: BLOSUM62
Gapop 10.0 , Gapext 0.5
Searched: 1 seqs, 444 residues
Total number of hits satisfying chosen parameters: 1
Database : US-18-645-166-7.pep:*
RESULT 1
US-18-645-166-7
Query Match 87.4%; Score 1943; DB 1; Length 444; Best Local Similarity 85.5%;
Matches 371; Conservative 28; Mismatches 35; Indels 0; Gaps 0;
Qy 1 MESRGKILMERYELGRLLGKGTFGKVHYARNLESNQSVAIKMMDKQQILKVGLSEQIRRE 60
|| |||||||||||||:||||||||||||:||||||||||||||| ::||||||||||||
Db 1 MEGRGKILMERYELGRMLGKGTFGKVHYAKNLESNQSVAIKMMDKDKVLKVGLSEQIRRE 60
Qy 61 ITTMRLVAHKNIVQLHEVMATRNKIYFVMEYVKGGELFEKVAKRGKLTEVVAHKYFQQLI 120
|||||||||||||:||||||||||||||||||||||||||: | ||||| |||||||||
Db 61 ITTMRLVAHKNIVELHEVMATRNKIYFVMEYVKGGELFEKIEKSGKLTEPAAHKYFQQLI 120
Qy 121 SAVDYCHSRGVYHRDLKPENLLLDENENLKVSDFGLSALSESKRQDGLLHTTCGTPAYVA 180
|||||||||||||||||||||||||:||||||||||||||||||||||||||||||||||
Db 121 SAVDYCHSRGVYHRDLKPENLLLDEDENLKVSDFGLSALSESKRQDGLLHTTCGTPAYVA 180
Qy 181 PEVISKIGYDGAKSDIWSCGVILFVLVAGYLPFQGPNLMEMYRKIQHGEFRCPGWFSRKL 240
|||||||||||||||||||||:||||||||||||||||||||||:|||:|||| ||| ||
Db 181 PEVISKIGYDGAKSDIWSCGVVLFVLVAGYLPFQGPNLMEMYRKVQHGDFRCPSWFSHKL 240
Qy 241 QKLLYKIMDPNPSTRISIQKIKESTWFRKGPEENRILKERTLNENTTKNVAPVLGVRRKK 300
:||||||:||||:||||||||||||||||||| | :||: || | | || | |||||
Db 241 KKLLYKILDPNPATRISIQKIKESTWFRKGPEGTRTVKEKIPCENATTNAAPTLSVRRKK 300
Qy 301 NAHEDVKPMSVTNLNAFEIISFSKGFDLSGMFIVKEWRNEARFTSDKSASTIISKLEDVA 360
| :|| ||::||||||||||||| ||||||:|: || | ||||||||||| || |:||||
Db 301 NPYEDAKPLTVTNLNAFEIISFSSGFDLSGLFLEKECRKEARFTSDKSASAIILKIEDVA 360
Qy 361 KALNLRVRKKDNGVVKMQGRKEGRNGVLQFDIEIFEVTTSYHIIEMKQTSGDSLEYRQLL 420
| ||||||||||||||:|||||||||||||| ||||:| :|::|||||||| |||::|
Db 361 KMLNLRVRKKDNGVVKIQGRKEGRNGVLQFDTEIFEITPLHHLVEMKQTSGDFLEYQKLF 420
Qy 421 EEGIRPALKDIVLA 434
|| ||||||||| |
Db 421 EEDIRPALKDIVWA 434
The Applicant also does not describe editing the coding region of the CIPK15 gene itself in green foxtail (VsCIPK15) to substitute the native valine (V) at position 48 with isoleucine (I). The Applicant does not describe if overexpressing the green foxtail VsCIPK15 polypeptide or a mutated VsCIPK15 polypeptide containing only the valine (V) to isoleucine substitution at position 48 while keeping the rest of the SEQ ID NO: 7, intact would improve growth, yield and/or root development in the transgenic or genome-edited green foxtail or any other plant.
Similarly, the instant SEQ ID NO: 19 (mutant BdCIPK15 from Brachypodium distanchyon with amino acid substitution V48I), as recited in claim 4, contains 39 mismatches with SEQ ID NO: 1, as shown below.
Title: US-18-645-166-1
Perfect score: 2224
Sequence: 1 MESRGKILMERYELGRLLGK..........EYRQLLEEGIRPALKDIVLA 434
Scoring table: BLOSUM62
Gapop 10.0 , Gapext 0.5
Searched: 1 seqs, 444 residues
Total number of hits satisfying chosen parameters: 1
Database : US-18-645-166-19.pep:*
RESULT 1
US-18-645-166-19
Best Local Similarity 80.4%; Query Match 81.7%; Score 1816; DB 1; Length 444;
Matches 349; Conservative 44; Mismatches 39; Indels 2; Gaps 2;
Qy 1 MESRGKILMERYELGRLLGKGTFGKVHYARNLESNQSVAIKMMDKQQILKVGLSEQIRRE 60
|:| ||::: |||:||||||| |||||||:||:||:||||||:||::|||||||||:|||
Db 1 MDSSGKVVLGRYEVGRLLGKGAFGKVHYAKNLKSNRSVAIKMLDKEKILKVGLSEQVRRE 60
Qy 61 ITTMRLVAHKNIVQLHEVMATRNKIYFVMEYVKGGELFEKVAKRGKLTEVVAHKYFQQLI 120
|||||||||||||:||||||||:||||||||||||:||:|:: ||||| |||||||||
Db 61 ITTMRLVAHKNIVKLHEVMATRSKIYFVMEYVKGGQLFDKISNGGKLTESAAHKYFQQLI 120
Qy 121 SAVDYCHSRGVYHRDLKPENLLLDENENLKVSDFGLSALSESKRQDGLLHTTCGTPAYVA 180
|||||||||||||||||||||||||:||||||||||||||||||||||||| ||:|||||
Db 121 SAVDYCHSRGVYHRDLKPENLLLDEHENLKVSDFGLSALSESKRQDGLLHTICGSPAYVA 180
Qy 181 PEVISKIGYDGAKSDIWSCGVILFVLVAGYLPFQGPNLMEMYRKIQHGEFRCPGWFSRKL 240
|||||| ||||||||||||||:||||||||||||| |||||| ||: |:|:|||| | ||
Db 181 PEVISKGGYDGAKSDIWSCGVVLFVLVAGYLPFQGQNLMEMYMKIEQGDFKCPGWVSIKL 240
Qy 241 QKLLYKIMDPNPSTRISIQKIKESTWFRKGPEENRILKERTLNENTTKNVAPVLGVRRKK 300
:|||:|||||:|| ||||||||||||||||||| : || || | || | :||:|
Db 241 RKLLHKIMDPDPSKRISIQKIKESTWFRKGPEET-LTMERIPIENAPTNAAPTL-MRRRK 298
Qy 301 NAHEDVKPMSVTNLNAFEIISFSKGFDLSGMFIVKEWRNEARFTSDKSASTIISKLEDVA 360
|:| | ||::||||||||||||| ||||||:|: || : | ||||: || |||||||||
Db 299 NSHGDAKPLAVTNLNAFEIISFSTGFDLSGLFVEKESKKETRFTSENPASAIISKLEDVA 358
Qy 361 KALNLRVRKKDNGVVKMQGRKEGRNGVLQFDIEIFEVTTSYHIIEMKQTSGDSLEYRQLL 420
|||||||||||||||||||||||||||:||| |||::| |||:|||||||||||||::||
Db 359 KALNLRVRKKDNGVVKMQGRKEGRNGVVQFDSEIFQITPSYHLIEMKQTSGDSLEYQKLL 418
Qy 421 EEGIRPALKDIVLA 434
|:|||||||||| |
Db 419 EDGIRPALKDIVWA 432
The Applicant does not describe if overexpression of SEQ ID NO: 19 (mutant BdCIPK15 from Brachypodium distanchyon with just one amino acid substitution V48I) polypeptide under the control of any promoter including endogenous rice CIPK15 promoter would improve growth, yield and/or root development in the transgenic or genome-edited Brachypodium distanchyon.
The Applicant does not provide any guidance to mutate the promoter region and/or the coding region of an endogenous CIPK15 gene in green foxtail or Brachypodium distanchyon, except at the position corresponding to position 48 of SEQ ID NO: 1, that would promote growth.
The nearest prior art Xiang et al. describes the transgenic rice plants overexpressing the cDNA of OsCIPK15 gene enhance growth and development of its root (Fig. 7 B-D) and increase salt tolerance (page 1420, right column, para 2). However, current status of the art does not provide any guidance to mutate the CIPK15 polypeptide for promoting growth, yield and/or root development. It is also not known if overexpressing a CIPK15 protein from other non-rice plants that do not have an isoleucine at a position corresponding to position 48 of SEQ ID NO: 1 is sufficient to achieve same or similar traits including increased growth, yield and/or root length.
Further experimentation is needed to understand the importance of the specific position 48 in any CIPK15 protein, irrespective of whether it is isoleucine or some other amino acid, in both rice and non-rice plants. The Applicant compares CIPK15 from green foxtail (SevCIPK15) and maize (ZmCIPK15) with rice CIPK15 (OsCIPK15, SEQ ID NO: 1) (Fig. 19). There are many amino acid positions) other than position 48, that have a different amino acid compared to rice CIPK15; e.g, position 47 has in maize and green foxtail CIPK15 have lysine (K) while OSCIPK15 has a glutamine (Q) (Fig. 19). Neither the Applicant nor the prior art teach mutating the native isoleucine at position 48 of with, say valine (as present in OsCIPK14, ZmCIK15 and SevCIPK15), to evaluate if that substitution abolished the function of the OsCIPK15 in terms of the claimed traits. Similarly, there is no evidence, either by the Applicant or any other reference, to overexpress any non-rice CIPK15 protein and/or substitute only the native amino acid at position 48 in a CIPK15 protein in any non-rice plant (e.g., ZmCIPK15 and/or SevCIPK15) to evaluate the function of the CIPK15 protein in terms of the claimed traits.
Given the differences in amino acid sequence between CIPK15 homologs of various plant species, and the lack of characterization of the importance of residue I48 in rice CIPK15, undue experimentation by one skilled in the art would be required to determine if this one amino acid difference alone is sufficient to practice the claimed method and make the claimed plants with any CIPK15 sequence, from any given plant species. Based on breadth of the claims, lack of any working example, lack of guidance in the instant description or in prior art, the specification at the time of the application filed would not have taught one skilled in the art how to use the full scope of the claimed invention without performing undue experiments.
Response to Applicant’s Argument: The Applicant’s response dated 2/17/2026 is fully considered but not found persuasive. In regard to 112(a) scope of enablement rejection, the Applicant argues, “Example 2.7 demonstrates the Ile48 residue essential for CIPK15's activation, in view of that substitution of Ile 48 with Val (I48V) in rice CIPK15 in Setaria could not activate the rice ACS1 promoter (Fig. 18g); and conversely substitution of Val 48 with Ile (V48I) in Setaria CIPK15 leading to Setaria CIPK15(V48I) variant could activate the rice ACS1 and αAmy3 promoters” (response, page 11, para 1, line 14-18). The Examiner disagrees. Example 2.7 describes expressing OsCIPK15 promoter driving the expression of OsCIPK15 coding sequence in green foxtail (S. viridis) (Spec, page 36, para 000198, line 3-4). Moreover, both the substitutions are linked to activation or lack thereof for ACS1 and/or αAmy3 promoter(s), which is not recited in the claims and nor does it evidence that activation of ACS1 and/or αAmy3 promoters confer(s) the claimed phenotype(s).
It is known that ACS1 gene (besides other ACS genes) is activated by several factors including hypoxia (Khan et al. The Ethylene Biosynthetic Enzymes,1-Aminocyclopropane-1-Carboxylate (ACC) Synthase (ACS) and ACC Oxidase (ACO): The Less Explored Players in Abiotic Stress Tolerance and ethylene and both the conditions activate many genes, 2024, Biomolecules, 14:90; page 2, para 1, line 19-20). Moreover, besides CIPK15, many other factors including AGL30, AGL104, ERF008, NAC71, Dof1.2, HSFB2a, HSFB3 (page 4, para 1, line 4-7), ERF9 (page 4, para 1, line 12-13) and NACs (1-4) (page 4, para 1, line 10-11) are found to interact with the promoter of ACS1 and directly control ACS1 transcription, thus regulating ethylene production (page 4, para 1, line 6-7).
Written Description
Claim 4 is 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 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 inventors, at the time the application was filed, had possession of the claimed invention.
Claim 4 depends from claim 1, and is drawn to a method for promoting growth, yield and/or root development of a plant by overexpressing CIPK15, wherein the CIPK15 comprises (a) an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-4 or an amino acid sequence selected from the group consisting of SEQ ID NOs: 19-32; or (b) an amino acid sequence having a sequence identity of at least 80% with the amino acid sequence of (a) and having an isoleucine (Ile) residue at position 48 of SEQ ID NO: 1.
The Applicant describes expressing full-length CIPK15 cDNA under the control of i) inducible promoter (spec, page 25, para 000136, line 1-2), ii) a 2 kb CIPK15 promoter region plus 1.4 kb 5’ untranslated region (UTR) including the first intron in rice OsCIPK15 gene (spec, page 25, para 000136, line 4-5), and iii) a constitutive ubiquitin promoter (spec, page 25, para 000138). Rice and green foxtail (S. vridis) plants are transformed with a construct containing the rice CIPK15 cDNA under the control of rice CIPK15 promoter (OsCIPK15:OsCIPK15) (page 27, para 000150). The Applicant describes that overexpression of CIPK15 under the control of strong constitutive ubiquitin (Ubi) promoter severely inhibits the growth of transgenic rice plants (spec, page 30, para 000174, line 5-6). However, the Applicant also describes that grain yield of CIPK15 overexpressing lines (carrying CIPK15:CIPK15) showed increased yield by 26-46% (spec, page 32, para 000183).
Rice is the only plant species where the native CIPK15 polypeptide consisting of SEQ ID NO: 1 has an isoleucine at position 48 (page 36, para 000200). SEQ ID NO: 1 contains 434 amino acids. Mutating up to 20% would allow mutating up to 86 amino acids in the polypeptide. The Applicant does not describe any transgenic plant including green foxtail overexpressing the native CIPK15 polypeptide comprising at least one mutation resulting in a substitution of the native amino acid to isoleucine at position 48 corresponding to SEQ ID NO: 1. There is no representative working example of any transgenic plant expressing a mutated polypeptide comprising less than 100% sequence identity to SEQ ID NO: 1. There is no representative working examples of the broad genus claimed.
The Applicant describes that CIPK15 has two domains- i) N-terminal catalytic/kinase domain and ii) C-terminal NAF domain. The NAF domain directly interact with the catalytic domain (spec, page 34, para 000194). The Applicant described deleting the entire NAF domain and concluded that NAF domain is essential for CPIK15 activity (page 34, para 000193). It is clear that even the highly conserved core amino acids (Asn-Ala-Phe) in the NAF domain are not essential for CIPK15 activity, in terms of activating its downstream target gene ACS1 (page 35, para 000195). The Applicant does not describe the any structure function relationship between the domains and/or crucial amino acids in CIPK15 polypeptide and promoting growth, yield and/or root development.
The nearest prior art Xiang et al. (Characterization of Stress-Responsive CIPK Genes in Rice for Stress Tolerance Improvement, 2007, Plant Physiology, 144:1416–1428) describes the transgenic rice plants overexpressing the cDNA of OsCIPK15 gene enhance growth and development of its root (Fig. 7 B-D) and increase salt tolerance (page 1420, right column, para 2). However, current status of the art does not establish any structure function relationship between the domains and/or crucial amino acids in CIPK15 polypeptide and promoting growth, yield and/or root development.
Considering the breadth of the claims, lack of representative species of the broad genus claimed, lack of structure function relationship of the broad genus claimed, the Applicant does not appear to have been in possession of the claimed genus at the time this application was filed.
Response to Applicant’s Argument: In regard to 112(a) written description rejection, the Applicant argues, “Example 2.7 demonstrates the Ile48 residue essential for CIPK15's activation, in view of that substitution of Ile 48 with Val (I48V) in rice CIPK15 in Setaria could not activate the rice ACS1 promoter (Fig. 18g); and conversely substitution of Val 48 with Ile (V48I) in Setaria CIPK15 leading to Setaria CIPK15(V48I) variant could activate the rice ACS1 and αAmy3 promoters” (response, page 11, para 1, line 14-18). The Applicant also argues that “NAF domain is essential for CIPK15 activity” (response, page 11, para 1, line 7-8). Applicant’s argument is fully considered but not found persuasive. Example 2.7 describes expressing OsCIPK15 promoter driving the expression of OsCIPK15 coding sequence in green foxtail (S. viridis) (Spec, page 36, para 000198, line 3-4). Moreover, both the substitutions are linked to activation or lack of it for ACS1 and/or αAmy3 promoter(s), which is not recited in the claims and nor does it evident that activation of ACS1 and/or αAmy3 promoters confer(s) the claimed phenotype(s). The Applicant is reminded that NAF domain is not just isoleucine 48 (I48) in SEQ ID NO: 1 and, moreover, that does not describe why the specific position 48 in relation to rice CIPK15 is crucial in regard to the claimed traits.
Claim Rejections - 35 USC § 103
Claims 1-2, 4-10, 12-13, 16-17, 19-28, 30-31 and 35-36 are rejected under 35 U.S.C. 103 as being unpatentable over Xiang et al. (Characterization of Stress-Responsive CIPK Genes in Rice for Stress Tolerance Improvement, 2007, Plant Physiology, 144:1416–1428) and in evidence of Schneider et al. (Root angle in maize influences nitrogen capture and is
regulated by calcineurin B-like protein (CBL)-interacting serine/threonine-protein kinase 15 (ZmCIPK15), 2021, Plant, Cell & Environment, 45:837–853).
Xiang et al. teaches a method of producing transgenic rice plants (a monocot, as recited in claims 12-13 and 30-31) overexpressing the rice CIPK15 gene (OsCIPK15) (abstract) (as recited in claims 2 and 17) encoding a protein containing an isoleucine (Ile or I) at position 48 (highlighted in grey) and comprising 100% sequence identity to SEQ ID NO: 1, as shown below.
RESULT 1
A2ZAR9_ORYSI
ID A2ZAR9_ORYSI Unreviewed; 434 AA.
AC A2ZAR9;
DT 20-MAR-2007, integrated into UniProtKB/TrEMBL.
DT 20-MAR-2007, sequence version 1.
DT 27-NOV-2024, entry version 107.
FUNCTION, AND INDUCTION.
RX PubMed=17535819; DOI=10.1104/pp.107.101295;
RA Xiang Y., Huang Y., Xiong L.;
RT "Characterization of stress-responsive CIPK genes in rice for stress
RT tolerance improvement.";
RL Plant Physiol. 144:1416-1428(2007).
CC -!- FUNCTION: Involved in salt stress tolerance. CIPK serine-threonine
CC protein kinases interact with CBL proteins. Binding of a CBL protein to
CC the regulatory NAF domain of CIPK protein lead to the activation of the
CC kinase in a calcium-dependent manner. {ECO:0000269|PubMed:17535819}.
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 -!- 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 -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC -!- INDUCTION: By drought and salt stresses and abscisic acid (ABA).
CC {ECO:0000269|PubMed:17535819}.
CC -!- DOMAIN: The activation loop within the kinase domain is the target of
CC phosphorylation/activation by upstream protein kinases. The PPI motif
CC mediates the interaction with the ABI (abscisic acid-insensitive)
CC phosphatases (By similarity). {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the protein kinase superfamily. CAMK Ser/Thr
CC protein kinase family. SNF1 subfamily. {ECO:0000305}.
CIPKF_ORYSJ
ID CIPKF_ORYSJ Reviewed; 434 AA.
AC Q2RBF0; A0A0P0XY79;
DT 10-JUN-2008, integrated into UniProtKB/Swiss-Prot.
DT 24-JAN-2006, sequence version 1.
DT 27-NOV-2024, entry version 119.
DE RecName: Full=CBL-interacting protein kinase 15;
DE EC=2.7.11.1;
DE AltName: Full=OsCIPK15;
GN Name=CIPK15; OrderedLocusNames=Os11g0113700, LOC_Os11g02240;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Nipponbare;
RA Kurusu T., Hamada J., Kuchitsu K.;
RT "Oryza sativa (japonica cultivar-group) CBL-interacting protein kinase
RT mRNA.";
RL Submitted (JUN-2006) to the EMBL/GenBank/DDBJ databases.
RN [2]
DR EMBL; AB264037; BAF34613.1; -; mRNA.
DR EMBL; DP000010; ABA91173.1; -; Genomic_DNA.
DR EMBL; AP008217; BAF27419.1; -; Genomic_DNA.
DR EMBL; AP014967; BAT12391.1; -; Genomic_DNA.
DR RefSeq; XP_015617455.1; XM_015761969.1.
DR AlphaFoldDB; Q2RBF0; -.
DR SMR; Q2RBF0; -.
DR STRING; 39947.Q2RBF0; -.
DR PaxDb; 39947-Q2RBF0; -.
DR EnsemblPlants; Os11t0113700-01; Os11t0113700-01; Os11g0113700.
DR EnsemblPlants; Os11t0113700-02; Os11t0113700-02; Os11g0113700.
DR Gramene; Os11t0113700-01; Os11t0113700-01; Os11g0113700.
DR Gramene; Os11t0113700-02; Os11t0113700-02; Os11g0113700.
DR eggNOG; KOG0583; Eukaryota.
DR HOGENOM; CLU_000288_59_0_1; -.
DR InParanoid; Q2RBF0; -.
DR InterPro; IPR017441; Protein_kinase_ATP_BS.
DR InterPro; IPR008271; Ser/Thr_kinase_AS.
DR PANTHER; PTHR43895; CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE KINASE-RELATED;
PE 2: Evidence at transcript level;
KW ATP-binding; Kinase; Manganese; Nucleotide-binding; Reference proteome;
KW Serine/threonine-protein kinase; Transferase.
FT CHAIN 1..434
FT /note="CBL-interacting protein kinase 15"
FT /id="PRO_0000338373"
FT DOMAIN 12..267
FT /note="Protein kinase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159"
FT DOMAIN 298..333
FT /note="NAF"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00256"
FT REGION 153..182
FT /note="Activation loop"
FT /evidence="ECO:0000250"
FT REGION 338..367
FT /note="PPI"
FT /evidence="ECO:0000250"
FT ACT_SITE 135
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159,
FT ECO:0000255|PROSITE-ProRule:PRU10027"
FT BINDING 18..26
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159"
FT BINDING 41
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00159"
SQ SEQUENCE 434 AA; 49698 MW; 1EB615196F262147 CRC64;
ALIGNMENT:
Query Match 100.0%; Score 2224; Length 434; Best Local Similarity 100.0%;
Matches 434; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MESRGKILMERYELGRLLGKGTFGKVHYARNLESNQSVAIKMMDKQQILKVGLSEQIRRE 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MESRGKILMERYELGRLLGKGTFGKVHYARNLESNQSVAIKMMDKQQILKVGLSEQIRRE 60
Qy 61 ITTMRLVAHKNIVQLHEVMATRNKIYFVMEYVKGGELFEKVAKRGKLTEVVAHKYFQQLI 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 ITTMRLVAHKNIVQLHEVMATRNKIYFVMEYVKGGELFEKVAKRGKLTEVVAHKYFQQLI 120
Qy 121 SAVDYCHSRGVYHRDLKPENLLLDENENLKVSDFGLSALSESKRQDGLLHTTCGTPAYVA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 SAVDYCHSRGVYHRDLKPENLLLDENENLKVSDFGLSALSESKRQDGLLHTTCGTPAYVA 180
Qy 181 PEVISKIGYDGAKSDIWSCGVILFVLVAGYLPFQGPNLMEMYRKIQHGEFRCPGWFSRKL 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 PEVISKIGYDGAKSDIWSCGVILFVLVAGYLPFQGPNLMEMYRKIQHGEFRCPGWFSRKL 240
Qy 241 QKLLYKIMDPNPSTRISIQKIKESTWFRKGPEENRILKERTLNENTTKNVAPVLGVRRKK 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 QKLLYKIMDPNPSTRISIQKIKESTWFRKGPEENRILKERTLNENTTKNVAPVLGVRRKK 300
Qy 301 NAHEDVKPMSVTNLNAFEIISFSKGFDLSGMFIVKEWRNEARFTSDKSASTIISKLEDVA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 NAHEDVKPMSVTNLNAFEIISFSKGFDLSGMFIVKEWRNEARFTSDKSASTIISKLEDVA 360
Qy 361 KALNLRVRKKDNGVVKMQGRKEGRNGVLQFDIEIFEVTTSYHIIEMKQTSGDSLEYRQLL 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 KALNLRVRKKDNGVVKMQGRKEGRNGVLQFDIEIFEVTTSYHIIEMKQTSGDSLEYRQLL 420
Qy 421 EEGIRPALKDIVLA 434
||||||||||||||
Db 421 EEGIRPALKDIVLA 434
Xiang et al. teaches transgenic rice plants comprising maize (Zea mays) ubiquitin promoter operably linked to the nucleotide sequence encoding rice OsCIPK15 polypeptide (page 1426, left column, para 3, line 20-21). Xiang et al. also describes selection of the transgenic plants and growing selected rice plants overexpressing the CIPK15 transgene (page 1420, right column, para 2, line 1-6) and having enhanced growth and development of its root (Fig. 7 B-D).
The rice plants with CIPK15 overexpression had significantly longer root (Fig. 7, B and C) and higher fresh weight per plant (read on to “yield”) under salt stress growing condition (page 1420, right column, para 2, line 12-16).
Xiang et al. also teaches that CIPK15 gene (GenBank accession No. AK121773; page 1418, Table 1) is strongly induced by salt stress (abstract, line 7-9; page 1419, bridging paragraph between left column, last 3 lines and right column, first 2 lines), implying that the native CIPK15 promoter is an inducible promoter and induced by salt stress.
Before the effective filing date of the invention, it would have been obvious to an ordinarily skilled artisan to introduce one or more extra copy(ies) of the native CIPK15 gene comprising native salt-stress inducible promoter, as described by Xiang et al., in a plant.
The artisan would have been motivated to introduce one or more extra copy(ies) of the native CIPK15 gene (encoding a polypeptide having 100% sequence identity to SEQ ID NO: 1 that has an isoleucine at position 48) which includes its native salt-stress inducible promoter (as recited in claims 1, 6, 16, 21 and 23) with a realistic objective to overexpress CIPK15 gene under salt-stress condition, which would help increasing the root length and yield under salt stress condition.
Regarding claims 4, 19 and 35-36, Xiang et al. teaches a rice CIPK15 polypeptide comprising an amino acid sequence having 100% sequence identity to SEQ ID NO: 1 which is having an isoleucine (Ile) residue at position 48, as discussed above.
Regarding claims 5 and 20, Xiang et al. teaches that CIPK15 gene is “strongly induced” (emphasis added) by salt stress (page 1419, bridging paragraph between left column, last 3 lines and right column, first 2 lines), implying that the native CIPK15 promoter is an inducible promoter which is induced by salt stress. It is also known that maize CIPK15 (Zm00001d033316) is expressed in roots with higher expression in crown root nodes (Schneider et al., page 841, right column, para 3, line 8-10; Fig. 2) implying that any induction of endogenous CIPK15 promoter (e.g., by salt stress) would be root-specific induction.
Regarding claims 7 and 25, The transgenic plants overexpressing the CPIK15 gene is grown initially in a growth chamber (page 1426, para 5, line 25-26) and then transferred to pots filled with soil (page 1426, para 5, line 29). It is implied that the transgenic plants are grown under aerobic condition. Xiang et al. also teaches growing 2-week-old transgenic rice seedlings under hypoxic condition as the seedlings have been submerged in 100 mM (page 1420, right column, para 2, line 10-12) and 200mM NaCl solution for evaluating salt-stress (page 1426, left column, para 4, line 11-12).The transgenic plants growing on salt-containing medium show significantly longer shoot and root length ((page 1420, right column, para 2, line 13-15).
Regarding claims 8 and 24, the transgenic rice plants overexpressing CIPK15 are shown to have increased plant height, longer shoot, and longer root (page 1423, right column, Fig. 7C). The plants showing increased plant height, longer shoot, and longer root are grown under aerobic condition, as recited in claim 25, and as discussed above.
Regarding claims 9-10 and 26-28, the transgenic rice plants overexpressing CIPK15 are shown to have enhanced tolerance to an abiotic (higher salt and higher salinity) stress (page 1420, right column, para 2; Fig. 7D). It also reads on to an “environmental stress” as described by the Applicant, comprising “drought, salinity, and flooding stresses, and/or increased ethylene production” (page 4, para 00011, last 2 lines).
Regarding claims 12-13 and 30-31, Xiang et al. teaches that rice is an important crop and a monocot (page 1422, right column, para 4, line 1-2).
Regarding claims 16-17, the recombinant construct comprises the CIPK15 gene from rice, as described above.
Regarding claim 22, Xiang et al. describes introducing the recombinant construct in an expression vector (page 1426, left column, para 3, line 18).
Claims 14-15 and 32-33 are rejected under 35 U.S.C. 103 as being unpatentable over Xiang et al. as applied to claims 1-2, 4, 7-10, 12-13, 16-17, 19, 22-28, 30-31, and 34-36 above, and further in view of Liu et al. (Overexpression of Rice NAC Gene SNAC1 Improves Drought and Salt Tolerance by Enhancing Root Development and Reducing Transpiration Rate in Transgenic Cotton, 2014, PLoS ONE, 9(1):e86895).
Claims 14-15 and 32-33 are drawn to a transgenic dicot plant comprising Arabidopsis, soybean, peanut, sunflower, safflower, cotton, tobacco, tomato, pea, chickpea, pigeon pea or potato plant overexpressing a CIPK15 protein having an isoleucine (Ile) residue at position 48 of SEQ ID NO: 1.
Xiang et al. describes a method for promoting growth and yield in rice by transforming and overexpressing OsCIPK15 polypeptide comprising an isoleucine (Ile) residue at a position corresponding to position 48 of SEQ ID NO: 1, and the OsCIPK15 gene being expressed under the control of a constitutive promoter or a native CIPK15 promoter, which is induced under salt-stress condition, as discussed above.
However, Xiang et al. does not describe transforming any dicot plant including Arabidopsis.
Liu et al. describes transforming cotton plants overexpressing a rice NAC gene SNAC1 to produce transgenic cotton plants with enhanced drought and salt tolerance (title and abstract).
Before the effective filing date of the invention, it would have been obvious to an ordinarily skilled artisan to modify the method described by Liu et al. to use the cDNA of OsCIPK15 gene, as described by Xiang et al., to overexpress the OsCIPK15 cDNA in cotton using native CIPK15 promoter to enhance salt tolerance resulting in improved growth and yield under salt stress in the transgenic cotton plants.
Before the effective filing date, an ordinarily skilled artisan would have been motivated to produce transgenic cotton plants by overexpressing the rice CIPK15 cDNA under the control of its native CIPK15 promoter to enhance growth and yield under salt stress in cotton which is an important crop worldwide.
Response to Applicant’s Arguments: In response to 35 U.S.C. 103 rejections, the Applicant argues, “Xiang's transgenic plants did not exhibit increased growth, yield and/or root development under normal growth conditions” (response, page 14, para 3, line 7-8) and “a gene that confers stress tolerance does not necessarily promote growth under non-stress conditions” (page 14, para 4, line 1-2).
The Examiner disagrees. Xiang et al. describes rice plants with CIPK15 overexpression had significantly longer root (Fig. 7, B and C) and higher fresh weight per plant (reads on to “yield”) under salt stress growing condition (page 1420, right column, para 2, line 12-16). The claims do not explicitly recite non-stress growth conditions and/or exclude plant growth under stress conditions.
Conclusion
No claim is allowed.
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.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JAY CHATTERJEE whose telephone number is (703)756-1329. The examiner can normally be reached (Mon - Fri) 8.30 am to 5.30 pm..
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Jay Chatterjee
Patent Examiner
Art Unit 1662
/Jay Chatterjee/Examiner, Art Unit 1662
/BRATISLAV STANKOVIC/Supervisory Patent Examiner, Art Units 1661 & 1662