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 .
Election/Restrictions
Applicant's election without traverse of species of polynucleotide sequence SEQ ID NO: 152, Zea mays DNA sequence of ZM-UBA-DELTA, and its corresponding polypeptide sequence SEQ ID NO: 436 for initial search and examination in the reply filed on 04/13/2026 is acknowledged.
Therefore claims 1-12 are pending and the claims 1-12 along with Applicant’s elected species of SEQ ID NOs: 152 and 436 are examined in this office action.
Specification
The use of the terms “Sorenson” in page 50, paragraph 068, “Transit” in page 50, paragraph 0688, “mMessage mMachine” in page 54, paragraph 0705, which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore, the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM, or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Claims 1, 10 and 11 are objected to because of the following informalities:
Claims 1, 10 and 11 recite “SEQ ID NOS:” which is advised to change to “SEQ ID NOs:”, see MPEP § 2412.04.
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.
Claims 1-9 and 12 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter 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. All dependent claims are included in these rejections unless they include a limitation that overcomes the deficiencies of the parent claim.
Claim 1 is drawn to a method of improving yield of a plant, comprising introducing into a plant cell a heterologous polynucleotide comprising a sequence at least 90% identical to a polynucleotide described as SEQ ID NO: 152, or the heterologous polynucleotide encoding a heterologous polypeptide comprising a sequence at least 90% identical to polypeptide of SEQ ID NO: 436. It further drawn to regenerating a plant, subjecting it to environmental condition, and assessing one or more characteristics of the plant. It further recites the characteristics demonstrate increased yield or improved agronomic characteristic of the plant compared to isolines.
The term “heterologous” in claim 1 is a relative term which renders the claim indefinite. The term “heterologous” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Heterologous is relative term. It is relative in terms it could be “heterologous” to the promoter or untranslated region (UTR) or other expression elements. The polynucleotide could also be “heterologous” to the plant cell (i.e. a rye sequence being introduced into a non-rye plant cell), and because the claim does not recite anything in particular that the polynucleotide is heterologous to, it is unclear what the metes and bounds are.
Regarding claim 12, nucleotide sequence and genomic locus are physical structures. It is not clear how a introduced nucleotide changes at a genomic loci is the effect of such changes as described in claim 12 (a), (b), and (g) as reduced expression of a polynucleotide, reduced activity of the polypeptide and repression of an enhancer motif. Since the change in physical structure like genomic loci can be deletion, or frameshift mutation or other mutation types known in art, reciting the one or more introduced changes are their function like reduced expression or activity renders the claim indefinite.
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 1-12 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.
Analysis of Breadth of Claims
Claim 1 recite a large genus of polynucleotide comprising a sequence at least 90% identical to SEQ ID NO:152 and
Claim 1 recite a large genus of polypeptide comprising a sequence at least 90% identical to SEQ ID NO: 436.
The terms “yield” and “agronomic characteristic” of plant in claim 1 would comprise large number of traits.
The phrase “an environmental condition” would comprise large genus of environmental conditions for example different levels of heat, water, nitrogen or other nutrients etc.
Site-directed modification would comprise any modification in any site of genomic locus encoding SEQ ID NO:436 (claim 11).
What is Described in the Specification
Applicant describes the following:
SEQ ID NO:152 is the Zea mays DNA sequence of ZM-UBA-DELTA and SEQID NO:436 is the Zea mays PRT sequence of ZM-UBA-DELTA. (pages 7 and 16, paragraphs 0158 and 0442 respectively).
Difference Between What was described and What is Claimed
Applicant has not described any nucleotide comprising a sequence at least 90% identical to SEQ ID NO:152. (claims 1 and 10).
Applicant has not described any polypeptide comprising a sequence at least 90% identical to SEQ ID NO: 436 (claims 1 and 11).
Applicant has not described any effect on yield or agronomic characteristics (claim 1), plant height, biomass, leaf color etc. (claim 8) caused by SEQ ID NOs: 152 and 436 in any environmental conditions (claim 1) or in water limitation, water overabundance, nitrogen limitation etc. (claim 7) in any plants.
Applicant has not described assessing any improvement in agronomic characteristics would increase yield of the plant.
Applicant has not described that any site-directed modification of applicant’s SEQ ID NO: 152 encoding SEQ ID NO:436 would have any effect to the yield or agronomic characteristics (claims 11 and 12).
Applicant has not described that the genomic locus encoding polypeptide of at least 95% identical to SEQ ID NO: 436 would be found in any other plant other than maize to carry out the method of site-directed modification (claim 11).
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 any nucleotide sequence encoding at least for example 90% identity to SEQ ID NO: 436 would have genetic diversity to select for increased yield or improved agronomic characteristics. For example, a polypeptide sequence of SEQ ID NO: 436 is 842 amino acids (AA) long. For example, a 90% identity to SEQ ID NO: 436 would have ~44 AA changes (i.e., substitutions, deletions, insertions, or additions) relative to SEQ ID NO: 436, and this encompasses a genus of proteins that includes at least ~2044 molecules. For this reason, the genus of proteins having at least 90% identity to SEQ ID NO: 436 is a very large genus of molecules. Similarly, a polynucleotide sequence of SEQ ID NO: 152 is 2529 nucleotides (NA) long. For example, a 90% identity to SEQ ID NO: 152 would have ~252 NA changes (i.e., substitutions, deletions, insertions, or additions) relative to SEQ ID NO: 152, and this encompasses a genus of polynucleotides that includes at least ~4252 molecules. For this reason, the genus of proteins having at least 90% identity to SEQ ID NO: 152 is a very large genus of molecules.
Furthermore, the state of the art at the time of the instant invention was that although the skilled artisan would appreciate the polypeptide and polynucleotide sequence comprising SEQ ID NOs: 436 and 152, one would not be able to readily predict function of polypeptide which has at least 90% identity to SEQ ID NO: 436 and it is impossible to predict such a broad sequence variation would have genetic diversity to select for increased yield or improved agronomic characteristics. 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).
Alignment of the applicant’s recited polypeptide of SEQ ID NO: 436 showed the protein is a NBR1-like protein (see alignment below). For example Li et al. (Plants 2026, 15, 1350, https://doi.org/10.3390/plants15091350) teaches NBRI has diverse effects on the plant growth and development, male fertility, plant stress responses, lateral root initiations, cellular homeostasis, carbon starvation-associated response (page 7, paragraphs 4-5), drought and heat tolerance (page 8, last paragraph), chilling tolerance (page 10, paragraph 4), salt tolerance (page 11, second to last paragraph), metal tolerance (page 12, first and second paragraphs) and resistance to bacteria, fungus and virus (page 16, paragraph 2, page 18, paragraph 3). Li et al. teaches NBRI’s are involved in signaling response involved in various phytohormones such as ABA, SA, BRs etc. (pages 19 and 20, last and first paragraphs). Li et al. teaches NBR1-mediated selective autophagy complements bulk autophagy by conferring substrate specificity, particularly under abiotic and biotic stress conditions hat intensify proteotoxic and oxidative damage (page3, paragraph 2).
Li et al. teaches molecular mechanisms governing hormone-mediated regulation of NBR1, particularly under heat, drought, salinity, and cold stresses, are still largely unexplored and he precise substrates and ubiquitin-like conjugation pathways targeted by NBR1 under specific stress conditions remain to be identified. (page 20, second paragraph).
Furthermore, Zhang et al. (Published: 2020, Journal: Cells 9, 2562; doi:10.3390/cells9122562) teaches presence of functional diversification of NBRI homologs in plants (page 4, Figure 1). Zhang et al. teaches in search of sequenced genome there were evolutionary tree for genes encoding NBR1 homologs and identified 27 NBR1-encoding genes from 2 spore-bearing and 15 seed plants (Figure 1) and there were three major clades (pages 3 and 4, last and first paragraphs). Zhang et al. teaches many selective autophagy receptors identified in plants are plant-specific (page 3, paragraph 2) and are involved in various selective autophagy in plant stress responses.
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Therefore, it would require to understand which of the function the specific NBR1 would diversity to select for. Instead, application has not described any function of any sequence that has 90% identity to SEQ ID NO:436 encoded by a sequence that has 90% identity to SEQ ID NO:152.
Furthermore, Applicant has not described any effect on yield or agronomic characteristics (claim 1), plant height, biomass, leaf color etc. (claim 8) caused by SEQ ID NOs: 152 and 436 in any environmental conditions (claim 1) or in water limitation, water overabundance, nitrogen limitation etc. (claim 7) in any plants. Applicant defines in Spec, paragraph 0586 “An "increased yield" can refer to any increase in biomass or seed or fruit weight, seed size, seed number per plant, seed number per unit area, bushels per acre, tons per acre, kilo per hectare, or carbohydrate yield.” Which does not specifically define the limit of the traits because of use of term “can”, therefore it would mean improvement in any of the leaf, stem, root, fruit, flower or any specified organ of the plant yield. Therefore, there is dearth of description whether the protein having amino acid sequence with at least 90% identity to SEQ ID NO:436 would create any genetic diversity in any plant to select for any improvement in yield or agronomic characteristics. Similar a broad definition of agronomic traits i.e. is provided in Spec, paragraph 0457 which would comprise any measurable property of the plant related to any of the agronomic practice.
Instead, applicant has not described effect of SEQ ID NO:436 encoded by SEQ ID NO:152 would create any genetic diversity to select for any of the agronomic or yield traits in any plants. Therefore, there is dearth of description whether the protein of SEQ ID NO:436 would create any genetic diversity in any plant to select for any improvement in yield or agronomic characteristics.
Applicant has not described assessing any improvement in agronomic characteristics would increase yield of the plant. Claim 1 line 1 recite method of improving yield of the plant and in claim 1 lines 11-12, the claim recites assessing characters that demonstrate increased yield or improved agronomic characteristics of the plant. Spec, page 21, paragraph 0575, Applicant sates the Agronomic traits chiefly to loosely refer to trait targets yield enhancement (YE), drought tolerance (DRT), nitrogen use efficiency (NUE), all three of which have varied definitions and complex interrelationships. Applicant states occasionally it includes other component traits involving plant architecture, maturity traits, and physiological traits driving intrinsic plant performances such as photosynthetic efficiency. Applicant states collectively Agronomic Traits broadly includes many mechanisms whether molecular or physiological, touching diverse aspects of plant biology. The statements are clear that the improved agronomic characteristics does not always require improvement in yield. The draught tolerance can be improved in a plant without improvement in actual yield or with same level of yield. Therefore, applicant has not described assessing any improvement in agronomic characteristics would increase yield of the plant.
Applicant has not described that any modification of applicant’s SEQ ID NO: 152 encoding SEQ ID NO:436 would have any effect to the yield or agronomic characteristics (claim 11). Leal et al. (Published: 2017, Journal: Cell 171, 470–480) teaches the modular organization and inherent redundancy among cis regulating elements make it extremely challenging to define useful targets, especially for generating specific desired modifications for a quantitative trait (such as yield) (page472, left paragraph 2). Leal et al. teaches specific cis-regulatory mutations influence locule number variation in SICLV3 promoter of tomato (page 474, right last paragraph) wherein some mutation has very few changes in the SICLV3 or SIWUS genes than other (seepage 475, Figure 4). Therefore, specific modification in specific region of the gene would have been required to cause improvement in yield or agronomic characteristics. Instead, applicant has not described any modification of applicant’s SEQ ID NO: 152 encoding SEQ ID NO:436 would have any effect to the yield or agronomic characteristics.
Applicant has not described that the genomic locus encoding polypeptide of at least 90% identical to SEQ ID NO: 436 would be found in any other plant other than maize to carry out the method of site-directed modification (claim 11). The sequence alignment to the Uniprot database showed there is no any other protein that is at least 90% identical to SEQ ID NO: 436 other than in maize (see alignment result above). Thus, there is no any other genomic locus in any plant other than maize that has a protein that is at least 90% identical SEQ ID NO: 436 that can be modified to effect on yield. Therefore, there is dearth of description of the method of site-directed modification of genomic locus comprising at least 90% identical to SEQ ID NO: 436 would be effective against any other plant other than maize (claims 11 and 12).
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Given the large structural variable associated with these embodiments, the claims read on an extremely broad and highly diverse structures that would require to have specific function of improving yield and agronomic characteristics. 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 improving any yield or agronomic characteristics.
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 in possession of the claimed genus at the time this application was filed.
Alignment of SEQ ID NO: 436 to Uniprot database:
RESULT 1
C0PDQ4_MAIZE
ID C0PDQ4_MAIZE Unreviewed; 842 AA.
AC C0PDQ4;
DT 05-MAY-2009, integrated into UniProtKB/TrEMBL.
DT 05-MAY-2009, sequence version 1.
DT 28-JAN-2026, entry version 81.
DE SubName: Full=Protein NBR1-like protein {ECO:0000313|EMBL:AQK72238.1};
GN Name=LOC100275089 {ECO:0000313|EnsemblPlants:Zm00001eb245950_P002};
GN ORFNames=ZEAMMB73_Zm00001d017072 {ECO:0000313|EMBL:AQK72238.1};
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:ACN33320.1};
RN [1] {ECO:0000313|EMBL:ACN33320.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=B73 {ECO:0000313|EMBL:ACN33320.1};
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 [2] {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., et al, RT "The B73 maize genome: complexity, diversity, and dynamics.";
RL Science 326:1112-1115(2009).
RN [3] {ECO:0000313|EMBL:AQK72238.1}
RP NUCLEOTIDE SEQUENCE.
RC TISSUE=Seedling {ECO:0000313|EMBL:AQK72238.1};
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 [4] {ECO:0000313|EnsemblPlants:Zm00001eb245950_P002}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. B73 {ECO:0000313|EnsemblPlants:Zm00001eb245950_P002};
RA Seetharam A., Woodhouse M., Cannon E.;
RL Submitted (JUL-2019) to the EMBL/GenBank/DDBJ databases.
RN [5] {ECO:0000313|EnsemblPlants:Zm00001eb245950_P002}
RP IDENTIFICATION.
RC STRAIN=cv. B73 {ECO:0000313|EnsemblPlants:Zm00001eb245950_P002};
RG EnsemblPlants;
RL Submitted (MAY-2021) to UniProtKB.
CC -!- SUBCELLULAR LOCATION: Cytoplasmic vesicle, autophagosome
CC {ECO:0000256|ARBA:ARBA00004419}.
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
DR EMBL; BT066423; ACN33320.1; -; mRNA.
DR EMBL; CM000781; AQK72238.1; -; Genomic_DNA.
DR RefSeq; XP_008645886.1; XM_008647664.2.
DR AlphaFoldDB; C0PDQ4; -.
DR SMR; C0PDQ4; -.
DR IntAct; C0PDQ4; 26.
DR STRING; 4577.C0PDQ4; -.
DR PaxDb; 4577-GRMZM2G092447_P01; -.
DR EnsemblPlants; Zm00001eb245950_T002; Zm00001eb245950_P002; Zm00001eb245950.
DR GeneID; 100275089; -.
DR Gramene; Zm00001eb245950_T002; Zm00001eb245950_P002; Zm00001eb245950.
DR KEGG; zma:100275089; -.
DR eggNOG; KOG4351; Eukaryota.
DR eggNOG; KOG4582; Eukaryota.
DR HOGENOM; CLU_017180_0_0_1; -.
DR OrthoDB; 661148at2759; -.
DR Proteomes; UP000007305; Chromosome 5.
DR ExpressionAtlas; C0PDQ4; baseline and differential.
DR GO; GO:0005776; C:autophagosome; IEA:UniProtKB-SubCell.
DR GO; GO:0031410; C:cytoplasmic vesicle; IEA:UniProtKB-KW.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-KW.
DR CDD; cd14947; NBR1_like; 1.
DR CDD; cd14319; UBA_NBR1; 1.
DR Gene3D; 3.30.60.90; -; 1.
DR Gene3D; 1.10.8.10; DNA helicase RuvA subunit, C-terminal domain; 2.
DR Gene3D; 2.60.40.10; Immunoglobulins; 1.
DR Gene3D; 3.10.20.90; Phosphatidylinositol 3-kinase Catalytic Subunit, Chain A, domain 1; 1.
DR InterPro; IPR013783; Ig-like_fold.
DR InterPro; IPR032350; Nbr1_FW.
DR InterPro; IPR053793; PB1-like.
DR InterPro; IPR000270; PB1_dom.
DR InterPro; IPR015940; UBA.
DR InterPro; IPR009060; UBA-like_sf.
DR InterPro; IPR056893; UBA_Nbr1_C.
DR InterPro; IPR000433; Znf_ZZ.
DR InterPro; IPR043145; Znf_ZZ_sf.
DR PANTHER; PTHR20930; OVARIAN CARCINOMA ANTIGEN CA125-RELATED; 1.
DR PANTHER; PTHR20930:SF0; PROTEIN ILRUN; 1.
DR Pfam; PF16158; N_BRCA1_IG; 1.
DR Pfam; PF00564; PB1; 1.
DR Pfam; PF24932; UBA_NBR1_C; 2.
DR Pfam; PF00569; ZZ; 1.
DR SMART; SM00666; PB1; 1.
DR SMART; SM00291; ZnF_ZZ; 1.
DR SUPFAM; SSF54277; CAD & PB1 domains; 1.
DR SUPFAM; SSF57850; RING/U-box; 1.
DR SUPFAM; SSF46934; UBA-like; 2.
DR PROSITE; PS51745; PB1; 1.
DR PROSITE; PS50030; UBA; 1.
DR PROSITE; PS50135; ZF_ZZ_2; 1.
PE 1: Evidence at protein level;
KW Cytoplasmic vesicle {ECO:0000256|ARBA:ARBA00023329};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723};
KW Proteomics identification {ECO:0007829|PeptideAtlas:C0PDQ4};
KW Reference proteome {ECO:0000313|Proteomes:UP000007305};
KW Zinc {ECO:0000256|ARBA:ARBA00022833};
KW Zinc-finger {ECO:0000256|ARBA:ARBA00022771, ECO:0000256|PROSITE-
KW ProRule:PRU00228}.
FT DOMAIN 23..108
FT /note="PB1"
FT /evidence="ECO:0000259|PROSITE:PS51745"
FT DOMAIN 401..451
FT /note="ZZ-type"
FT /evidence="ECO:0000259|PROSITE:PS50135"
FT DOMAIN 754..792
FT /note="UBA"
FT /evidence="ECO:0000259|PROSITE:PS50030"
FT REGION 196..232
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 285..312
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 289..298
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 842 AA; 92621 MW; BB04805B420A9614 CRC64;
Query Match 100.0%; Score 4468; Length 842;
Best Local Similarity 100.0%;
Matches 842; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MSDWSSPAAPTFFPFGPQAEGWDVTFKVKYGDTLKRFYGCANGSHFDMNLSALRARIDTA 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MSDWSSPAAPTFFPFGPQAEGWDVTFKVKYGDTLKRFYGCANGSHFDMNLSALRARIDTA 60
Qy 61 FKFGPDVDFVLTYTDEDGDIVMLDDDDDLRDAALRQRLNPLRITVQLKKNQPTEKKDTSA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 FKFGPDVDFVLTYTDEDGDIVMLDDDDDLRDAALRQRLNPLRITVQLKKNQPTEKKDTSA 120
Qy 121 PVKSAAQDPLSQLMSAIEGLKPVQEDSLAHIKSAIGEAIKSIPEPIPDALAKLSHEILDA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 PVKSAAQDPLSQLMSAIEGLKPVQEDSLAHIKSAIGEAIKSIPEPIPDALAKLSHEILDA 180
Qy 181 APPPLAELMKPFAQLMAPNNNGNGPSDVHAEGSSSSSSAQVPAEAKNEPKVRPSLGLKTV 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 APPPLAELMKPFAQLMAPNNNGNGPSDVHAEGSSSSSSAQVPAEAKNEPKVRPSLGLKTV 240
Qy 241 LKEAAGPVPNAGASQVQQPLMYPSVEEMLFPCNSVDKSVCKGKIDAQSKGKSVTSSGIQP 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 LKEAAGPVPNAGASQVQQPLMYPSVEEMLFPCNSVDKSVCKGKIDAQSKGKSVTSSGIQP 300
Qy 301 APHSLRTHAPPPPHPCISEWSRAQRSQHRQLKFEDNAKATNDSRWRIPMYKMPYAPPPPA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 APHSLRTHAPPPPHPCISEWSRAQRSQHRQLKFEDNAKATNDSRWRIPMYKMPYAPPPPA 360
Qy 361 VPPPGYVPSPHFPYPGRLLSSGHPYGDLAGNMENSAPHSLHRWIQCDGCGAQPIVGPRYK 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 VPPPGYVPSPHFPYPGRLLSSGHPYGDLAGNMENSAPHSLHRWIQCDGCGAQPIVGPRYK 420
Qy 421 SNVKEDYDLCDSCFQRMGNEMEYTKIDKPILPHRFLRDPHVYRKVHHPRVLMKSRREKLE 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 SNVKEDYDLCDSCFQRMGNEMEYTKIDKPILPHRFLRDPHVYRKVHHPRVLMKSRREKLE 480
Qy 481 SRFILDVTVLDGTLMTPSTPFTKIWRMHNNGSVVWPRGTQLVWVGGDQFALQTSVPLEIP 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 SRFILDVTVLDGTLMTPSTPFTKIWRMHNNGSVVWPRGTQLVWVGGDQFALQTSVPLEIP 540
Qy 541 VDGFPVDKEIDVPVDFVAPTRPGRYISYWRLASPSGQKFGQRVWVHIQVEDPSFVNDNNR 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 VDGFPVDKEIDVPVDFVAPTRPGRYISYWRLASPSGQKFGQRVWVHIQVEDPSFVNDNNR 600
Qy 601 NAAINLNLPPESYSSNTTNLIDVNIEPADSALSAHAKRTKEFHFCSTDFPEPSKSVPFTL 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 NAAINLNLPPESYSSNTTNLIDVNIEPADSALSAHAKRTKEFHFCSTDFPEPSKSVPFTL 660
Qy 661 ATTSLSAAAPTNQTGDVPMSSTPAAACLPSVNVPMHEVVTTHTPSPITPVLPTTIHFSAP 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 ATTSLSAAAPTNQTGDVPMSSTPAAACLPSVNVPMHEVVTTHTPSPITPVLPTTIHFSAP 720
Qy 721 VSAPAIA PELASGAVGVPPPVSAVVPELSELDVHNEEKLLRELEEMGFRQVDLNKEILRQ 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 721 VSAPAIA PELASGAVGVPPPVSAVVPELSELDVHNEEKLLRELEEMGFRQVDLNKEILRQ 780
Qy 781 NNYNLEQSVDDLCGVNEWDPLLAELEEMGFDDTEMNKELLAKNEGSIKRAVMELIAREKK 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 781 NNYNLEQSVDDLCGVNEWDPLLAELEEMGFDDTEMNKELLAKNEGSIKRAVMELIAREKK 840
Qy 841 DK 842
||
Db 841 DK 842
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Anticipated by Emmanuel et al.
Claims 1-5, and 7-10 are rejected under 35 U.S.C. 102 “(a)(1)” or “(a)(2)” or both as being anticipated by Emmanuel et al. (US Patent Application Pub. No.US 2013/0125258, Pub. Date: May 16, 2013).
Claims are drawn to method of improving yield of a plant by introducing polynucleotide sequence at least 90% identical to a polynucleotide of SEQ ID NO:152 that encodes a polypeptide sequence at least 90% identical to a polypeptide of SEQ ID NO:436, regenerating the plant, subjecting to environmental conditions and assessing one or more characteristics.
Regarding claim 1, Emmanuel et al. discloses a method of introducing a maize gene LYM372 in Arabidopsis which is applicant’s SEQ ID NO:152 that encodes SEQ ID NO:436 (see alignment below and Emmanuel et al., page 25, Table 1).), wherein transgenic seeds of Arabidopsis were grown in the growth media and T2 transgenic seedlings were planted (i.e. (b) regenerated) in specific environments in greenhouse until mature seeds were produced which were harvested (page 90, paragraph 0532-0533). Emmanuel et al. discloses several characteristics for example overall seed growth rates, seed yield, dry matter index was measured (page 90, paragraphs 0535-0553).
Emmanuel et al. discloses in Table 34 it showed genes showing improved plant performance at specific growth conditions under regulation of At6669 promoter (page 91, Table 33).
Emmanuel et al. discloses LYM372 is maize gene maizelgbl 701AW499159 as nucleotide sequence of SEQ ID NO: 354 that encodes the protein of SEQ ID NO: 760 which has been identified genes for increasing yield, growth rate, vigor, biomass, growth rate, oil content, abiotic stress tolerance, nitrogen use efficiency, water use efficiency and fertilizer use efficiency of a plant (page 25, Table 1).
Emmanuel et al. discloses test of expression of the gene LYM372 in Arabidopsis (Example 11) had higher plot coverage compared to control plant (77.6 vs 71.1 cm2) (page 93, Table 34). Higher rosette area (cm2) (8.9 vs. 9.7 cm2), higher harvest index (0.3 vs. 0.2) compared to control plant (page 95, Table 36), higher fresh weight (3779.2 vs. 2926.6) compared to control plant (page 101, Table 38), higher plot coverage, rosette area and rosette diameter (page 104, Table 39), higher related growth rate (page 107, Table 40), increased relative growth rate (RGR) of root length (page119, Table 45).
Alignment of SEQ ID NO:436 to pubpaa__le40000 database:
RESULT 1
US-13-695-094A-760
(NOTE: this sequence has 5 duplicates in the database searched)
Sequence 760, US/13695094A
Publication No. US20130125258A1
GENERAL INFORMATION
APPLICANT: Evogene Ltd.
APPLICANT: Emmanuel, Eyal
APPLICANT: Karchi, Hagai
TITLE OF INVENTION: ISOLATED POLYNUCLEOTIDES AND POLYPEPTIDES, AND METHODS OF USING
TITLE OF INVENTION: SAME FOR INCREASING PLANT YIELD AND/OR AGRICULTURAL
TITLE OF INVENTION: CHARACTERISTICS
FILE REFERENCE: 54786
CURRENT APPLICATION NUMBER: US/13/695,094A
CURRENT FILING DATE: 2012-10-29
PRIOR APPLICATION NUMBER: PCT/IB2011/051843
PRIOR FILING DATE: 2011-04-27
PRIOR APPLICATION NUMBER: US 61/328,692
PRIOR FILING DATE: 2010-04-28
PRIOR APPLICATION NUMBER: US 61/378,003
PRIOR FILING DATE: 2010-08-30
PRIOR APPLICATION NUMBER: US 61/405,260
PRIOR FILING DATE: 2010-10-21
PRIOR APPLICATION NUMBER: US 61/437,715
PRIOR FILING DATE: 2011-01-31
NUMBER OF SEQ ID NOS: 5159
SEQ ID NO 760
LENGTH: 842
TYPE: PRT
ORGANISM: Zea mays
Query Match 100.0%; Score 4468; Length 842;
Best Local Similarity 100.0%;
Matches 842; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MSDWSSPAAPTFFPFGPQAEGWDVTFKVKYGDTLKRFYGCANGSHFDMNLSALRARIDTA 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MSDWSSPAAPTFFPFGPQAEGWDVTFKVKYGDTLKRFYGCANGSHFDMNLSALRARIDTA 60
Qy 61 FKFGPDVDFVLTYTDEDGDIVMLDDDDDLRDAALRQRLNPLRITVQLKKNQPTEKKDTSA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 FKFGPDVDFVLTYTDEDGDIVMLDDDDDLRDAALRQRLNPLRITVQLKKNQPTEKKDTSA 120
Qy 121 PVKSAAQDPLSQLMSAIEGLKPVQEDSLAHIKSAIGEAIKSIPEPIPDALAKLSHEILDA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 PVKSAAQDPLSQLMSAIEGLKPVQEDSLAHIKSAIGEAIKSIPEPIPDALAKLSHEILDA 180
Qy 181 APPPLAELMKPFAQLMAPNNNGNGPSDVHAEGSSSSSSAQVPAEAKNEPKVRPSLGLKTV 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 APPPLAELMKPFAQLMAPNNNGNGPSDVHAEGSSSSSSAQVPAEAKNEPKVRPSLGLKTV 240
Qy 241 LKEAAGPVPNAGASQVQQPLMYPSVEEMLFPCNSVDKSVCKGKIDAQSKGKSVTSSGIQP 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 LKEAAGPVPNAGASQVQQPLMYPSVEEMLFPCNSVDKSVCKGKIDAQSKGKSVTSSGIQP 300
Qy 301 APHSLRTHAPPPPHPCISEWSRAQRSQHRQLKFEDNAKATNDSRWRIPMYKMPYAPPPPA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 APHSLRTHAPPPPHPCISEWSRAQRSQHRQLKFEDNAKATNDSRWRIPMYKMPYAPPPPA 360
Qy 361 VPPPGYVPSPHFPYPGRLLSSGHPYGDLAGNMENSAPHSLHRWIQCDGCGAQPIVGPRYK 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 VPPPGYVPSPHFPYPGRLLSSGHPYGDLAGNMENSAPHSLHRWIQCDGCGAQPIVGPRYK 420
Qy 421 SNVKEDYDLCDSCFQRMGNEMEYTKIDKPILPHRFLRDPHVYRKVHHPRVLMKSRREKLE 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 SNVKEDYDLCDSCFQRMGNEMEYTKIDKPILPHRFLRDPHVYRKVHHPRVLMKSRREKLE 480
Qy 481 SRFILDVTVLDGTLMTPSTPFTKIWRMHNNGSVVWPRGTQLVWVGGDQFALQTSVPLEIP 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 SRFILDVTVLDGTLMTPSTPFTKIWRMHNNGSVVWPRGTQLVWVGGDQFALQTSVPLEIP 540
Qy 541 VDGFPVDKEIDVPVDFVAPTRPGRYISYWRLASPSGQKFGQRVWVHIQVEDPSFVNDNNR 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 VDGFPVDKEIDVPVDFVAPTRPGRYISYWRLASPSGQKFGQRVWVHIQVEDPSFVNDNNR 600
Qy 601 NAAINLNLPPESYSSNTTNLIDVNIEPADSALSAHAKRTKEFHFCSTDFPEPSKSVPFTL 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 NAAINLNLPPESYSSNTTNLIDVNIEPADSALSAHAKRTKEFHFCSTDFPEPSKSVPFTL 660
Qy 661 ATTSLSAAAPTNQTGDVPMSSTPAAACLPSVNVPMHEVVTTHTPSPITPVLPTTIHFSAP 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 ATTSLSAAAPTNQTGDVPMSSTPAAACLPSVNVPMHEVVTTHTPSPITPVLPTTIHFSAP 720
Qy 721 VSAPAIA PELASGAVGVPPPVSAVVPELSELDVHNEEKLLRELEEMGFRQVDLNKEILRQ 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 721 VSAPAIA PELASGAVGVPPPVSAVVPELSELDVHNEEKLLRELEEMGFRQVDLNKEILRQ 780
Qy 781 NNYNLEQSVDDLCGVNEWDPLLAELEEMGFDDTEMNKELLAKNEGSIKRAVMELIAREKK 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 781 NNYNLEQSVDDLCGVNEWDPLLAELEEMGFDDTEMNKELLAKNEGSIKRAVMELIAREKK 840
Qy 841 DK 842
||
Db 841 DK 842
Alignment of SEQ ID NO:152 to pubpna__le40000 database:
RESULT 2
US-13-695-094A-354
(NOTE: this sequence has 3 duplicates in the database searched)
Sequence 354, US/13695094A
Publication No. US20130125258A1
GENERAL INFORMATION
APPLICANT: Evogene Ltd.
APPLICANT: Emmanuel, Eyal
APPLICANT: Karchi, Hagai
TITLE OF INVENTION: ISOLATED POLYNUCLEOTIDES AND POLYPEPTIDES, AND METHODS OF USING
TITLE OF INVENTION: SAME FOR INCREASING PLANT YIELD AND/OR AGRICULTURAL
TITLE OF INVENTION: CHARACTERISTICS
FILE REFERENCE: 54786
CURRENT APPLICATION NUMBER: US/13/695,094A
CURRENT FILING DATE: 2012-10-29
PRIOR APPLICATION NUMBER: PCT/IB2011/051843
PRIOR FILING DATE: 2011-04-27
PRIOR APPLICATION NUMBER: US 61/328,692
PRIOR FILING DATE: 2010-04-28
PRIOR APPLICATION NUMBER: US 61/378,003
PRIOR FILING DATE: 2010-08-30
PRIOR APPLICATION NUMBER: US 61/405,260
PRIOR FILING DATE: 2010-10-21
PRIOR APPLICATION NUMBER: US 61/437,715
PRIOR FILING DATE: 2011-01-31
NUMBER OF SEQ ID NOS: 5159
SEQ ID NO 354
LENGTH: 2908
TYPE: DNA
ORGANISM: Zea mays
Query Match 100.0%; Score 2529; Length 2908;
Best Local Similarity 100.0%;
Matches 2529; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 ATGTCTGACTGGAGCTCGCCGGCTGCGCCGACGTTCTTCCCTTTTGGCCCGCAGGCCGAG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 242 ATGTCTGACTGGAGCTCGCCGGCTGCGCCGACGTTCTTCCCTTTTGGCCCGCAGGCCGAG 301
Qy 61 GGGTGGGACGTCACCTTCAAGGTCAAATATGGTGATACACTTAAAAGGTTTTATGGTTGT 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 302 GGGTGGGACGTCACCTTCAAGGTCAAATATGGTGATACACTTAAAAGGTTTTATGGTTGT 361
Qy 121 GCCAATGGGAGTCATTTTGACATGAATTTATCTGCTCTACGGGCGAGGATTGATACTGCC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 362 GCCAATGGGAGTCATTTTGACATGAATTTATCTGCTCTACGGGCGAGGATTGATACTGCC 421
Qy 181 TTTAAGTTTGGTCCTGACGTTGACTTTGTTCTGACTTACACCGATGAGGATGGTGATATT 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 422 TTTAAGTTTGGTCCTGACGTTGACTTTGTTCTGACTTACACCGATGAGGATGGTGATATT 481
Qy 241 GTCATGCTAGATGATGATGATGACTTGCGTGATGCAGCTCTCCGTCAGAGATTAAACCCT 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 482 GTCATGCTAGATGATGATGATGACTTGCGTGATGCAGCTCTCCGTCAGAGATTAAACCCT 541
Qy 301 CTCAGGATTACTGTTCAACTGAAGAAAAATCAACCAACTGAAAAAAAAGATACTTCTGCA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 542 CTCAGGATTACTGTTCAACTGAAGAAAAATCAACCAACTGAAAAAAAAGATACTTCTGCA 601
Qy 361 CCAGTGAAATCCGCTGCTCAGGATCCACTATCCCAGTTAATGTCAGCTATTGAAGGTTTG 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 602 CCAGTGAAATCCGCTGCTCAGGATCCACTATCCCAGTTAATGTCAGCTATTGAAGGTTTG 661
Qy 421 AAGCCTGTTCAGGAAGATAGTCTGGCCCATATAAAATCAGCTATTGGTGAAGCAATCAAG 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 662 AAGCCTGTTCAGGAAGATAGTCTGGCCCATATAAAATCAGCTATTGGTGAAGCAATCAAG 721
Qy 481 TCTATCCCAGAGCCAATACCTGATGCCCTTGCAAAACTTTCTCATGAAATACTTGATGCA 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 722 TCTATCCCAGAGCCAATACCTGATGCCCTTGCAAAACTTTCTCATGAAATACTTGATGCA 781
Qy 541 GCACCACCACCATTAGCTGAGCTGATGAAACCTTTTGCACAATTGATGGCACCAAACAAT 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 782 GCACCACCACCATTAGCTGAGCTGATGAAACCTTTTGCACAATTGATGGCACCAAACAAT 841
Qy 601 AATGGCAATGGGCCATCTGATGTGCATGCTGAGGGGTCATCTAGCTCTTCCAGTGCACAG 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 842 AATGGCAATGGGCCATCTGATGTGCATGCTGAGGGGTCATCTAGCTCTTCCAGTGCACAG 901
Qy 661 GTGCCAGCTGAAGCTAAAAATGAGCCCAAAGTTAGGCCAAGTTTGGGTCTTAAGACCGTG 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 902 GTGCCAGCTGAAGCTAAAAATGAGCCCAAAGTTAGGCCAAGTTTGGGTCTTAAGACCGTG 961
Qy 721 TTGAAAGAGGCTGCTGGACCTGTTCCTAATGCTGGAGCTTCTCAGGTTCAACAGCCATTA 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 962 TTGAAAGAGGCTGCTGGACCTGTTCCTAATGCTGGAGCTTCTCAGGTTCAACAGCCATTA 1021
Qy 781 ATGTATCCATCTGTTGAGGAGATGCTGTTCCCCTGTAATTCAGTCGACAAATCTGTTTGC 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1022 ATGTATCCATCTGTTGAGGAGATGCTGTTCCCCTGTAATTCAGTCGACAAATCTGTTTGC 1081
Qy 841 AAAGGGAAGATTGATGCTCAAAGTAAGGGAAAATCTGTTACGTCCTCAGGCATCCAACCT 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1082 AAAGGGAAGATTGATGCTCAAAGTAAGGGAAAATCTGTTACGTCCTCAGGCATCCAACCT 1141
Qy 901 GCTCCTCATTCTCTTCGTACTCATGCCCCACCTCCACCACATCCGTGCATTTCAGAATGG 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1142 GCTCCTCATTCTCTTCGTACTCATGCCCCACCTCCACCACATCCGTGCATTTCAGAATGG 1201
Qy 961 TCCCGAGCACAAAGAAGCCAACACCGTCAATTGAAATTTGAAGACAATGCAAAAGCCACT 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1202 TCCCGAGCACAAAGAAGCCAACACCGTCAATTGAAATTTGAAGACAATGCAAAAGCCACT 1261
Qy 1021 AATGATTCTAGATGGCGCATTCCGATGTATAAAATGCCCTATGCACCACCACCTCCAGCA 1080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1262 AATGATTCTAGATGGCGCATTCCGATGTATAAAATGCCCTATGCACCACCACCTCCAGCA 1321
Qy 1081 GTGCCACCCCCAGGCTATGTACCTTCTCCACATTTTCCTTATCCAGGCCGCCTCTTATCT 1140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1322 GTGCCACCCCCAGGCTATGTACCTTCTCCACATTTTCCTTATCCAGGCCGCCTCTTATCT 1381
Qy 1141 TCTGGGCATCCATACGGAGATCTCGCTGGTAACATGGAAAACTCAGCACCACATAGTCTG 1200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1382 TCTGGGCATCCATACGGAGATCTCGCTGGTAACATGGAAAACTCAGCACCACATAGTCTG 1441
Qy 1201 CATAGATGGATTCAGTGTGATGGCTGTGGAGCGCAACCAATTGTTGGTCCACGTTATAAA 1260
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1442 CATAGATGGATTCAGTGTGATGGCTGTGGAGCGCAACCAATTGTTGGTCCACGTTATAAA 1501
Qy 1261 TCTAATGTGAAGGAAGACTATGATTTATGTGATTCCTGTTTCCAGCGCATGGGAAATGAA 1320
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1502 TCTAATGTGAAGGAAGACTATGATTTATGTGATTCCTGTTTCCAGCGCATGGGAAATGAA 1561
Qy 1321 ATGGAGTACACCAAAATAGACAAGCCTATTTTACCCCACAGGTTTCTAAGAGATCCCCAT 1380
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1562 ATGGAGTACACCAAAATAGACAAGCCTATTTTACCCCACAGGTTTCTAAGAGATCCCCAT 1621
Qy 1381 GTGTACCGGAAGGTGCACCATCCACGGGTTCTAATGAAGTCAAGACGGGAGAAACTTGAA 1440
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1622 GTGTACCGGAAGGTGCACCATCCACGGGTTCTAATGAAGTCAAGACGGGAGAAACTTGAA 1681
Qy 1441 AGTCGCTTCATTTTGGATGTGACTGTTCTTGATGGAACACTGATGACACCTTCTACCCCG 1500
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1682 AGTCGCTTCATTTTGGATGTGACTGTTCTTGATGGAACACTGATGACACCTTCTACCCCG 1741
Qy 1501 TTCACTAAGATTTGGCGCATGCATAACAATGGGTCTGTTGTGTGGCCACGGGGCACACAG 1560
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1742 TTCACTAAGATTTGGCGCATGCATAACAATGGGTCTGTTGTGTGGCCACGGGGCACACAG 1801
Qy 1561 CTTGTCTGGGTTGGTGGAGATCAGTTTGCATTGCAGACATCTGTTCCATTAGAGATTCCT 1620
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1802 CTTGTCTGGGTTGGTGGAGATCAGTTTGCATTGCAGACATCTGTTCCATTAGAGATTCCT 1861
Qy 1621 GTGGATGGTTTTCCTGTGGACAAAGAGATTGATGTTCCTGTTGATTTTGTGGCACCTACA 1680
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1862 GTGGATGGTTTTCCTGTGGACAAAGAGATTGATGTTCCTGTTGATTTTGTGGCACCTACA 1921
Qy 1681 AGGCCAGGGAGGTACATATCTTACTGGAGGTTGGCTTCCCCTTCTGGTCAGAAATTTGGT 1740
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1922 AGGCCAGGGAGGTACATATCTTACTGGAGGTTGGCTTCCCCTTCTGGTCAGAAATTTGGT 1981
Qy 1741 CAGCGAGTTTGGGTTCATATCCAGGTGGAAGACCCTTCTTTTGTTAATGACAATAACAGG 1800
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1982 CAGCGAGTTTGGGTTCATATCCAGGTGGAAGACCCTTCTTTTGTTAATGACAATAACAGG 2041
Qy 1801 AATGCTGCTATTAACCTGAATCTGCCTCCAGAGAGCTATAGTTCAAACACAACCAACTTA 1860
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2042 AATGCTGCTATTAACCTGAATCTGCCTCCAGAGAGCTATAGTTCAAACACAACCAACTTA 2101
Qy 1861 ATTGATGTGAACATTGAGCCTGCTGACTCAGCCCTTAGTGCACATGCTAAGCGCACAAAG 1920
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2102 ATTGATGTGAACATTGAGCCTGCTGACTCAGCCCTTAGTGCACATGCTAAGCGCACAAAG 2161
Qy 1921 GAGTTCCATTTCTGTTCAACTGATTTTCCTGAACCCAGTAAGTCTGTGCCTTTTACGTTG 1980
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2162 GAGTTCCATTTCTGTTCAACTGATTTTCCTGAACCCAGTAAGTCTGTGCCTTTTACGTTG 2221
Qy 1981 GCCACTACCTCTTTGTCTGCAGCAGCTCCTACAAACCAAACTGGTGATGTTCCCATGTCC 2040
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2222 GCCACTACCTCTTTGTCTGCAGCAGCTCCTACAAACCAAACTGGTGATGTTCCCATGTCC 2281
Qy 2041 AGTACACCTGCTGCTGCTTGTTTGCCCTCTGTTAATGTGCCTATGCATGAAGTCGTTACT 2100
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2282 AGTACACCTGCTGCTGCTTGTTTGCCCTCTGTTAATGTGCCTATGCATGAAGTCGTTACT 2341
Qy 2101 ACTCATACACCGTCACCTATTACGCCTGTCTTGCCTACAACTATACACTTTTCAGCCCCA 2160
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2342 ACTCATACACCGTCACCTATTACGCCTGTCTTGCCTACAACTATACACTTTTCAGCCCCA 2401
Qy 2161 GTATCTGCTCCTGCAATTGCCCCTGAGCTTGCATCAGGGGCTGTTGGTGTGCCTCCACCT 2220
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2402 GTATCTGCTCCTGCAATTGCCCCTGAGCTTGCATCAGGGGCTGTTGGTGTGCCTCCACCT 2461
Qy 2221 GTTAGTGCTGTGGTACCTGAGCTGTCAGAACTGGATGTTCACAATGAGGAGAAGTTGCTG 2280
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2462 GTTAGTGCTGTGGTACCTGAGCTGTCAGAACTGGATGTTCACAATGAGGAGAAGTTGCTG 2521
Qy 2281 AGGGAGCTGGAGGAAATGGGTTTTAGGCAGGTCGATCTCAACAAGGAAATCCTCAGGCAG 2340
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2522 AGGGAGCTGGAGGAAATGGGTTTTAGGCAGGTCGATCTCAACAAGGAAATCCTCAGGCAG 2581
Qy 2341 AACAATTACAATCTGGAGCAGTCTGTCGATGACCTATGTGGCGTCAATGAATGGGATCCT 2400
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2582 AACAATTACAATCTGGAGCAGTCTGTCGATGACCTATGTGGCGTCAATGAATGGGATCCT 2641
Qy 2401 CTCCTTGCAGAGCTGGAAGAGATGGGATTTGATGACACAGAGATGAACAAGGAGCTGCTT 2460
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2642 CTCCTTGCAGAGCTGGAAGAGATGGGATTTGATGACACAGAGATGAACAAGGAGCTGCTT 2701
Qy 2461 GCGAAGAATGAGGGAAGCATCAAGCGAGCTGTGATGGAGCTCATTGCCAGGGAGAAGAAG 2520
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2702 GCGAAGAATGAGGGAAGCATCAAGCGAGCTGTGATGGAGCTCATTGCCAGGGAGAAGAAG 2761
Qy 2521 GACAAGTGA 2529
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Db 2762 GACAAGTGA 2770
Regarding claim 2, Emmanuel et al. discloses in Table 34 the genes were under regulation of At6669 promoter (page 91, Table 33).
Regarding claims 3 and 4, Emmanuel et al. discloses their disclosed nucleotides are used with At6669 as promoter is a constitutive promoter and also can be with tissue specific promoters (page 11, paragraphs 0158, and 0160-0161).
Regarding claim 5, Emmanuel et al. discloses the transformation was Agrobacterium mediated (page 89, Example 10).
Regarding claim 7, Emmanuel et al. claim 19-20 recites growing the plant expressing said exogenous polynucleotide under the abiotic stress wherein abiotic stress ins water deprivation, flood (i.e. water overabundance) etc.
Regarding claim 8, Emmanuel et al. claim 21 recite, yield comprise seed yield. Furthermore, Emmanuel et al. discloses test of expression of the gene LYM372 (i.e. Applicant’s SEQ ID NO:152 encoding SEQ ID NO: 436) in Arabidopsis (Example 11) had higher plot coverage compared to control plant (77.6 vs 71.1 cm2) (page 93, Table 34). Higher rosette area (cm2) (8.9 vs. 9.7 cm2), higher harvest index (0.3 vs. 0.2) compared to control plant (page 95, Table 36), higher fresh weight (3779.2 vs. 2926.6) compared to control plant (page 101, Table 38), higher plot coverage, rosette area and rosette diameter (page 104, Table 39), higher related growth rate (page 107, Table 40), increased relative growth rate (RGR) of root length (page119, Table 45).
Regarding claim 9, Emmanuel et al. page 10, paragraphs 0148-0149 disclose the plant useful in the method of the invention include maize plant. Emmanuel et al. page, 76, Example 7 discloses maize hybrids comprising the transcripts of LYM372 which were grown in specific environments and various traits for example dry weight per plant, plant height etc. Since applicant has not specifically defined the term “heterologous” (see analysis above), the method of producing the hybrid would have transferred locus from one maize plant to other by the method of hybridization by human intervention.
Regarding claim 10, Emmanuel et al. discloses SEQ ID NO:760 (i.e. gene LYM372) is cloned in pUC19c plasmid (page 87, Table 32) (i.e. in recombinant construct).
Therefore Emmanuel et al. anticipates the claims.
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 Emmanuel et al. and further in view of Shi et al.
Claims 1, 6, and 11-12 are rejected under 35 U.S.C. 103 as being unpatentable over, Emmanuel et al., and further in view of Shi et al. (Published: 2017, Journal: Plant biotechnology journal, 15(2), 207-216).
Claims 1 and 6 are drawn to method of improving yield of a plant by introducing polynucleotide sequence at least 90% identical to a polynucleotide of SEQ ID NO:152 that encodes a polypeptide sequence at least 90% identical to a polypeptide of SEQ ID NO:436, regenerating the plant, subjecting to environmental conditions, assessing one or more characteristics and further introducing into the cell a Cas endonuclease and a guide polynucleotide. Claims 11-12 are drawn to site-directed modification of genomic locus comprising the polynucleotide encoding the polypeptide that modify its expression.
Regarding claim 1, Emmanuel et al. teaches a method of introducing a maize gene LYM372 which is applicant’s SEQ ID NO:152 that encodes SEQ ID NO:436 (see analysis above) wherein transgenic seeds of Arabidopsis were grown in the growth media and T2 transgenic seedlings were planted (i.e. (b) regenerated) in specific environments in greenhouse until mature seeds were produced which were harvested (page 90, paragraph 0532-0533). Emmanuel et al. teaches several characteristics for example overall seed growth rates, seed yield, dry matter index were measured (page 90, paragraphs 0535-0553).
Emmanuel et al. teaches in Table 34 showed genes showing improved plant performance under regulation of At6669 promoter (page 91, Table 33) compared to control plants. Emmanuel et al. teaches LYM372 is maize gene maizelgbl 701AW499159 as nucleotide sequence of SEQ ID NO: 354 that encodes the protein of SEQ ID NO: 760 which has been identified genes for increasing yield, growth rate, vigor, biomass, growth rate, oil content, abiotic stress tolerance, nitrogen use efficiency, water use efficiency and fertilizer use efficiency of a 12lant (page 25, Table 1).
Emmanuel et al. teaches modification and variation of their disclosed proteins and nucleotide sequence would have been apparent to the skilled in the art (page 123, paragraph 0594).
Emmanuel et al. does not teach the method further comprise introducing into the cell a Cas endonuclease and guide polynucleotide.
Shi et al. teaches a method of improving maize grain yield under drought stress conditions by generating variants of ARGOS8, a negative regulator of ethylene response, by introducing into the maize immature embryo a Cas endonuclease and guide polynucleotide (page 213, left column third paragraph) to improve grain yield under drought stress environments which had increased plant height, ear height, and approximately five bushels per acre more grain yield than the control in flowering stress environments (page 210, right column 3-4).
Thus, it would have been obvious to one skilled in the art before the effective filing date of the claimed invention to apply known method of introducing Cas endonuclease and guide polynucleotide for site directed modifications from teaching, suggestion, or motivation in Shi et al. to a genomic locus taught by Emmanuel et al. and screen the genomic edit variants to select for the plant with improved agronomic characters or yield.
Regarding claim 11, Emmanuel et al. teaches modification and variation of their disclosed proteins and nucleotide sequence would have been apparent to the skilled in the art (page 123, paragraph 0594).
Emmanuel et al. does not teach the method of increasing grain yield and/or one more agronomic characteristics of a plant comprises introducing one or more nucleotide modifications through a targeted site-directed modification at the genomic locus encoding at a polypeptide at least 90% identical to SEQ ID NO:436 such that its expression and/or activity is modified.
Shi et al. teaches a method of improving maize grain yield under drought stress conditions by generating variants of ARGOS8, a negative regulator of ethylene response, by introducing into maize immature embryo repair template and genome editing reagents using particle bombardment (page 208, right column second paragraph).
Shi et al. teaches a method of improving maize grain yield under drought stress conditions by generating variants of ARGOS8, a negative regulator of ethylene response, by introducing into the maize immature embryo a Cas endonuclease and guide polynucleotide (page 213, left column third paragraph) to improve grain yield under drought stress environments which had increased plant height, ear height, and approximately five bushels per acre more grain yield than the control in flowering stress environments (page 210, right column 3-4).
Thus, it would have been obvious before the effective filing date of the claimed invention from teaching, suggestion, or motivation in Shi et al. that would have led one of ordinary skill in the art to modify the genomic locus encoding at a polypeptide at least 90% identical to SEQ ID NO:436 taught by Emmanuel et al. to arrive the claimed invention of a method of increasing grain yield and/or one more agronomic characteristics of a plant by introducing one or more site directed nucleotide modifications.
Regarding claim 12, Emmanuel et al. teaches modification and variation of their disclosed proteins and nucleotide sequence would have been apparent to the skilled in the art (page 123, paragraph 0594). Shi et al. teaches using site-directed modification of ARGOS8 locus in maize using CRISPR-Cas9 system to improve grain yield under drought stress environments which had increased plant height, ear height, and approximately five bushels per acre more grain yield than the control in flowering stress environments (page 210, right column 3-4).
Shi et al. teaches a method using an RNA-guided Ca9 nuclease to modify one or more nucleotide by integrating the GOS2 PRO (a maize GOS2 promoter and 5’-UTR with an intron) into the upstream region of ARGOS8 via homology directed DNA repair (Figure 2a, page 208, right second column). It further show deletion of the promoter region (Fig 2c, 2e). It further teaches deletion of the 550 bp genomic DNA fragment between CTS3 and CTS1 removed part of the ARGOS8 5’-UTR and the upstream promoter sequence (Figure 2b and 3a, page 210, left column fourth paragraph). The variants were found to have improved grain yield under drought stress environment (page 210, right column 3-4).
Thus it would have been obvious before the effective filing date of the claimed invention from teaching, suggestion, or motivation in Shi et al. that would have led one of ordinary skill in the art to introduce one or more nucleotide changes or deletion of a regulatory element operably linked to the expression of the genomic loci taught by Emmanuel et al. to arrive the claimed invention of a method of increasing grain yield and/or any of the agronomic characteristics of a plant by introducing one or more site directed nucleotide modifications. Since Emmanuel et al. teaches complete sequence, then it would have been obvious to carry out the site-directed modification in the genomic locus comprising SEQ ID NO:152 encoding SEQ ID NO:436, that would have created variation in any of the agronomic traits to screen for improvement in any of the agronomic traits of the plant.
Summary
No claim is allowed.
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/SANTOSH SHARMA/Examiner, Art Unit 1663
/DAVID H KRUSE/Primary Examiner, Art Unit 1663
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