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 with traverse of Group I in the reply filed on 10/24/2025 is acknowledged. The Applicant also elected the following species, with traverse.
Woody plant, in claims 9-10 and 22-23
Populus Spp., in claims 10 and 23.
The traversal is on the grounds that, “Mishra does not teach a method for obtaining a genetically modified plant having improved yield and/or drought tolerance by modifying the genomic DNA in at least one cell of the plant to increase expression of a FTSHi3 gene in the plant” (response, page 10, para 7, line 3-6). This is not found persuasive because:.
All the groups require the common technical feature of, “a genetically modified plant having its FTSHi3 gene expression modified to improve yield and/or drought tolerance”, as described in the Office action dated 08/26/2025. That technical feature is not a special technical feature as it does not make a contribution over the prior art in view of Mishra et al.
Mishra et al. describes a homozygous ftshi3-2 mutant which shows enhanced cold tolerance after exposure to 4°C for 16 weeks (Supplementary Fig. S3A). Under the cold stress condition, the ftshi3-2 plants (page 2179, right column, para 2, line 1-7) show improved yield in terms of plant biomass, and that is also expected to be reflected in increased seed yield (Supplementary Fig. 3A).
Moreover, as provided in 37 CFR 1.475 (b), a national stage application containing claims to different categories of invention will be considered to have unity of invention if the claims are drawn only to one of the following combinations of categories:
(1) A product and a process specially adapted for the manufacture of said product; or
(2) A product and a process of use of said product; or
(3) A product, a process specially adapted for the manufacture of the said product, and a
use of the said product; or
(4) A process and an apparatus or means specifically designed for carrying out the said
process; or
(5) A product, a process specially adapted for the manufacture of the said product, and an
apparatus or means specifically designed for carrying out the said process.
Otherwise, unity of invention might not be present. See 37 CFR 1.475 (c).
In this case, there are more than one (two) different product inventions and more than one (two) different process (to make the said products) inventions. The invention of Group I and II are directed to methods; in contrast, the inventions of Group III and IV are directed to a product (a genetically modified plant), as described in the Office action dated 08/26/2025.
The requirement is still deemed proper and is therefore made FINAL.
Claim Status
Claims 1-3, 6-10, 13-16 and 19-25 are pending.
Claims 6-7, 13-16, 19-21, 23-24 are withdrawn from examination as being part of non-elected inventions.
Claims 4-5, 11-12 and 17-18 are cancelled by the Applicant.
The Applicant added a new claim, claim 25. Claim 25 would have been included in Group I invention and, thus, is being examined.
Claims 1-3, 8-10, 22 and 25 are being examined.
Priority
Acknowledgment is made of applicant's claim for foreign priority based on an application filed in Sweden on 05/20/2022. It is noted, however, that applicant has not filed a certified copy of the SWEDEN 2150653-0 application as required by 37 CFR 1.55.
Should applicant desire to obtain the benefit of foreign priority under 35 U.S.C. 119(a)-(d) prior to declaration of an interference, a certified English translation of the foreign application must be submitted in reply to this action. 37 CFR 41.154(b) and 41.202(e).
Failure to provide a certified translation may result in no benefit being accorded for the non-English application.
Information Disclosure Statement
The listing of references on pages 46-47 of the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Claim Rejections - 35 USC § 112(a)
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.
Written Description
Claim 3 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 inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 3 is drawn to a polypeptide sequence encoded by FTSHi3 gene and comprising SEQ ID NO: 2 or SEQ ID NO: 4, or the broad genus comprising any polypeptide having at least 60% sequence identity to SEQ ID NO: 2 or SEQ ID NO: 4.
SEQ ID NO: 2 contains 622 amino acid residues while SEQ ID NO: 4 contains 647 amino acid residues. Mutating at least 40% of the polypeptide would allow mutating up to 248 and 258 amino acid residues, respectively. The Applicant does not describe any structure function relationship to enable a skilled artisan to mutate up to 248 or up to 258 amino acid residues in the polypeptide sequences while retaining and/or achieving one or more of the function(s) of the native FTSHi3 gene which include(s) drought tolerance and improved yield.
Instant description teaches that, “All FtsH proteases contain a putative AAA ATPase domain, an ATPase AAA core and an M41 peptidase domain. In addition to active FtsH proteases, pseudo-proteases, termed FtsHi (i for inactive) have been detected in the genomes of plants (Spec, page 1, line 22-25) where the protease domain is mutated (spec, page 1, line 28). There are 12 genes encoding proteolytically active members of the FtsH family in the genome of Arabidopsis along with the five FtsHi genes coding for members that are proteolytically inactive due to mutations in the protease domain (Spec, page 1, line 26-28). The zinc-binding motif (HEXXH) comprising 5 amino acid residues within M41 peptidase domain is assumed to correspond to proteolytically active proteases (Mishra et al., Reduced expression of the proteolytically inactive FtsH members has impacts on the Darwinian fitness of Arabidopsis thaliana, 2019, Journal of Experimental Botany, 70:2173–2184; page 2176, Fig. 1). Mutating one or more of the 5 amino acids within the M41 protease domain in any of the 12 proteolytic active Ftsh polypeptides encoded by the Ftsh genes would also give rise to a polypeptide having more than 60% sequence identity to SEQ ID NO: 2 with unpredictable outcome in terms of improved yield and/or drought tolerance. On the other hand, mutating one or more critical amino acid(s) in the native FTSHi3 polypeptide having at least 60% sequence identity also potentially can have unpredictable outcome on the function(s) of the protein. It is prudent to mention here that Arabidopsis FTSHi3 (SEQ ID NO: 2) and Populus FtSHi3 (SEQ ID NO: 4) do not share significant sequence identity (less than 63%) yet they both share the same functions.
An ordinarily skilled artisan would know that mutating just one amino acid can lead to drastic change in the function(s) of a protein, as we see often observe in missense SNP mutants leading to a novel trait and/or abolishing a trait (which was previously present in the native polypeptide) altogether. Prior art also does not establish any structure function relationship in this regard.
An invention described solely in terms of a method of making and/or its function would lack written descriptive support where there is no described (in the specification) or art-recognized correlation between the disclosed function and the structure(s) responsible for the function. See MPEP § 2163.
Considering the breadth of the claims, lack of structure function relationship of the broad genus claimed, and unpredictability of the art, the Applicant does not appear to have been in possession of the claimed genus at the time this application was filed.
Scope of Enablement
Claim 3 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a polypeptide having 100% sequence identity to SEQ ID NO: 2 and/or SEQ ID NO: 4, does not reasonably provide enablement for a FTSHi3 homologous/orthologous polypeptide having at least 60% identity to the amino acid sequence according to SEQ ID NO: 2 or SEQ ID NO: 4. 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.
SEQ ID NO: 2 contains 622 amino acid residues while SEQ ID NO: 4 contains 647 amino acid residues while. Mutating 40% of the polypeptide would allow mutating up to 248 and 258 amino acid residues, respectively. The Applicant does not provide any guidance that would enable a skilled artisan to mutate up to 248 or up to 258 amino acid residues, respectively, in the polypeptide sequence(s) while retaining and/or achieving one or more of the function(s) of the native FTSHi3 gene which include(s) improved yield and/or drought tolerance.
Instant description teaches that, “All FtsH proteases contain a putative AAA ATPase domain, an ATPase AAA core and an M41 peptidase domain. In addition to active FtsH proteases, pseudo-proteases, termed FtsHi (i for inactive) have been detected in the genomes of plants (Spec, page 1, line 22-25) where the protease domain is mutated (spec, page 1, line 28). There are 12 genes encoding proteolytically active members of the FtsH family in the genome of Arabidopsis along with the five FtsHi genes coding for members that are proteolytically inactive due to mutations in the protease domain (Spec, page 1, line 26-28). The zinc-binding motif (HEXXH) comprising 5 amino acid residues within M41 were assumed to correspond to proteolytically active proteases (Mishra et al., Reduced expression of the proteolytically inactive FtsH members has impacts on the Darwinian fitness of Arabidopsis thaliana, 2019, Journal of Experimental Botany, 70:2173–2184; page 2176, Fig. 1).
An ordinarily skilled artisan would know that mutating just one amino acid can lead to drastic change in the function(s) of a protein, as we see often in missense SNP mutants leading to a novel trait or abolishing a trait altogether.
Mutating one or more of the 5 amino acids within the M41 protease domain in any of the 12 proteolytic active FTSH polypeptides encoded by the Ftsh genes in Arabidopsis would also give rise to a polypeptide having more than 60% sequence identity to SEQ ID NO: 2 but without the protease activity. However, it remains unpredictable if the mutant polypeptide, if overexpressed (or downregulated), would improve yield and/or drought tolerance. On the other hand, mutating one or more critical amino acid(s) in the native FTSHi3 polypeptide also potentially can have unpredictable outcome on the function(s) of the protein.
Prior art also does not guidance in this regard. Undue trial and error experimentations would be needed to make myriads of possible combinations involving as many as 248 amino acids (for SEQ ID NO: 2) or up to 258 amino acid residues (for SEQ ID NO: 4) along the entire length of the protein while ascertaining the function of the mutated proteins in terns of yield and/or drought tolerance.
Based on breadth of the claims, 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.
Claim Rejections - 35 USC § 112(b)
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 1-3, 8-10, 22 and 25 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.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c).
In the present instance, claim 1 recites the broad recitation “… improved yield and/or drought tolerance” (line 2), and the claim also recites “… and (d) selecting a genetically modified plant having improved drought tolerance” (line 10-11), which is the narrower statement of the range/limitation. It is unclear to the Examiner if both the features (improved yield and drought tolerance) are needed or if “improved yield” alone (as interpreted by “improved yield or drought tolerance) is sufficient to satisfy all the limitations of the claim.
All the claims directly or indirectly depend from claim 1 inherit the same indefiniteness.
Further regarding claims 9 , the phrase "such as" renders the claim(s) indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention or recited in the claim as examples. See MPEP § 2173.05(d).
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
Claims 1-3 are rejected under 35 U.S.C. 103 as being unpatentable over Mishra et al. (Reduced expression of the proteolytically inactive FtsH members has impacts on the Darwinian fitness of Arabidopsis thaliana, 2019, Journal of Experimental Botany, 70:2173–2184).
Claim 1 is drawn to a method for obtaining a genetically modified plant having improved yield and/or drought tolerance via increased expression of a FTSHi3 gene.
Mishra et al. describes exposing the FtsHi3 mutant plants to fluctuating water supply (page 2174, right column, last para, line 9-10), which imply exposing the plants either to flooding, drought, or both (i.e., obtaining genetically modified plant having improved yield and/or drought tolerance). But the data on the effect of “fluctuating water supply” are not explicitly described there. Nonetheless, the same plants show enhanced cold tolerance (Supplementary Fig. S3A). Under the cold stress condition, the ftshi3 plants (page 2179, right column, para 2, line 1-7) show improved yield in terms of plant biomass, and that is expected to be reflected in increased seed yield of the plants compared to wild type plants grown under the same condition (Supplementary Fig. 3A). Mishra et al. also teaches that the homozygous T-DNA insertion ftshi3 mutant plants do not abolish expression of the FTSHi3 gene, but maintained an expression level which is 10-30% of the wild-type (WT) level (page 2179, right column, para 2, line 11-14). Mishra et al. also describes a native FTSHi3 gene that comprises FTSHi3 promoter (as recited in claim 2) and the gene product having 100% sequence identity (GenBank Accession No. AT3G02450; Mishra et al., page 2175, right column, last para, line 1-2) to the amino acid sequence set forth in SEQ ID NO: 2, as recited in claim 3, as shown below.
RESULT 1
A0A178VIN9_ARATH
ID A0A178VIN9_ARATH Unreviewed; 622 AA.
AC A0A178VIN9; A0A5S9X9G8;
DT 07-SEP-2016, integrated into UniProtKB/TrEMBL.
DT 07-SEP-2016, sequence version 1.
DT 08-OCT-2025, entry version 42.
DE RecName: Full=AAA+ ATPase domain-containing protein {ECO:0000259|SMART:SM00382};
GN OrderedLocusNames=AXX17_At3g01670 {ECO:0000313|EMBL:OAP04762.1};
GN ORFNames=AN1_LOCUS11512 {ECO:0000313|EMBL:VYS56058.1}, C24_LOCUS11351
GN {ECO:0000313|EMBL:CAA0381095.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702 {ECO:0000313|EMBL:OAP04762.1, ECO:0000313|Proteomes:UP000078284};
RN [1] {ECO:0000313|Proteomes:UP000078284}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Landsberg erecta {ECO:0000313|Proteomes:UP000078284};
RX PubMed=27354520; DOI=10.1073/pnas.1607532113;
RA Zapata L., Ding J., Willing E.M., Hartwig B., Bezdan D., Jiao W.B.,
RA Patel V., Velikkakam James G., Koornneef M., Ossowski S., Schneeberger K.;
RT "Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent
RT of translocation and inversion polymorphisms.";
RL Proc. Natl. Acad. Sci. U.S.A. 113:E4052-E4060(2016).
RN [2] {ECO:0000313|EMBL:OAP04762.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC TISSUE=Leaf {ECO:0000313|EMBL:OAP04762.1};
RA Zapata L., Schneeberger K., Ossowski S.;
RT "Full-length assembly of Arabidopsis thaliana Ler reveals the complement of
RT translocations and inversions.";
RL Submitted (MAR-2016) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000313|EMBL:VYS56058.1, ECO:0000313|Proteomes:UP000426265}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. An-1 {ECO:0000313|Proteomes:UP000426265}, and cv. C24
RC {ECO:0000313|Proteomes:UP000434276};
RA Jiao W.-B., Schneeberger K.;
RL Submitted (NOV-2019) to the EMBL/GenBank/DDBJ databases.
CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000256|ARBA:ARBA00004141}; Multi-
CC pass membrane protein {ECO:0000256|ARBA:ARBA00004141}. Plastid,
CC chloroplast {ECO:0000256|ARBA:ARBA00004229}.
CC -!- SIMILARITY: Belongs to the AAA ATPase family.
CC {ECO:0000256|ARBA:ARBA00006914, ECO:0000256|RuleBase:RU003651}
DR EMBL; CACSHJ010000089; CAA0381095.1; -; Genomic_DNA.
DR EMBL; LUHQ01000003; OAP04762.1; -; Genomic_DNA.
DR EMBL; CACRSJ010000106; VYS56058.1; -; Genomic_DNA.
DR RefSeq; NP_186894.1; NM_111112.4.
DR AlphaFoldDB; A0A178VIN9; -.
DR SMR; A0A178VIN9; -.
DR Gramene; AT3G02450.1; AT3G02450.1; AT3G02450.
DR KEGG; ath:AT3G02450; -.
DR OMA; MPSLMGR; -.
DR OrthoDB; 1413014at2759; -.
DR Proteomes; UP000078284; Chromosome 3.
DR Proteomes; UP000426265; Unassembled WGS sequence.
DR Proteomes; UP000434276; Unassembled WGS sequence.
DR ExpressionAtlas; A0A178VIN9; baseline and differential.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0016020; C:membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:InterPro.
DR GO; GO:0004176; F:ATP-dependent peptidase activity; IEA:InterPro.
DR GO; GO:0004222; F:metalloendopeptidase activity; IEA:InterPro.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR CDD; cd19501; RecA-like_FtsH; 1.
DR FunFam; 3.40.50.300:FF:000277; ATP-dependent zinc metalloprotease FtsH; 1.
DR FunFam; 1.10.8.60:FF:000061; Probable inactive ATP-dependent zinc metalloprotease FTSHI 4, chloroplastic; 1.
DR Gene3D; 1.10.8.60; -; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR041569; AAA_lid_3.
DR InterPro; IPR003959; ATPase_AAA_core.
DR InterPro; IPR003960; ATPase_AAA_CS.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR011546; Pept_M41_FtsH_extracell.
DR PANTHER; PTHR23076:SF110; INACTIVE ATP-DEPENDENT ZINC METALLOPROTEASE FTSHI 3, CHLOROPLASTIC-RELATED; 1.
DR PANTHER; PTHR23076; METALLOPROTEASE M41 FTSH; 1.
DR Pfam; PF00004; AAA; 1.
DR Pfam; PF17862; AAA_lid_3; 1.
DR Pfam; PF06480; FtsH_ext; 1.
DR SMART; SM00382; AAA; 1.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
DR PROSITE; PS00674; AAA; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|RuleBase:RU003651};
KW Chloroplast {ECO:0000256|ARBA:ARBA00022528};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801};
KW Membrane {ECO:0000256|ARBA:ARBA00023136, ECO:0000256|SAM:Phobius};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741,
KW ECO:0000256|RuleBase:RU003651}; Plastid {ECO:0000256|ARBA:ARBA00022640};
KW Protease {ECO:0000256|ARBA:ARBA00022670};
KW Transit peptide {ECO:0000256|ARBA:ARBA00022946};
KW Transmembrane {ECO:0000256|ARBA:ARBA00022692, ECO:0000256|SAM:Phobius};
KW Transmembrane helix {ECO:0000256|ARBA:ARBA00022989,
KW ECO:0000256|SAM:Phobius}.
FT TRANSMEM 147..164
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT DOMAIN 366..502
FT /note="AAA+ ATPase"
FT /evidence="ECO:0000259|SMART:SM00382"
FT REGION 600..622
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 622 AA; 69410 MW; 1E22381B11D4A6A8 CRC64;
Query Match 100.0%; Score 3166; Length 622; Best Local Similarity 100.0%;
Matches 622; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MATFNVLCSNRFRFNGGYSPEKFNRKVSSRSSELNVCVSRIRTQSFSCRRLGGFMEIGET 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MATFNVLCSNRFRFNGGYSPEKFNRKVSSRSSELNVCVSRIRTQSFSCRRLGGFMEIGET 60
Qy 61 RLGVIRVHGDSRNRFSCNSEIKRLVTGDYGDKETRIGENGRNKGKRRRFSLRLRPRLRLV 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 RLGVIRVHGDSRNRFSCNSEIKRLVTGDYGDKETRIGENGRNKGKRRRFSLRLRPRLRLV 120
Qy 121 RMRLGRFDFRASMEDFRYFLKKNLKRVILSTGVALIFGLCYLFLRLTAVPSPSIVPYSDF 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 RMRLGRFDFRASMEDFRYFLKKNLKRVILSTGVALIFGLCYLFLRLTAVPSPSIVPYSDF 180
Qy 181 VTNLRGGSVSKVLLEEGSRRIYYNTDENVEVVDDVHKSETLEDPAIQIDGGTVTEAVTKD 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 VTNLRGGSVSKVLLEEGSRRIYYNTDENVEVVDDVHKSETLEDPAIQIDGGTVTEAVTKD 240
Qy 241 DTPRKVRALPPVWKYVTRKVDHDEKFLLSLMREKGITYSSAPQSALMSMRTTLITIISLW 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 DTPRKVRALPPVWKYVTRKVDHDEKFLLSLMREKGITYSSAPQSALMSMRTTLITIISLW 300
Qy 301 IPLTPLMWLLYRQLSASNSPAKKRRSKNPTVGFDDVEGVDSAKDELVEIVSCLQGSINYK 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 IPLTPLMWLLYRQLSASNSPAKKRRSKNPTVGFDDVEGVDSAKDELVEIVSCLQGSINYK 360
Qy 361 KLGARLPRGVLLVGPPGTGKTLLARAVAGEAGVPFFSVSASEFVELFVGRGAARIRDLFN 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 KLGARLPRGVLLVGPPGTGKTLLARAVAGEAGVPFFSVSASEFVELFVGRGAARIRDLFN 420
Qy 421 AARKNSPSIIFIDELDAVGGKRGRSFNDERDQTLNQLLTEMDGFESDTKVIVIAATNRPE 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 AARKNSPSIIFIDELDAVGGKRGRSFNDERDQTLNQLLTEMDGFESDTKVIVIAATNRPE 480
Qy 481 ALDSALCRPGRFSRKVLVAEPDQEGRRKILAIHLRDVPLEEDAFLICDLVASLTPGFVGA 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 ALDSALCRPGRFSRKVLVAEPDQEGRRKILAIHLRDVPLEEDAFLICDLVASLTPGFVGA 540
Qy 541 DLANIVNEAALLAARRGGEAVAREDIMEAIERAKFGINDKEARPRTLGNELSKMFPWMPS 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 DLANIVNEAALLAARRGGEAVAREDIMEAIERAKFGINDKEARPRTLGNELSKMFPWMPS 600
Qy 601 LARRNGPDQDGLQGPLGYQTLS 622
||||||||||||||||||||||
Db 601 LARRNGPDQDGLQGPLGYQTLS 622
Mishra et al. teaches that gene expression in the ftsh3-2 homozygous line is reduced by 88-90% (page 2177, right column, last para, line 26-27). Nonetheless, the homozygous T-DNA mutant lines somehow manage to make functional transcripts, up to 30% of the wild type plants, and thus, able to produce functional FTSHi3 protein. The Applicant does not provide any data on the protein level of FTSHi3 polypeptide in the homozygous FtsHi3 plants in comparison to the wild type plants.
Mishra et al. describes that there is no significant difference in seed viability between ftshi3-2 mutant and the wild type (page 2181, left column, para 1, line 15-18) and the molecular mechanism remains to be elucidated (page 2181, left column, para 1, line 20-21).
It is known in the art that the relationship between the mRNA level and the protein it encodes is not always linear, especially for the genes crucial for survival of the plant (embryo-lethal mutants) where the plant maintains a critical level of the protein irrespective of the level of the transcript. Any selection for such mutants is essentially screening for survival mutants (seedlings) that could overcome the lethality arising due to total loss-of-function of the gene/protein. An ordinarily skilled artisan would also acknowledge that increasing a gene's transcription (cellular mRNA level) doesn't necessarily lead to a proportional increase or any increase in the protein level in a cell for various reasons1.
It is also known in the art that overexpression of a wild-type gene not only can develop its own/unique phenotype(s) but also can cause mutant phenotypes with varying degrees of expressivity/penetrance, which provides an alternative yet powerful tool to identify loss-of-function (mutant) phenotype(s)2. Overexpression also provides a tool to identify mechanism and/or pathway components that might remain undetected using traditional loss-of-function analysis2.
Dosage effect, in terms of gene expression, can lead to new trait(s) and/or having mutant plants with varying degrees of penetrance and/or expressivity, especially for the genes crucial for survival of the plant (embryo-lethal mutants) where the cells maintain a stable protein level irrespective of the level of the transcript. It would have been obvious to try by an ordinarily skilled artisan to study the dosage effect of the FtsHi3 gene with a realistic objective to get different mutant line(s) with a new trait and/or mutant plants with varying degrees of penetrance and/or expressivity of the economically important traits (e.g. cold tolerance and consequential yield increase under specific growing condition in cold), as described by Mishra et al.
Thus, it would have been obvious to an ordinarily skilled artisan to generate an FtsHi3 overexpressing lines by introducing a nucleic acid molecule encoding a FTSHi3 gene product operably linked to a promoter (as recited in claim 2), considering the teachings of Mishra et al. describing a partial knockdown mutant line while not being able to recover a full knockdown mutant line for FtsHi3, and is described as not embryo- or seed-lethal (Mishra et al., page 2179, right column, para 2, line 11-14).
One with ordinary skill in the art would have been motivated to develop FtsHi3 overexpressing lines with a realistic objective to develop mutant line(s) with a new trait and/or having mutant plants with varying degrees of penetrance and/or expressivity (conferring tolerance to colder condition) of the economically important trait of cold tolerance that increases yield under specific growing condition.
Regarding claim 2, using the native promoter is a standard method in the art1 and would have been obvious to an ordinarily skilled artisan to maintain the specific gene expression profile in the overexpressing line by increasing the number of the gene in the genome. Using a strong consecutive promoter is also a standard practice in the art to either replace the native promoter (by well-known CRISPR-Cas technique) or introducing at least one transgene driven by a constitutive promoter like 35S CaMV1 to achieve ectopic overexpression.
Claims 8-10, 22 and 25 are rejected under 35 U.S.C. 103 as being unpatentable over Mishra et al. as applied to reject claims 1-3 under 35 U.S.C. 103 above, and further in view of Jangale et al. (Independent and combined abiotic stresses affect the physiology and expression patterns of DREB genes differently in stress-susceptible and resistant genotypes of banana, 2019, Physiologia Plantarum, 165:303–318) and Yue et al. (Identification and characterization of two members of the FtsH gene family in maize, 2010, Mol. Biol. Rep., 37:855–86)
Claim 8 is drawn to a method for obtaining a genetically modified plant having improved drought tolerance.
Claim 25 is drawn to aspen or hybrid aspen plant.
Mishra et al. describes the obviousness and motivation to develop FtsHi3 overexpressing mutant line(s) with a realistic goal to get varying degrees of penetrance/expressivity of the economically important trait of cold tolerance that increases yield under specific growing condition in cold, as discussed above. Mishra et al. also describes exposing the FtsHi3 mutant plants to fluctuating water supply (page 2174, right column, last para, line 9-10).
However, Mishra et al. does not explicitly describe the response of the FtsHi3 mutant line in terms of “fluctuating water supply” or drought tolerance.
It is known in the art that plant growth is greatly affected by water-limited conditions such as drought and salinity, as well as extreme temperature conditions including cold. It is also known in the art that genes activated in response to various stresses, including cold and drought, reveal significant overlap in gene networks and distinct pathways for each stress type; for example, RNA-seq results show that 45 DREB genes in sugarcane are deregulated under cold stress while 35 of the same genes were found to be involved in responding to drought stress as well3.
Yue et al. describes cold, high salt, Polyethylene glycol (PEG) (widely used to mimic drought stress), and ABA dependent expression pattern of a member of the FtsH gene family in maize (abstract, line 14-18). The AtFTSHi3 mRNA (GeneBank Accession No. NM_111112, first published in 2000 as part of Arabidopsis genome sequencing project) also has an abscisic acid (ABA)-responsive element (ACGTGT) in its promoter, starting at position 126 (sequence identity data not shown).
Jangale et al. teaches that most of the DEHYDRATION-RESPONSIVE ELEMENT BINDING (DREB) genes had abscisic acid (ABA)-responsive elements in their promoters and were also activated by ABA (abstract, line 17-18). Jangale et al. describes that within the DREB gene family, the DREB A1 and DREB A2 group of genes (page 304, right column, para 1, line 7-9; Fig. 3-4), have shown greater association with abiotic stresses including cold and drought in plants including Arabidopsis, rice, soybean, cotton, Eucalyptus, and bamboo (page 314, left column, para 2, line 7-13).
It would have been obvious to an ordinarily skilled artisan to try to develop FtsHi3 mutant lines (as described by Mishra et al.) including overexpressing lines in different plants including aspen (as recited in claim 25) with an objective to improve economically important traits like cold and/or drought tolerance by up deregulating other ABA responsive genes, which include DREB A genes, involved abiotic stress response including cold and drought tolerance, as described by Jangale et al.
It is a standard practice in the art to regenerate matured mutant/transgenic plants, harvest seeds and grow next generation of mutant/transgenic plants for various purposes including propagation of the commercially important plant varieties. Identification of the native FtsHi3 gene4 encoding a protein (GenBank Accession No. TKR85660) having more than 60% (98.8%) sequence identity to instant SEQ ID NO: 4 in an aspen sp. (white poplar) would help developing the overexpressing aspen line using native FTSHi3 gene, besides using the same gene from other plant species including from Arabidopsis with a realistic expectation to achieve the same objective to develop cold and/or drought tolerant aspen plant.
An ordinarily skilled artisan would have been motivated to improve economically important traits like drought tolerance and/or cold tolerance by overexpressing FTSHi3 gene, in different plants including aspen.
Regarding claims 9-10 and 22, Jangale et al. describes crop plants like rice (Oryza spp.), soybean (Glycine spp.), and cotton (Gossypium hirsutum); woody plant species comprising Eucalyptus ( Eucalyptus sp.) and bamboo ( Bambusa sp.), as recited in claims 9-10 and 22 (page 314, left column, para 2, line 7-13).
Improper Markush Group
Claim 10 is rejected under the judicially-created basis that it contains an improper Markush grouping of alternative species. See In re Harnisch, 631 F.2d 716, 721-722 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. and Int. 1984). The improper Markush grouping includes species of the claimed invention that do not share both a substantial structural feature and a common use that flows from the substantial structural feature.
The members of the improper Markush grouping do not share a substantial feature and a common use that flows from the substantial structural feature for the following reasons: the claim is drawn to “crop plant species”. However, the alternatives in the long list in claim 10 also encompass non-crop plant species like Cola spp., Agrostis stolonifera, etc.
Thus, the species of claim 10 do not share a substantial structural feature recited as a claim limitation of being a crop plant.
In response to this rejection, Applicants should either amend the claim to recite only individual species or grouping of species that are crop plants or present a sufficient showing that the species recited in the alternative of the claim in fact are in fact, crop plants.
Conclusion
No claim is allowed.
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..
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Bratislav Stankovic can be reached at (571) 270-0305. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
Jay Chatterjee
Patent Examiner
Art Unit 1662
/Jay Chatterjee/Examiner, Art Unit 1662
/BRATISLAV STANKOVIC/Supervisory Patent Examiner, Art Units 1661 & 1662
1 Lubman et al. (Two-dimensional liquid separations–mass mapping of proteins from human cancer cell lysates, 2002, Journal of Chromatography B, 782:183–196) provides the evidence that cellular levels of mRNA and protein are not always linear (page 184, left column, para 1, line 7-9).
2 Prelich, G (Gene Overexpression: Uses, Mechanisms, and Interpretation, 2012, Genetics, 190:841–854) provides the evidence that overexpression of a wild-type gene can also cause loss-of-function trait(s) and became a useful tool for geneticists (abstract, line 2-4; page 841, right column, para 1, line 1-4). It also provides the evidence of developing systematic high-copy libraries that express genes from endogenous promoters (page 843, right column, last para last line; Table 1) and also consecutive 35S CaMV promoter (Table 1).
3 Huang et al. (Genome-Wide Analysis of the DREB Subfamily in Saccharum spontaneum Reveals Their Functional Divergence During Cold and Drought Stresses, 2020, Front. Genet., 10:1326) provides the evidence that that 45 DREB genes are deregulated under cold stress while 35 of the same genes in sugarcane were found to be involved in responding to drought stress as well (abstract).
4 Liu et al. (De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China, 2019, Sci. China Life Sci., 62:609–618) provides the evidence of Identification of the native FtsHi3 gene in an aspen plant (white poplar).