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 .
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) is acknowledged. As such, the effective filing date of Claims 1, 3-4, 6-7, 9-11, 13, 15, 17, 19-20, 22, 24, 27-29, 31-32, and 34 is 06/22/2020.
Election/Restrictions
Applicant’s election of SEQ ID NO: 134 in the reply filed on 1/30/2025 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Status of the Claims
Claims 1, 3-4, 6-7, 9-11, 13, 15, 17, 19-20, 22, 24, 27-29, 31-32, and 34 are pending.
Claims 1, 3-4, 6-7, 9-11, 13, 15, 17, 19-20, 22, 24, 27-29, 31-32, and 34 are examined herein.
Claims 1, 3-4, 6-7, 9-11, 13, 15, 17, 19-20, 22, 24, 27-29, 31-32, and 34 are rejected.
Information Disclosure Statement
The Information Disclosure Statement filed on 05/21/2023 is in compliance with the provisions of 37 CFR 1.97 and has been considered in full. A signed copy of the list of references cited is included with this Office Action.
Specification
Applicant is reminded of the proper language and format for an abstract of the disclosure.
The abstract should be in narrative form and generally limited to a single paragraph on a separate sheet within the range of 50 to 150 words in length. The abstract should describe the disclosure sufficiently to assist readers in deciding whether there is a need for consulting the full patent text for details.
The language should be clear and concise and should not repeat information given in the title. It should avoid using phrases which can be implied, such as, “The disclosure concerns,” “The disclosure defined by this invention,” “The disclosure describes,” etc. In addition, the form and legal phraseology often used in patent claims, such as “means” and “said,” should be avoided.
The abstract of the disclosure is objected to because it is less than 50 words in length and recites, in part, "The present disclosure describes...". A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
The disclosure is objected to because of the following informalities:
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code on pg. 170. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
The listing of references in 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.
Appropriate correction is required.
Claim Objections
Claims 1, 2, 4, 13, 19, and 32 are objected to because of the following informalities:
Claim 1 recites “npr1” and “NPR1” which are abbreviations/acronyms. As Claim 1 is the first recitation of both “npr1” and “NPR1”, Applicant is advised to clearly define the full name of the abbreviation/acronym.
Claim 2, line 4 should recite “…and the promoter and the one or more uORFs” rather than “…or the promoter and the one or more uORFs”.
Claim 4 recites “TBF1”, “tCUP”, “Rsyn7”, ”In2-2”, and “PR-1a” which are abbreviations/acronyms. As Claim 4 is the first recitation of the previously listed terms, Applicant is advised to clearly define the full name of the abbreviation/acronym.
Claim 13 recites “CUL3” which is an abbreviation/acronym. As Claim 13 is the first recitation of “CUL3”, Applicant is advised to clearly define the full name of the abbreviation/acronym.
Claim 19 recites “∆CTD npr1 ∆CTD”, “BTB”, and “sim3” which are abbreviations/acronyms. As Claim 19 is the first recitation of the previously listed terms, Applicant is advised to clearly define the full name of the abbreviation/acronym.
Claim 32 recites “EDS1” and “WRKY” which are abbreviations/acronyms. As Claim 32 is the first recitation of “EDS1” and “WRKY”, Applicant is advised to clearly define the full name of the abbreviation/acronym.
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 3-4, 6-7, 9-11, 13, 15, 17, 19-20, 22, 24, 27-29, 31-32, and 34 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.
Claims 1, 9, 13, and 15 recite a nucleic acid encoding a “npr1” protein, which renders the claim indefinite. Claims 1, 9, 13, and 15 are drawn to a nucleic acid encoding an npr1 protein, wherein the npr1 protein forms salicylic acid-independent NPR1 condensates, wherein the specification defines that npr1 proteins included in the scope of the claims can be “a nucleic acid encoding: (a) a protein comprising the amino acid sequence of any of SEQ ID NOs: 134-160 or an ortholog thereof; or (b) a protein having at least 70%, identity to a protein comprising the amino acid sequence of any of SEQ ID NOS: 134-160, wherein the protein retains salicylic acid-independent NPR1 condensate formation function” (paragraph 0066). However, when examining sequences with 100% sequence identity to SEQ ID NO: 134 (elected species of npr1 protein), the prior art shoes that these mutated NPR1 proteins are given several different names, such as NIM1 and SAI1 (See first result in TAIR_BLAST_SEQ_ID_NO_134 located in file wrapper), making the nomenclature for what constitutes a “npr1” protein unclear and inconsistent. As such, the nomenclature regarding npr1, as defined by the specification and in view of the prior art is not consistent, making the metes and bounds of the claimed invention unclear. It is not clear, even with the definition provided in the specification, what constitutes a “npr1” protein in the present invention, and one of ordinary skill in the art would not be reasonably apprised of the scope of the claims.
Claims 3-4, 6-7, 9-11, 13, 15, 17, 19-20, 22, 24, 27-29, 31-32, and 34 ultimately depend from Claim 1 and are therefore rejected for the same reasons as given above.
Claim 7 recites the limitation "expression control elements" in line 1. There is insufficient antecedent basis for this limitation in the claim. Claim 7 depends from cancelled Claim 5, therefore the recited “expression control elements” and other elements recited in Claim 7 lack antecedent basis because the limitations depend from a cancelled claim. For examination purposes, Claim 7 is interpreted to depend from the nucleic acid of Claim 6. However, this determination does not relieve Applicant from their duty to amend the claim in further correspondence.
Claims 11 and 15 recite mutations corresponding to amino acid positions relative to SEQ ID NO: 1 which renders the claim indefinite. The claims are drawn to mutations in the RDR of any npr1 protein known in the art from any species of plant, wherein the mutations correspond to the recited amino acid positions relative to the 593 amino acids long SEQ ID NO: 1. Taking the species of npr1 proteins provided by Applicant (SEQ ID NOs: 134-160) as an example, it is noted that npr1 proteins vary in length (between 576-608 amino acids long); therefore, it is unclear how these regions identified in Claims 11 and 15 correspond to sequences other than SEQ ID NO: 1 and closely related sequences that are 593 amino acids in length. As such, the metes and bounds of the claims are unclear.
Claim 17 depends from Claim 15 and is therefore rejected for the same reasons as given above.
Claim Rejections - 35 USC § 112
Written Description
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1, 3-4, 6-7, 9-11, 13, 15, 17, 19-20, 22, 24, 27-29, 31-32, and 34 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.
The Federal Circuit has clarified the written description requirement. The court stated that a written description of an invention "requires a precise definition, such as by structure, formula, [or]chemical name, of the claimed subject matter sufficient to distinguish it from other materials". University of California v. Eli Lilly and Co., 119 F.3d 1559, 1568; 43 USPQ2d 1398, 1406 (Fed. Cir. 1997). The court also concluded that "naming a type of material generally known to exist, in the absence of knowledge as to what that material consists of, is not description of that material". Id. Further, the court held that to adequately describe a claimed genus, Patent Owner must describe a representative number of the species of the claimed genus, and that one of skill in the art should be able to "visualize or recognize the identity of the members of the genus". Id.
The claims are broadly directed to a nucleic acid encoding a NPR1 mutant protein (denoted as npr1), a plant expressing the npr1 mutant, and a method of increasing stress tolerance in a plant which expresses the npr1 mutant, all of which require a nucleic acid that encodes a npr1 protein (a NPR1 mutant), wherein npr1 proteins that are included in the scope of the claims appear to encompass all npr1 proteins known in the art or homologs thereof from any species of plant, with untold numbers of mutations to the protein, at any position in the protein, wherein the npr1 protein forms salicylic acid-independent NPR1 condensates.
Applicant describes:
Nonmutated NPR1 from Arabidopsis thaliana that contains three redox-sensitive intrinsically disordered regions (RDR) located at amino acids 140-160, 368-404, and 510-539 relative to SEQ ID NO: 1 (paragraph 0052)
Methods of identifying homologs and/or orthologues of the A. thaliana NPR1 RDR2 (paragraph 0053)
Nonmutated orthologues of SEQ ID NO: 1 denoted as SEQ ID NOs: 2-12 and 30-34 (paragraph 0052)
Mutated nucleic acid sequences encoding NPR1 proteins denoted as SEQ ID NOs: 134-160 (paragraph 0066)
Mutations to A. thaliana NPR1 proteins performed in the instant invention and known in the art at the time of filing (paragraph 00153; Table 4)
Applicant does not describe:
-mutations at any position of any nucleic acid sequence encoding an NPR1 protein from any diverse source other than A. thaliana, that forms salicylic acid-independent NPR1 condensates.
-expression of npr1 from any diverse source known in the art, in any plant known in the art.
- expression of npr1 from any diverse source known in the art, in any plant known in the art, wherein the npr1 protein forms salicylic acid-independent NPR1 condensates.
- Mutated nucleic acids sequences encoding NPR1 proteins other than the sequences denoted as SEQ ID NOs: 134-160.
-whether all mutated nucleic acids sequences encoding NPR1 proteins denoted as SEQ ID NOs: 134-160 are able to form condensates in the nucleus or the cytoplasm in the absence of SA.
-whether all mutations to all NPR1 proteins known in the art, at any position in the sequence, result in the formation of NPR1 condensates in the absence of SA.
-mutated nucleic acids sequences encoding NPR1 proteins from sources other than A. thaliana that form salicylic acid-independent NPR1 condensates.
-mutated nucleic acids sequences encoding npr1 proteins from sources other than A. thaliana having one or more mutations in at least one redox-sensitive intrinsically disordered region (RDR), wherein the one or more mutations result in the npr1 protein forming salicylic acid-independent NPR1 condensates.
- mutated nucleic acids sequences encoding npr1 proteins from sources other than A. thaliana that are expressed in any plant known in the art, wherein the one or more mutations result in the npr1 protein forming salicylic acid-independent NPR1 condensates.
-the amino acid positions of any homologues and orthologues of A. thaliana NPR1 that align to SEQ ID NO: 1 and what those amino acid positions would be in the homologues and orthologues of A. thaliana NPR1 relative to SEQ ID NO: 1.
- whether mutations to A. thaliana NPR1 proteins known in the art at the time of filing resulted in the npr1 protein forming salicylic acid-independent NPR1 condensates.
Applicant’s exemplified species appear to be a broadly claimed genus of nucleic acids encoding npr1 proteins and homologues or orthologues thereof from any plant species capable of forming NPR1 condensates in the absence of salicylic acid when expressed in any plant, using any method known in the art to mutate any part of the nucleic acids encoding any NPR1 protein from any diverse source and subsequently express said npr1 protein in any plant.
The structural features that distinguish npr1 proteins and homologues and orthologues thereof, that function to form NPR1 condensates in the absence of salicylic acid, when expressed in any plant known in the art are not described in the specification, nor is any direction given to be able to find npr1 proteins and homologues and orthologues thereof in any plant species that function to form NPR1 condensates in the absence of salicylic acid due to the lack of disclosure regarding the structural features that cause NPR1 mutants (with an undefined number of mutations to any part of the sequence) from any plant known in the art to be able to form NPR1 condensates in the absence of salicylic acid.
When examining sequences with 100% sequence identity to the npr1 protein encoded in SEQ ID NO: 134 (elected species), the prior art shows that these mutated NPR1 proteins are given several different names, such as NIM1 and SAI1 (See first result in TAIR_BLAST_SEQ_ID_NO_134 located in file wrapper), making the nomenclature for what constitutes a “npr1” protein unclear and inconsistent, in view of the specification and the prior art. The npr1 proteins with 100% sequence identity to SEQ ID NO: 134 appear to encompass a group of polypeptides (NIM1 and SAI1) and it is not clear, based on Applicant’s definition of npr1 proteins, if these polypeptides are included in the broadly claimed genus of npr1 proteins that form salicylic acid-independent NPR1 condensates when expressed in a plant, as they are not given the name “npr1” despite being identical to SEQ ID NO: 134.
The state of the art for inferring a structure function relationship based on sequence homology is highly unpredictable. The functional prediction of a protein based on structural comparison is not consistent with an empirical assessment of its function. For example, Doerks et al. (TIG, 14:248-250, 1998) teaches that sequence homology is not sufficient to determine functionality of an uncharacterized protein. The homologs that scored best in PSI-BLAST analysis failed to share same catalytic activity. The reference clearly emphasizes that computer analysis of genome sequences is flawed, and overpredictions are common because the highest scoring database protein does not necessarily share the same or even similar functions (pg. 248, first paragraph; page 248, right column, second paragraph). Also, Smith et al. (Nature Biotechnology, 15:1222-1223, 1997) teaches that there are numerous cases in which proteins of very different functions are homologous (pg. 1222, last paragraph). Also, Bork et al. (TIG, 12:425-427, 1996) teaches that homology search methods are stretched and spurious hits are taken as real. The reference further teaches that similarities determined by homology search might only be restricted to certain domains of the uncharacterized protein, whereas the whole protein is required for the functionality of the protein (pg. 426, right column, first paragraph).
The Applicant does not describe the structural features of npr1 proteins and homologues and orthologues thereof from any plant with an undefined number of mutations to any part of the sequence, that form NPR1 condensates in the absence of salicylic acid, that confer the recited function of increasing stress tolerance in a plant when the recited proteins are expressed in any plant known in the art. Applicant does not describe the structure-function requirements relative to npr1 proteins and homologues and orthologues thereof from any plant species with an undefined number of mutations to any part of the sequence, that form NPR1 condensates in the absence of salicylic acid, that confer the recited function of increasing stress tolerance in any plant known in the art from npr1 proteins and homologues and orthologues thereof from any plant species with an undefined number of mutations to any part of the sequence that cannot form NPR1 condensates in the absence of salicylic acid when expressed in any plant species known in the art.
Additionally, Applicant does not describe salicylic acid-independent NPR1 condensates in such a way that one of ordinary skill in the art would be able to identify their formation in the nucleus or cytoplasm of a plant cell from any plant species known in the art. Applicant define salicylic acid-dependent condensates as “cytoplasmic organelle-like structures that contain NPR1 protein and Cullin 3 RING E3 ligase (CLR3) and are enriched in proteins that regulate death, redox metabolism, DNA damage response, and protein quality control machineries, including ubiquitination” (paragraph 0042); however, the salicylic acid-independent NPR1 condensates are only defined as “NPR1 condensates that are functionally similar to SINCs and form in the absence of salicylic acid” (paragraph 0043). Applicant only describes the salicylic acid-independent NPR1 condensates by function relative to SINCs, rather than describing the actual structural components that comprise the NPR1 condensates, so one of ordinary skill in the art would be able to differentiate cellular components that are NPR1 condensates from cellular components that are not NPR1 condensates. Even in the description of the structures that are denoted as SINCs, there is a broad genus of undefined proteins that regulate death, redox metabolism, DNA damage response, and protein quality control machineries, including ubiquitination that are considered to be NPR1 condensates formed in the presence of SA, but are not defined in a way that one of ordinary skill in the art would be able to distinguish them from proteins that regulate death, redox metabolism, DNA damage response, and protein quality control machineries, including ubiquitination that are not considered NPR1 condensates.
In the absence of a clear description of what comprises the salicylic acid-independent NPR1 condensates (i.e., what components or proteins are present in the cell of any plant species that expresses the mutated NPR1 protein), it is unclear how one of ordinary skill in the art would be able to identify if any nucleic acid encoding an npr1 protein or homologue or orthologue thereof from any species of plant actually forms salicylic acid-independent NPR1 condensates.
The state of the art regarding mutant NPR1 proteins teaches that mutations to the NPR1 gene are highly unpredictable when said mutant is expressed in a plant. Després et al. (2000) teaches that A. thaliana NPR1 mutants expressed in A. thaliana that lacked ankyrin-like repeats (mutation within amino acids 354-593) resulted in npr1 mutants that were unable to establish SAR and/or ISR, increasing the plants susceptibility to disease (Abstract). Després et al. (2000) does not describe any structural features that would differentiate npr1 genes that confer the recited function of increasing stress tolerance in a plant, or structural features that would differentiate npr1 genes that form NPR1 condensates in the absence of SA.
Cao et al. (1997) describes npr1-1, npr1-2, npr1-3, and npr1-4 mutant alleles that altered the highly conserved histidine (residue 334) in the third ankyrin-repeat consensus sequence to a tyrosine, changed a cysteine (residue 150) to a tyrosine, introduced a nonsense codon (residue 400) that should result in a truncated protein lacking 194 amino acids of the C-terminal end of the protein, and destroyed the acceptor site of the third intron junction, wherein all of the point mutations were GC-to-AT transitions (pg. ). The npr1 mutants described in Cao et al. (1997) resulted in plants that displayed little expression of pathogenesis-related (PR) genes and exhibiting increased susceptibility to infections (Abstract). Cao et al. (1997) does not describe any structural features that would differentiate npr1 genes that confer the recited function of increasing stress tolerance in a plant, or structural features that would differentiate npr1 genes that form NPR1 condensates in the absence of SA.
The prior art does not supplement the specification because the instant application appears to be the first disclosure of any nexus between mutant npr1 proteins and homologues and orthologue thereof and the formation of NPR1 condensates in the absence of salicylic acid.
As such, neither the specification nor the prior art describe the structural features that distinguish npr1 proteins and homologues and orthologues thereof from any plant species with an undefined number of mutations to any part of the sequence, that form NPR1 condensates in the absence of salicylic acid, that confer the recited function of increasing stress tolerance in a plant when the recited proteins are expressed in any plant known in the art from npr1 proteins and homologues and orthologues thereof from any plant species with an undefined number of mutations to any part of the sequence, that cannot form NPR1 condensates in the absence of salicylic acid.
One of ordinary skill in the art would not recognize that the Applicant was in possession of the necessary common attributes or features of the claimed genus in view of the disclosed species.
Hence, Applicant has not, in fact, adequately described the broad genus of nucleic acids encoding npr1 proteins and homologues or orthologues thereof from any plant species, with an undefined number of mutations to any part of the sequence, capable of forming NPR1 condensates in the absence of salicylic acid when expressed in any plant species.
Claim Rejections - 35 USC § 112
Scope of Enablement
Claims 1, 3-4, 6-7, 9-11, 13, 15, 17, 19-20, 22, 24, 27-29, 31-32, and 34 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a nucleic acid encoding a npr1 protein comprising the amino acid sequence of any of SEQ ID NOs: 134-160, wherein the npr1 protein form salicylic acid-independent NPR1 condensates and a method of increasing stress tolerance in an Arabidopsis thaliana plant comprising expressing in the plant the nucleic acid encoding any of SEQ ID NOs: 134-160, does not reasonably provide enablement for nucleic acids encoding npr1 proteins and homologues or orthologues thereof from any plant species, with an undefined number of mutations to any part of the sequence relative to SEQ ID NO: 1, wherein the npr1 protein forms NPR1 condensates in the absence of salicylic acid when expressed in any plant species. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make or use the invention commensurate in scope with these claims.
The claimed invention is not supported by an enabling disclosure taking into account the Wands factors. In re Wands, 858/F.2d 731, 8 USPQ2d 1400 (Fed. Cir. 1988). In re Wands lists a number of factors for determining whether or not undue experimentation would be required by one skilled in the art to make and/or use the invention. These factors are: the quantity of experimentation necessary, the amount of direction or guidance presented, the presence or absence of working examples of the invention, the nature of the invention, the state of the prior art, the relative skill of those in the art, the predictability or unpredictability of the art, and the breadth of the claim.
The claims are broadly directed to a nucleic acid encoding a NPR1 mutant protein (denoted as npr1), a plant expressing the npr1 mutant, and a method of increasing stress tolerance in a plant which expresses the npr1 mutant, all of which require a nucleic acid that encodes a npr1 protein (a NPR1 mutant), wherein npr1 proteins that are included in the scope of the claims appear to encompass all npr1 proteins known in the art or homologs thereof from any species of plant, with untold numbers of mutations to the protein, at any position in the protein, wherein the npr1 protein forms salicylic acid-independent NPR1 condensates.
Applicant teaches:
Nonmutated NPR1 from Arabidopsis thaliana that contains three redox-sensitive intrinsically disordered regions (RDR) located at amino acids 140-160, 368-404, and 510-539 relative to SEQ ID NO: 1 (paragraph 0052)
Methods of identifying homologs and/or orthologues of the A. thaliana NPR1 RDR2 (paragraph 0053)
Nonmutated orthologues of SEQ ID NO: 1 denoted as SEQ ID NOs: 2-12 and 30-34 (paragraph 0052)
Mutated nucleic acid sequences encoding NPR1 proteins denoted as SEQ ID NOs: 134-160 (paragraph 0066)
Mutations to A. thaliana NPR1 proteins performed in the instant invention and known in the art at the time of filing (paragraph 00153; Table 4)
Applicant does not teach:
-mutations at any position of any nucleic acid sequence encoding an NPR1 protein from any diverse source other than A. thaliana, that forms salicylic acid-independent NPR1 condensates.
-expression of npr1 from any diverse source known in the art, in any plant known in the art.
- expression of npr1 from any diverse source known in the art, in any plant known in the art, wherein the npr1 protein forms salicylic acid-independent NPR1 condensates.
- Mutated nucleic acids sequences encoding NPR1 proteins other than the sequences denoted as SEQ ID NOs: 134-160.
-whether all mutated nucleic acids sequences encoding NPR1 proteins denoted as SEQ ID NOs: 134-160 are able to form condensates in the nucleus or the cytoplasm in the absence of SA.
-whether all mutations to all NPR1 proteins known in the art, at any position in the sequence, result in the formation of NPR1 condensates in the absence of SA.
-mutated nucleic acids sequences encoding NPR1 proteins from sources other than A. thaliana that form salicylic acid-independent NPR1 condensates.
-mutated nucleic acids sequences encoding npr1 proteins from sources other than A. thaliana having one or more mutations in at least one redox-sensitive intrinsically disordered region (RDR), wherein the one or more mutations result in the npr1 protein forming salicylic acid-independent NPR1 condensates.
- mutated nucleic acids sequences encoding npr1 proteins from sources other than A. thaliana that are expressed in any plant known in the art, wherein the one or more mutations result in the npr1 protein forming salicylic acid-independent NPR1 condensates.
-the amino acid positions of any homologues and orthologues of A. thaliana NPR1 that align to SEQ ID NO: 1 and what those amino acid positions would be in the homologues and orthologues of A. thaliana NPR1 relative to SEQ ID NO: 1.
- whether mutations to A. thaliana NPR1 proteins known in the art at the time of filing resulted in the npr1 protein forming salicylic acid-independent NPR1 condensates.
The claims are directed to nucleic acids encoding npr1 proteins and homologues or orthologues thereof from any plant species capable of forming NPR1 condensates in the absence of salicylic acid when expressed in any plant, using any method known in the art to mutate any of the nucleic acids encoding any NPR1 protein from any diverse source and subsequently express said npr1 protein in any plant.
The structural features that distinguish npr1 proteins and homologues and orthologues thereof, that function to form NPR1 condensates in the absence of salicylic acid, when expressed in any plant known in the art are not taught in the specification, nor is any direction given to be able to find npr1 proteins and homologues and orthologues thereof in any plant species that function to form NPR1 condensates in the absence of salicylic acid due to the lack of disclosure regarding the structural features that cause NPR1 mutants (with an undefined number of mutations to any part of the sequence) from any plant known in the art to be able to form NPR1 condensates in the absence of salicylic acid.
The state of the art for inferring a structure function relationship based on sequence homology is highly unpredictable. The functional prediction of a protein based on structural comparison is not consistent with an empirical assessment of its function. For example, Doerks et al. (TIG, 14:248-250, 1998) teaches that sequence homology is not sufficient to determine functionality of an uncharacterized protein. The homologs that scored best in PSI-BLAST analysis failed to share same catalytic activity. The reference clearly emphasizes that computer analysis of genome sequences is flawed, and overpredictions are common because the highest scoring database protein does not necessarily share the same or even similar functions (pg. 248, first paragraph; page 248, right column, second paragraph). Also, Smith et al. (Nature Biotechnology, 15:1222-1223, 1997) teaches that there are numerous cases in which proteins of very different functions are homologous (pg. 1222, last paragraph). Also, Bork et al. (TIG, 12:425-427, 1996) teaches that homology search methods are stretched and spurious hits are taken as real. The reference further teaches that similarities determined by homology search might only be restricted to certain domains of the uncharacterized protein, whereas the whole protein is required for the functionality of the protein (pg. 426, right column, first paragraph).
The Applicant does not describe the structural features of npr1 proteins and homologues and orthologues thereof from any plant with an undefined number of mutations to any part of the sequence, that form NPR1 condensates in the absence of salicylic acid, that confer the recited function of increasing stress tolerance in a plant when the recited proteins are expressed in any plant known in the art. Applicant does not teach the structure-function requirements relative to npr1 proteins and homologues and orthologues thereof from any plant species with an undefined number of mutations to any part of the sequence, that form NPR1 condensates in the absence of salicylic acid, that confer the recited function of increasing stress tolerance in any plant known in the art from npr1 proteins and homologues and orthologues thereof from any plant species with an undefined number of mutations to any part of the sequence that cannot form NPR1 condensates in the absence of salicylic acid when expressed in any plant species known in the art. It would require undue experimentation to discover all npr1 proteins and homologues and orthologues thereof from any plant with an undefined number of mutations to any part of the sequence, and subsequently determine if all npr1 proteins and homologues and orthologues thereof from any plant with an undefined number of mutations to any part of the sequence form NPR1 condensates in the absence of salicylic acid, and confer the recited function of increasing stress tolerance in a plant when the recited proteins are expressed in any plant known in the art.
Additionally, Applicant does not teach salicylic acid-independent NPR1 condensates in such a way that one of ordinary skill in the art would be able to identify their formation in the nucleus or cytoplasm of a plant cell from any plant species known in the art. Applicant teaches that salicylic acid-dependent condensates are “cytoplasmic organelle-like structures that contain NPR1 protein and Cullin 3 RING E3 ligase (CLR3) and are enriched in proteins that regulate death, redox metabolism, DNA damage response, and protein quality control machineries, including ubiquitination” (paragraph 0042); however, the salicylic acid-independent NPR1 condensates are only taught to be “NPR1 condensates that are functionally similar to SINCs and form in the absence of salicylic acid” (paragraph 0043). Applicant only teaches the salicylic acid-independent NPR1 condensates by function relative to SINCs, rather than describing the actual structural components that comprise the NPR1 condensates, so one of ordinary skill in the art would be able to differentiate cellular components that are NPR1 condensates from cellular components that are not NPR1 condensates. Even the definition of the structures that are considered to be SINCs fails to provide adequate teachings regarding the scope of “undefined proteins that regulate death, redox metabolism, DNA damage response, and protein quality control machineries, including ubiquitination” encompassed by NPR1 condensates formed in the presence of SA. Applicant does not provide adequate guidance of the scope of NPR1 condensates formed in the presence of SA, so one of ordinary skill in the art would be able to distinguish them from proteins that regulate death, redox metabolism, DNA damage response, and protein quality control machineries, including ubiquitination that are not considered NPR1 condensates.
In the absence of a clear guidance of what comprises the salicylic acid-independent NPR1 condensates (i.e., what components or proteins are present in the cell of any plant species that expresses the mutated NPR1 protein), it would require undue experimentation by one of ordinary skill in the art to identify what cellular components and proteins are comprised within the scope of “NPR1 condensates”, and subsequently determine if all nucleic acids encoding npr1 proteins and homologues and orthologue thereof (with an undefined number of mutations to any part of the sequence) from any species of plant actually form NPR1 condensates, much less form NPR1 condensates in a salicylic acid-independent manner.
The state of the art regarding mutant NPR1 proteins teaches that mutations to the NPR1 gene are highly unpredictable when said mutant is expressed in a plant. Després et al. (2000) teaches that A. thaliana NPR1 mutants expressed in A. thaliana that lacked ankyrin-like repeats (mutation within amino acids 354-593) resulted in npr1 mutants that were unable to establish SAR and/or ISR, increasing the plants susceptibility to disease (Abstract). Després et al. (2000) does not teach any structural features that would differentiate npr1 genes that confer the recited function of increasing stress tolerance in a plant, or structural features that would differentiate npr1 genes that form NPR1 condensates in the absence of SA.
Cao et al. (1997) describes npr1-1, npr1-2, npr1-3, and npr1-4 mutant alleles that altered the highly conserved histidine (residue 334) in the third ankyrin-repeat consensus sequence to a tyrosine, changed a cysteine (residue 150) to a tyrosine, introduced a nonsense codon (residue 400) that should result in a truncated protein lacking 194 amino acids of the C-terminal end of the protein, and destroyed the acceptor site of the third intron junction, wherein all of the point mutations were GC-to-AT transitions (pg. ). The npr1 mutants described in Cao et al. (1997) resulted in plants that displayed little expression of pathogenesis-related (PR) genes and exhibiting increased susceptibility to infections (Abstract). Cao et al. (1997) does not teach any structural features that would differentiate npr1 genes that confer the recited function of increasing stress tolerance in a plant, or structural features that would differentiate npr1 genes that form NPR1 condensates in the absence of SA.
The prior art does not supplement the specification because the instant application appears to be the first disclosure of any nexus between mutant NPR1 proteins and homologues and orthologue thereof and the formation of NPR1 condensates in the absence of salicylic acid.
In the absence of adequate guidance, it would require undue experimentation to determine the structural features that distinguish npr1 proteins and homologues and orthologues thereof from any plant species with an undefined number of mutations to any part of the sequence, that form NPR1 condensates in the absence of salicylic acid, that confer the recited function of increasing stress tolerance in a plant when the recited proteins are expressed in any plant known in the art from npr1 proteins and homologues and orthologues thereof from any plant species with an undefined number of mutations to any part of the sequence, that cannot form NPR1 condensates in the absence of salicylic acid, as encompassed by the breadth and scope of the claims.
Given the breadth of the claims, unpredictability of the art and lack of guidance of the specification, as discussed above, undue experimentation would be required by one skilled in the art to make and use the claimed invention commensurate in scope with the claims.
Conclusion
No claims are allowed.
The claims appear to be free of the prior art, given that the prior art fails to teach any nexus between mutant NPR1 proteins (npr1) and homologues and orthologues thereof and the formation of NPR1 condensates in the absence of salicylic acid.
The closest prior art in regard to the claims can be found in Lai et al. (Proceedings of the National Academy of Sciences 115.22 (2018): E5203-E5212; IDS Document) which teaches Arabidopsis npr1-6 null mutant plants (Col-0; SAIL_708F09) which displayed enhanced resistance to chronic ER stress in the root growth and wherein the induction of unfolded protein response (UPR) genes in npr1 plants was significantly higher relative to Col-0 plants. However, Lai does not teach or suggest that the npr1-6 null mutant plants for salicylic acid-independent or insensitive NPR1 condensates, nor suggest or provide any rational to assay the Arabidopsis npr1-6 null mutant plants to determine the presence or absence of any condensates in the nucleus or cytoplasm of the plant cells after expression of the npr1-6 mutant protein in Arabidopsis in an environment that is absent of salicylic acid.
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/KELSEY L MCWILLIAMS/Examiner, Art Unit 1663
/CHARLES LOGSDON/Primary Examiner, Art Unit 1662