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 .
Claim Status
Claims 1-2, 4-17 & 19-35 are under examination on the merits.
Priority
Claims 1-2, 4-17 & 19-35 receive the U.S. effective filing date of 29 August 2023.
Previous rejection of claims 1-16 under 35 U.S.C. 112(b) is withdrawn in light of Applicant’s amendment to the claims.
Previous rejection of claims 15 & 16 under 35 U.S.C. 101 is withdrawn in light of Applicant’s amendment to the claims.
Previous rejection of claims 1-14 under 35 U.S.C. 102(a)(1) as being anticipated by Wu is withdrawn in light of Applicant’s amendment to the claims.
Claim Rejections - 35 USC § 112
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 1-2 & 4-16 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.
This rejection is newly made in view of Applicant’s claim amendments submitted 14 July 2026. Claim 1 has been amended to recite that the proteins encompassed are now limited to those possessing a ‘subtilase activity’.
Original claims covered endogenous genes which would be expected to have conserved endogenous function. Amended claims now recite recombinant gene(s) drawn to subtilases. The action of such polypeptides would be unknown in a non-native host (i.e. what is ‘subtilase activity’ in non-native hosts). Dependent claims 2 & 4-16 include this limitation in referencing subtilase function(s).
Claims are indefinite because it is unclear what constitutes ‘subtilase activity’ in a protein, or if Applicant means to imply ‘subtilase activity’ is synonymous with nitrogen fixation. The specific characteristics of ‘subtilase activity’ or protein function are not indicated in claim 1, and referring to the written description Applicant does not directly define such ‘subtilase activity’.
Rather, Applicant’s written description only indicates subtilases are a broad category of proteins found in all kingdoms of life, with broad functional roles not limited to nitrogen fixation (i.e. there are highly varied ‘subtilase activities’) [par.42]. Applicant states various subtilase activities include symbiosis, disease resistance, stress response, embryogenesis, organogenesis, senescence, and cell death [id]. ‘Subtilase activity’ could be interpreted to mean protein activity in any one or more of these diverse physiological functions, including functions not related to nitrogen fixation or the subject matter of the instant application. This description is essentially uninformative as to what activity or function is being limited in claim 1 via the amended language, absent other functional limitations.
Broadest reasonable interpretation of this claim due to the newly introduced language would now potentially include proteins with functions completely unrelated to nitrogen fixation or Applicant’s claimed invention. Lacking a specific definition of ‘subtilase activity’ and presented with numerous functional possibilities, one reading the claims would not be able to ascertain the metes and bounds of Applicant’s invention or how to avoid infringing. Because of this, claims 1-2 & 4-16 are rejected as indefinite.
Applicant is advised to amend claims and recite the specific, defined function of the protein(s) in claim 1.
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 1-2, 4-15 & 19-35 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 claims contain 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.
Due to Applicant’s amendment of the claims, this rejection is modified from that set forth in the Office action mailed 26 March 2026 as applied to claims 1-35. Applicant’s arguments 14 July 2026 have been considered but are not persuasive.
Claims 1 & 15 require a Mt12a protein with at least 80% identity to SEQ ID NO.5; thus, the claim is broad and reads on numerous unspecified polynucleotides. Dependent claims 2, 4-14 & 16 also include this limitation.
Proteins with 80% identity to the 771-residue long SEQ ID NO.5 encompass polypeptides with approximately 154 random amino acid substitutions to the primary structure of the protein of SEQ ID NO.5. Describing a genus of polypeptides with all possible single amino acid substitutions relative to the 771-amino-acids-long polypeptide of SEQ ID NO:5 would require describing 15420 polypeptide sequences; most of which were not in Applicant's possession at the time of filing. It is reasonable to consider that such wide breadth of structurally variable proteins have variable functions.
Further, the claim is drawn to a genus of molecules of as little as 80% sequence identity that hybridize to SEQ ID NO.5 under non-specified stringency conditions [claim 1(c)]; thus, the claim is broad and reads on virtually any protein.
The only species described in the specification is SEQ ID NO.3, which encodes the Mt12a protein of SEQ ID NO.5. This naturally occurring Mt12a gene encodes a subtilase which influences symbiosis with nitrogen-fixing microbes, but the specific functional domains or structural characteristics of the protein responsible for this activity are not defined.
Subtilases are a class of proteolytic enzymes with highly varied physiological effects in plants [Schaller et al. Physiologia Plantarum 145: 52–66. 2012 2011, p.52, ‘Abstract’; Published 21 Nov 2011]. Applicant indicates the specific Mt12a protein is newly described, and sequence search returns only a corresponding 95.6% genomic DNA match on chromosome 7 of Medicago [TIGR, Medicago genome, accession: AC148994; Published 1 Jan 2013] and a nearest similar sequences (54% identity) associated with root nodulation/symbiosis in soybean [Indigo Ag Inc., WO2016200987-A1, claim 19, SEQ ID NO.1999; Published 15 Dec 2016].
Sequence search of the protein SEQ ID NO.5 returns matches for Medicago protease inhibitor (100% identity) [Yang et al. Nat. Genet. 54:1553-1563(2022), Ref Seq XP_003624104.2] and subtilisin-like protease (82.3% identity) [Young et al. Nature 480:520-524(2011), ID A0A9D4Y1F6_PEA] from sequences submitted to Uniprot.
No protein motifs encoded by SEQ ID NO.5 are described in the specification and structural characterization of Mt12a is limited to identifying it as part of the broad class of subtilases. Applicant describes use of Mt12a mutants and phenotypic assessments of plants but does not indicate which features of the Mt12a protein are necessary for correct function or activity [p.59-p.62, Examples 1-8]. Applicant describes native Mt12a protein and disrupted, loss-of-function mutant sequences caused by transposon insertion but does not describe what polypeptide features identify or are causative for the specific activity of Mt12a which distinguish it from the incredibly broad class of ‘subtilases’.
The specification does not describe sufficient structural elements of this protein regarding its ability to increase nitrogen fixation or improve symbiosis with nitrogen fixing microbes, emphasizing relevant “molecular mechanisms remain elusive” [Specification, par.38]. As such, the specification fails to make up for the lack of knowledge on the art and what necessary structural elements would confer the claimed function to generic subtilase proteins with as little as 80% identity to SEQ ID NO.5.
Research reports describe that subtilases share several structures identifying them as a distinct type of protease within plants identifiable via a ‘subtilisin domain’ a ‘protease-associated domain’ [Schaller, p.60, col.1, par.2 & col.2, par.2]. However, these shared domains used to generically identify subtilases does not indicate which specific one of the many different physiological processes a given subtilase is involved in, of which their role in nitrogen fixation appears to be only one of many. Prior art emphasizes the relatively uncharacterized state of subtilases and states that additional biological roles and novel functions are waiting to be discovered for these enzymes [Schaller, p.61, col.1, par.3 – col.2, par.1].
The structural features that distinguish native Mt12a enzymes from other encoded proteins with 80% identity to SEQ ID NO.5 are not described in the specification in such a manner as to allow a reader to reasonably identify a protein that was not only a subtilase per se, but that also would predictably retain any particular ‘subtilase function’ due to their highly-varied roles in physiological processes. One of skill in the art would not recognize that Applicant was in possession of the necessary common attributes or features of their broadly claimed genus of more than 5.62e43 molecular variants in view of the limited disclosed species, Applicant having fully described only three species/sequences.
Hence, Applicant has not, in fact, described the nucleic acids that encode Mt12a variants over the full scope of the claims, and the specification fails to provide adequate written description of the claimed invention. Therefore, given the lack of written description in the specification with regard to the structural and functional characteristics of the claimed compositions, Applicant does not appear to have been in possession of the claimed genus at the time this application was filed.
Claim 17 requires a nucleic acid fragment of the Mt12a promoter with at least 80% identity to SEQ ID NO.4. Dependent claims 19-35 therefore also include this limitation.
Claim 17 is drawn to a genus of nucleic acids encoding the Mt12a protein promoter, reciting polynucleotides with as little as 80% sequence identity to SEQ ID NO.4; thus, the claim is broad and reads on numerous unspecified polynucleotides. Nucleic acids with 80% identity to the 2,000bp long SEQ ID NO.4 would have 400 nucleotide substitutions relative to SEQ ID NO.4. This would reasonably alter the structure & function of such a promoter region, depending on the arrangement of such substituted nucleotides. Sequences with only 80% identity to SEQ ID NO.4 would encompass a broad genus of potential promoter molecules.
The only species described in the specification is SEQ ID NO.4, which is the natural promoter of the Mt12a protein of SEQ ID NO.5. This naturally occurring Mt12a promoter drives production of Mt12a as identified by Applicant, but the specific functional domains or structural characteristics responsible for its efficacy in expression of the Mt12a subtilase are not defined.
The research literature describes that while having certain conserved features (i.e. TATA boxes), plant promoters are structurally diverse. A review of this in the context of synthetic promoter design is provided by Yasmeen et al. [Plant Comm., 2023-07, Vol.4 (4); Published 10 July 2013, p.2, col.1, par.3 ‘Promoter Architecture in Plants’]. Diverse and variable arrangement exists for critical structural components of promoters such as cis elements [Yasmeen et al., p.2, col.2, par.2]. Understanding the structure of such regions in native promoters is important to achieving their functional effects. This is because there is a direct relationship between promoter structure and function. Thus, the specific structural features required of a promoter that regulates Mt12a in response to microbial infection are critical information.
Further sequence search for corresponding structural features from other reports returns only a corresponding 95.6% genomic DNA match on chromosome 7 of Medicago [TIGR, Medicago genome, accession: AC148994] and a nearest similar sequences (54% identity) associated with root nodulation/symbiosis in soybean [See Indigo Ag Inc., WO2016200987-A1, claim 19, SEQ ID NO.1999]. Moreover, the regulation of the gene encoding Mt12a relies on signals from the external environment during microbial infection, as described in Applicant’s expression assays [Specification, p.61, par.171]. Review of the literature surrounding subtilases and their promoters indicates the required structural features of such a newly described promoters involved in subtilase activation during the symbiotic infection process are as yet uncharacterized.
No specific structural motifs or necessary promoter elements encoded by SEQ ID NO.4 are described in the specification and structural characterization of the region is limited to describing its use in expressing Mt12a as part of the broad class of subtilases. The specification does not describe sufficient structural elements of this promoter critical to its ability to facilitate expression of subtilases in response to stimuli from rhizobia or any other nitrogen fixing microbes. As such, the specification fails to make up for the lack of knowledge on the art and what necessary structural elements would confer the claimed function to the promoters encoded by sequences with as little as 80% identity to SEQ ID NO.4.
The structural features that distinguish the effective Mt12a promoter with 80% identity to SEQ ID NO.4 from other potentially ineffective promoters with 80% identity to SEQ ID NO.4 are not described in the specification. One of skill in the art would not recognize that Applicant was in possession of the necessary common attributes or features of the broad genus in view of the limited disclosed species.
Hence, Applicant has not, in fact, fully described the nucleic acids required of the Mt12a promoter over the full scope of the claims, and the specification fails to provide adequate written description of the claimed invention. Therefore, given the lack of written description in the specification with regard to the structural and functional characteristics of the claimed compositions, Applicant does not appear to have been in possession of the broadly claimed genus at the time this application was filed.
Applicant is advised to amend claims to recite only sequences which are reasonably described in the Specification.
Response to Arguments
Applicant urges that rejection under U.S.C. 112(a) for lack of possession is improper because they provide both structural context and functional characterization of the claimed proteins and promoter sequences.
With respect to claimed proteins, Applicant argues that comparative sequence matches to generic 'subtilases' in other legumes and/or sequence-based identification of orthologs provides requisite structural context to predictably determine protein function (i.e. nitrogen fixation attributes). [p.10, par.2; p.10, par.4-p.11, par.1] Applicant further argues that detailed functional characterization has been provided in that the Mt12a via phenotypic description of two loss-of-function mutants unable to fix nitrogen. [p.9, par.4 & p.10, par.3].
With respect to claimed promoter sequences, Applicant argues requisite structural information is provided by the Mt12a promoter sequence and description of fragments thereof [p.11, par.4; p.12, par.1]. Applicant further argues that functional characterization of promoter activity is provided by generation of constructs utilizing the promoter and assessment in reporting assays [p.11, par.4—p.12, par.2].
Regarding claimed proteins; it is unconvincing that the ability to match a sequence of 80% identity with the disclosed sequence of Mt12a combined with the two non-functional mutant sequences provides reasonable description to predict a gain-of-function in nitrogen fixation from a genus encompassing more than 5.62e43 proteins. Applicant argues that narrowing to such molecules retaining 'subtilase function' would facilitate such protein identification by way of inclusion of this functional limitation. However, one skilled in the art would recognize that three sequences, none of which identify specific critical functional domains imparting nitrogen-fixing qualities would identify subtilases broadly but not predictably indicate those conferring nitrogen-fixing qualities to plants.
Further, arguments that requiring ‘subtilase function’ would be informative of identifying structural features is not persuasive as subtilase functions are incredibly diverse and appear to include variable protein structures or domains, many of which may have little or no relation to nitrogen fixation or the subject matter of the instant application. See new 112b rejection above, p.3.
Regarding claimed promoter sequences; it is again unconvincing that description of a single native promoter sequence and its validation provides sufficient description of variants having as little as 80% sequence identity. Applicant points to description of fragments or chimeric forms of the promoter listed in their specification [Remarks, p.12, par.1; Specification par.139-141], however, the indicated sections merely state that fragments of the promoter sequence provided may be used [par.139] and then provide definitions for the terms ‘chimeric’ and ‘variant’ [par.140-141].
None of the referenced sections indicate any fragment or sequence of less than 100% sequence identity to SEQ ID NO.4 was tested for promoter activity or function [par.178-181, Examples 6-8]. Further, the newly amended claim now requires claimed sequences to have promoter activity. No sequences of less than 100% similarity to SEQ ID NO.4 have been described, tested, or validated as having predictable promoter activity [id]. For this reason, arguments are not persuasive and the previous rejection of claims 17 & 19-35 is maintained.
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.
Claims 1-2 & 4-14 are rejected under 35 U.S.C. 103 as being unpatentable over Taylor [Molecular Plant-Microbe Interactions 2017 30:6, 489-501. Pub. 8 May 2017], in view of Istvanek [Front Plant Sci 8, 367 (2017); Published 22 March 2017], and Wu [US-9029636-B2; Published 12 May 2015].
This rejection is newly made in view of Applicant’s claim amendments submitted 14 July 2026. Claim 1 has been amended to recite proteins encompassed are now limited to those possessing a ‘subtilase activity’. Dependent claims 2 & 4-16 include this limitation in referencing subtilase function(s) in the context of non-native hosts.
Taylor teaches that subtilases are important in the formation of root nodules [p.489, col.2, ¶.2—p.491, col.2, ¶1 & Table 1]. They teach that subtilases are important to restructuring cellular surfaces during plant/microbe interactions and thus are critical to symbiotic nodule formation in the plant host [id].
Taylor teaches that subtilases are critical proteins for plants to form mutualistic associations with soil microbes and formation of root nodules in legumes.
Taylor does not teach sequences identifying subtilases, or the use of such sequences in exogenous DNA constructs or as applied in creating transgenic plants.
Istvanek teaches sequences and molecular markers useful in the breeding of nitrogen-fixing legumes, specifically in red clover [p.2, col.2, ¶.3—p.3, col.1, ¶.2; p.5, col.1, ¶.5—p.7, col.1, ¶.2]. They teach that there are conserved molecular features and relationships among genes and proteins among red clover, barrel medic, and soybean [p.3, col.1, ¶.2]. They teach a sequence of 81.87% identity to Applicant’s claimed SEQ ID NO.5, and which is a subtilase (i.e. having ‘subtilase activity’ in native hosts) [p.14, Supplementary Material, locus PNY17185]. This is Accession KAK236188.1 by NCBI BLAST comparison to Applicant’s SEQ ID NO.5:
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Istvanek teaches the identification of the claimed sequence which is a subtilase in a nitrogen-fixing legume crop (i.e. red clover) and its use in cross-application of such to other legumes including Medicago truncatula and Glycine max.
Wu teaches the use sequences from soybean associated with enhanced agronomic traits and their use in recombinant DNA molecules [col.1, l.39-67]. They describe these in soybean, which is a nitrogen fixing crop that is in contact with soil rhizobia in the field. They teach sequences of structural similarity, as one of their sequences used to enhance agronomic traits is 71% identical to Applicant's claimed SEQ ID NO.3 [Wu, SEQ ID NO.175391], which encodes the subtilase of SEQ ID NO.5 claimed in the instant Application.
Wu describes the use of such genes and proteins which are structurally similar to Applicant’s in a recombinant DNA construct with a promoter (i.e. heterologous promoter), operably linked to the DNA molecule of SEQ ID NO.5 [col.2, 1.63 - col.3, 1.3]. They describe recombinant DNA constructs with non-natural promoters, including non-plant promoters, that can be used with a target sequence such as SEQ ID NO.5 [col.9, l.43—col.10, l.45; col.15, l.36—col.16, l.62]. This is described in a corn plant, and seeds of such plants, having a stably integrated, recombinant DNA construct (i.e. plants have undergone transformation), as recited in Applicant's claim 11 [id].
Wu's sequence is a fragment of a subtilase protein as claimed by Applicant, because the sequence of Wu partially matches (i.e. is a fragment thereof) of SEQ ID NO.5 which Applicant defines as a subtilase protein.
Wu teaches that genes and/or proteins identified as subtilases in nitrogen-fixing legumes (i.e. soybean) based on molecular structure can be used to make transgenic constructs and transfer said genes to other plants (i.e. maize).
Before the effective filing date of the claimed invention, it would have been obvious to one of ordinary skill to target subtilases which are involved in nitrogen-fixing symbiosis as described by Taylor, with the corresponding structural/sequences from nitrogen-fixing legumes as described by Istvanek for the purpose of genetically engineering or transferring such a beneficial trait to non-leguminous plants, as described by Wu.
One would be motivated to do so because the ability to induce nodulation and nitrogen-fixation qualities in non-leguminous plants would reduce the need for application of exogenous nitrogen fertilizers, which is widely recognized as both a production constraint limiting crop yields as well as a major global source of pollution and environmental degradation due to nitrate contamination. One would be motivated to genetically engineer components or entire biosynthetic pathways associated with such beneficial nitrogen-fixing genes and proteins into non-leguminous plants as a potential solution to this long recognized but as yet unresolved problem in global food production.
Regarding claims 1-2 & 14; they recite limitations of a recombinant DNA molecule comprising a heterologous promoter linked to sequence encoding a subtilase or fragment thereof with at least 80% identity to SEQ ID NO.5, and which has improved nitrogen fixation. These are met by Istvanek who teaches a subtilase sequence of >80% identity to SEQ ID NO.5 [p.14, Supplementary Material, locus PNY17185], Taylor who describes nodulation and nitrogen fixation as a subtilase activity when plants come into contact with nitrogen-fixing microbes such as Rhizobium spp. [p.489, col.2, ¶.2—p.491, col.2, ¶1 & Table 1; p.495, col.1, ¶.4—col.2, ¶.1], and Wu who describes use of transgenic constructs of related subtilase sequences (i.e. structures) to transfer agronomically beneficial traits from legumes to non-legume plants and plant cells via use of artificial vectors [col.2, 1.63 - col.3, 1.3].
Regarding claims 4-6; they recite additional limitations of the transgenic cell(s) in which such constructs are expressed as bacterial host cells chosen from Agrobacterium or Escerichia coli. These are met by Wu who describes methods of preparing similar transgenic constructs using both Agrobacterium or E. coli cells, which are routinely used in the art to create and screen plasmids [col.12, l.40-63; see incorporated references].
Regarding claims 7-11; they recite additional limitations of transgenic plants or plant cells being a monocot, such as corn. These are met by Wu who describes similar transgenic constructs to transfer agronomically beneficial genes applied to the monocot grass maize (i.e. corn) [col.9, l.43—col.10, l.45; col.15, l.36—col.16, l.62].
Regarding claims 12-13; they recite additional limitations of a seed or progeny seed harvested from transgenic plants. These are met by Wu who describes transgenic plants producing seeds and the recovery of transgenic progeny (i.e. harvested progeny seed) from such plants [col.15, l.36—col.16, l.51].
Because of these reasons, claims 1-2 & 4-14 of the instant Application would have been obvious to one of ordinary skill at the time of filing, and thus are rejected.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KEITH R WILLIAMS whose telephone number is (571)272-3911. The examiner can normally be reached Mon - Fri, 9:30 - 5:30 EST.
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/KEITH R. WILLIAMS/Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663
