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 1-35 are under examination on the merits.
Priority
Claims 1-35 receive the U.S. effective filing date of 29 August 2023.
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 1-16 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.
Claim 1 recites a protein that ‘comprises the amino acid sequence of SEQ ID NO.3, an amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, or about 100% sequence identity to SEQ ID NO.3, and hybridizes under stringent conditions to a polynucleotide having the nucleotide sequence of SEQ ID NO.3’, and claim 15 recites a ‘subtilase protein or fragment or variant thereof as set forth in SEQ ID NO.3 or at least 70% identical to SEQ ID NO.3’. Similarly, claim 15 recites that SEQ ID NO.3 is a protein.
However, SEQ ID NO.3 lists a polynucleotide sequence (i.e. DNA), not a polypeptide sequence (i.e. protein). Therefore, claims 1 & 15, as well as their dependent claims 2-14 & 16, are rendered indefinite.
For purposes of examination, the claims will be treated as though they were reciting SEQ ID NO.5, the protein encoded by SEQ ID NO.3. Such treatment does not relive Applicant of the responsibility to respond to this rejection.
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 1-35 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. Claims are being interpreted as though they were reciting SEQ ID NO.5, the protein encoded by SEQ ID NO.3. (See p.3, par.2-3 above).
Claims 1 & 15 require a Mt12a protein with at least 70% identity to SEQ ID NO.5; thus, the claim is broad and reads on numerous unspecified polynucleotides. Dependent claims 2-14 & 16 therefore also include this limitation.
Proteins with 70% identity to the 771-residue long SEQ ID NO.5 encompass polypeptides with approximately 231 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 23120 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 would have correspondingly variable functionality.
Further, the claim is drawn to a genus of molecules of as little as 70% 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 functionally is shown to influence symbiosis with nitrogen-fixing microbes, but the specific functional domains or structural characteristics responsible for this in protein Mt12a 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 describing it as part of the broad class of subtilases. The specification does not include 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/or what necessary structural elements would confer the claimed function to proteins with as little as 70% identity to SEQ ID NO.5.
Prior art describes subtilases share several structures identifying them as a distinct type of protease within plants identifiable via ‘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 with from other encoded proteins with 70% identity to SEQ ID NO.5 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 genus in view of the limited disclosed species.
Hence, Applicant has not, in fact, described the nucleic acids that encode Mt12a 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 encoding the Mt12a promoter with at least 70% identity to SEQ ID NO.4. Dependent claims 18-35 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 70% sequence identity to SEQ ID NO.4; thus, the claim is broad and reads on numerous unspecified polynucleotides. Nucleic acids with 70% identity to the 2,000bp long SEQ ID NO.4 would have 667 nucleotide substitutions relative to SEQ ID NO.4. This would reasonably alter the structure & function such a promoter region, depending on the arrangement of such substituted nucleotides. Sequences with only 70% sequence 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 effective 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.
Prior art demonstrates 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 appears to indicate 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 regarding 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/or what necessary structural elements would confer the claimed function to the promoters encoded by sequences with as little as 70% identity to SEQ ID NO.4.
The structural features that distinguish the effective Mt12a promoter with 70% identity to SEQ ID NO.4 from other potential promoters with 70% 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 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 claimed genus at the time this application was filed.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 15 & 16 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon without significantly more. The claims recite methods of increasing symbiotic nitrogen fixation in a plant via expression of the subtilase protein encoded by SEQ ID NO:3. This judicial exception is not integrated into a practical application because the subtiliase protein claimed is a naturally occurring protein, encoded by a naturally occurring gene in Medicago. Claims are being interpreted as though they are reciting SEQ ID NO.5, the protein encoded by SEQ ID NO.3. (See p.3, par.2-3 above).
The protein encoded by SEQ ID NO:3 is naturally occurring in Medicago. Sequence search of this sequence encoding the specific Mt12a protein returns a corresponding 95.6% genomic DNA match on chromosome 7 of Medicago [TIGR, Medicago genome, accession: AC148994]. Further, in Applicant’s specification they identify and confirm the function of Mt12a via use of common mutant stocks obtained from the public Medicago truncatula mutant database, based on their identification of the gene from expression studies of naturally occurring, extant (i.e. wild-type) germplasm [Specification, p.59, par.164; p.60, par.167;p.61, par. 171].
Medicago plants naturally express nodulation-associated genes or encoded proteins when forming (i.e. increasing) associations with symbiotic nitrogen fixing microbes [Xu et al. 2023, p.R552, col.2, par.2 – p.R553, col.1, par.1]. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because they merely recite this natural relationship as a ‘method’. Such symbiotic relationships exist in nature, and such ‘methods’ are naturally performed by plants as they modulate expression of such subtilases in response to developmental or environmental queues, as characterized by Applicant in their own experiments comparing wild-type plants to those lacking native, functional Mt12a alleles [par.164, 168; Example 1 & 2].
Because no additional inventive steps are included beyond the description of this naturally occurring phenomenon, claims 15 & 16 do not rise to the level of an inventive practical application and are therefore rejected.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-14 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Wu [US-9029636-B2; Published 12 May 2015].
Claim 1 recites a protein with at least 70% sequence identity to the protein of SEQ ID NO.5 and its expression in a plant via a recombinant DNA molecule. This protein, or a fragment thereof, is encoded by SEQ ID NO.3.
Sequence search of SEQ ID NO.3 reveals the prior publication of Wu describing 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. One of their sequences is 71% identical to Applicant’s claimed SEQ ID NO.3 [Wu, SEQ ID NO.175391].
Use of Wu’s nucleotide sequence would encompass transgenic production of a protein that is at least 70% identical to Applicant’s SEQ ID NO.5. Wu describes its use 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, l.63 – col.3, l.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.10, l.45 – col.11, l.45]. 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.
Because the disclosed plant(s) are transformed with a construct encoding a protein with at least 70% identity to SEQ ID NO.3, which improves symbiotic nitrogen fixation, the resulting plant therefore would have the quality of ‘improved symbiotic nitrogen fixation’ as a result of the transgene.
Thus, prior art discloses a protein at least 70% identity to SEQ ID NO.5 as in claim 1 and dependent claims 2-14.
As such, claims 1-14 are anticipated by Wu and therefore rejected.
Conclusion
No claims are allowed.
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
/Anne Kubelik/Primary Examiner, Art Unit 1663