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 .
DETAILED ACTION
Election/Restrictions
1. Applicant's election with traverse of Group VII, claims 35, 36 (part), 37, 38 (part), and species “an ectodomain of an EPR3a polypeptide” and an ectodomain of an EPR3 polypeptide in the reply filed on September 23, 2023 is acknowledged.
The traversal is on the ground(s) that the special technical feature linking the pending claims is the use of an EPR3a polypeptide outside of its endogenous context. Applicant further argues that Ware, Wu et al. do not teach such special technical feature and thus fail to provide contribution over prior art (response, pages 9-11).
Applicant’s arguments are carefully considered but are deemed to be unpersuasive.
It is important to note that the instant application is a national stage entry of a PCT Application (PCT/EP2020/073164, filed 08/19/2020) and is subject to restriction requirement under 35 U.S.C. 121 and 372.
It is maintained that the inventions listed as Groups I-VII do not relate to a single general inventive concept under PCT Rule 13.1 because, under PCT Rule 13.2, they lack the same or corresponding special technical features.
It is maintained that the technical feature linking Groups I-VII is a EPR3a and/or modified EPR3 polypeptide and its role in providing a beneficial commensal microbe.
Contrary to Applicant’s arguments, it may be noted that the breadth and scope of recitations “EPR3a polypeptide”, “EPR3 polypeptide”, “EPR3a polypeptide moiety”, “modified EPR3 polypeptide”, “modified EPR3a polypeptide”, “an ectodomain of an EPR3a polypeptide and/or “an ectodomain of an EPR3 polypeptide” is so broad that it reads on any polypeptide from any source, including the one taught by WU et al. who disclose recombinant DNA constructs expressed in transgenic seeds, wherein SEQ ID NO: 183760 having 100% identity to instant SEQ ID NO: 4 (an EPR3 sequence) is expressed from said construct. The property of increased selectivity for a beneficial commensal would be inherent to said transgenic plants. See in particular, claims 1, 4, 9 and 11. More importantly, also see, Kawaharada et al. (Nat Commun 8, 14534 (2017). https://doi.org/10.1038/ncomms14534) who teach that Lotus japonicus LysM receptor kinase, and EPR3 promotes increased selectivity for a beneficial commensal microbe. See in particular abstract, figures 1-7. Likewise, Kawaharada et al. (Nature, 523(7560):308-312, 2015) teach overexpression of EPR3 protein from a recombinant construct in Nicotiana benthamiana leaves. The reference further teaches EPR3 function in Lotus japonicus in sensing bacterial exopolysaccharides. See in particular, abstract, page 314. As discussed in previous Office action, Ware (NCBI, GenBank Sequence Accession No. ONM41523.1, pages 1-2, Published February 6, 2017; see page 2) disclose recombinant DNA encoding a polypeptide having 100% identity to instant SEQ ID NO: 91 (EPR3a polypeptide as per instant specification). The property of increased selectivity for a beneficial commensal upon expression in a plant would be inherent to said Ware polypeptide, unless Applicant provides evidence to contrary. It may be noted that Applicant’s arguments are not in commensurate with the scope and breadth of the instantly claimed invention. Applicant’s attention is drawn to MPEP 2145 [R-08.2012] VI which says: “Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims”. See for example, In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993), Constant v. Advanced Micro-Devices, Inc., 848 F.2d 1560, 1571-72, 7 USPQ2d 1057, 1064-1065; Ex parte McCullough, 7 USPQ2d 1889, 1891 (Bd. Pat. App. & Inter. 1987).
It is therefore, maintained that the technical feature linking the inventions of Groups I-VII does not constitute a special technical feature as defined by PCT Rule 13.2, as it does not define a contribution over the prior art.
Applicant is also reminded that different nucleotide sequences and amino acid sequences are structurally distinct chemical compounds and are unrelated to one another. These sequences are thus deemed to normally constitute different inventive concepts.
Thus, claims 20-34 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected inventions, there being no allowable generic or linking claim. Species an
an M1 domain of an EPR3a polypeptide, an M2 domain of an EPR3a polypeptide, and a LysM3 domain of an EPR3a polypeptide (claim 36); and species an M1 domain of an EPR3 polypeptide, an M2 domain of an EPR3 polypeptide, and a LysM3 domain of an EPR3 polypeptide (claim 38) are also withdrawn as being drawn to a nonelected inventions. Applicant timely traversed the restriction (election) requirement in the reply filed on September 23, 2025.
Accordingly, claims 35-38 in conjunction with elected species (an ectodomains of EPR3a and EPR3 polypeptides) are examined on merits in the present Office action. This restriction is made FINAL.
Applicant is reminded that upon the cancellation of claims to a non-elected invention, the inventorship must be amended in compliance with 37 CFR 1.48(b) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. Any amendment of inventorship must be accompanied by a request under 37 CFR 1.48(b) and by the fee required under 37 CFR 1.17(i).
Information Disclosure Statement
2. Initialed and dated copies of Applicant’s IDS form 1449 filed 04/26/2022, 10/08/2024 and 09/23/2025 are attached to the instant Office action. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Specification
The disclosure is objected to because of the following informalities:
3. The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. For example, see specification at line 13 of paragraph [0121]; line 4 of paragraph [0123]; and line 2 of paragraph [0154].
Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code. See MPEP § 608.01.
Claim Objections
4. Claims 35-38 are objected to because of the following informalities:
Claims 35 and 36 are objected for not reciting full form of the recitation “EPR3a” in parenthesis.
Claims 37 and 38 are objected for not reciting full form of the recitation “EPR3” in parenthesis.
Claims 36 and 38 are objected for having non-elected subject matter.
In claim 35, the recitation “detecting binding of the microbe” in line 1 of part (c), implies that microbe binds to ectodomain of EPR3a which is not technically correct because it is the ligand produced by the microbe such as EPS that binds to the ectodomain of EPR3a or EPR3 polypeptide not the microbe itself. It appears that it is not Applicant’s intention that microbe should bind to the ectodomain of EPR3a or EPR3 polypeptide. Applicant’s clarification with appropriate claim amendments are requested. Failing to do so will invoke 112(b) rejection.
Appropriate action is required.
Claim Rejections - 35 USC § 112
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.
5. Claims 35-38 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 recently clarified the application of 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 a 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.
Finally, the court held:
A description of a genus of cDNAs may be achieved by means of a recitation of a representative number of cDNAs, defined by nucleotide sequence, falling within the scope of the genus or a recitation of structural features common to members of the genus, which features constitute a substantial portion of the genus. Id.
See also MPEP Section 2163, page 174 of Chapter 2100 of the August 2005 version, column 1, bottom paragraph, where it is taught that
[T]he claimed invention as a whole may not be adequately described where an invention is described solely in terms of a method of its making coupled with its function and there is no described or art-recognized correlation or relationship between the structure of the invention and its function. A biomolecule sequence described only by a functional characteristic, without any known or disclosed correlation between that function and the structure of the sequence, normally is not a sufficient identifying characteristic for written description purposes, even when accompanied by a method of obtaining the claimed sequence.
See also Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ 2d 1016 at 1021, (Fed. Cir. 1991) where it is taught that a gene is not reduced to practice until the inventor can define it by "its physical or chemical properties" (e.g. a DNA sequence).
Claims are broadly drawn to a method of identifying a beneficial commensal microbe capable of participating in a plant root microbiota comprising: (a) providing a first polypeptide comprising an EPR3a polypeptide moiety; (b) contacting the first polypeptide with a sample comprising a microbe or a molecule produced by the microbe selected from the group consisting of an EPS, a beta-glucan, a cyclic beta- glucan, a LPS, or a surface carbohydrate; (c) detecting binding of the microbe or the molecule produced by the microbe to the first polypeptide, wherein binding of the microbe or the molecule produced by the microbe to the first polypeptide indicates that the microbe is a beneficial commensal microbe capable of participating in the plant root microbiota; optionally wherein the detecting is by a functional assay, optionally selected from (i) detecting enrichment of taxa in Burkholderiales and/or Rhizobiales in a plant rhizosphere or endosphere, wherein enrichment of taxa in Burkholderiales and/or Rhizobiales in the plant rhizosphere or endosphere indicates that the microbe is a beneficial commensal microbe capable of participating in a plant root microbiota; (ii) detecting nodulation in a plant root system, wherein nodulation indicates that the microbe is a beneficial commensal microbe capable of participating in a plant root microbiota; and/or (iii) detecting mycorrhization in a plant root system, wherein mycorrhization indicates that the microbe is a beneficial commensal microbe capable of participating in a plant root microbiota, or optionally wherein the detecting is by a direct binding assay, optionally selected from (1) a competition assay optionally with a known signaling saccharide, or (2) an affinity assay optionally wherein the detected affinity is compared to the affinity for the known signaling saccharide; and optionally further comprising: (d) culturing the beneficial commensal microbe if binding is detected in step (c); and (e) applying the beneficial commensal microbe to the plant or a part thereof or applying the beneficial commensal microbe, optionally in admixture with a soil-compatible carrier, a fungal carrier, or a growth medium, optionally soil, to where the plant is growing or is to be grown or wherein the EPR3a polypeptide moiety is selected from the group consisting of an EPR3a polypeptide, and an ectodomain of an EPR3a polypeptide, or wherein the method further comprising providing a second polypeptide comprising an EPR3 moiety in step (a), wherein the second polypeptide is in contact with the first polypeptide, or wherein the EPR3 polypeptide moiety is selected from the group consisting of an EPR3 polypeptide and an ectodomain of an EPR3 polypeptide.
The essential feature of claim 35 is directed to an EPR3a polypeptide moiety having the function of identifying a beneficial commensal microbe.
The breadth of claim 35 and claims dependent thereon encompasses a very large genus comprising species having structures comprising any part of any EPR3a polypeptide of any size and with any amino acid sequence and derived from any source (e.g. plant, animals, lower eukaryotes etc.).
The breadth and scope of claims encompass a very large genus with unknown and/or undescribed structures and having the function of identifying any beneficial commensal microbe of this universe.
The essential feature of claim 37 is directed to an EPR3 polypeptide moiety having the function of identifying a beneficial commensal microbe.
The breadth of claim 37 encompasses a very large genus comprising species having structures comprising any part of any EPR3 polypeptide of any size and with any amino acid sequence and derived from any source (e.g. plant, animals, lower eukaryotes etc.).
The breadth and scope of claims encompass a very large genus with unknown and/or undescribed structures and having the function of identifying any beneficial commensal microbe of this universe.
The essential feature of claim 36 is directed to an ectodomain of an EPR3a polypeptide moiety having the function of identifying any beneficial commensal microbe.
The breadth of claim 36 encompasses a very large genus comprising species having structures comprising any ectodomain of any EPR3a polypeptide moiety of any size and with any amino acid sequence and derived from any source (e.g. plant, animals, lower eukaryotes etc.).
The breadth and scope of claims encompass a very large genus with unknown and/or undescribed structures and having the function of identifying any beneficial commensal microbe of this universe.
The essential feature of claim 38 is directed to an ectodomain of an EPR3 polypeptide moiety having the function of identifying any beneficial commensal microbe.
The breadth of claim 38 encompasses a very large genus comprising species having structures comprising any ectodomain of any EPR3 polypeptide moiety of any size and with any amino acid sequence and derived from any source (e.g. plant, animals, lower eukaryotes etc.).
The breadth and scope of claims encompass a very large genus with unknown and/or undescribed structures and having the function of identifying any beneficial commensal microbe of this universe.
Breadth of claims also encompass any microbe from this universe or any molecule produced by said microbe which are capable of interacting directly or with said molecule comprising any EPS, any beta-glucan, any cyclic beta-glucan, any LPS or any surface carbohydrates and having the function of inducing nodulation upon binding with any EPR3 and EPR3 ED as encompassed by the breadth and scope of claims.
The breadth and scope of claims encompass a very large genus with unknown and/or undescribed structures and having the function of identifying any beneficial commensal microbe of this universe.
The specification, however, only describes isolation of low molecular mass (LMM) exopolysaccharides (EPS) isolated and purified from rhizobial strains R. leguminosarum bv. viciae 3855 and Sinorhizobium meliloti. The specification also describes expression and purification of Lotus japonicus Exopolysaccharide Receptor 3 (EPR3) ectodomain. The specification further describes high binding affinity of said EPR3 ED (ectodomain) with said EPS. The specification further describes expression and purification of Lotus japonicus Exopolysaccharide Receptor 3a (EPR3a) ectodomain. The specification also describes high binding affinity of said EPR3a ED (ectodomain) with said EPS. The specification also describes plate nodulation assays by growing L. japonicus plants on agar with or without the addition of M. loti strain R7A, and the number of nodules per plant counted. See in particular, examples 1-6; Figures 1-34.
The specification does not describe (except prophetic guidance) expressing said EPR3 or EPR3 ED and/or EPR3a or EPR3a ED to induce nodulation and shaping soil microbiota diversity as encompassed by the breadth and scope of the instantly claimed method. The specification also does not describe (except prophetic guidance) induction of nodulation and shaping soil microbiota diversity by expressing transgenically said EPR3 or EPR3 ED and said EPR3a or EPR3a ED in a plant as encompassed by the breadth and scope of the instantly claimed method.
The specification does not describe the structure for a representative members of a genus comprising EPR3a and EPR3a ED from diverse sources (bacteria to mammals as encompassed by the breadth of claims) and thus their function of identifying any beneficial commensal microbe of this universe is unknown.
The specification does not describe the structure for a representative members of a genus comprising EPR3 and EPR3 ED from diverse sources (bacteria to mammals as encompassed by the breadth of claims) and thus their function of identifying any beneficial commensal microbe of this universe is unknown.
The specification does not describe the structure for a representative members of a genus comprising any microbe or microbes producing any EPS, any beta-glucan, any cyclic beta-glucan, any LPS or any surface carbohydrates and having the function of inducing nodulation upon binding with any EPR3 and EPR3 ED as encompassed by the breadth and scope of claims.
Applicant fails to describe representative structures of Applicant’s broadly claimed genus and thus instantly claimed function is either unknown or unpredictable.
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. See for example, Doerks et al., (TIG, 14:248-250, 1998) who teach 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 over predictions are common because the highest scoring database protein does not necessarily share the same or even similar functions. See example 30, tables 10A-10B at pages 143-144 of the specification.
Also, see Smith et al. (Nature Biotechnology, 15:1222-1223, 1997) who teach that there are numerous cases in which proteins of very different functions are homologous. See in particular, page 1222, last paragraph.
Also, see Bork et al. (TIG, 12:425-427, 1996) who teach 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. See page 426, right column, 1st paragraph.
State of the art related to LysM Receptor-like kinases suggests that members of LysM Receptor-like kinase gene family are involved in diverse functions. See for example, Buendia et al. (Frontiers in Plant Science, 9:1-24, 2018), who describe that members of this gene family is involved in defense responses against pathogens. See in particular, abstract; Figures 4-7. Also see Buist et al. (Molecular Microbiology, 68:838-847, 2008) who teach diverse function of LysM motif binding to glycans among diverse organisms, such as bacteria, animals, including plants. See in particular, abstract, Figures 1-3, Table 1 and Table S1.
Thus one of skilled in the art would not expect all EPR3, EPR3a and Ectodomains thereof proteins result in instantly claimed function. The specification does not teach which EPR3, EPR3a and Ectodomains thereof would confer instantly claimed function and which would not.
There is no description of the structure required for the recited function, and no description of the necessary and sufficient elements of a functional EPR3a/EPR3a ED and EPR3/EPR3 ED from any source as encompassed by the breadth and scope of claims and further described above.
There is no description of the structure required for the recited function, and no description of the necessary and sufficient elements of a functional microbe or microbes producing any EPS, any beta-glucan, any cyclic beta-glucan, any LPS or any surface carbohydrates from any microbial source and having the function of inducing nodulation upon binding with any EPR3 and EPR3 ED as encompassed by the breadth and scope of claims and further described above.
Applicant’s broadly claimed genus encompasses structures whose function is unrelated to different elements as encompassed by the breadth and scope of instantly claimed method. The specification fails to describe the function of identifying any beneficial commensal microbe of this universe is unknown.
The only species described in the specification is EPR3a/EPR3a ED and EPR3/EPR3 ED from L. japonicus plants and exopolysaccharides (EPS) from few rhizobial strains as discussed above.
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 disclosed species. Since the disclosure fails to describe the common attributes that identify members of the genus, and because the genus is highly divergent and species described above are insufficient to describe the claimed genus.
Therefore, given the lack of written description in the specification with regard to the structural and functional characteristics of the claimed compositions, it is not clear that Applicant was in possession of the claimed genus at the time this application was filed.
Accordingly, there is lack of adequate description to inform a skilled artisan that applicant was in possession of the claimed invention at the time of filing. See Written Description guidelines published in Federal Register/Vol.66, No. 4/Friday, January 5, 2001/Notices; p. 1099-1111.
6. Claims 35-38 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.
Neither the instant specification nor the originally filed claims appear to provide support for the phrase “moiety”. The instant specification, provides support for EPR3a and EPR3 polypeptides and specific domains therein as recited in claims 36 and 38, respectively. However, the specification fails to provide support for the full scope of instantly claimed phrase “EPR3a polypeptide moiety” and “EPR3 polypeptide moiety”. The recitation “moiety” reads on any amino acid segment of any size and function of an EPR3a polypeptide moiety” and “EPR3 polypeptide moiety”. Thus, such a phrase constitutes NEW MATTER. Applicant is required to point to support for the phrase “EPR3a polypeptide moiety” and “EPR3 polypeptide moiety” or to cancel the new matter.
7. Claims 35-38 are rejected under 35 U.S.C. 112, first paragraph, because the specification, while being enabling for identifying a beneficial commensal microbe from the rhizobium species capable of participating in a nodule forming leguminous plant root microbiota comprising transforming said nodule forming leguminous plant with a construct comprising a first nucleic acid sequence encoding an exopolysaccharide receptor (EPR3a) kinase polypeptide as set forth in SEQ ID NO: 62 from said nodule forming leguminous plant or an ectodomain thereof operably linked to its kinase domain from said nodule forming leguminous plant and/or transforming said nodule forming leguminous plant with a construct comprising a root-specific promoter operably linked to a second nucleic acid sequence encoding an exopolysaccharide receptor (EPR3) kinase polypeptide as set forth in SEQ ID NO: 1 from said nodule forming leguminous plant or an ectodomain thereof operably linked with its kinase domain from said nodule forming leguminous plant, wherein overexpression of said EPR3a and EPR3 kinase polypeptides or said ectodomains thereof, respectively results in the identification of a beneficial commensal microbe from the rhizobium species capable of participating in a nodule forming leguminous plant root microbiota by binding of EPS, beta-glucan, a cyclic beta glucan or LPS molecules produced by said rhizobium species, does not reasonably provide enablement for (a) any EPR3a and EPR3 polypeptide and ectodomains thereof from any source; (b) any microbe or a molecule produced from any such microbe including any surface carbohydrate; and (c) providing and increasing expression of in a plant said EPR3a and EPR3 kinase polypeptides or said ectodomains thereof having its kinase domains by a method other than transforming said plant with said nucleic acids. 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 and/or use the invention commensurate in scope with these claims.
Claims are broadly drawn to a method of identifying a beneficial commensal microbe capable of participating in a plant root microbiota comprising: (a) providing a first polypeptide comprising an EPR3a polypeptide moiety; (b) contacting the first polypeptide with a sample comprising a microbe or a molecule produced by the microbe selected from the group consisting of an EPS, a beta-glucan, a cyclic beta- glucan, a LPS, or a surface carbohydrate; (c) detecting binding of the microbe or the molecule produced by the microbe to the first polypeptide, wherein binding of the microbe or the molecule produced by the microbe to the first polypeptide indicates that the microbe is a beneficial commensal microbe capable of participating in the plant root microbiota; optionally wherein the detecting is by a functional assay, optionally selected from (i) detecting enrichment of taxa in Burkholderiales and/or Rhizobiales in a plant rhizosphere or endosphere, wherein enrichment of taxa in Burkholderiales and/or Rhizobiales in the plant rhizosphere or endosphere indicates that the microbe is a beneficial commensal microbe capable of participating in a plant root microbiota; (ii) detecting nodulation in a plant root system, wherein nodulation indicates that the microbe is a beneficial commensal microbe capable of participating in a plant root microbiota; and/or (iii) detecting mycorrhization in a plant root system, wherein mycorrhization indicates that the microbe is a beneficial commensal microbe capable of participating in a plant root microbiota, or optionally wherein the detecting is by a direct binding assay, optionally selected from (1) a competition assay optionally with a known signaling saccharide, or (2) an affinity assay optionally wherein the detected affinity is compared to the affinity for the known signaling saccharide; and optionally further comprising: (d) culturing the beneficial commensal microbe if binding is detected in step (c); and (e) applying the beneficial commensal microbe to the plant or a part thereof or applying the beneficial commensal microbe, optionally in admixture with a soil-compatible carrier, a fungal carrier, or a growth medium, optionally soil, to where the plant is growing or is to be grown or wherein the EPR3a polypeptide moiety is selected from the group consisting of an EPR3a polypeptide, and an ectodomain of an EPR3a polypeptide, or wherein the method further comprising providing a second polypeptide comprising an EPR3 moiety in step (a), wherein the second polypeptide is in contact with the first polypeptide, or wherein the EPR3 polypeptide moiety is selected from the group consisting of an EPR3 polypeptide and an ectodomain of an EPR3 polypeptide.
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.
Claim 35 is directed to an EPR3a polypeptide moiety having the function of identifying a beneficial commensal microbe.
The breadth of claim 35 and claims dependent thereon encompasses any part of any EPR3a polypeptide of any size and with any amino acid sequence and derived from any source (e.g. plant, animals, lower eukaryotes etc.).
Claim 37 is directed to an EPR3 polypeptide moiety having the function of identifying a beneficial commensal microbe.
The breadth of claim 37 encompasses any part of any EPR3 polypeptide of any size and with any amino acid sequence and derived from any source (e.g. plant, animals, lower eukaryotes etc.).
Claim 36 is directed to an ectodomain of an EPR3a polypeptide moiety having the function of identifying a beneficial commensal microbe having the function of identifying a beneficial commensal microbe.
The breadth of claim 36 encompasses any ectodomain of any EPR3a polypeptide moiety of any size and with any amino acid sequence and derived from any source (e.g. plant, animals, lower eukaryotes etc.).
Claim 38 is directed to an ectodomain of an EPR3 polypeptide moiety having the function of identifying a beneficial commensal microbe having the function of identifying a beneficial commensal microbe.
The breadth of claim 38 encompasses any ectodomain of any EPR3 polypeptide moiety of any size and with any amino acid sequence and derived from any source (e.g. plant, animals, lower eukaryotes etc.).
The specification, however, only provides guidance on isolation of low molecular mass (LMM) exopolysaccharides (EPS) were isolated and purified from rhizobial strains R. leguminosarum bv. viciae 3855 and Sinorhizobium meliloti. The specification also provides guidance on expression and purification of Lotus japonicus Exopolysaccharide Receptor 3 (EPR3) ectodomain. The specification further provides guidance on high binding affinity of said EPR3 ED (ectodomain) with said EPS. The specification further provides guidance on expression and purification of Lotus japonicus Exopolysaccharide Receptor 3a (EPR3a) ectodomain. The specification also provides guidance on high binding affinity of said EPR3a ED (ectodomain) with said EPS. The specification also provides guidance on plate nodulation assays by growing L. japonicus plants on agar with or without the addition of M. loti strain R7A, and the number of nodules per plant was counted. See in particular, examples 1-6; Figures 1-34.
The specification provides prophetic guidance on expressing said EPR3 or EPR3 ED and/or EPR3a or EPR3a ED to induce nodulation and shaping soil microbiota diversity. The specification also provides prophetic guidance on induction of nodulation and shaping soil microbiota diversity by expressing transgenically said EPR3 or EPR3 ED and EPR3a or EPR3a ED in a plant. See paragraphs [0096] – [0111).
The instant specification fails to provide guidance on how to make nucleic acid sequences encoding homologues, orthologues or paralogues of EPR3a, EPR3 and ectodomains thereof as encompassed by the breadth and scope of claims from any source and having the functional activity of identifying a beneficial commensal microbe when introduced and expressed in a transgenic plant environment.
The specification at paragraph [0110] of published Application says:
“Nucleic acids and proteins of the present invention can also encompass homologues of the specifically disclosed sequences. Homology (e.g., sequence identity) can be 50%-100%. In some instances, such homology is greater than 80%, greater than 85%, greater than 90%, or greater than 95%. The degree of homology or identity needed for any intended use of the sequence(s) is readily identified by one of skill in the art. As used herein 132 WO 2021/032769 PCT/EP2020/073164 percent sequence identity of two nucleic acids is determined using an algorithm known in the art, such as that disclosed by Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 87:2264- 2268, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877. Such an algorithm is incorporated into the BLASTN, BLASTP, and BLASTX, programs of Altschul et al. (1990) J. Mol. Biol. 215:402-410. BLAST nucleotide searches are performed with the BLASTN program, score=100, wordlength=12, to obtain nucleotide sequences with the desired percent sequence identity. To obtain gapped alignments for comparison purposes, Gapped BLAST is used as described in Altschul et al. (1997) Nucl. Acids. Res. 25:3389- 3402. When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs (BLASTN and BLASTX) are used. See www.ncbi.nih.gov. One of skill in the art can readily determine in a sequence of interest where a position corresponding to amino acid or nucleic acid in a reference sequence occurs by aligning the sequence of interest with the reference sequence using the suitable BLAST program with the default settings (e.g., for BLASTP: Gap opening penalty: 11, Gap extension penalty: 1, Expectation value: 10, Word size: 3, Max scores: 25, Max alignments: 15, and Matrix: blosumé62; and for BLASTN: Gap opening penalty: 5, Gap extension penalty:2, Nucleic match: 1, Nucleic mismatch -3, Expectation value: 10, Word size: 11, Max scores: 25, and Max alignments: 15).”
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. See for example, Doerks et al., (TIG, 14:248-250, 1998) who teach 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. See in particular, page 248, 1st paragraph; page 248, right column, 2nd paragraph.
Also see Smith et al. (Nature Biotechnology, 15:1222-1223, 1997) who teach that there are numerous cases in which proteins of very different functions are homologous. See in particular, page 1222, last paragraph.
Also see Bork et al. (TIG, 12:425-427, 1996) who teach 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. See page 426, right column, 1st paragraph.
Thus, in the absence of guidance, analyzing a plant cell or plant with instantly claimed function of identifying a beneficial commensal microbe comprising any nucleic acid sequence encoding any biologically active EPR3a or ectodomain thereof and biologically active EPR3 or ectodomain thereof would require undue experimentation.
The specification does not provide guidance in the specification with respect to making amino acid changes in a functional active EPR3a or ectodomain thereof and biologically active EPR3 or ectodomain.
Thus, from the guidance in the specification, it would appear that the vast majority of
the amino acids in a fully-functional active EPR3a or ectodomain thereof and biologically active EPR3 or ectodomain protein could be changed with any other amino acid.
The instant specification fails to provide guidance for which amino acids of active EPR3a or ectodomain thereof and biologically active EPR3 or ectodomain can be altered and to which other amino acids, and which amino acids must not be changed, to maintain biological activity of the encoded protein. The specification also fails to provide guidance for which amino acids can be deleted and which regions of the protein can tolerate insertions and still produce a functional polypeptide.
Making amino acid changes in fully functional protein is unpredictable. While it is known that many amino acid substitutions, additions or deletions are generally possible in any given protein the positions within the protein's sequence where such amino acid changes can be made with a reasonable expectation of success (without altering protein function) are limited. Certain positions in the sequence are critical to the protein's structure/function relationship, e.g. such as various sites or regions directly involved in binding, activity and in providing the correct three-dimensional spatial orientation of binding and active sites. These regions can tolerate only relatively conservative substitutions or no substitutions (see for example, Wells, Biochemistry 29:8509-8517, 1990, see pages 8511-8512, tables 1-2; Ngo et al., The Protein Folding Problem and Tertiary Structure Prediction, K. Merz., and S. Le Grand (eds.) pp. 492-495,1994; see page 491, 1st paragraph).
Furthermore, Keskin et al. (Protein Science, 13:1043-1055, 2004, see page 1043, abstract) teach that proteins with similar structure may have different functions. Furthermore, Thornton et al. (Nature structural Biology, structural genomics supplement, November 2000, page 992, 2nd paragraph bridging columns 1 and 2) teach that structural data may carry information about the biochemical function of the protein. Its biological role in the cell or organism is much more complex and actual experimentation is needed to elucidate actual biological function under in vivo conditions. Thus, making and analyzing proteins with large number of amino acid changes that also have the biological activity of increasing seed yield or plant growth would require undue experimentation.
The instant specification also fails to provide guidance on how to make nucleic acid sequences encoding variants, homologues, paralogues, or orthologues of a fully functional active EPR3a or ectodomain thereof and biologically active EPR3 or ectodomain as encompassed by the breadth and scope of claims, and having the property of identifying a beneficial commensal microbe when overexpressed in a transgenic plant environment.
State of the art related to LysM Receptor-like kinases suggests that members of LysM Receptor-like kinase gene family are involved in diverse functions. See for example, Buendia et al. (Frontiers in Plant Science, 9:1-24, 2018), who teach that members of this gene family is involved in defense responses against pathogens. See for example abstract; Figures 4-7. Also see Buist et al. (Molecular Microbiology, 68:838-847, 2008) who teach diverse function of LysM motif binding to glycans among diverse organisms, such as bacteria, animals, including plants. See in particular, abstract, Figures 1-3, Table 1 and Table S1.
Thus one of skilled in the art would not expect all EPR3, EPR3a and Ectodomains thereof proteins result in instantly claimed function. The specification does not teach which EPR3, EPR3a and Ectodomains thereof would confer instantly claimed function and which would not.
In the absence of guidance, undue experimentation would have been required by a skilled artisan at the time the claimed invention was made to isolate other EPR3, EPR3a and Ectodomains thereof from diverse sources and use them in a method of obtaining instantly claimed function.
Given the claim breath, unpredictability, and lack of guidance as discussed above, undue experimentation would have been required by one skilled in the art to develop and evaluate any and all EPR3, EPR3a and Ectodomains thereof to obtain instantly claimed function
In the absence of guidance, undue trial and error experimentation would be required to screen through the myriad of nucleic acids encompassed by the claims and plants transformed therewith, to identify those with instantly claimed function when expressed in a plant, if such plants are even obtainable. See Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016 at page 1027, where it is taught that the disclosure of a few gene sequences did not enable claims broadly drawn to any analog thereof.
Claim 35 and claims dependent thereof are directed to identifying a beneficial commensal microbe by contacting EPR3, EPR3a and Ectodomains thereof. The instant specification, however, only provides prophetic guidance on expressing said EPR3 or EPR3 ED and/or EPR3a or EPR3a ED to induce nodulation and shaping soil microbiota diversity. The specification also provides prophetic guidance on induction of nodulation and shaping soil microbiota diversity by expressing transgenically said EPR3 or EPR3 ED and EPR3a or EPR3a ED in a plant. See paragraphs [0096] – [0111).
The specification fails to provide guidance on a method of identifying a beneficial commensal microbe in any manner other than transforming a plant with a nucleic acid sequence encoding said EPR3 or EPR3 ED and/or EPR3a or EPR3a ED. The specification does not provide guidance on co-factors, or positive regulators of said EPR3 or EPR3 ED and/or EPR3a or EPR3a ED, for example that makes the said EPR3 or EPR3 ED and/or EPR3a or EPR3a ED gene to overexpress to produce a plant with said characteristics. The specification provides no guidance on up-stream regulatory factors, for example, that may be necessary in stimulating the overexpression endogenous said EPR3 or EPR3 ED and/or EPR3a or EPR3a ED, and thereby increase the activity of endogenous said EPR3 or EPR3 ED and/or EPR3a or EPR3a ED.
In the absence of guidance, undue experimentation would have been required to identifying a beneficial commensal microbe by increasing expression of endogenous EPR3 or EPR3 ED and/or EPR3a or EPR3a ED gene as encompassed by the breadth of the claims.
Breadth of claims also encompass any microbe from this universe or any molecule produced by said microbe which are capable of interacting directly or with said molecule comprising any EPS, any beta-glucan, any cyclic beta-glucan, any LPS or any surface carbohydrates and having the function of inducing nodulation upon binding with any EPR3 and EPR3 ED as encompassed by the breadth and scope of claims.
The specification, however, only provides guidance on isolation of low molecular mass (LMM) exopolysaccharides (EPS) were isolated and purified from rhizobial strains R. leguminosarum bv. viciae 3855 and Sinorhizobium meliloti. The specification also provides guidance on expression and purification of Lotus japonicus Exopolysaccharide Receptor 3 (EPR3) ectodomain. The specification further provides guidance on high binding affinity of said EPR3 ED (ectodomain) with said EPS. The specification further provides guidance on expression and purification of Lotus japonicus Exopolysaccharide Receptor 3a (EPR3a) ectodomain. The specification also provides guidance on high binding affinity of said EPR3a ED (ectodomain) with said EPS. The specification also provides guidance on plate nodulation assays by growing L. japonicus plants on agar with or without the addition of M. loti strain R7A, and the number of nodules per plant was counted. See in particular, examples 1-6; Figures 1-34.
The specification does not provide guidance on contacting or any microbe by itself or any EPS, beta-glucan, any cyclic beta-glucan, any LPS or any surface carbohydrates produced by any microbe which are capable of binding to any EPR3a, EPR3a ED, EPR3 and EPR3 ED and thus help in identifying a beneficial commensal microbe capable of participating in a plant root microbiota.
In the absence of guidance, it would require undue experimentation without undue experimentation, to make and use any microbe by itself or any EPS, beta-glucan, any cyclic beta-glucan, any LPS or any surface carbohydrates produced by any microbe which are capable of binding to any EPR3a, EPR3a ED, EPR3 and EPR3 ED and thus help in identifying a beneficial commensal microbe capable of participating in a plant root microbiota.
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.
Claim Rejections - 35 USC § 102
(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.
8. Claim(s) 35, 37 and 38 are rejected under 35 U.S.C. 102 (a)(1) as being anticipated by Kawaharada et al. (Nature, 523:308-312, 2015 with supplementary data).
Kawaharada et al. disclose a method of identifying a beneficial commensal microbe capable of participating in plant root microbiota by describing Lotus japonicus EPR3 function in sensing bacterial (rhizobium sp.) exopolysaccharides (EPS). The reference clearly disclose that legume-rhizobium symbiosis, bacterial exopolysaccharides (EPS) are essential for the infected root nodules (beneficial commensal microbe). The reference further discloses method steps of isolation, purification and binding with subsequent detection of said EPR3 or EPR3-ED (ectodomain) thereof directly to said EPS using appropriate assays, such as mass spectrometry analysis. The reference further discloses that plant-bacterial compatibility and bacterial access to legume roots is regulated by sequential receptor-mediated recognition of Nod factor and EPS signal. The data provided in the reference clearly indicates (i) EPS serves as a signal perceived by EPR3 receptor or EPR3 ED thereof.; and (ii) method steps of contacting, binding and detection of said EPS with said EPR3 receptor or EPR3 ED thereof clearly indicates identification of a bacterial strain like rhizobium species having symbiotic relationship with leguminous plant through the formation of nodules in the roots to fix Nitrogen for the plant and provides space and nutrients for said bacteria to survive. Additionally, the reference discloses transformation of Nicotiana benthamiana leaves with an EPR3 overexpression construct to demonstrate EPR3 protein was localized in plasma membrane. Furthermore, phenotypic characterization suggested said EPR3 monitoring of said EPS, and control of bacterial (rhizobium sp.) passage through the root epidermis. This was shown through transgenic expression of a Gus reporter protein using EPR3 promoter. See in particular, abstract, figures 1-6, methods, pages 308-812, also see supplementary information for methods, extended data under Figures 1-8 and Tables 1-2.
Accordingly, Kawaharada et al. anticipated the claimed invention.
This rejection is made because the recitation “moiety” in claim 35 is so broad as it reads on any Exopolysaccharide receptor (ERP) protein kinase and its domains including EPR3 and EPR3 ED disclosed by Kawaharada et al.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
9. Claim(s) 35-38 are rejected under 35 U.S.C. 103 as being unpatentable over Kawaharada et al. (Nature, 523:308-312, 2015 with supplementary data) and further in view of (UniProtKB/TrEMBL database accession number V7C918, pages 1-3, published 2014 and also published as Schmutz et al. (Nat. Genet. 46:707-713, 2014).
Kawaharada et al. teach a method of identifying a beneficial commensal microbe capable of participating in plant root microbiota by describing Lotus japonicus EPR3 function in sensing bacterial (rhizobium sp.) exopolysaccharides (EPS). The reference clearly teaches that legume-rhizobium symbiosis, bacterial exopolysaccharides (EPS) are essential for the infected root nodules (beneficial commensal microbe). The reference further teaches method steps of isolation, purification and binding with subsequent detection of said EPR3 or EPR3-ED (ectodomain) thereof directly to said EPS using appropriate assays, such as mass spectrometry analysis. The reference further teaches that plant-bacterial compatibility and bacterial access to legume roots is regulated by sequential receptor-mediated recognition of Nod factor and EPS signal. The data provided in the reference clearly indicates (i) EPS serves as a signal perceived by EPR3 receptor or EPR3 ED thereof.; (ii) method steps of contacting, binding and detection of said EPS with said EPR3 receptor or EPR3 ED thereof clearly indicates identification of a bacterial strain like rhizobium species having symbiotic relationship with leguminous plant through the formation of nodules in the roots to fix Nitrogen for the plant and provides space and nutrients for said bacteria to survive. Additionally, the reference teaches transformation of Nicotiana benthamiana leaves with an EPR3 overexpression construct to demonstrate EPR3 protein was localized in plasma membrane. Furthermore, phenotypic characterization suggested said EPR3 monitoring of said EPS, and control of bacterial (rhizobium sp.) passage through the root epidermis. This was shown through transgenic expression of a Gus reporter protein using EPR3 promoter. See in particular, abstract, figures 1-6, methods, pages 308-812, also see supplementary information for methods, extended data under Figures 1-8 and Tables 1-2.
Kawaharada et al. do not teach EPR3a.
UniProtKB/TrEMBL database accession number V7C918, pages 1-3, published 2014 and also published as Schmutz et al. (Nat. Genet. 46:707-713, 2014) teach a CERK1/LYK3-like protein from nodule forming legume bean (Phaseolus vulgaris)plant having 100% identity instant EPR3a amino acid sequence as set forth in instant SEQ ID NO: 85. The homology results are shown as below:
V7C918_PHAVU
ID V7C918_PHAVU Unreviewed; 615 AA.
AC V7C918;
DT 19-FEB-2014, integrated into UniProtKB/TrEMBL.
DT 19-FEB-2014, sequence version 1.
DT 18-JUN-2025, entry version 51.
DE RecName: Full=Protein kinase domain-containing protein {ECO:0008006|Google:ProtNLM};
GN ORFNames=PHAVU_003G063700g {ECO:0000313|EMBL:ESW25765.1};
OS Phaseolus vulgaris (Kidney bean) (French bean).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade;
OC NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Phaseolus.
OX NCBI_TaxID=3885 {ECO:0000313|EMBL:ESW25765.1, ECO:0000313|Proteomes:UP000000226};
RN [1] {ECO:0000313|Proteomes:UP000000226}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. G19833 {ECO:0000313|Proteomes:UP000000226};
RX PubMed=24908249; DOI=10.1038/ng.3008;
RA Schmutz J., McClean P.E., Mamidi S., Wu G.A., Cannon S.B., Grimwood J.,
RA Jenkins J., Shu S., Song Q., Chavarro C., Torres-Torres M., Geffroy V.,
RA Moghaddam S.M., Gao D., Abernathy B., Barry K., Blair M., Brick M.A.,
RA Chovatia M., Gepts P., Goodstein D.M., Gonzales M., Hellsten U.,
RA Hyten D.L., Jia G., Kelly J.D., Kudrna D., Lee R., Richard M.M.,
RA Miklas P.N., Osorno J.M., Rodrigues J., Thareau V., Urrea C.A., Wang M.,
RA Yu Y., Zhang M., Wing R.A., Cregan P.B., Rokhsar D.S., Jackson S.A.;
RT "A reference genome for common bean and genome-wide analysis of dual
RT domestications.";
RL Nat. Genet. 46:707-713(2014).
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000256|ARBA:ARBA00004162};
CC Single-pass membrane protein {ECO:0000256|ARBA:ARBA00004162}.
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DR EMBL; CM002290; ESW25765.1; -; Genomic_DNA.
DR RefSeq; XP_007153771.1; XM_007153709.1.
DR AlphaFoldDB; V7C918; -.
DR SMR; V7C918; -.
DR STRING; 3885.V7C918; -.
DR EnsemblPlants; ESW25765; ESW25765; PHAVU_003G063700g.
DR Gramene; ESW25765; ESW25765; PHAVU_003G063700g.
DR eggNOG; ENOG502QQIN; Eukaryota.
DR OMA; EFIDVGW; -.
DR OrthoDB; 4062651at2759; -.
DR Proteomes; UP000000226; Chromosome 3.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0019199; F:transmembrane receptor protein kinase activity; IEA:InterPro.
DR GO; GO:0045087; P:innate immune response; IEA:InterPro.
DR CDD; cd00118; LysM; 1.
DR FunFam; 1.10.510.10:FF:000468; PTI1-like tyrosine-protein kinase 3; 1.
DR Gene3D; 3.10.350.10; LysM domain; 1.
DR Gene3D; 3.30.200.20; Phosphorylase Kinase, domain 1; 1.
DR Gene3D; 1.10.510.10; Transferase(Phosphotransferase) domain 1; 1.
DR InterPro; IPR044812; CERK1/LYK3-like.
DR InterPro; IPR011009; Kinase-like_dom_sf.
DR InterPro; IPR018392; LysM_dom.
DR InterPro; IPR036779; LysM_dom_sf.
DR InterPro; IPR000719; Prot_kinase_dom.
DR InterPro; IPR017441; Protein_kinase_ATP_BS.
DR InterPro; IPR008271; Ser/Thr_kinase_AS.
DR PANTHER; PTHR46204; CHITIN ELICITOR RECEPTOR KINASE 1-RELATED; 1.
DR PANTHER; PTHR46204:SF8; PROTEIN KINASE DOMAIN-CONTAINING PROTEIN; 1.
DR Pfam; PF01476; LysM; 1.
DR Pfam; PF00069; Pkinase; 1.
DR SMART; SM00257; LysM; 1.
DR SMART; SM00220; S_TKc; 1.
DR SUPFAM; SSF54106; LysM domain; 1.
DR SUPFAM; SSF56112; Protein kinase-like (PK-like); 1.
DR PROSITE; PS51782; LYSM; 1.
DR PROSITE; PS00107; PROTEIN_KINASE_ATP; 1.
DR PROSITE; PS50011; PROTEIN_KINASE_DOM; 1.
DR PROSITE; PS00108; PROTEIN_KINASE_ST; 1.
PE 4: Predicted;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|PROSITE-
KW ProRule:PRU10141}; Disulfide bond {ECO:0000256|ARBA:ARBA00023157};
KW Kinase {ECO:0000256|ARBA:ARBA00022777};
KW Membrane {ECO:0000256|ARBA:ARBA00023136, ECO:0000256|SAM:Phobius};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|PROSITE-
KW ProRule:PRU10141}; Reference proteome {ECO:0000313|Proteomes:UP000000226};
KW Signal {ECO:0000256|ARBA:ARBA00022729, ECO:0000256|SAM:SignalP};
KW Transferase {ECO:0000256|ARBA:ARBA00022679};
KW Transmembrane {ECO:0000256|ARBA:ARBA00022692, ECO:0000256|SAM:Phobius};
KW Transmembrane helix {ECO:0000256|ARBA:ARBA00022989,
KW ECO:0000256|SAM:Phobius}.
FT SIGNAL 1..23
FT /evidence="ECO:0000256|SAM:SignalP"
FT CHAIN 24..615
FT /note="Protein kinase domain-containing protein"
FT /evidence="ECO:0000256|SAM:SignalP"
FT /id="PRO_5004757499"
FT TRANSMEM 224..248
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT DOMAIN 156..202
FT /note="LysM"
FT /evidence="ECO:0000259|PROSITE:PS51782"
FT DOMAIN 311..592
FT /note="Protein kinase"
FT /evidence="ECO:0000259|PROSITE:PS50011"
FT BINDING 339
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU10141"
SQ SEQUENCE 615 AA; 68862 MW; 88013D677312423B CRC64;
Query Match 100.0%; Score 3175; Length 615;
Best Local Similarity 100.0%;
Matches 615; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MASFTPLLAFVFPLLTTFPTVFAFEVSIKATNLSPLYCSAKITTCNASLYHTSHNLTIHQ 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MASFTPLLAFVFPLLTTFPTVFAFEVSIKATNLSPLYCSAKITTCNASLYHTSHNLTIHQ 60
Qy 61 ISSFYSVTSSHITPIKHGTKQDYLLRVPCSCKHTSDLSGYFYDTTYKVRPHDTFSNISNL 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 ISSFYSVTSSHITPIKHGTKQDYLLRVPCSCKHTSDLSGYFYDTTYKVRPHDTFSNISNL 120
Qy 121 VFSGQAWPVNGTLHPDENLAIHIPCGCSESDSQIVVTYTVQPNDTPTLIANLLNASLADM 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 VFSGQAWPVNGTLHPDENLAIHIPCGCSESDSQIVVTYTVQPNDTPTLIANLLNASLADM 180
Qy 181 LSMNKILDPNFKFIDVGWVLFVPKGSKGLLPSTAAGNEEKKLKWATTIIGILAGVTFLSV 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 LSMNKILDPNFKFIDVGWVLFVPKGSKGLLPSTAAGNEEKKLKWATTIIGILAGVTFLSV 240
Qy 241 ITTIILIVRVNKENQKNSEDSRLISRRSIANRTISSKYNFQKEYIEDVVSLESERPIAYN 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 ITTIILIVRVNKENQKNSEDSRLISRRSIANRTISSKYNFQKEYIEDVVSLESERPIAYN 300
Qy 301 LEVIEEATNNFDESRRIGSGGYGTVYYGVLGNKEVAVKKMRSNKSKEFYAELKVLCKIHH 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 LEVIEEATNNFDESRRIGSGGYGTVYYGVLGNKEVAVKKMRSNKSKEFYAELKVLCKIHH 360
Qy 361 INIVELLGYANGEDDLYLVYEYVPNGSLSDHLHDPLLKGNQPLSWSVRVQIALDAAKGLE 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 INIVELLGYANGEDDLYLVYEYVPNGSLSDHLHDPLLKGNQPLSWSVRVQIALDAAKGLE 420
Qy 421 YIHDYTKARYVHRDIKSSNILLNDKFRAKVGDFGLAKLVDRTDDENFIATRLVGTPGYLP 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 YIHDYTKARYVHRDIKSSNILLNDKFRAKVGDFGLAKLVDRTDDENFIATRLVGTPGYLP 480
Qy 481 PESLKELQVTPKTDVFAFGVVLSELLTGKRALFRESQEEIKMKSLISVVNKIFQDDDPEI 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 PESLKELQVTPKTDVFAFGVVLSELLTGKRALFRESQEEIKMKSLISVVNKIFQDDDPEI 540
Qy 541 ALEDAIDKNLEASYRMEDVYKMAEIAEWCLQEDPIERPEMRDIIGALSQIVMSSTEWEAS 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 ALEDAIDKNLEASYRMEDVYKMAEIAEWCLQEDPIERPEMRDIIGALSQIVMSSTEWEAS 600
Qy 601 LCGNSQVFSGLYSGR 615
|||||||||||||||
Db 601 LCGNSQVFSGLYSGR 615
Kawaharada et al. teach a method for identifying beneficial commensal microbes that associate with plant root microbiota. Specifically, they teach how Lotus japonicus employs the receptor EPR3 to sense rhizobial exopolysaccharides (EPS), with EPR3 or its ectodomain (EPR3-ED) directly binding to EPS.
It would have been obvious to a person of ordinary skill in the art, prior to the earliest filing date of the present application, to substitute the EPR3 or EPR3-ED of Kawaharada et al. with an EPR3-like protein from another root-nodule–forming legume, such as the bean plant. This is taught by UniProtKB/TrEMBL database accession number V7C918 (published 2014) and by Schmutz et al., which discloses a protein having 100% amino acid sequence identity with SEQ ID NO: 85 of the present application (an EPR3a protein).
It would also have been a matter of routine design choice to incorporate such EPR3 and/or EPR3a proteins, and/or their ectodomains, into the method of Kawaharada et al. and to screen them for identifying beneficial commensal microbes capable of participating in plant root microbiota. A person of ordinary skill would have had a reasonable expectation of success in doing so, and no evidence of unexpected results has been provided.
It is further important to note that KSR forecloses the argument that a specific teaching, suggestion or motivation is required to support a finding of obviousness. See the recent Board decision Ex parte Smith, -- USPQ2d --, slip op. at 20, (Bd. Pat. App. & Interf. June 25, 2007) (citing KSR, 82 USPQ2d at 1396)
Accordingly, the claimed invention as a whole is prima facie obvious in view of the combined teachings of the prior art.
Conclusions
10. Claims 35-38 are rejected.
Contact Information
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/VINOD KUMAR/ Primary Examiner, Art Unit 1663