DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Priority
Acknowledgment is made of applicant’s claim for benefit under 35 U.S.C. 119(e).
Election/Restrictions
Applicant’s election without traverse of the invention of Group 1 in the reply filed on 02/19/2026 is acknowledged.
Status of the Claims
Claims 1-4, 6-8, 15-16, 18-21, 23-30 are pending.
Claims 23-24 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 02/19/2026.
Claims 3 and 7 are withdrawn as being directed toa non-elected species (the required polypeptides exclude the elected species of SEQ ID NO:81 and 96).
Claims 1-2, 4, 6, 8, 15-16, 18-21, 25-30 are examined herein.
Claim Interpretation
The recitation of “modified” in Claims 1-2, 4, 6, 8, 15-16, 18-19, 21, 25, 27 and 30 is reasonably interpreted to mean that the motifs in the modified polypeptide are structurally different from unmodified polypeptides. For example, a LysM receptor polypeptide wherein motifs from the juxtamembrane domain amino acid residues have been deleted and then replaced by the same amino acid residues would be excluded from Applicant’s invention, as the resultant product would not be distinguishable from an unmodified LysM receptor polypeptide. The recitation of “a second αA motif of an unmodified plant LysM receptor polypeptide” is reasonably interpreted to mean that the unmodified plant LysM receptor polypeptide is the starting unmodified state of the modified LysM receptor polypeptide, and does not encompass any other plant LysM receptor polypeptide, as such an interpretation would render the limitation meaningless.
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.
Claims 1-2, 4, 6, 8, 15-16, 18-21, 25-30 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for mutating juxtamembrane domains of LysM-domain comprising polypeptides, does not reasonably provide enablement for a use of said polypeptides across the scope of the claims.
In re Wands, 858 F.2d 731 (Fed. Cir. 1988) lists the following eight factors for determining whether undue experimentation would be required to practice an invention: (1) quantity of experimentation necessary; (2) amount of direction or guidance supplied; (3) presence or absence of working examples; (4) nature of the invention; (5) state of the prior art; (6) relative skill of those in the art; (7) predictability or unpredictability or the prior art; (8) breadth of the claims.
Biotechnology is generally held to be an unpredictable art. In re Vaeck, 947 F.2d 488, 496, 20 U.S.P.Q.2d 1438, 1445 (Fed. Cir. 1991).
Applicant claims a modified plant LysM receptor polypeptide comprising: (i) a juxtamembrane domain comprising a first αA motif, wherein the first αA motif has been modified as compared to a second αA motif of an unmodified plant LysM receptor polypeptide by insertion, deletion, or substitution of one or more amino acids, two or more amino acids, three or more amino acids, four or more amino acids, five or more amino acids, six or more amino acids, all seven amino acids, or wherein the juxtamembrane domain lacks the first αA motif and the second αA motif is inserted into the corresponding position in the juxtamembrane domain wherein the first αA motif, the second αA motif, or both are selected from a polypeptide with 70% identity, 80% identity, 90% identity, 95% identity, or 99% identity to SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 110, or SEQ ID NO: 159 and organisms comprising said modified LysM receptor polypeptide and methods of making the same.
Even in the claims that recite 70% identity to sequence identifiers, the scope of the claims is vast. SEQ ID NO:81 (elected herein) for example is only 10 amino acid residues in length. As such at 70% identity, 3 of the ten amino acids could be added, deleted or substituted – for a total of over 823,000 different combinations in this small motif. Critically, these variations are only directed to one small part of the claimed receptor polypeptides and provide no limitations on the overall structure of the LysM receptors outside of the recited motifs. The genus of polypeptides as encompassed by the claims is accordingly vast.
Applicant has not provided teaching sufficient to enable a use for the vast genus of polypeptides as encompassed by the scope of the claims, without undue experimentation. In contrast to the vast claimed scope, Applicant provides little to no guidance as to how the protein can be changed and still function in the instant invention.
Applicant teaches that LysM receptors are involved in recognition of chemicals produced by bacteria and fungi. Applicant teaches that the LysM receptor kinase NFR5 is required for the perception of rhizobial nod factors and the subsequent initiation of root nodule symbiosis between legumes and nitrogen-fixing rhizobia bacteria. NFR5 is composed of an extracellular domain of three lysin-motifs (LysM), which selectively binds the nod factor signal produced by the symbiont of Lotus, Mesorhizobium loti. NFR5 is embedded in the plant plasma membrane via a single transmembrane helix and on the intracellular side contains an N-terminal juxtamembrane part followed by a protein kinase domain and a C-terminal tail region. The receptor partner NFR1, contains a conventional protein kinase and NFR1 phosphorylation activity is required for symbiosis signaling.
Modeling data was used to identify two alpha helices comprising the juxtamembrane domain, named αA and αA’.
NFR5 (residues 276-595; SEQ ID NO: 146) and NFR1 (residues 263-599; SEQ ID NO: 152) expression constructs were cloned and crystal structures of the intracellular domains of NFR5 were determined. Constructs were made with the native NFR5 promoter upstream (or driving) NFR5 or mutant NFR5 and those constructs were transformed back into Lotus japonicus. The transformants were assayed for nodulation capacity. It appears that the results confirmed that the juxtamembrane domain was important for NFR5 signaling. Applicant then performed the nodulation assay using substitution mutants of the αA motif and found that the ability to form nodules was lost. Applicant then performed nodulation assays using a chimera of the barley NFR5-type receptor RLK10. RLK10 is not normally involved in promoting nodulation, but Applicant found that attaching the juxta membrane domain from NFR5 produced a chimera that promoted nodulation in Lotus japonicus. Applicant speculates that such chimeras or mutants of NFR5-related polypeptides could be used to extend nodulation into cereals. (Specification, ¶ 0115-0151).
Applicant’s experiments have only resulted in the elimination of the capacity of plants to form root nodules and then add it back in plants that already had this ability with a chimeric polypeptide.
Applicant fails to provide any guidance as to how to use the claimed invention across the broad scope of the claims.
The basic quid pro quo contemplated by the Constitution and the Congress for granting a patent monopoly is the benefit derived by the public from an invention with substantial utility. Unless and until a process is refined and developed to this point-where specific benefit exists in currently available form, there is insufficient justification for permitting an application to engross what may prove to be a broad field
Brenner v. Manson, 383 U.S. 519, 534-35, 148 USPQ 689, 695 (1966). Further, “a patent is not a hunting license. It is not a reward for the search, but compensation for its successful conclusion. "[A] patent system must be related to the world of commerce, rather than to the realm of philosophy. . . ." Id., 383 U.S. at 536, 148 USPQ at 696 (quoting In re Ruschig, 52 CCPA 1238, 343 F.2d 965, 970, 145 USPQ 274, 279).
The claimed invention is not enabled across the scope of the claims because the effects of mutating or substituting juxtamembrane domain components in LysM receptors is unpredictable. Applicant has not demonstrated a use for the vast majority of the variants encompassed by the claimed genus of variants. Other than speculation that the substitution or alteration of alpha helix motifs in the juxtamembrane domain of NFR5-like polypeptides could be used to introduce nodulation into plants that normally do not exhibit this useful trait, Applicant has only provided evidence of the importance of this domain by way of eliminating its function.
One of skill in the art, after reading the specification, would be uncertain as to how to use a modified LysM receptor to function within the instant invention. One of skill in the art would find it difficult to predict which of the claimed sequence variants could be used in the instant invention, and which could not. Although testing individual sequences can be routine, Applicant has provided no guidance as to how to proceed.
Given the claim breadth regarding variant sequences, combined with the unpredictability in the art, and lack of guidance as discussed above, undue experimentation is required to practice Applicant’s invention. Applicant’s claimed invention would require undue trial and error experimentation with no reasonable expectation of success.
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 1,4,8,18-21, 25-30 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 21 recites in part “A method of making the genetically modified plant or part thereof of claim 19”. There is insufficient antecedent basis for this limitation in the claim. Claim 19 is directed to a method. For examination purposes the claim is interpreted to be dependent from Claim 18. This does not relieve Applicant of the duty to amend the claims to address the cited deficiency.
Claim 29 recites “A method of reducing NFR5 nodulation signaling comprising: introducing a genetic alteration via an expression vector, isolated DNA molecule, or recombinant nucleic acid of claim 25, wherein the cell is a plant cell.” There is insufficient antecedent basis for this limitation in the claim. Claim 25 does not recite any plant cell. For examination purposes the wherein clause is ignored. This does not relieve Applicant of the duty to amend the claims to address the cited deficiency.
Claims 1,4,8,18-19, 21, 25, 30 are rejected as indefinite for the recitation of “plant LysM receptor polypeptide” and “juxtamembrane domain comprising a first αA (or αA’) motif”. The Specification provides the following with respect to what a LysM receptor polypeptide is: LysM receptors may be defined as proteins that contain three tandem LysM domains in their extracellular region, namely LysM1, LysM2, and LysM3, which are present in this order on the protein sequence and separated by CxC motifs. This definition is open-ended as to what the requirements are to qualify as a plant LysM receptor polypeptide.
This definition does not provide objective boundaries for determining which proteins qualify as plant LysM receptor polypeptides within the meaning of the claims. In particular, the specification loosely defines the term at a high level of generality based on the presence of certain domains and broad functional groupings, but does not set forth sufficiently definite criteria such as the required number, arrangement, or sequence conservation of LysM motifs, the degree of sequence identity or homology required, whether all recited domains must be present and functional, what receptor activity or signaling capability is required, or how such activity is to be assessed. Thus, neither the claims nor the specification provide an objective standard for determining which proteins fall within the recited genus and which do not.
This ambiguity is especially significant because the term receptor denotes a functional classification, yet the claims do not provide a reasonably certain boundary for distinguishing the recited plant LysM receptor polypeptides from other structural relate LysM-containing or receptor-linked proteins. The uncertainty in genus membership is further compounded because the claims broadly recite modifications to juxtamembrane domains comprising a first αA or αA’ motif. It is unclear whether equivalent domains are present in all LysM receptor polypeptides and if so whether they share corresponding position or even similar or the same naming. A review of the art reveals some polypeptides that comprise what appear to be LysM domains but it is unclear whether other parts of the polypeptides comprise juxtamembrane domains comprising a first αA (or αA’) motif, as this nomenclature appears to be limited to art referencing only a subset of LysM domain-containing polypeptides. As such, it is unclear where such motifs start and end in many polypeptides comprising LysM domains. As such the metes and bounds of the claims are unclear.
Dependent claims are included in this rejection because they do not include additional limitations to resolve the ambiguity.
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 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.
Claim 1-2, 4, 6, 8, 18-20, 25-29 rejected under 35 U.S.C. 102(a)(1) as being anticipated by Bozsoki et al. "Ligand-recognizing motifs in plant LysM receptors are major determinants of specificity." Science 369.6504 (2020): 663-670.
Applicant claims a modified plant LysM receptor polypeptide comprising: (i) a juxtamembrane domain comprising a first αA motif, wherein the first αA motif has been modified as compared to a second αA motif of an unmodified plant LysM receptor polypeptide by insertion, deletion, or substitution of one or more amino acids, two or more amino acids, three or more amino acids, four or more amino acids, five or more amino acids, six or more amino acids, all seven amino acids, or wherein the juxtamembrane domain lacks the first αA motif and the second αA motif is inserted into the corresponding position in the juxtamembrane domain (Claim 1), the modified plant LysM receptor polypeptide of claim 1, wherein the first αA motif, the second αA motif, or both are selected from a polypeptide with 70% identity, 80% identity, 90% identity, 95% identity, or 99% identity to SEQ ID NO: 81 (elected herein) (Claim 2), the modified plant LysM receptor polypeptide of claim 1, wherein the modification comprises disruption of the first αA motif, wherein disruption of the first αA motif includes removing, replacing, or substituting one or more residues, two or more residues, three or more residues, four or more residues, five or more residues, six or more residues, or all seven residues within the first αA motif (Claim 4), the modified plant LysM receptor polypeptide of The modified plant LysM receptor polypeptide of wherein the first αA' motif, the second αA' motif, or both are selected from a polypeptide with 70% identity, 80% identity, 90% identity, 95% identity, or 99% identity to SEQ ID NO: 96 (elected herein) (Claim 6), the modified plant LysM receptor polypeptide of the modified plant LysM receptor polypeptide of wherein the modification comprises disruption of the first αA' motif, wherein disruption of the first αA' motif includes removing, replacing, or substituting one or more residues, two or more residues, three or more residues, four or more residues, five or more residues, six or more residues, or all seven residues within the first αA' motif (Claim 8), a genetically modified plant or part thereof comprising the modified plant LysM receptor polypeptide of claim 1 (Claim 18), a method of making the genetically modified plant or part thereof of claim 18, comprising introducing a genetic alteration to the plant or part thereof comprising a nucleic acid sequence encoding a heterologous plant LysM receptor polypeptide comprising a juxtamembrane domain comprising a modified αA motif and/or a modified αA' motif, wherein the nucleic acid sequence is operably linked to a promoter (Claim 19), the method of claim 19, wherein the promoter is a root specific promoter, an inducible promoter, a constitutive promoter, or a combination thereof (Claim 20), an expression vector, isolated DNA molecule, or recombinant nucleic acid comprising one or more nucleic acid sequences encoding a heterologous plant LysM receptor polypeptide comprising a juxtamembrane domain comprising a modified αA motif (Claim 25), a bacterial cell or an Agrobacterium cell comprising the expression vector, isolated DNA molecule, or recombinant nucleic acid of claim 25 (Claim 26), a genetically modified plant, plant part, plant cell, or seed comprising the expression vector, isolated DNA molecule, or recombinant nucleic acid of claim 25 (Claim 27), a composition or kit comprising the expression vector, isolated DNA molecule, or recombinant nucleic acid of claim 25 with a bacterial cell (Claim 28), a method of reducing NFR5 nodulation signaling comprising: introducing a genetic alteration via an expression vector, isolated DNA molecule, or recombinant nucleic acid of claim 25 (Claim 29).
Bozsoki discloses a series of experiments designed to determine the components of some plant LysM receptors that re responsible for target recognition. Bozsoki discloses that chimeras between the NFR1 (a kinase) and CERK6 (another kinase) proteins from Lotus japonicus were created by swapping various domains in the nucleic acids encoding the proteins, putting the chimeric sequences under the control of the NFR1 (a root-specific) promoter. (p. 2 left col. ¶ 2 – middle col. ¶ 1, Supplement, Materials and Methods). Bozsoki discloses that constructs encoding the chimeras were moved into Agrobacterium rhizogenes and then transformed into Medicago truncatula (a legume). (Supplement, Materials and Methods). Bozsoki discloses that two of the chimeras that were tested were chimeras wherein the transmembrane and juxtamembrane domain of NFR1 and CERK6 were swapped into one another. (Figure 1, part B). NFR1 comprises αA and αA’ motifs that match both SEQ ID NO:81 and 96 at 100% identity. This domain swapping reasonably reads on the complete deletion of the αA and αA’ motifs of the juxtamembrane domains of both NFR1 and CERK6 and their replacement with heterologous αA and αA’ motifs. Bozsoki discloses that the NFR1 polypeptide comprising the CERK6 transmembrane and juxtamembrane appears to have reduced nodulation activity. (Figure 1, part B). The instant disclosure provides evidence that the juxtamembrane domain is involved in signaling. Because Bozsoki discloses that the LysM domains were responsible for target recognition, it is reasonable to conclude that the reduction in nodulation activity is caused by disrupted signaling.
As such, the claimed inventions are anticipated by the disclosures of the prior art.
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 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 of this title, 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.
Claim 21 is rejected under 35 U.S.C. 103 as being unpatentable over Bozsoki et al. "Ligand-recognizing motifs in plant LysM receptors are major determinants of specificity." Science 369.6504 (2020): 663-670 in view of Zhao, Yongping, et al. "An alternative strategy for targeted gene replacement in plants using a dual-sgRNA/Cas9 design." Scientific reports 6.1 (2016): 23890.
Applicant claims a method of making the genetically modified plant or part thereof of claim 18 (see 112b rejection herein), comprising genetically modifying the plant or part thereof by transforming the plant or part thereof with one or more gene editing components that target an endogenous nuclear genome sequence encoding an endogenous plant LysM receptor polypeptide comprising a juxtamembrane domain comprising an αA motif, wherein the αA motif is genetically modified by removing, replacing, or substituting one or more residues, two or more residues, three or more residues, four or more residues, five or more residues, six or more residues, or all seven residues within the αA motif, wherein the one or more gene editing components comprise a ribonucleoprotein complex that targets the nuclear genome sequence; a vector comprising a TALEN protein encoding sequence, wherein the TALEN protein targets the nuclear genome sequence; a vector comprising a ZFN protein encoding sequence, wherein the ZFN protein targets the nuclear genome sequence; an oligonucleotide donor (OND), wherein the OND targets the nuclear genome sequence; or a vector CRISPR/Cas enzyme encoding sequence and a targeting sequence, wherein the targeting sequence targets the nuclear genome sequence.
Bozsoki discloses a series of experiments designed to determine the components of some plant LysM receptors that re responsible for target recognition. Bozsoki discloses that chimeras between the NFR1 (a kinase) and CERK6 (another kinase) proteins from Lotus japonicus were created by swapping various domains in the nucleic acids encoding the proteins, putting the chimeric sequences under the control of the NFR1 (a root-specific) promoter. (p. 2 left col. ¶ 2 – middle col. ¶ 1, Supplement, Materials and Methods). Bozsoki discloses that constructs encoding the chimeras were moved into Agrobacterium rhizogenes and then transformed into Medicago truncatula (a legume). (Supplement, Materials and Methods). Bozsoki discloses that two of the chimeras that were tested were chimeras wherein the transmembrane and juxtamembrane domain of NFR1 and CERK6 were swapped into one another. (Figure 1, part B). NFR1 comprises αA and αA’ motifs that match both SEQ ID NO:81 and 96 at 100% identity. This domain swapping reasonably reads on the complete deletion of the αA and αA’ motifs of the juxtamembrane domains of both NFR1 and CERK6 and their replacement with heterologous αA and αA’ motifs. Bozsoki discloses that the NFR1 polypeptide comprising the CERK6 transmembrane and juxtamembrane appears to have reduced nodulation activity. (Figure 1, part B). The instant disclosure provides evidence that the juxtamembrane domain is involved in signaling. Because Bozsoki discloses that the LysM domains were responsible for target recognition, it is reasonable to conclude that the reduction in nodulation activity is caused by disrupted signaling.
However, Bozsoki does not teach that the domain swapping (replacing) is accomplished using a gene editing system.
Zhao teaches a dual-sgRNA/Cas9 system for targeted gene replacement in plants. Zhao teaches that the method was successful in replacing a primary micro RNA sequence - AtMIR827a. (p. 2 ¶ 1 – p. 6 ¶ 2, See Figure 1).
It would have been prima facie obvious to a person of ordinary skill in the art at the time of filing to modify the method of Bozsoki such that the domain swapping was accomplished using a gene editing system as taught by Zhao. One having ordinary skill in the art would have been motivated to do this because Zhao teaches that the dual-sgRNA/Cas9 system is successful in targeted gene replacement and the size of the replaced segment (607 nucleotides) would be adequate to encompass the domains swapped by Bozsoki. As such, one of ordinary skill in the art would have a reasonable expectation of success. The traditional molecular biology approach used in Bozsoki and the dual-sgRNA/Cas9 system of Zhao are reasonably deemed to be functional equivalents known for the same purpose and as such their substitution are prima facie obvious.
As such, the claimed inventions are obvious in view of the teachings of the prior art.
Conclusion
No claims are allowed.
Claims 15, 16 and 30 appear to be free of the prior art. The closest prior art is Bozsoki et al. "Ligand-recognizing motifs in plant LysM receptors are major determinants of specificity." Science 369.6504 (2020): 663-670. However, Bozsoki teaches that the juxtamembrane domain is not involved in target recognition and indicates that swapping the domains reduced nodulation and otherwise does not motivate one of ordinary skill to make such changes to NFR5 polypeptides.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CHARLES A LOGSDON whose telephone number is (571)270-0282. The examiner can normally be reached M-F 8:30 - 5:00 pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Bratislav Stankovic can be reached at (571) 270-0305. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/CHARLES LOGSDON/Primary Examiner, Art Unit 1662
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