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
Claim 29 is newly added by the Applicant and entered.
Claims 1-29 are pending.
Claims 9-17, 21-25 and 27-28 are withdrawn from examination as being part of non-elected groups.
Claims 1-8, 18-20, 26 and 29 are being examined.
Claim Rejections - 35 USC § 112(b)
Claims 1-8, 18-20, 26 and 29 are newly rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention. This is a new rejection necessitated by the claim amendments.
It is not clear to the Examiner if the method comprises:
The first subunit polypeptide (comprising an affinity polypeptide) binds to the second subunit polypeptide, OR
The affinity polypeptide (fused to the first subunit polypeptide) binds the second subunit polypeptide.
In the interest of compact prosecution, the claims are nonetheless examined.
Response to Applicant’s Arguments: Regarding rejections under 35 U.S.C. § 112(b), the Applicant amended claim 20.
However, present rejections under 35 U.S.C. § 112(b) are new rejections necessitated by the claim amendments.
Claim Rejections - 35 USC § 112(a)
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.
Enablement
Claims 1-8, 18-20, 26 and 29 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 enablement requirement. The claims contain subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention. This is a new rejection necessitated by the claim amendments.
The first enablement issue is related to activating TM receptor signaling in the absence of a stimulus (in form of oligomerization of the first subunit polypeptide and the second subunit polypeptide).
Claim 1 is drawn to a genetically modified cell comprising a transmembrane (TM) receptor complex comprising a first subunit comprising a heterologous affinity polypeptide that binds to the second subunit polypeptide, intracellularly inducing oligomerization of the first subunit polypeptide and the second subunit polypeptide activating TM receptor signaling in the absence of a stimulus for the TM receptor complex.
The Applicant describes symbiotic receptors NFRl and NFR5 as proof-of-principle (spec, p.134, para 0168, line 2-3). The Applicant describes that expression of (heavy-chain variable domain) VHH-tagged NFRl receptor construct would specifically recognize and bind the kinase domain of the native NFR5 receptor forming a heteromeric complex (spec, p.134, para 0168, line 5-8) in plant roots using Agrobacterium rhizogenes produces nodules in absence of rhizobia or Nod factors (NF) to show that “receptor assembly is the key step in symbiotic signaling” (spec, p.134, para 0168, line 9-13). The Applicant assert that the assembly of NFR1 and NFR5 is necessary and sufficient for nodule formation (spec, p.134, para 0169, line 1-2).
Current status of the art teaches that NFR1 and NFR5 do interact by itself in absence of any Nod Factor (NF) or bacteria or any other stimulus/signal as shown in
bimolecular fluorescence complementation (BiFC) assay in tobacco (Wong et al., A Lotus japonicus cytoplasmic kinase connects Nod factor perception by the NFR5 LysM receptor to nodulation, 2019, 116: 14339–14348; bridging paragraph between page 14339 and 14340). It is also known in the art that purified NFR1 and NRF5 directly and independently binds to the NF (i.e., the signal/stimulus) produced by rhizobia bacteria (Wong et al.; p.14339, left column, para 1, line 17-18). Thus, a skilled artisan would acknowledge that under normal circumstances (as in wild type plants) neither the assembly (binding) of NFR1 and NFR5 is necessary nor sufficient for activating the TM receptor signaling (as recited in claim 1) resulting in nodule formation.
There are several genes (not NFR1 or NRF5), when mutated, are known to induce spontaneous nodule formation in absence of rhizobia (Tirichine et al., Spontaneous Root-Nodule Formation in the Model Legume Lotus japonicus: A Novel Class of Mutants Nodulates in the Absence of Rhizobia and NF, 2006, MPMI, 19:373-382; title and abstract). A skilled artisan would acknowledge that Agrobacterium mediated transformation would introduce the transgene(s) in the host genome and integrate the transgene(s) anywhere in the genome. The Applicant does not show that expression or activity of the gene(s) involved in spontaneous nodule formation in absence of rhizobia is altered during Agrobacterium mediated transformation.
Undue trial and error experimentations would be needed to express NFRl and NFR5 receptors to form a heteromeric complex (spec, p.134, para 0168, line 5-8) activating the receptor signaling process leading to nodule formation in absence of rhizobia or Nod factors (NF).
Based on breadth of the claims, lack of guidance in the instant description or in prior art, the specification at the time of the application filed would not have taught one skilled in the art how to make and use the full scope of the claimed invention without performing undue experiments.
The second (scope of ) enablement issue is related to the role of posttranslational modification of the polypeptides in a specific organism in terms of its function comprising activating TM receptor signaling.
Claims 1-8, 18-20, 26 and 29 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a genetically modified cell which has the same posttranslational modification capability for the target proteins including NFR1 and NFR5, does not reasonably provide enablement for a genetically modified cell which does not possess the same posttranslational modification capability for the target proteins including NFR1 and NFR5. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
Claim 1 is drawn to a genetically modified cell comprising a transmembrane (TM) receptor complex comprising a first subunit comprising a heterologous affinity polypeptide that binds to the second subunit polypeptide, intracellularly inducing oligomerization of the first subunit polypeptide and the second subunit polypeptide activating TM receptor signaling in the absence of a stimulus for the TM receptor complex.
Broghammer et al. teaches that glycosylation, especially N-glycosylation, is a common posttranslational modification of plasma membrane-localized proteins like NFR1 and NFR5, and can be involved in posttranslational processing (p.13860, left column, last para, line 1-3) of the biologically active proteins. Matured or fully processed NFR proteins including NFR5 are highly N-glycosylated (p.13863, left column, first para, line 1; p.13860, left column, last para, line 3-5). A growing body of evidence suggest that glycosylation of glycosylated proteins is essential for various functional activities such as playing a key role, inter alia, in protein function (He et al., Glycosylation: mechanisms, biological functions and clinical implications, 2024, Sig. Transduct. Target Ther., 9:194; abstract, line 4-5).
The Applicant describes expressing the NFR1 and NFR5 proteins (i.e., the first subunit polypeptide and the second subunit polypeptide) in E coli only to generate NFR5 VHH fusion protein (spec, p.115, para 0157-0161). The Applicant also describes expressing the NFR1 and NFR5 proteins in plant cells (spec, para 0164-0165; para 0171; para 0173-0175; para 0183-0184).
The Applicant does not describe expressing the NFR1 and NFR5 (fusion) proteins in any cell other than a plant cell while the claims include any cell from any organism.
Undue trial and error experimentations would be needed to express NFRl and NFR5 protein in a genetically modified cell having the same or similar functional glycosylation pattern of the proteins which would be capable of activating the receptor signaling process leading to nodule formation in absence of a stimulus.
Based on breadth of the claims, lack of guidance in the instant description or in prior art, the specification at the time of the application filed would not have taught one skilled in the art how to make and use the full scope of the claimed invention without performing undue experiments.
Written Description
Claims 1-8, 18-20, 26 and 29 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. This is a new rejection necessitated by the claim amendments.
Claim 1 is drawn to a genetically modified cell comprising a transmembrane (TM) receptor complex comprising a first subunit comprising a heterologous affinity polypeptide that binds to the second subunit polypeptide, intracellularly inducing oligomerization of the first subunit polypeptide and the second subunit polypeptide activating TM receptor signaling in the absence of a stimulus for the TM receptor complex.
Broghammer et al. teaches that glycosylation especially N-glycosylation is a common posttranslational modification of plasma membrane-localized proteins like NFR1 and NFR5, and is involved in posttranslational processing (p.13860, left column, last para, line 1-3) of the biologically active proteins. Matured or fully processed NFR proteins including NFR5 are highly N-glycosylated (p.13863, left column, first para, line 1; p.13860, left column, last para, line 3-5). A growing body of evidence suggests that glycosylation is essential for various functional activities in different organisms, such as playing a key role, inter alia, in protein function (He et al., abstract, line 4-5). It is known in the art that different eukaryotic cells (plant, animal and fungal cells) have very different glycosylation pattern while bacterial cells often do not possess any glycosylation capability.
The Applicant describes expressing the NFR1 and NFR5 proteins in E coli only to generate NFR5 VHH (spec, p.115, para 0157-0161). The Applicant also describes expressing the NFR1 and NFR5 proteins in plant cells (spec, para 0164-0165; para 0171; para 0173-0175; para 0183-0184).
The Applicant does not provide examples of a genetically modified cell other than a plant cell to express the NFR1 and NFR5 proteins while claiming the broad genus of any cell.
The Applicant also does not describe any structure function relationship between glycosylation of NFR1 and/or NFR5 in terms of its ability to activate the receptor signaling process leading to nodule formation in absence of a stimulus.
Considering the breadth of the claims, lack of representative species of the broad genus claimed, lack of structure function relationship of the broad genus claimed, and unpredictability of the art, the Applicant does not appear to have been in possession of the claimed genus at the time this application was filed.
Claim Rejections - 35 USC § 102(a)(1)
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 1-3, 5-7, 18-20, 26 and 29 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Broghammer et al. (Legume receptors perceive the rhizobial lipochitin oligosaccharide signal molecules by direct binding, 2012, PNAS, 109:13859-13864) in evidence of Ried et al. (Spontaneous symbiotic reprogramming of plant roots triggered by receptor-like kinases, 2014, Elife, 3:e03891) and Jensen, et al. (Enhanced Fluorescence Resonance Energy Transfer between Spectral Variants of Green Fluorescent Protein through Zinc-Site Engineering, 2001, Biochemistry, 40:938-945).
Broghammer et al. teaches that lotus (Lotus japonicus) (as recited in claim 19) Nod Factor Receptor 1 (NFR1) and Nod Factor Receptor 5 (NFR5) binds Nod factor (NF) directly and play an important role in root nodule symbiosis leading towards nitrogen fixation in a plant (Abstract). It teaches genetically modified cells (as recited in claims 1, 18, 20 and 26) and the method of making (as recited in claims 20 and 29) such cells where full length NFR1 and NFR5 are ectopically expressed in tobacco and Arabidopsis cells (which are eukaryotic and plant cells, as recited in claims 5-6) as GFP/YFP fusion proteins (page 13860, left column, para 3, line 15-16; page 13863, right column, last 2 lines; Supporting Information, page 1, para 1). Ectopic overexpression of NFR1 and/or NFR5 would activate(s) TM receptor signaling as it is also known in the art that ectopic (over) expression of NFR1 and/or NFR5 initiate(s) spontaneous nodule organogenesis and nodulation-related gene expression in the absence of rhizobia (evidence provided by Ried et al., p.1091, left column, para 2, line 1-4) (as recited in claim 1) underscoring the critical need for tight control over NFR1/NFR5 protein level in terms of NF initiated signal transduction.
Broghammer et al. describes that all NFR proteins including NFR1 and NFR5 are transmembrane proteins (page 13859, right column, para 1, line 11-13) and forms a transmembrane (protein) receptor complex (page 13859, right column, para 1, line 19-20), as recited in claim 1. The NFR1 and NFR5 heterocomplex (NFR complex) is capable of initiating or activating transmembrane (TM) signal transduction process after perceiving the NF (page 13859, right column, para 2, line 1-7). Broghammer et al. teaches that all NFRs including NRF1 and NRF5 comprise lysin motif (LysM) receptor (page 13859, left column, para 1, line 7-8), as recited in claim 6.
Broghammer et al. describes a split YFP system using (full length) NFR1 and NFR5 proteins (page 13859, right column, para 1, line 20-21), where the fluorescent protein polypeptide (as recited in claim 3), YFP, is divided in two halves. One half of the YFP is fused to NFR1 while the other half is fused to NFR5, and these two halves bind directly (as recited in claim 2) due to high affinity to each other. It is known in the art that the split YFP assay (a Bimolecular Fluorescence Complementation, BiFC, assay) shows high intrinsic affinity of YFP’s two halves (YN and YC) to spontaneously reassemble into a functional, fluorescent Yellow Fluorescent Protein (YFP) when brought close together by interacting proteins creating a signal that visualizes the protein-protein interaction (PPI) in real-time within living cells.
The Applicant describes, “an affinity polypeptide can be any polypeptide that enables any stable protein-protein dimerization (e.g., two proteins that bind). Protein dimerization by affinity polypeptides can be or can be derived from known dimers, known protein interactions, or proteins that bind in silico” (page 99, para 98, line 1-4). The instant description teaches, “the term “epitope tag” or “affinity tag” or “tag polypeptides” refers to a site on or fused to a target polypeptide to which an affinity polypeptide binds” (examples are excluded) (page 99, para 99, line 1-4). Thus, the two halves of YFP (YC and YN), which are heterologous to both NFR1 and NFR 5, can be described as, and reads on to, “tag polypeptide” as well as “affinity polypeptide”.
Moreover, besides a truncated versions of YFP (as discussed above), Broghammer et al. also describes ectopically (over-) expressing NFR1 and NFR5 proteins fused to an affinity polypeptide comprising (full length) GFP or YFP (page 13862, right column, para 1, line 2-4). The NFR1 and NFR5 can be used interchangeably to read on to “first subunit polypeptide” and “second subunit polypeptide” (as recited in claims 1-2, 6-7 and 20) of the oligomer they form. All these interactions happen inside a cell, i.e., intracellularly, as recited in claim 1. Both the GFP and/or YFP fused to NFR1 and/or NFR5 qualify as “affinity polypeptide” as it is known in the art that various versions of GFP/YFP including the wild type GFP and YFP do form dimers (evidence provided by Jensen, et al., p.939, left column, para 1, line 5-7; Fig-1; p.941, left column, para 2, line 2-3; p.941, left column, para 3, line 2-10).
Claim Rejections - 35 USC § 103
Claim 4 is rejected under 35 U.S.C. 103 as being unpatentable over Broghammer et al. as applied to rejected claims 1-3, 5-7, 18-20, 26 and 29 under 35 U.S.C. 102(a)(1) above, and further in view of Rothbauer et al. (A Versatile Nanotrap for Biochemical and Functional Studies with Fluorescent Fusion Proteins, 2008, Molecular & Cellular Proteomics, Molecular & Cellular Proteomics.7:282-9).
Claim 4 depends from claim 1 and is drawn to the genetically modified cell wherein the affinity polypeptide is a heavy-chain variable domain (VHH) and/or a synthetic version of it.
Broghammer et al. describes a genetically modified cell comprising a transmembrane (TM) receptor complex comprising a first subunit polypeptide fused to a heterologous affinity polypeptide and binds to a second subunit polypeptide forming an oligomer and activates TM receptor signaling in absence of a stimulus, as discussed above.
However, Broghammer et al. does not teach any heavy-chain variable domain (VHH) and/or a synthetic version of it.
Rothbauer et al. describes developing a specific binder for fluorescent proteins including GFP and YFP (page 283, left column, para 2, line 1-6; page 183, para 3, line 3), which are the most widely used labeling tags in cell biology (page 282, right column, line 12-13), based on a 13-kDa GFP binding fragment derived from a llama single chain antibody (Abstract), which is also referred to as VHH (heavy-chain variable domain) (page 282, right column, line 18-19). These VHHs, which represent the smallest intact antigen-binding units, are highly soluble and stable, and can be efficiently produced in heterologous systems (page 282, right column, line 20-24).
Rothbauer et al. also describes that a GFP-binding protein (GBP) derived from Ilama single chain antibody (VHH) (abstract) allows a fast and efficient (one-step) isolation of GFP and YFP fusion proteins and their interacting factors for biochemical analyses including mass spectroscopy and enzyme activity measurements, as GBP also recognizes (and binds to) YFP (forming heterodimer) as well (page 284, right column, para 3, line 3-4). Moreover, the GBP is also suitable for chromatin immune-precipitations from cells expressing fluorescent DNA-binding proteins including GFP and YFP. Most importantly, the GBP can be fused with cellular proteins to ectopically recruit GFP/YFP fusion proteins allowing targeted manipulation of cellular structures and processes in living cells (abstract).
Before the effective filing date of the invention, it would have been obvious to an ordinarily skilled artisan to fuse the heavy-chain variable domain (VHH), as described by Rothbauer et al., with specific proteins including NFR1 and/or NFR5 for various objectives. Such objectives would comprise purifying the fused proteins with the VHH affinity polypeptide, isolate and/or identify the interacting partners of the fused protein(s) in a protein complex while having the useful option to visualize the fused or interacting fluorescent protein(s) like GFP or YFP in-vivo.
Nitrogen fixation via nodulation in legume plants where NFR1 and NFR5 proteins play important roles, is of great economic importance. Understating the process and other proteins that interact with NFR1 and/or NFR5 would have been of great academic and commercial interests.
Before the effective filing date, an ordinarily skilled artisan would have been motivated to fuse the heavy-chain variable domain (VHH) capable to bind GFP/YFP fused to NFR1 or NFR5 for various goals. Such goals would include to purify the fused protein with this small affinity polypeptide more efficiently or easily, isolate and/or identify the interacting partners of the fused protein(s) in a protein complex while having the useful option to visualize the fused or interacting fluorescent protein(s) like GFP or YFP in-vivo.
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Broghammer et al. as applied to reject claims 1-3, 5-7, 18-20, 26 and 29 under 35 U.S.C. 102(a)(1) above, and further in view of Andedrsen et al. (US 2021/0233608 A1, published on July 29, 2021).
Claim 8 indirectly depends from claim 1 and is drawn to any of the recited SEQ ID NOs encoding NFR1, LYK3, or RLK4; and any of the recited sequences encoding NFR5, NFP, or RLK10. The list of SEQ ID NOs comprise NFR1 encoded by SEQ ID NO: 4 and NFR5 encoded by SEQ ID NO: 5.
Broghammer et al. describes expressing full length cDNA encoding full length NFR1 and NFR5 proteins (page 13860, left column, para 3, line 15-16; page 13863, right column, last 2 lines; Supporting Information, page 1, para 1). Broghammer et al. also describes a genetically modified cell comprising a transmembrane (TM) receptor complex comprising a first subunit polypeptide fused to a heterologous affinity polypeptide that binds to a second subunit polypeptide forming an oligomer and activates TM receptor signaling in absence of a stimulus, as discussed above.
However, Broghammer et al. does not explicitly teach a NFR1 protein encoded by SEQ ID NO: 4 and a NFR5 protein encoded by SEQ ID NO: 5.
Andedrsen et al. teaches a NFR1 protein from lotus (Lotus japonicus) encoded by SEQ ID NO: 70 (page 12, para 0048, line 13) which is having 100% sequence identity to instant SEQ ID NO: 4, as shown below.
RESULT 1
US-17-267-240-70
Filing date in PALM: 2021-02-09
Sequence 70, US/17267240
Publication No. US20210233608A1
GENERAL INFORMATION
APPLICANT: Aarhus Universitet
TITLE OF INVENTION: GENETICALLY ALTERED LYSM RECEPTORS WITH ALTERED AGONIST
TITLE OF INVENTION: SPECIFICITY AND AFFINITY
FILE REFERENCE: 79454-20004.00
CURRENT APPLICATION NUMBER: US/17/267,240
CURRENT FILING DATE: 2021-02-09
PRIOR APPLICATION NUMBER: PCT/EP2019/071705
PRIOR FILING DATE: 2019-08-13
PRIOR APPLICATION NUMBER: US 62/718,282
PRIOR FILING DATE: 2018-08-13
NUMBER OF SEQ ID NOS: 106
SEQ ID NO 70
LENGTH: 623
TYPE: PRT
ORGANISM: Lotus japonicus
Query Match 100.0%; Score 3198; Length 623; Best Local Similarity 100.0%;
Matches 623; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MKLKTGLLLFFILLLGHVCFHVESNCLKGCDLALASYYILPGVFILQNITTFMQSEIVSS 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MKLKTGLLLFFILLLGHVCFHVESNCLKGCDLALASYYILPGVFILQNITTFMQSEIVSS 60
Qy 61 NDAITSYNKDKILNDINIQSFQRLNIPFPCDCIGGEFLGHVFEYSASKGDTYETIANLYY 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 NDAITSYNKDKILNDINIQSFQRLNIPFPCDCIGGEFLGHVFEYSASKGDTYETIANLYY 120
Qy 121 ANLTTVDLLKRFNSYDPKNIPVNAKVNVTVNCSCGNSQVSKDYGLFITYPIRPGDTLQDI 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 ANLTTVDLLKRFNSYDPKNIPVNAKVNVTVNCSCGNSQVSKDYGLFITYPIRPGDTLQDI 180
Qy 181 ANQSSLDAGLIQSFNPSVNFSKDSGIAFIPGRYKNGVYVPLYHRTAGLASGAAVGISIAG 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 ANQSSLDAGLIQSFNPSVNFSKDSGIAFIPGRYKNGVYVPLYHRTAGLASGAAVGISIAG 240
Qy 241 TFVLLLLAFCMYVRYQKKEEEKAKLPTDISMALSTQDGNASSSAEYETSGSSGPGTASAT 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 TFVLLLLAFCMYVRYQKKEEEKAKLPTDISMALSTQDGNASSSAEYETSGSSGPGTASAT 300
Qy 301 GLTSIMVAKSMEFSYQELAKATNNFSLDNKIGQGGFGAVYYAELRGKKTAIKKMDVQAST 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 GLTSIMVAKSMEFSYQELAKATNNFSLDNKIGQGGFGAVYYAELRGKKTAIKKMDVQAST 360
Qy 361 EFLCELKVLTHVHHLNLVRLIGYCVEGSLFLVYEHIDNGNLGQYLHGSGKEPLPWSSRVQ 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 EFLCELKVLTHVHHLNLVRLIGYCVEGSLFLVYEHIDNGNLGQYLHGSGKEPLPWSSRVQ 420
Qy 421 IALDAARGLEYIHEHTVPVYIHRDVKSANILIDKNLRGKVADFGLTKLIEVGNSTLQTRL 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 IALDAARGLEYIHEHTVPVYIHRDVKSANILIDKNLRGKVADFGLTKLIEVGNSTLQTRL 480
Qy 481 VGTFGYMPPEYAQYGDISPKIDVYAFGVVLFELISAKNAVLKTGELVAESKGLVALFEEA 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 VGTFGYMPPEYAQYGDISPKIDVYAFGVVLFELISAKNAVLKTGELVAESKGLVALFEEA 540
Qy 541 LNKSDPCDALRKLVDPRLGENYPIDSVLKIAQLGRACTRDNPLLRPSMRSLVVALMTLSS 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 LNKSDPCDALRKLVDPRLGENYPIDSVLKIAQLGRACTRDNPLLRPSMRSLVVALMTLSS 600
Qy 601 LTEDCDDESSYESQTLINLLSVR 623
|||||||||||||||||||||||
Db 601 LTEDCDDESSYESQTLINLLSVR 623
Andedrsen et al. also teaches a NFR5 protein from lotus (Lotus japonicus) encoded by SEQ ID NO: 11 (page 13, para 0052, line 5-6) which is having 100% sequence identity to instant SEQ ID NO: 5, as shown below.
RESULT 1
US-17-267-240-11
Filing date in PALM: 2021-02-09
Sequence 11, US/17267240
Publication No. US20210233608A1
GENERAL INFORMATION
APPLICANT: Aarhus Universitet
TITLE OF INVENTION: GENETICALLY ALTERED LYSM RECEPTORS WITH ALTERED AGONIST
TITLE OF INVENTION: SPECIFICITY AND AFFINITY
FILE REFERENCE: 79454-20004.00
CURRENT APPLICATION NUMBER: US/17/267,240
CURRENT FILING DATE: 2021-02-09
PRIOR APPLICATION NUMBER: PCT/EP2019/071705
PRIOR FILING DATE: 2019-08-13
PRIOR APPLICATION NUMBER: US 62/718,282
PRIOR FILING DATE: 2018-08-13
NUMBER OF SEQ ID NOS: 106
SEQ ID NO 11
LENGTH: 591
TYPE: PRT
ORGANISM: Lotus japonicus
Query Match 100.0%; Score 3028; Length 591; Best Local Similarity 100.0%;
Matches 591; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MTSFFLFTNTLFLALMMFFSTTHHILAQLSHTNGTNFSCPVDSPPSCDTYVTYFAQSPNF 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MTSFFLFTNTLFLALMMFFSTTHHILAQLSHTNGTNFSCPVDSPPSCDTYVTYFAQSPNF 60
Qy 61 LTLTSISDLFDTSPLSIARASNIKDENQNLVPGQLLLVPVTCACSGSNSFSNISHMIKEG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 LTLTSISDLFDTSPLSIARASNIKDENQNLVPGQLLLVPVTCACSGSNSFSNISHMIKEG 120
Qy 121 ESYYYLSTTSYENLTNWETVQDSNPNYNPYLLPVGIKVVIPLFCKCPSNYHLNKGIEYLI 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 ESYYYLSTTSYENLTNWETVQDSNPNYNPYLLPVGIKVVIPLFCKCPSNYHLNKGIEYLI 180
Qy 181 TYVWHNNDNVSLVASKFGVSTQDIISENNFSHQNFTAATNFPILIPVTQLPSLSQSYSSS 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 TYVWHNNDNVSLVASKFGVSTQDIISENNFSHQNFTAATNFPILIPVTQLPSLSQSYSSS 240
Qy 241 ERKRSNHIHIIISIGISLGSTLLIALLVLVSVTCLRKRKSSENKSLLSVEIAGKKLISGV 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 ERKRSNHIHIIISIGISLGSTLLIALLVLVSVTCLRKRKSSENKSLLSVEIAGKKLISGV 300
Qy 301 SNYVSKSILYEFRLIMEATLNLNEQCKIGESVYKAKLDGQVLAVKKVKEDVTEEVMILQK 360
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Db 301 SNYVSKSILYEFRLIMEATLNLNEQCKIGESVYKAKLDGQVLAVKKVKEDVTEEVMILQK 360
Qy 361 VNHLNLVKLMGVSSGHDGNHFLVYEFAENGSLHNWLFSNSSTGSRFLTWSQRISIAVDVA 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 VNHLNLVKLMGVSSGHDGNHFLVYEFAENGSLHNWLFSNSSTGSRFLTWSQRISIAVDVA 420
Qy 421 MGLQYMHEHTQPSIVHRDITSSNILLDSNFKAKIANFSVARTSINPMILKVDVFGYGVVL 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 MGLQYMHEHTQPSIVHRDITSSNILLDSNFKAKIANFSVARTSINPMILKVDVFGYGVVL 480
Qy 481 LELLSGKKSLTNNEINHIREIFDLKEKREERIRRWMDPKIESLYPIDDALSLAFLAMNCT 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 LELLSGKKSLTNNEINHIREIFDLKEKREERIRRWMDPKIESLYPIDDALSLAFLAMNCT 540
Qy 541 SEKPLSRPTMGEVVLSLSLLMTQHSPTTLERSWTCGLDVDVTEMQTLIAAR 591
|||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 SEKPLSRPTMGEVVLSLSLLMTQHSPTTLERSWTCGLDVDVTEMQTLIAAR 591
Before the effective filing date of the invention, it would have been obvious to an ordinarily skilled artisan to modify the method, as described by Broghammer et al., and use NFR1 and NFR5 proteins (as described by Andedrsen et al.) from lotus, a commercially important crop, as described by Andedrsen et al., to understand the TM receptor signaling process via NFR1 and NRF5, which is involved in root nodule symbiosis leading to nitrogen fixation, as described by Broghammer et al.
Before the effective filing date, an ordinarily skilled artisan would have been motivated to produce a genetically modified cell of a lotus plant, which is a commercially important crop, using any specific NFR1 and NFR5 proteins including the ones described by Andedrsen et al.) to understand the TM receptor signaling process via NFR1 and NRF5 involved in root nodule symbiosis and nitrogen fixation in lotus.
Response to Applicant’s Arguments: Regarding rejections under 35 U.S.C. § 102(a)(1) and 35 U.S.C. § 103, the Applicant argues, “Broghammer does not teach or describe a genetically modified cell comprising a transmembrane receptor complex comprising a first subunit polypeptide comprising a heterologous affinity polypeptide that binds to a second subunit polypeptide, intracellularly inducing oligomerization of the first subunit polypeptide and the second subunit polypeptide, wherein the induced oligomerization of the first subunit polypeptide and the second subunit polypeptide occurs in the absence of a stimulus for the TM receptor complex, as recited in amended claim 1” (response, p.14, para 3). The Applicant also argues that “the split YFP system described in Broghammer does not involve a heterologous affinity polypeptide that mediates an interaction between NFR1 and NFR5. Rather, the split YFP system is used as a reporter for the naturally occurring complex formation between NFR1 and NFR5, and does not induce protein-protein interactions that would not otherwise occur absent the affinity between the YFP halves” response, p.15, para 2, line 4-8).
The Examiner disagrees. Besides the split YFP polypeptides (which is also known to induce protein-protein interactions), both the GFP and/or YFP fused to NFR1 and/or NFR5 qualify as “affinity polypeptide” (as per Applicant’s definition of the term “affinity polypeptide”, as discussed above) as it is known in the art that various versions of GFP/YFP including the wild type GFP and YFP do form dimers (Jensen, et al., p.939, left column, para 1, line 5-7; Fig-1; p.941, left column, para 2, line 2-3; p.941, left column, para 3, line 2-10). It is also known in the art that ectopic (over-) expression of NFR1 and/or NFR5 initiate(s) spontaneous nodule organogenesis and nodulation-related gene expression in the absence of rhizobia (Ried et al., p.1091, left column, para 2, line 1-4) implying that ectopic (over)expression NFR1 or NFR5 protein fused with wild-type GFP, YFP or the split YFP polypeptides would also initiate spontaneous TM receptor signaling in form of nodule organogenesis and nodulation-related gene expression in the absence of rhizobia.
Conclusion
No claim is allowed.
Applicant's claim amendments and submission of new information in an information disclosure statement under 37 CFR 1.97(c) necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Communication
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JAY CHATTERJEE whose telephone number is (703)756-1329. The examiner can normally be reached (Mon - Fri) 8.30 am to 5.30 pm..
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J.C.
/Jay Chatterjee/ Examiner, Art Unit 1662
/BRATISLAV STANKOVIC/Supervisory Patent Examiner, Art Units 1661 & 1662
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