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 .
Election/Restrictions
Applicant’s election of Group I (claims 1-3, 5-6, 9-10, 12-13, 15 and 20-22) in the reply filed on 6/17/2026 is acknowledged. In response to the species election requirement Applicant elects a viral protein from Tobacco Rattle Virus (TRV) (in claim 10); a viral protein from Tobacco Rattle Virus (TRV) (in claim 12); and c) an RNA-guided nuclease (in claim 20).
Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
The requirement is still deemed proper and is therefore made FINAL.
Claim Status
Claims 1-3, 5-6, 9-10, 12-13, 15 and 20-22 are pending and being examined.
The Applicant canceled all the non-elected claims, i.e., claims 23-28.
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.
Written Description
Claims 1-3, 5-6, 9-10, 12-13, 15 and 20-22 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.
Claim 1 is drawn to a method for modifying a plant genome using a recombinant DNA construct encoding a site-specific endonuclease operably linked to a viral protein, grafting a scion lacking the recombinant DNA construct to said transgenic plant, and selecting at least a first cell from said scion comprising a genomic modification resulting from the presence of said site-specific endonuclease.
The claim encompasses any viral protein. However, the Applicant describes TRV RNA2 fused to Cas9 as cloned in the pFGR32 vector (spec, p.10, para 0047; p.53, Table 1; p.55, para 0219, line 3). The TRV2 (TRV RNA2) encodes a TRV coat protein set forth by the SEQ ID NO: 42 (spec, p.12, para 0088) encoded by the polynucleotide sequence at position from 9634 to 10248 in pFGR32 (SEQ ID NO: 1) (data not shown). The Applicant does not describe any viral protein other than the TRV coat protein operably linked to a DNA construct encoding a site-specific endonuclease.
The invention needs the viral protein to be able to move from cell-to-cell and capable for long distance transport in a plant, to spread systemically via the vasculature and across a graft junction (specification, paragraph bridging p. 13-14). Such movement would enable a fusion protein fused to the viral (movement) protein. The Applicant does not describe the protein structure and function relationship for a viral protein to be able to move long distance systematically inside a plant.
Current status of the art does not describe any exhaustive list of viral proteins capable to move long distance systematically inside a plant. Current status of the art also does not describe any structure and function relationship for a viral protein to be able to move long distance systematically inside a plant. In many plant viruses, the Coat Protein (CP) is not able to move from cell to cell and/or is not required for cell-to-cell movement. Based on the requirement for coat protein (CP) and on the form that the specialized Movement Protein (MP) adopts during cell-to-cell movement, three different transport mechanisms have been reported. Two of the methods do not need the coat protein while the third mechanism does need the coat protein (Herranz et al., Mutational analysis of the RNA-binding domain of the Prunus necrotic ringspot virus (PNRSV) movement protein reveals its requirement for cell-to-cell movement, 2005, Virology, 339:3-41; p.31, the bridging paragraph between left and right column). Thus, the TRV coat protein is not representative of the genus of viral proteins for this function.
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.
Scope of Enablement
Claims 1-3, 5-6, 9-10, 12-13, 15 and 20-22 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 TRV coat protein and other known viral movement proteins including from TRV, does not reasonably provide enablement for all viral proteins. 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 use the invention commensurate in scope with these claims.
The Applicant describes TRV RNA2 fused to Cas9 as cloned in the pFGR32 vector (spec, p.10, para 0047; p.53, Table 1; p.55, para 0219, line 3). The specific TRV virus and the TRV RNA2 encoded by the viral geome encodes a TRV coat protein set forth by the SEQ ID NO: 42 (spec, p.12, para 0088) encodes by the polynucleotide sequence in position from 9634 to 10248 in p pFGR32 (SEQ ID NO: 1), data not shown.
The viral protein needs to be able to move from cell-to-cell and capable for long distance transport in a plant. That would enable a fusion protein fused to the viral (movement) protein. The applicant does not describe a viral protein other than TRV coat protein able to move long distance systematically inside a plant.
The Applicant does not provide any guidance how on to create a fusion protein between a site-specific endonuclease (like Cas9) and a viral protein that is capable to move long distance systematically inside a plant.
Current status of the art does not teach any exhaustive list of viral proteins (from all the known viruses), other than movement proteins and few other proteins, capable to move long distance systematically inside a plant. In many plant viruses, the Coat Protein (CP) is not required for cell-to-cell movement or systemically in the plant. Based on the requirement for coat protein (CP) and on the form that the MP adopts during cell-to-cell movement, three different transport mechanisms have been reported and two of the methods do not need the coat protein while the third mechanism does need the coat protein (Herranz et al.; p.31, the bridging paragraph between left and right column).
Undue trial and error experimentations would be needed to make a viral protein which is capable to move long distance systematically inside a plant as a fused protein with another protein.
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.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
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.
Claims 1-3, 5-6, 9-10, 12-13, 15 and 20-22 are rejected under 35 U.S.C. 103 as being unpatentable over Yang et al. (Heritable transgene-free genome editing in plants by grafting of wild-type shoots to transgenic donor rootstocks, 2023, Nature Biotechnology, 41:958-967; published on 2 January 2023) in view of Deng et al. (Modification of Tobacco rattle virus RNA1 to Serve as a VIGS Vector Reveals That the 29K Movement Protein Is an RNA Silencing Suppressor of the Virus, 2013, MPMI, 26:503–514), Lucas W. J. (Plant viral movement proteins: Agents for cell-to-cell trafficking of viral genomes, 2006, Virology, 344:169 – 184) and Wang et al. (Increasing the efficiency of CRISPR/Cas9-based gene editing by suppressing RNAi in plants, 2019, Sci. China Life Sci., 62:982–984).
Claim 1 is drawn to a method for modifying a plant genome using a recombinant DNA construct encoding a site-specific endonuclease operably linked to a viral protein, grafting a scion lacking the recombinant DNA construct to said transgenic plant, and selecting at least a first cell from said scion comprising a genomic modification resulting from the presence of said site-specific endonuclease.
Yang et al. describes a graft-mobile gene editing system that enables the production of transgene-free offspring in one generation without the need for transgene elimination and culture recovery by using recombinant DNA constructs encoding fusions of a RNA-guided site-specific endonuclease (Cas9) (as recited in claim 20) and guide RNA transcripts to tRNA-like sequence motifs (TLS) that move RNAs from transgenic rootstocks to grafted wild-type shoots (scions) (that does not have the transgene) and achieve heritable gene editing in wild-type Arabidopsis thaliana and Brassica rapa (abstract).
Transcript mobility is introduced by tRNA-like sequence (TLS) motif and variants thereof to enable transport of protein encoding transcripts including mRNA in Arabidopsis and Nicotiana tabacum (p.963, right column, para 1, line 24-25) (as recited in claim 13) over graft junctions (p.958, left column, para 1, last 3 lines). The Cas9 along with other transcripts encoding gRNAs fused to TLS expressed in rootstock are detected in grafted plants in scion tissues (p.961, left column, para 2, line 21-23). The Cas9-TLS, gNIA1-TLS, gVenus1 and gVenus2 fusions are delivered to wild-type flowers and cause heritable edits (deletion) in the germline cells (p.961, left column, para 2, line 8-10; p.961, right column, para 2, line 3-4). The NIA1 gene (part of it is deleted) (p.960, Fig. 2; p.962, Fig. 3) and Venus fluorescence gene (encoding the Venus fluorescent protein) (p.959, left column, para 1, line 1-3) (reads on to “transcribable region of the genome”, as recited in claim 21) is edited, as recited in claim 13, in the grafted wild type scion. The genome editing resulted in alerted phenotype as it shows loss of Venus fluorescence in the homozygous lines (p.961, right column, para 3, line 21-25; p.974, Fig. 4), as recited in claim 22.
The polynucleotide sequences encoding Cas9, TLS motif, and the gRNA reads on to “heterologous DNA molecule”, as recited in claim 13. Yang et al. describes using 35S promoter (p.961, right column, para 2-3) operably linked to the transcribable DNA sequence, as recited in claim 15.
Yang et al. teaches that the wild-type scion cultivar grafted onto a given transgenic rootstock donor can belong to a very distant plant family. For example, A. thaliana and Nicotiana sp. can easily be used as rootstocks for a very wide range of quite distantly related species including tomato, carrots, soybean, and onions (p.966, left column, para 2, line 3-7), implying that N. tabacum can be used as both the wild-type scion and/or transgenic rootstock, as recited in claim 13.
Yang et al. describes that the grafting method enables Cas9-TLS mRNA and gRNA-TLS fusions to be delivered directly to germline progenitor cells where they edit the genome (p.965, bridging paragraph between right column and left column). Yang et al. describes generating a plant while using antibiotics as selection agent (p.968, left column, para 4, last 3 lines). It is implied that the polynucleotide sequence encoding the selectable marker gene (antibiotic resistance gene) is stably integrated into the plant genome (as recited in claim 6) as it’s heritable through subsequent generations. Yang et al. also teaches the well-known regeneration and selection of the edited plant material which includes a cell from the genome edited scion (reads on to “the first cels”), as recited in claims 1-3. It is well known in the art that selection of a transgenic or a genome edited cell/tissue to regenerate a plant involve using a selection agent and involve organogenesis which produces roots and shoots, as recited in claims 3 and 5.
However, Yang et al. does not describe any viral protein (e.g. viral movement protein) able to move systemically within a plant.
Deng et al. describes Tobacco Rattle Virus (TRV) (as recited in claim 10) genome encodes two proteins, 29K and 16K (as recited in claim 12), that function as movement proteins and a suppressor of RNA silencing, which is a basal cellular antiviral defense mechanism that targets double-stranded RNA including the replicative forms of viral RNA (p. 503, bridging paragraph between left column and right column).
Lucas W.J. describes that proteins fused to a viral movement protein (p.173, left column, para 1, line 6-9), and/or DNA or RNA (including mRNA) bound to the movement protein(s) can travel long distance within a plant through plasmodesmata by means of vascular system (abstract), which develops in/around the graft junction for successful grafting to keep the scion alive and thrive.
Before the effective filing date of the invention, it would have been prima facie obvious to an ordinarily skilled artisan to modify the method as described by Yang et al. by replacing the TLS sequence with the polynucleotide sequence encoding TRV viral movement protein(s) 29K and/or 16K (which reads on to “second DNA construct encoding a movement protein, as recited in claim 9), as described by Deng et al.
Before the effective filing date, the ordinarily skilled artisan would have been motivated to modify the method described by Yang et al. by replacing the TLS sequence with the polynucleotide sequence encoding the TRV viral movement protein(s) 29K and/or 16K. Using the TRV movement protein(s) like 29K and/or 16K would offer an added advantage by suppressing virus-induced gene silencing (or RNA silencing or post-transcription gene silencing, PTGS) that that targets double-stranded RNAs, would have a realistic expectation to increase genome editing efficiency while using CRISPR-Cas technique, as described by Wang et al. (title; p.984, right column, para 2, last 7 lines), by suppressing endogenous RNA silencing pathway (including RNAi) while improving editing efficiency by CRISPR-Cas.
Conclusion
No claim is allowed.
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..
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
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.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
J.C.
/Jay Chatterjee/Examiner, Art Unit 1662
/BRATISLAV STANKOVIC/Supervisory Patent Examiner, Art Units 1661 & 1662
Prosecution Insights