DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Status
Claims 1, 3, 8, and 14 are amended.
Claims 10, 13, and 17 are cancelled.
Claims 1-3, 5-6, 8-9, 11-12, 14-16, and 18-20 are pending.
Claims 1-3, 5-6, 8-9, 11-12, 14-16, and 18-20 are examined on the merits.
Response to Amendment
The rejection under 35 U.S.C. 112(a) is withdrawn in view of the amendment.
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.
Claims 1-3, 5-6, 8-9, 11, 14-16 and 20 are rejected under 35 U.S.C. §103 as being unpatentable over Mullineaux (WO2022129856A1, filed 2021-11-18, published 2022-06-23) as applied claim 3 and 14, in view of Li (Li, Wenlan et al. Functional & integrative genomics 17.6, pp: 653-666, 2017), and further in view of Qi (Qungang Qi et. al., Journal of Biological Chemistry (2012) VOL 287, Number 37, pp31482-31493).
The rejection is applied to the claimed BBX10(DBB4) alternative. The DBB6 alternative is not relied upon for this rejection.
Claim 1 recites a guide nucleic acid that binds to a target site within an endogenous B-BOX(BBX) gene encoding a BBX transcription factor, the endogenous BBX gene comprising a sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:70 or SEQ ID NO:73; and encoding a polypeptide comprising a sequence having at least 90% sequence identity to the amino acid sequence of SEQ ID NO:71 or SEQ ID NO:74; and the target site comprising a nucleotide sequence encoding the B-BOX domain of the BBX transcription factor, wherein the B-BOX domain comprises an amino acid sequence having at least 90% sequence identity to any one of SEQ ID NOs:83-85, and wherein the BBX gene is a BBX10 (DBB4) gene or a DBB6 gene.
Mullineaux teaches guide nucleic acids used in CRISPR-Cas editing systems, wherein the guide nucleic acid comprises a spacer sequence that binds to at target site within an endogenous BBX gene encoding a BBX transcription factor, and further identifies Arabidopsis BBX32 as a BBX transcription factor that may be targeted and modified using the disclosed CRISPR-Cas (claim 9, and 11, and p29, line 15-30). Mullineaux further teaches using the guide nucleic acid to target and modify an endogenous BBX gene in a plant (claim 21 and 22, p29, line 15-30).
Mullineaux does not expressly teach that the endogenous BBX gene is a corn BBX10(DBB4) gene having the claimed sequence identity to SEQ ID NO: 70 and encoding a polypeptide having the claimed sequence identity to SEQ ID NO:71, or specifically targeting a region encoding the claimed B-Box domain.
Li teaches ZmDBB4 gene as GRM2M2G019335 (Chr4: 137141449-137142700 (-)). The instant application identifies DBB4/BBX10 as Zm00001d051018 (Zm00001d051018 Chr4: 137141449-137142700 (-)) (paragraph 0344), with SEQ ID NO: 69, 70, and 71 as genomic sequence, cDNA sequence and polypeptide sequence. Therefore, Li teaches the same gene as claimed DBB4/BBX10 (sequence information and alignment see below). Li further teaches that DBB4 comprises two B-BOX domains (Title; Abstract).
Qi further teaches the same Arabidopsis AtBBX32 contains an N-terminal B-BOX domain that is required for protein-protein interaction. Qi specifically demonstrates through deletion and site-directed mutagenesis that disruption of the B-BOX domain causes loss or substantial reduction of BBX32 binding activity. For example, deletion of N-terminal residues 1-17 resulted in loss of binding p31488, whereas mutation of conserved B-BOX metal-binding residues caused dramatic reduction in binding ; in contrast, a deletion outside the B-BOX did not significantly affect binding (p31488, Fig. 4B). Qi therefore teaches that the B-BOX is a functionally critical region of a BBX protein and that mutation of the B-BOX is an effective means for altering BBX activity (p31488-31489, Figs. 4-5).
It would have been obvious to one of ordinary skill in the art to apply the CRISPR-Cas BBX editing system of Mullineaux to the maize BBX10(DBB4) gene taught by Li, because Mullineaux teaches targeted genome editing of BBX transcription factor genes, and Li identifies maize BBX10(DBB4) as maize BBX/DBB transcription factor genes. It further would have been obvious to target the B-BOX domain because Qi teaches that the B-BOX is a functionally critical region of BBX32 and that mutation disrupting the B-BOX substantially reduces or eliminates BBX32 protein interaction. Thus, a skilled artisan seeking to alter BBX transcription-factor activity would have had reason to target a B-BOX-encoding region of Li’s maize DBB4 gene. A person of ordinary skill would have had a reasonable expectation of success because CRISPR-Cas guide nucleic acids are designed based on sequence complementarity to a selected genomic target site.
Accordingly, claim 1 is prima facie obvious over Mullineaux in view of Li and Qi.
Claim 2 is drawn to the guide nucleic acid of claim 1, , wherein the guide nucleic acid comprises a spacer having the nucleotide sequence of SEQ ID NO:86 or SEQ ID NO:87.
Regarding claim 2, Mullineaux in view of Li and Qi teaches the limitations of claim 2 for the same reasons set forth with respect to claim 1. It would have been obvious to one of ordinary skill in the art to selecta a spacer sequence complementary to a target site within the maize BBX10(DBB4) gene taught by Li, including the spacer sequences recited in claim 2, in order to direct site-specific CRISPR-Cas cleavage of the selected BBX10(DBB4) target site. SEQ ID NO:86 matching a segment within the cDNA of ZmDBB4 (GRMZM2G019335) (below). Therefore, claim 2 is prima facie obvious.
Claim 3 recites a gene editing system comprising a CRISPR-Cas effector protein in association with a guide nucleic acid, wherein the guide nucleic acid comprises a spacer sequence that binds to a B-BOX (BBX) gene encoding a BBX transcription factor, wherein the BBX gene is a BBX10 (DBB4) gene or a DBB6 gene, wherein the spacer sequence binds to a region of the BBX gene encoding the B-BOX domain of the BBX transcription factor, and wherein the BBX gene comprises a sequence having at least 80% sequence identity to the nucleotide sequence of SEQ ID NO:70 or SEQ ID NO:73 and encodes a polypeptide comprising a sequence having at least 90% sequence identity to the amino acid sequence of SEQ ID NO:71 or SEQ ID NO:74.
Regarding claim 3, Mullineaux in view of Li teaches the limitations of claim 3 for the same reasons set forth with respect to claim 1. Claim 3 further recites a gene editing system comprising a CRISPR-Cas effector protein in association with the guide nucleic acid. Mullineaux teaches a CRISPR-Cas effector protein in association with a guide nucleic acid comprising a spacer sequence that binds to a BBX gene (p29, line 15-30). Qi provides the reason to select the B-BOX-encoding region as the target, as discussed above. Therefore, claim 3 is prima facie obvious.
Claim 5 is drawn to the gene editing system of claim 3, wherein the guide nucleic acid comprises a spacer having SEQ ID NO:86 or SEQ ID NO:87.
Claim 5 is rejected for the same reasons set forth above with respect to claim 2 because claim 5 recites the same spacer sequence limitation, SEQ ID NO: 86 in the gene editing system of claim 3.
Claim 6 recites the gene editing system of claim 3, further comprising a tracr nucleic acid that associates with the guide nucleic acid and a CRISPR-Cas effector protein, optionally wherein the tracr nucleic acid and the guide nucleic acid are covalently linked.
Mullineaux discloses tracrRNA, CRISPR-Cas effector protein and sgRNA concepts directly (page 29, line 15-30). Accordingly claim 6 is obvious over Mullineaux, Li and Qi.
Claim 8 recites a method of editing a specific site in the genome of a corn plant cell using a CRISPR-Cas system directed to an endogenous BBX10(DBB4) gene or DBB6 gene having the recited sequence identities, wherein the edit results in a mutation in the B-BOX domain of the BBX transcription factor encoded by the endogenous BBX gene.
Regarding claim 8, Mullineaux in view of Li and Qi teaches the limitations of claim 8 for the same reasons set forth with respect to claim 3. Claim 8 further recites introducing the gene editing system into a corn plant cell and site -specific cleavage of the endogenous BBX10(DBB4) gene, thereby generating an edit in the endogenous BBX gene of the corn plant cell. Mullineaux teaches CRISPR-Cas mediated site-specific cleavage and editing of endogenous BBX genes in plant cells (p29, line15-30). It would have been obvious to apply the BBX-targeted CRISPR-Cas editing system of Mullineaux to the maize BBX10(DBB4) gene taught by Li in a corn plant cell and to generate the edit within the B-BOX domain because Qi teaches that mutations disrupting the B-BOX substantially alter BBX32 protein interaction/activity. Therefore, claim 8 is prima facie obvious.
Claims 9 is drawn to a method depending on claim 8, wherein a spacer sequence comprises a nucleotide sequence of SEQ ID NO:86 or SEQ ID NO:87 and is obvious for the same reasons set forth above with respect to claim 2.
Claim 11 is drawn to a method of claim 8, further comprising regenerating a corn plant from the corn plant cell comprising the edit in the endogenous BBX gene to produce a corn plant comprising the edit in its endogenous BBX gene.
Mullineaux teaches “In certain embodiments, one or more mutations are introduced into a least one plant cell and the plant is regenerated from the at least one mutated plant cell” (page 35, line 4-5). Therefore, claim 11 is prima facie obvious.
Claim 14 recites a method of generating variation in a plant BBX transcription factor, comprising contacting an endogenous BBX gene within a plant cell with a CRISPR-Cas editing system, wherein the system is targeted to a region of the gene that encodes the transcription factor, wherein the BBX gene is a BBX10(DBB4) or a DBB6 gene, and wherein variation is generated in a region of the BBX transcription factor comprising a B-BOX domain.
Mullineaux discloses a gene editing system(claim 9, 11, 12-14, 16, 18, 22, and page 29, line 15-30) to modify Arabidopsis BBX32 gene (a B-BOX transcription factor) through plant cell ( plant cell is plant part as claim 16 in Mullineaux). Qi further teaches that the B-BOX domain of BBX32 is functionally critical and that mutation within the B-BOX substantially reduces or eliminates BBX32 protein interaction. Accordingly, it would have been obvious to apply Mullineaux’s BBX editing system to Li’s maize BBX(DBB4) gene and generate the variation within its B-BOX domain in order to alter BBX activity, with a reasonable expectation of successfully introducing the targeted mutation.
Therefore, claim 14 is rejected as being unpatentable over Mullineaux in view of Li and Qi for the same reasons set forth above with respect to claim 1.
Claims 15 and 16 are drawn to the method of claim 14, wherein the endogenous BBX gene comprises a nucleotide sequence having at least 80% identity to SEQ ID NO: 70 or SE ID NO: 73 and encodes an amino acid sequence having at least 90% sequence identity of SEQ ID NO: 71 or SEQ ID NO:74 (claim 15), wherein the targeted region encodes an amino acid sequence having at least 90% sequence identity to any one of SEQ ID NOs:83-85 (claim16).
The sequence-identity limitations recited in claims 15 and 16 correspond to the BBX10(DBB4) gene and target-region limitations addressed above. Therefore, claims 15 and 16 are prima facie obvious for the same reasons set forth above.
Claim 20 recites a plant transformed with a recombinant DNA construct comprising a guide nucleic acid, wherein the guide nucleic acid comprises a spacer sequence that binds to a B- BOX (BBX) gene that comprises a region of homology of at least 98% sequence identity with at least 20 contiguous nucleotides with SEQ ID NO:86 or SEQ ID NO:87.
Mullineaux teaches plant transformation with a recombinant DNA construct/vector comprising a guide nucleic acid for CRISPR-Cas editing of an endogenous BBX gene in a plant cell (claim 9, and 11, 12, and p29, line 15-30). Mullineaux further teaches that the guide nucleic acid includes a spacer sequence complementary to a target site in the BBX gene and is used to introduce mutations into the endogenous BBX gene (claim 21 and 22, p29, line 15-30) .
Mullineaux does not expressly teach a guide nucleic acid that binds a BBX gene comprising a region having at least 98% sequence identity with at least 20 contiguous nucleotides of SEQ ID NO:86 or SEQ ID NO:87.
Li teaches maize BBX10/DBB4, the same maize DBB4 gene identified in the instant application, and the SEQ ID NO:86 matches a segment within the cDNA of ZmDBB4 /GRMZM2G019335. (below)
It would have been obvious to one of ordinary skill in the art to use the CRISPR guide/vector system of Mullineaux to target the maize DBB4/BBX10 gene sequence taught by Li, including a spacer sequence corresponding to a 20-nucleotide target region within the known DBB4 sequence, because selecting a guide spacer complementary to a known endogenous gene sequence is a routine CRISPR design step based on sequence complementarity and PAM compatibility.
Therefore, the recombinant DNA construct of claim 20 would have been obvious over Mullineaux in view of Li.
Claims 12, 18, and 19 are rejected under 35 U.S.C. §103 as being unpatentable over WO2022129856A1 (Mullineaux 2022), in view of Li (2017) and Qi (2012), as applied to claims 11 and 14 above, and further in view of Crocco (Carlos D. Crocco et. al., Nature communications 6:6202, pp1-10, 2015).
Claims 11 and 14 as the teachings of Mullineaux, Li and Qi are discussed above.
Claim 12 is interpreted as dependent of claim 11.
Claim 18 is interpreted as dependent of claim 14.
The rejection is applied to the claimed BBX10(DBB4) alternative. The DBB6 alternative is not relied upon for this rejection.
Claim 12 depends from claim 11 and is drawn to the corn plant comprising the edit in its endogenous BBX gene has an attenuated Shade Avoidance Response.
18 and 19 drawn to the method of producing edit plant and subsequent regenerating a plant from the edited cell, selfing the plant to obtain E1 progeny, and selecting progeny with reduced shade avoidance response relative to a control plant (claim 18), further comprising selfing the selected progeny to produce E2, and selecting progeny with reduced SAR relative to a control (claim 19).
Mullineaux teaches modifying an endogenous BBX transcription factor gene in a plant using targeted genome editing (e. g., CRISPR/Cas with a guide nucleic acid) to generate mutations in the endogenous BBX gene and to obtain plants having the resulting increasing photosynthesis and improving yield genotype (claim 24).
Mullineaux does not explicitly teach the particular maize BBX/DBB gene sequence set recited in claim12 (e. g., the specific SEQ ID NO selections and/or the “≥80% identity” framing as applied to the particular claimed maize BBX gene region/polypeptide).
Li teaches the identification/characterization of maize BBX/DBB genes, provides maize DBB/BBX genes sequence and structural (such as double B-box, without CCT domain)(fig 4, page 658), and points out BBX/DBB genes (DBB4/DBB6) “play an essential role in the light signaling pathway”(page 663), Li also teaches in BBX family “similar gene structures may share the similar gene functions”(page 663).
Qi teaches that mutation of the B-BOX domain can substantially disrupt BBX protein interaction, thereby providing the reason for generating the B-BOX-domain mutation required by amended claims 8 and 14.
Crocco teaches that BBX24 in Arabidopsis sharing the same structure as maize DBB4/6 (two B-Box)(page 2), and participating in light-response/photomorphogenesis networks (including shade avoidance response) (abstract). Crocco further teaches mutating BBX24 results “shade-response defect”(abstract).
It would have been obvious to one of ordinary skill in the art to apply Mullineaux’s CRISPR-based BBX editing approach to Li’s maize BBX10/DBB4, target the functionally important B-BOX domain as taught by Q1, regenerated plants and progeny, and screen the resulting edited plants for altered shade avoidance response in view of Crocco’s teaching that mutation of a BBX protein can produce a shade-response defect.
The claimed invention in claims 12, 18 and 19 as a whole is prima facie obvious over the combined teachings of the prior arts above.
Response to Applicant’s Remarks:
Applicant argues that Mullineaux and Li fail to teach or suggest targeting or mutating the B-BOX domain of BBX10 (DBB4) or DBB6 and fail to provide sufficient motivation for the claimed modification.
The arguments have been considered but are not persuasive in view of the rejection as presently formulated. Mullineaux is relied upon for CRISPR-Cas-mediated targeting and modification of an endogenous BBX transcription-factor gene, Li for maize BBX10(DBB4) and its B-BOX-containing structure, and Qi for teaching the functional importance of the B-BOX domain. Thus, the references in combination provide sufficient reason to target or modify the B-BOX domain as claimed.
Applicant further argues that the prior art does not teach disruption of BBX-DELLA interaction.
This argument is not persuasive because disruption of BBX-DELLA interaction is not a limitation of the pending claims. The claims require the recited targeting, mutation, or variation associated with the B-BOX domain, but do not require that such modification disrupt DELLA binding or operate through any particular mechanism.
With respect to claims 12, 18, and 19, Applicant’s arguments concerning the claimed shade-avoidance phenotype are likewise not persuasive because Crocco is relied upon for the additional teaching relating to shade-avoidance response, in combination with Mullineaux, Li, and Qi, as discussed in the rejection above.
Accordingly, Applicant’s arguments are not persuasive because the rejection is based on the combined teachings of the references.
PNG
media_image1.png
376
874
media_image1.png
Greyscale
PNG
media_image2.png
348
1024
media_image2.png
Greyscale
DBB4 from Li is 100% identity to BBX/DBB(SEQ ID NO:71)
PNG
media_image3.png
510
757
media_image3.png
Greyscale
The location of SEQ ID NO:86 is highlighted on GRMZM2G019335 cDNA
PNG
media_image4.png
587
975
media_image4.png
Greyscale
Arabidopsis BBX gene structure (Gangappa et al.,)
PNG
media_image5.png
808
773
media_image5.png
Greyscale
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-20 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 15, 24, 67, 89, 111, and 114 of copending Application No. US18593162 (reference application). Although the instant claims and the reference claims are not identical, they are not patentably distinct from each other because they do not add any non-obvious structural or procedural limitation beyond what is already claimed for editing the same endogenous BBX gene/target site.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Instant claims 8-17 recite introducing a targeted nuclease system (explicitly CRISPR-Cas) to cleave/edit the same endogenous BBX garget site defined by the same sequence identity limitations, thereby generating an edit/mutation, which is an obvious species/implementation of the reference’s claimed targeted nuclease editing of the same BBX loci (reference claim 67), including B-Box domain embodiments (reference claim 15) and reduced SAR embodiments (reference claims 24/89/114).
Instant claims 11, 18, and 19 add routine downstream steps (regenerating plants, selfing, assaying/sleeting progeny) that would have been obvious and conventional once the reference already claims producing plants having the BBX mutation and reduced SAR phenotype (reference claims 67, 89, 114). These steps do not render the claimed subject matter patentably distinct.
Instant claims 1-7 and 20 recite guides/CRISPR systems and transformed plants/constructs directed to binding /targeting the same BBX loci defined by the same sequence identity limitations. Such claims are obvious variants for practicing the reference’s claimed mutated plants and traits (reference claims 1, 24, 67, 89, 114), and therefore are not patentably distinct.
Accordingly, the claims 1-20 of application 18644352 are not patentably distinct from the claims of the reference application and a provisional obviousness-type double patenting rejection is appropriate.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to YANXIN SHEN whose telephone number is (571)272-7538. The examiner can normally be reached Monday-Friday.
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, Amjad A Abraham can be reached at (571)272-7058. 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.
/YANXIN SHEN/Examiner, Art Unit 1663
/WEIHUA FAN/Primary Examiner, Art Unit 1663
Prosecution Insights