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 without traverse of species of SEQ ID NO:5, including claims 1, 2, 4-20 in reply filed on 03/19/2026 is acknowledged.
Thus claims 1-2 and 4-20 are pending and the claim along with the elected species of SEQ ID NO:5 is examined in this office action.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code for example in page 17, lines 13 and 17. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claim 19 is rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter. The claim does not fall within at least one of the four categories of patent eligible subject matter because the claimed invention are directed to judicial exception (i.e., a law of nature, natural phenomenon, or an abstract idea) without significantly more.
Claim is drawn to a plant comprising a promoter comprising a cis regulatory element of as-1 like and a core promoter of a TATA box.
Singh et al. (US Patent No.: 5,847,102, Date of Patent: Dec. 8, 1998) discloses a winter B. napus cv Jet neuf where SEQ ID NO:1 was extracted (col. 7, lines 28-67, col.10 lines 21-25), wherein the transgenic expression to a B. napus cv. Wester showed increase GUS expression at low temperature (col. 9, lines 62-67). The sequence of SEQ ID NO:1 as showed in Figure 2 (see snippet of figure 2 below) showed the G box element of CACGTG and TATA box are 25 nucleotides apart. Furthermore, Teube et al. (Published: 2024, Journal: Theoretical and Applied Genetics 137:192 pages 1-23 https://doi.org/10.1007/s00122-024-04641-w) discloses B. napus cv Jet neuf is a traditionally bred cultivar since 1977 (page 16, left paragraph 2).
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The claim is interpreted as “product by process claim” wherein [E]ven though product by process claims are limited by and defined by the process, determination of patentability is based on the product itself. If the product in the product by process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process."
Thus, method of claim 1 would produce the SEQ ID NO:1 found in traditionally bred B. napus cv Jet neuf and the promoter is a naturally developed promoter.
Thus, the claims do not recite additional elements that amount to significantly more.
Claim Rejections - 35 USC § 112 - Indefiniteness
Claim 4 is 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.
Regarding claim 4, claim recite “wherein in step (i) less than 30 nucleotides are inserted, deleted and/or substituted at the first location and/or the second location” renders claim definite since less than 30 would also mean zero nucleotide inserted, deleted and/or substituted in the first and/or second location wherein claim 1 require introduction of at least a modification in the first and second position. Therefore the meets and bound of the claim cannot be determined since the dependent claim would need introduction of the CRE and CPE elements wherein the claim 4 that it depends would require any of less than 30 nucleotide inserted, deleted and/or substituted that would include no nucleotide modifications.
Claim Rejections - 35 USC § 112 – written description requirements
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 and 4-20 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
What is Described in the Specification?
Applicant describes:
The sequence of ZmCW13 is given in SEQ ID NO: 184.
The insertion of a cis-regulatory element (CRE) (E039g, SEQ ID NO: 5) in combination with an optimized TATA box (CTATAAATA) in the ZmCWl3 promoter led to a 110-fold increase in expression (SEQ ID NO: 189), wherein the two modifications alone only achieved a 5,6- or 21,2-fold increase (SEQ ID NOs: 186 and 187) (page 44, lines 6-10).
The CRE must be placed upstream of the TATA-box and if the CRE was placed downstream of the TATA-box, this resulted in a promoter activation not differing from the effect of the CRE alone (SEQ ID NO: 188) (see Figure 1) (page 44, lines 24-27).
In CWl3v3-2, the endogenous TATA box (CTACAAATA) was optimized by one point mutation to CTATAAATA (SEQ ID NO: 186). In CWl3v3-2-51-E039g, an as1-like CRE (E039g, SEQ ID NO: 5) is generated via site-directed mutagenesis at the -51 position, which is at an 18 bp distance to position v3-2 (SEQ ID NO: 219). The combining CRE and CPE leads to synergistic promoter activation of 194-fold and 246-fold (page 46 lines 36-38 and page 47, lines 1-5).
The as1 -like element E039g (SEQ ID NO: 5) is inserted via site-directed mutagenesis or oligo ligation at different positions upstream of the generated TATA-box in position v7 (Zm-prom7v7-50-E039g, Zm-prom7v7-1-E039g and Zm-prom7v7+8-E039g) in Zm-prom7 promoter wherein the CRE were in position -50, -1 and +8. The new combination of CRE and CPE leads to synergistic promoter activation of 241 to 417-fold (page 47, lines 10-20).
The effect of insertion of TATA box and as-1 like element of SEQ ID NO:5 to Zm-Prom8 promoter was also showed increase from 63 fold in case of TATA box insertion to 68 and 178 fold increase when CRE and CPE were combined (page 47, lines 24-37).
Difference Between What was Reduced to Practice and What is Claimed
Applicant has not described inserting or forming any of a cis regulatory element (CRE) the as1-like element, a G-box element, a double G-box element, a TEF-box promoter motif, a corn CYP promoter fragment and a corn adh1 promoter element in first position and a core promoter element (CPE) selected from a TATA box motif, a Y-patch motif, an initiator element and a downstream promoter element in second position would increase expression of any of a nuclei acid molecule of interest in any plant cell (claim 1).
Applicant has not described structure and associated function of any cis regulatory element (CRE) the as1-like element, a G-box element, a double G-box element, a TEF-box promoter motif, a corn CYP promoter fragment and a corn adh1 promoter element in first position and a core promoter element (claims 1 and 11).
Applicant has not described positioning any of the CRE and CPE at 5 to 225 would increase the expression of any gene (claims 1 and 11) and would increase expression by 20-fold (claims 10, 15).
Applicant has not described any modification with less than 30 nucleotides that are inserted, deleted and/or substituted at the first location and/or the second location” since the CRE and CPE would have more than 4 nucleotides to be inserted.
Applicant has not described increasing expression level of any nucleic acid molecule by introducing any CRE and CPE in any endogenous promoter other than promoter of specific sequence of genes ZmCWI3, BvHPPD1, Bv-prom3, BvHPPD2, Zm-prom6, BvFT2, Zm-prom2, Zm-prom7, Zm-prom8 (see Examples 1-11).
Applicant has not described a modified endogenous promoter comprising a cis regulatory element has 95% identity to SEQ ID NO:5 other than SEQ ID NO:5 itself (claims 16 and 17).
Applicant has not described a promoter sequence comprising CRE of SEQ ID NO:5 and CTATAAATA motif located downstream of the transcription start site (claim 18).
Applicant has not described the method of claim 20 utilizing SEQ ID NO:5 and CATAAATA in promoter of any gene can be used for increasing expression of any nucleic acid molecule in any plant cell.
Analysis
The purpose of the written description is to ensure that the inventor had possession at the time the invention was made, of the specific subject claimed. For a broad generic claim, the specification must provide adequate written description to identify the genus of the claim.
Applicant has not described inserting or forming any of a cis regulatory element (CRE) the as1-like element, a G-box element, a double G-box element, a TEF-box promoter motif, a corn CYP promoter fragment and a corn adh1 promoter element in first position and a core promoter element (CPE) selected from a TATA box motif, a Y-patch motif, an initiator element and a downstream promoter element in second position would increase expression of any of a nuclei acid molecule of interest in any plant cell (claim 1). For example, Xu et al. (Published: 1991, Nucleic Acids Research, Vol. 19(24): 6699-6704) teaches presence of gene specific TATA boxes wherein in mammals with various gene having different variants of TATA (page 6699, Abstract). Xu et al. teaches TATA box is a cluster of some 7 As and Ts flanked by more GC-rich sequence, and that the actual sequence would not be conserved where in some genes have specific TATA boxes conserved boxes (page 6704, left paragraph 1 and 2)). Furthermore, applicant’s definition of TATA box motif of Spec, page 11, lines 27-33 does not define specific TATA box instead showed large variants of sequences. Therefore, there is dearth of description of any TATA boxes would have increase the expression of any gene in any plant cell (claim 1). Furthermore, applicant has broad definition of a Y-patch motif, an initiator element and a downstream promoter element is formed (Spec, pages 11 and 12). Therefore there is dearth of description of inserting or forming any of a cis regulatory element (CRE) the as1-like element, a G-box element, a double G-box element, a TEF-box promoter motif, a corn CYP promoter fragment and a corn adh1 promoter element in first position and a core promoter element (CPE) selected from a TATA box motif, a Y-patch motif, an initiator element and a downstream promoter element in second position would increase expression of any of a nuclei acid molecule of interest in any plant cell (claim 1).
Applicant’s definition of as1-like element, a G-box element, a double G-box element, a TEF-box promoter motif, a corn CYP promoter fragment and a corn adh1 promoter element are broad (see Spec, page 10 and 11) where multiple variants are encompassed in the consensus sequence and open-ended definition of the cis acting regulatory elements (CRE). For example, Ishige et al. (Published: 1999, Journal: The Plant Journal 18(4): 443-448) teaches the various response of tissue specific gene expression enhancement by 11 different G box variants (page 445, last paragraph). Ishige et al. teaches G-box 5 is an inactive motif as it does not affect gene regulation wherein there are other variants for example 2-4, 8-10 that has lower expression compared to the 35s promoter (see part of Figure 1 below).
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Zhang et al. (Published: 2019, Journal: Plant Biotechnology Journal 17:724–735) teaches in both in native and synthetic soybean promoters changes to the core and flanking sequences of G-box elements lead to increases and decreases in gene expression in both native and synthetic soybean promoters (page724, abstract). Zhang et al. teaches G-boxes (CACGTG, GACGTG, TACGTG, CACGTT, AACGTG) (Figure 1a, c) in synthetic promoters using transient expression in lima bean cotyledons and stable expression in soybean hairy roots showed different levels of GFP expression driven by those G-box-containing sequences where changing the first and last nucleotide of G-boxes has lower promoter activity (Figure 1d–e) (page 728, last paragraph). Zhang et al. teaches the G-box variant ‘GACGTG’ had little, if any contribution to the high activity of the 4xEF4- M8C synthetic promoter (Figure 2) (page 729, left last paragraph). Therefore, specific sequence of CRE would have been required to have the function of recited increasing expression of the gene. Therefore, there is dearth of description of any of the recited CRE and CPE would increase expression of any of the nucleic acid of interest.
Applicant has not described a modified endogenous promoter comprising a cis regulatory element has 95% identity to SEQ ID NO:5 other than SEQ ID NO:5 itself (claim 16). Since the SEQ ID NO:5 is 9 nucleotide long the cis regulatory element has 95% identity to SEQ ID NO:5 comprise any of a point mutation in the sequence. There is dearth of description of which of the point mutation would increase expression of any of the genes in plant. For example, Zhang et al. teaches a slight variation such as ‘GACGTG’ had little, if any contribution to the high activity of the 4xEF4- M8C synthetic promoter (Figure 2) (page 729, left last paragraph).
Furthermore, Zhang et al. (Published: 2005, Journal: Bioinformatics, 21(14): 3074-3081) teaches cis-regulatory elements that are known to be responsible for the transcription of target genes (page 3074, Abstract Results) where in ACGT containing motifs are termed G-box (page3076, left paragraph 4). Zhang et al. teaches the ACGT core in ABREs is well conserved even though flanking sequences were beyond ACGT-core vary for example a rice ABRE is CGTACGTGTC, whereas an ABRE for maize is GACGTG and an ABRE for A. thaliana is CCACGTGG (page 3076, right paragraph 3). Therefore, there is dearth of description of any of the G box CRE with any structure would cause increased expression of any polynucleotides in any plant.
Furthermore, Applicant has not described positioning any of the CRE and CPE at 5 to 225 would increase the expression of any gene (claims 1 and 11) and would increase expression by 20-fold (claims 10, 15). For example, 5 showed the combination of CRE and CPE in the BvHPPD2 promoter has 17-fold increase in expression, Example 7 in the BvFT2 promoter had for example 14-fold increase. Therefore, there is dearth of description of introduction of any of the recited CRE and CPE in any promoter would have increased the expression at least 20-fold (claims 10, 15).
Given the large diversity in structure and function associated with claimed genus of a cis regulatory element (CRE) the as1-like element, a G-box element, a double G-box element, a TEF-box promoter motif, a corn CYP promoter fragment and a corn adh1 promoter element in first position and a core promoter element (CPE) selected from a TATA box motif, a Y-patch motif, an initiator element and a downstream promoter element in second position would increase expression of any of a nuclei acid molecule of interest in any plant cell, Applicant’s disclosure is not representative of the claimed genus as a whole. This point is particularly relevant because, as discussed above, the prior art speaks to the disconnection between the broadly claimed diverse structure of CRE and/or CPE and their function of increasing expression of any gene in any plant.
"The test for sufficiency is whether the disclosure of the application relied upon reasonably conveys to one skilled in the art that the inventor had possession of the claimed subject matter as of the filing date." Ariad Pharm, Inc, v EH Lilly & Co., 598 F.3d 1336, 1351 (Fed. Cir. 2010). To satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. Lockwood v. Amer. Airlines, ina, 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966 (Fed. Cir. 1997). "An applicant shows possession of the claimed invention by describing the claimed invention with all of its limitations. Lockwood, 107 F.3d at 1572, 41 USPG2d at 1966". While the written description requirement does not demand either examples or an actual reduction, actual "possession" or reduction to practice outside of the specification is not enough. Ariad Pharm, Inc. v. Eli Lilly & Co., 598 F,3d 1336,1352 (Fed. Cir. 2010). Rather, it is the specification itself that must demonstrate possession. Id.
Thus, based on the analysis above, Applicant has not met either of the two elements of the written description requirement as set forth in the court's decision in Eli Lilly. As a result, it is not clear that Applicant was in possession of the claimed genus at the time this application was filed.
Claim Rejections - 35 USC § 102
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 19 is rejected under 35 U.S.C. 102 (a)(1) and/or (a)(2) as being anticipated by Singh et al. (US Patent No.: 5,847,102, Date of Patent: Dec. 8, 1998).
Claim is drawn to a plant comprising a promoter comprising a cis regulatory element of as-1 like and a core promoter of a TATA box.
Following analysis based on the In re Thorpe, 777 F.2d 695, 698, 227 USPQ 964, 966 (Fed. Cir. 1985) which teaches “[E]ven though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process.” Hence a product-by-process claim may be properly rejectable over prior art teaching the same product produced by a different process, if the process of making the product fails to distinguish the two products.
Singh et al. teaches a winter B. napus cv Jet neuf where SEQ ID NO:1 was extracted (col. 7, lines 28-67, col.10 lines 21-25), wherein the transgenic expression to a B. napus cv. Wester showed increase GUS expression at low temperature (col. 9, lines 62-67). The sequence of SEQ ID NO:1 as showed in Figure 2 (see snippet of figure 2 above) showed the G box element of CACGTG and TATA box are 25 nucleotides apart.
Therefore Singh et al. anticipates the claim.
Anticipated by Banerjee et al.
Claim 19 is rejected under 35 U.S.C. 102 (a)(1) as being anticipated by Banerjee et al. (Published: 2015, Journal: Plant Mol Biol Rep (2015) 33:532–556 DOI 10.1007/s11105-014-0766-5).
Claim is drawn to a plant comprising a promoter comprising a cis regulatory element of as-1 like and a core promoter of a TATA box.
Following analysis based on the In re Thorpe, 777 F.2d 695, 698, 227 USPQ 964, 966 (Fed. Cir. 1985) which teaches “[E]ven though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process.” Hence a product-by-process claim may be properly rejectable over prior art teaching the same product produced by a different process, if the process of making the product fails to distinguish the two products.
Banerjee et al. discloses a region containing as-1-like sequence (TGGCCG, position −50 to −45 from TSS) upstream of the TATA box sequence which are 12 nucleotides apart (page 539, Figure 1). Banerjee et al. discloses expression of the nucleic acid in a tobacco seedling (page 542, Figure 3).
Banerjee et al. discloses in their experiments as-1-like element is the major determinant of the high level of expression of the DaMVSgt promoter (page 554, left paragraph 1). Banerjee discloses for example when as-1 like and TATA box motif were deleted for example in deletion variant 6 and 7 wherein the expression was very low compared to the variant with such motifs (see Figure 2 below). Banerjee et al. discloses the higher expression was observed when the expression was within 22 nucleotide the expression was highest (page 539, Figures 1 and 2, see figure 2 above).
Therefore Banerjee et al. anticipate the claim 19.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Obvious over Zhang et al. and further in view of Shrestha et al. and Grace et al.
Claims 7 and 10-15 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (Published: 2019, Journal: Plant Biotechnology Journal 17:724–735) and further in view of Shrestha et al. (Published: 2018, Journal: Plants. Mol. Plant. 11: 886–898), and further in view of Grace et al. (Published:2004, Journal: The journal of biological chemistry, 279(9)8102-8110).
Claims are drawn to a promoter which is endogenous to a plant cell which has been modified to have increased expression and the promoter comprise a heterologous G-box cis regulating element and a heterologous tata box motif of CTATAAATA.
Regarding claims 7 and 10-15, Zhang et al. teaches fusing fragment tetramers G-box elements to the 35S core promoter increase GFP expression by more than 120% (page 726, Figure 1) wherein the 35S core promoter is 35ScorepFLEV (GenBank accession number: KX814441) or GmScreamM8C-pFLEV plasmids (GenBank accession number: KX252740). The KX252740 showed there is the TATA box CTATAAATA at position 432-440 (see enclosed PDF for the access sequence).
Zhang et al. teaches introduction of G-box element from GmScream promoters in 35S core promoter in lima bean cotyledons would increase the expression of GFP by over 120-fold (page 726, Figure 1, page 725, right paragraph 1).
Furthermore, Grace et al. teaches the tata box sequence CTATAAATA as a Tata box T2 (page 8104, Fig. 1). Grace et al. teaches mutation in the CTATAAATA as mTATA2 yielded about half expression activity (i.e. 54%) compared to control, showing presence of full sequence would have increased expression. Grace et al. teaches statistically significant reduction in GUS activity due to these mutations indicates TATA2 as CTATAAATA contribute to the overall high level of expression from the phas promoter in common bean (P. vulgaris) plant (page 8104, right paragraph 1).
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Shrestha et al. teaches two adjacent key elements should be placed at least four to five base pairs apart to facilitate transcription (page 888, right first paragraph). Shrestha et al. teaches consideration of optimal element spacing is also required when engineering promoters because the size of each DNA fragment should match the physical conformation of the TF/cis-element binding complex.
Therefore, the space between the G-box element and TATA box element would be an optimization parameter.
The space between the G-box element and TATA box element are empirically determined and is an optimization of process parameters. According to section 2144.05 of the MPEP, “[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.” In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955). See also Peterson, 315 F.3d at 1330, 65 USPQ2d at 1382 (“The normal desire of scientists or artisans to improve upon what is already generally known provides the motivation to determine where in a disclosed set of percentage ranges is the optimum combination of percentages.”).
A particular parameter must first be recognized as a result-effective variable, i.e., a variable, which achieves a recognized result, before the determination of the optimum or workable ranges of said variable might be characterized as routine experimentation. In re Antonie, 559 F.2d 618, 195 USPQ 6 (CCPA 1977). Prior art teaches the fusion of a G-box element in a TATA box CTATAAATA containing promoter of 35S increased expression upto 120-fold of GFP, therefore, determining the effective spacing between the G box element and TATA box element is a routine experimentation.
Therefore it would have been obvious before the effective date of filling from some teaching, suggestion, or motivation in the Zhang et al. and Grace et al. to introduce specific G-box element upstream of the TATA box element of CTATAAATA in a endogenous promoter in a plant and would optimize the separation by 15-60 nucleotides as suggested by Shrestha et al. and Zhang et al. leading to the development of a modified promoters that could be screened to find increased expression of a nucleic acid.
Regarding claims 10 and 15, Zhang et al. teaches introduction of G-box element from GmScream promoters in 35S core promoter in lima bean cotyledons would increase the expression of GFP by over 120-fold (page 726, Figure 1, page 725, right paragraph 1).
Obvious over Zhang’17 et al. and further in view of Shrestha et al. and Banerjee et al.
Claims 1, 2, 4, 5-7 and 9 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang’17 et al. (Published: 2017, Journal: Plant Physiology, 173: 715–727), and further in view of Shrestha et al. (Published: 2018, Journal: Plants. Mol. Plant. 11: 886–898), and further in view of Banerjee et al. (Published: 2015, Journal: Plant Mol Biol Rep (2015) 33:532–556 DOI 10.1007/s11105-014-0766-5).
Claims are drawn to a method of increasing the expression level of a nuclei acid wherein the method comprise introducing a first cis regulatory element as an as I-like element, a G-box element, a double G-box element, a TEF-box promoter motif, a corn CYP promoter fragment and a corn adh1 and a second core promoter element as a TATA box motif, a Y-patch motif, an initiator element and a downstream promoter element. Claims are drawn wherein the first and second modifications are separated by 5-225 nucleotides.
Regarding claims 1 and 4, Shrestha et al. teaches plant promoters are modulate in nature and the domains of a plant promoter can be deleted or exchanged with others to reconstitute an engineered promoter module with an altered cis cloud, resulting in tailored functionality.
Shrestha et al. teaches the distance between the core promoter (or more precisely, the TATA box) and the proximal cis elements affects the level of gene expression which is either positively or negatively regulated by distal factors (page 887, right last paragraphs, see figure 1 lower panel below). Shrestha et al. teaches engineering any element in the proximal region (by addition, deletion, substitution, or duplication) inevitably affects the activity of the core promoter (page 888, left paragraph 1).
Shrestha et al. teaches two adjacent key elements should be placed at least four to five base pairs apart to facilitate transcription (page 888, right first paragraph).
Shrestha et al. teaches synthetic promoter can contain multiple cis-acting elements that respond to different activation pathways including salicylic acid, jasmonic acid, and ethylene due to for example presence of DRE, ABRE and as-1 elements on promoters (page 889, left paragraph 1).
Zhang’17 et al. teaches TATA-box insertion in the promoter region upstream of the coding region exhibited increased Iron-Regulated Transporter1 (IRT1) expression in apple plants leading to adaptation in Fe deficiency and enhancing expression (page 715, Abstract). Zhang et al. teaches that the insertion is -363 to -357 bp from the ATG start site (page 716, col. 2, para 2). Zhang’17 teaches at least a 4-fold increase in the expression level of the nucleic acid molecule of interest in cells containing the nucleic acid construct or expression cassette [Fig. 4] (regarding claims 1 and 4).
Banerjee et al. teaches a region containing as-1-like sequence (TGGCCG, position −50 to −45 from TSS) upstream of the TATA box sequence which are 12 nucleotide apart (page 539, Figure 1).
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Banerjee et al. teaches in their experiments as-1-like element is the major determinant of the high level of expression of the DaMVSgt promoter (page 554, left paragraph 1). Banerjee teaches for example when as-1 like and TATA box motif were deleted for example in deletion variant 6 and 7 the expression was very low compared to the variant with such motifs (see Figure 2 below). Therefore, it would have been obvious to insert TATA box and as-1 like motifs in the polynucleotide of variant 6 and 7 that would lead to the increased expression of the gene under DaMVSgt promoter.
Therefore it would have been obvious before the effective date of filling from some teaching, suggestion, or motivation in the Zhang’17 et al. to develop a method to insert TAT box in the promoter region upstream of the coding region of IRT1 gene in apple plant and enhance expression and furthermore, insert a as -1 like element as TGGCCG that was found have effect on increasing expression when places upstream to a TATA box that would lead to increase the expression of the nucleic acid molecule of interest.
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Regarding claim 2, since applicant has not defined negative term and the prior art would use negative (“-‘) sign showing upstream of transcription of start site. The negative sign here is interpreted as showing upstream of start codon as recited in the claim.
Banerjee et al. teaches the TATA box is located about 179 nucleotides upstream of start codon (page 539, Figure 1, see figure below).
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Greyscale
Regarding claim 4, it would have been obvious to introduce CRE of less than 30 nucleotides for example 1-like sequence is six nucleotide long (i.e.TGGCCG) (page 539, Figure 1).
Regarding claim 9, Banerjee et al. teaches the higher expression was observed when the expression was within 22 nucleotide the expression was highest (page 539, Figures 1 and 2, see figure 2 above). Therefore, it would have been obvious to separate the TATA box from as-1 element to be at least 15 nucleotides apart.
Obvious over Zhang’17 et al. and further in view of Shrestha et al. and Banerjee et al.
Claims 1 and 6 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang’17 et al. and further in view of Shrestha et al., and further in view of Banerjee et al. and further in view of Rodriguez et al. (Published: 2017, Journal: Cell 171: 470–480).
Regarding claim 1, Shrestha et al. teaches the distance between the core promoter (or more precisely, the TATA box) and the proximal cis elements affects the level of gene expression which is either positively or negatively regulated by distal factors (page 887, right last paragraphs, see figure 1 lower panel below). Shrestha et al. teaches engineering any element in the proximal region (by addition, deletion, substitution, or duplication) inevitably affects the activity of the core promoter (page 888, left paragraph 1). Shrestha et al. teaches CRISPR-Cas9 technology can be used for introducing CRE elements in promoter effecting transcription level of a gene of interest (page 889, left first paragraph).
Zhang’17 et al. teaches TATA-box insertion in the promoter region upstream of the coding region exhibited increased Iron-Regulated Transporter1 (IRT1) expression in apple plants leading to adaptation in Fe deficiency and enhancing expression (page 715, Abstract). Zhang et al. teaches that the insertion is -363 to -357 bp from the ATG start site (page 716, col. 2, para 2). Zhang’17 teaches at least a 4-fold increase in the expression level of the nucleic acid molecule of interest in cells containing the nucleic acid construct or expression cassette [Fig. 4] (regarding claims 1 and 4).
Banerjee et al. teaches a region containing as-1-like sequence (TGGCCG, position −50 to −45 from TSS) upstream of the TATA box sequence which are 12 nucleotides apart (page 539, Figure 1).
Shrestha et al. Zhang’17 et al. and Banerjee et al does not show insertion of the CRE of CPE using CRISPR Cas 9 system.
Rodriguez et al. teaches insertion, deletion and substitution in SICLV3 promoter cis regulatory region using CRISPR Cas9 mutagenesis using multiple guide RNAs wherein deletion, and insertion in different region causes variation in relative expression of the SICLV3 and SIWUS genes (Figure 4) (page 472, left paragraph 2).
Therefore, it would have been obvious to insert the as 1 like element as CRE and Tata box as CPE using more efficient and targeted insertion method of using a CRISPR Cas9 system leading to variation in expression of the gene of interest and it would have been obvious to select for increased expression of gene for example IRT1 that would have increased adaption to Fe deficiency.
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).
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Claims 1-2, 4-7, 11-14 and 19 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 11 of copending Application No. 17040943 (Hereafter referenced as ‘943) in view of Shrestha et al., Zhang et al. and Banerjee et al.
Regarding claims 1-2 and 7, copending Application ‘943 claim 1 teaches a method for increasing the expression level of a nuclei acid molecule of interest in a plant cell wherein the method comprises introducing promoter activating nuclei acid sequence identical to CTATAAATA (E59a).
copending Application ‘943 claim 1 teaches the CTATAAATA is inserted 50-500 nucleotide upstream of the transcription start site and >50 nucleotides of the stat codon of the nucleic acid molecule.
copending Application ‘943 does not teach inserting first a cis regulatory element (CRE) the as1-like element, a G-box element, a double G-box element, a TEF-box promoter motif, a corn CYP promoter fragment and a corn adh1 promoter element in first position.
Shrestha et al. teaches the distance between the core promoter (or more precisely, the TATA box) and the proximal cis elements affects the level of gene expression which is either positively or negatively regulated by distal factors (page 887, right last paragraphs, see figure 1 lower panel below). Shrestha et al. teaches engineering any element in the proximal region (by addition, deletion, substitution, or duplication) inevitably affects the activity of the core promoter (page 888, left paragraph 1).
Zhang et al. teaches fusing fragment tetramers G-box elements to the 35S core promoter increase GFP expression by more than 120% (page 726, Figure 1) wherein the 35S core promoter is 35ScorepFLEV (GenBank accession number: KX814441) or GmScreamM8C-pFLEV plasmids (GenBank accession number: KX252740). The KX252740 showed there is the TATA box CTATAAATA at position 432-430 (see enclosed PDF for the access sequence).
Banerjee et al. teaches a region containing CRE of as-1-like sequence (TGGCCG, position −50 to −45 from TSS) upstream of the TATA box sequence which are 22 nucleotide apart (page 539, Figure 1).
Banerjee et al. teaches in their experiments as-1-like element is the major determinant of the high level of expression of the DaMVSgt promoter (page 554, left paragraph 1). Banerjee teaches for example when as-1 like and TATA box motif were deleted for example in deletion variant 6 and 7 the expression was very low compared to the variant with such motifs (see Figure 2 below). Therefore, it would have been obvious to insert TATA box and as-1 like motifs in the polynucleotide of variant 6 and 7 that would lead to the increased expression of the gene under DaMVSgt promoter.
Therefore, it would have been obvious to insert a G Box element upstream of TATA box CTATAAATA leading to higher expression and the separate them for example 22 (i.e. 5 to 225) nucleotide apart since Banerjee found a CRE and TATA box when separated by 22 nucleotide apart had the highest expression of the gene.
Regarding claims 4 and 14, Banerjee et al. teaches the higher expression was observed when the expression was within 22 nucleotide the expression was highest (page 539, Figures 1 and 2, see figure 2 above). Therefore, it would have been obvious to separate the TATA box from as-1 element to be at least 15 nucleotides apart.
Regarding claims 5-6, copending Application ‘943 claims 1 and 11 teaches site specific CRISPR nuclease with guide RNA to insert the CTATAAATA.
Regarding claim 19, the plant cell would have been obviously produced by the method of claim 1.
Regarding claims 10 and 15, Zhang et al. teaches introduction of G-box element from GmScream promoters in 35S core promoter in lima bean cotyledons would increase the expression of GFP by over 120-fold (page 726, Figure 1, page 725, right paragraph 1).
Therefore, it would have been obvious to insert the Gbox element and the tata box element as CTATAAATA and screen the variants to find the 20-fold increase in expression of the genes in the variants.
This is a provisional nonstatutory double patenting rejection.
Summary
No claim is allowed.
Claims 8, 16-18 and 20 appear to be free of the prior art. The closest prior art is Zhang et al. teaches fusing fragment tetramers G-box elements to the 35S core promoter increase GFP expression by more than 120% (page 726, Figure 1) wherein the 35S core promoter is 35ScorepFLEV (GenBank accession number: KX814441) or GmScreamM8C-pFLEV plasmids (GenBank accession number: KX252740). The KX252740 showed there is the TATA box CTATAAATA at position 432-430 (see enclosed PDF for the access sequence). The patentable distinction is Zhang et al. does not teach inserting or forming a cis regulatory element of SEQ ID NO:5 or has a sequence being 95% identical to SEQ ID NO:5.
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/SANTOSH SHARMA/Examiner, Art Unit 1663
/DAVID H KRUSE/Primary Examiner, Art Unit 1663
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