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 .
This is a Final Office Action in response to amendment filed on September 29, 2025.
Claims 2-8 have been canceled. Claims 24-28 are newly added. Claims 1, 9, 10, 13, 17, 18, 20, 22, and 23 have been amended. Claims 1, 9-18, and 20-28 are pending and examined herein.
Response to Amendment
The objection to the Specification regarding Sequence Rules is withdrawn in view of the amendment and the submission of Sequence Listing.
The objection to the Specification regarding typographic errors of amino acid numbering is withdrawn in view of the amendment.
In view of the timely submitted certified English translation of the foreign application, the application is granted with the benefit of foreign priority, dated April 2, 2021.
The objection to Claims 7-8 regarding typographic errors of amino acid numbering is withdrawn in view of the amendment.
The rejection of Claims 1-2, 4-5, 7-18, and 20-23 under 35 U.S.C. 112(b) is withdrawn in view of the amendment.
The rejection of Claims 1-2, 5, 7-8, 10-13, under 35 U.S.C. 102(a)(1) and (a)(2) over [Johnson et al . US6018105A, 2000] regarding the embodiment of Y426M, is withdrawn in view of the amendment.
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.
Claims 10-13 and 22 remain, and claims 24-26 are newly rejected under 35 U.S.C. 101 because the claimed invention is directed to a product of nature which is a Judicial Exception without significantly more.
Claim 10 is directed to an isolated polynucleotide, which is a product, falling into one of the four categories under 101.
The isolated nucleotide comprises, especially, a nucleic acid sequence that hybridizes to 1)—which is nucleic acid sequence encoding the PPO polynucleotide according to claim l.
These encompass the nucleic acid of the naturally occurring nucleic acid reads on naturally occurring genomic DNA that, due to the minimal differences at the two positions of the encoded amino acid variance, can hybridize with the polynucleotide encoding the PPO variants of claim 1. For example, rice genomic locus LOC_Os10g33430 is a sequence that would hybridize with a nucleotide that encode the rice PPO polypeptide of SEQ ID NO: 1 even with the two amino acid mutations. Similarly, the genomic DNA of Arabidopsis thaliana also comprises a sequence that would hybridize with the nucleotide that encode the PPO polypeptide even with the two variations.
As such, the hybridizing sequence also reads on the naturally occurring plant genome DNA, or transcription product thereof, for that matter. Therefore, the claim is directed to a product of nature which is a judicial exception.
This judicial exception is not integrated into a practical application. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
Dependent claims 11 and 22, and new claim 26, is drawn to a plant genome comprising the polynucleotide. As discussed above, such a plant genome reads on the naturally occurring plant genome, a product of nature which is a judicial exception. This judicial exception is not integrated into a practical application. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
Claim 24 is drawn to “isolated” polynucleotide which is a DNA. This also reads on the naturally occurring genomic DNA. The word “isolated” does not make the claim markedly different from its natural counterpart.
Dependent claim 12 is drawn to a vector construct comprising the polynucleotide and the homologous promoter operably linked thereto. At the broadest sense, a vector construct reads on any DNA construct including isolated genomic DNA fragments. As such, it still reads on the naturally occurring plant genome with the native promoter, a product of nature which is a judicial exception. This judicial exception is not integrated into a practical application. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
Dependent claim 13, and new claim 25, is drawn to a host plant cell comprising the nucleic acid above. Therefore, it reads on the naturally occurring plant cell, a product of nature which is a judicial exception. This judicial exception is not integrated into a practical application. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
Therefore, claims 10-13 and 22 remain, and new claims 24-26 are, rejected under 101.
Response to Applicant’s Remarks:
Applicant responded to the rejection by amendment to delete "bioactive fragment" and "partial sequence" to “make more clear that the claims are not directed to a product of nature.”. Additionally, Applicant stated that in view of this amendment, “the claimed PPO polynucleotide comprises the variants to the LLLNYI motif, and as such it significantly differs from wild type proteins”.
As discussed above, the claims broadly encompass not only “PPO polynucleotide comprises the variants to the LLLNYI motif,” but also the nucleotide sequences that would hybridize to “PPO polynucleotide comprises the variants to the LLLNYI motif”. Since hybridization, even at the most stringent conditions, would occur at two polynucleotides of sufficient length (e.g., over a kb in encoding SEQ ID NO: 1) despite the two nucleotides that result in the amino acid variation (over 99% identity). Those hybridizing sequences reads on the natural product.
Therefore, the rejection is maintained.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (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, 9-18, 20, and 22-23 remain, and claims 24-28 are, rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by [Gocal et al. PGPUB US20180327773A1, published Nov. 18, 2018].
Claim 1 is drawn to a PPO polypeptide tolerant to a PPO-inhibiting herbicide, the polypeptide comprises the motif “LLLNYI”, wherein the leucine L at position 3 within the motif is substituted with any other amino acid, or the tyrosine Y at position 5 is substituted with any other amino acid.
Regarding claim 1, Gocal discloses a mutated PPX protein (protoporphyrinogen oxidase) that has increased resistance to one or more herbicides as compared to a reference protein, (p. 2-3, [0011]), comprising a mutation at one or more amino acid positions 424 or 426 of SEQ ID NO: 1, (p. 3, [0012]).
SEQ ID NO: 1 of the PPX (PPO, or PPOX) protein of Gocal is the reference sequence of Arabidopsis thaliana At4g0169 (Table 3A) which is the same as the instant SEQ ID NO: 15, and has the motif “LLLNYI” with the L at position 3 and Y at position 5 corresponding to amino acid positions 423 or 425 of SEQ ID NO: 1.
Gocal discloses the mutations: a leucine to serine (S) at a position corresponding to position 423 of SEQ ID NO: 1; a tyrosine (Y) to isoleucine (I) at a position corresponding to position 425 of SEQ ID NO: 1; (L423S/Y425I) a tyrosine to leucine (L) at a position corresponding to position 425 of SEQ ID NO: 1; a tyrosine to valine (V) at a position corresponding to position 425 of SEQ ID NO: 1; (p. 4, right column; and Table 1; Table 2;)
Gocal discloses the mutant PPX protein comprising two or more mutation combinations selected from Table 1, therefore encompassing the combination L423S/Y425I, for example.
Gocal discloses the instant SEQ ID NO: 15, and the corresponding mutations, as discussed above. Additionally, Gocal also discloses rice, potato, sorghum, PPO proteins (included in the instant SEQ ID NO: 1-19).
Gocal discloses the rice PPO (SEQ ID NO: 15) and the mutation corresponding to L423S (numbered 423), therefore, the instant SEQ ID NO: 20.
Gocal discloses the encoding DNA, vectors, host cells, and transgenic plants ([0005]; for example).
Gocal discloses method for a targeted mutation in a protoporphyrinogen IX oxidase (PPX) gene to produce a plant cell with a PPX gene, (claim 7) and the plant cell, plant generated thereof (Claims 1-12).
Gocal discloses the method of weed control ([0119]; e.g.)
Gocal discloses the plant being potato, maize, cotton, soybean, or rice, (claim 9).
Gocal discloses the herbicide being flumioxazin (Table 8, e.g.,); Saflufenacil (Example 2, e.g.).
Therefore, claims 1-2, 4-5, 7-18, 20, and 22-23 are anticipated by Gocal.
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 20-21 remain rejected under 35 U.S.C. 103 as being unpatentable over Gocal et al . PGPUB US20180327773A1, published Nov. 18, 2018, in view of [ Sung et al . US 10717985B2, July 21, 2020].
Claims 20-21 are drawn to a method for controlling weeds in a plant cultivation site, comprising applying to the cultivation site a herbicidally effective amount of PPO-inhibiting herbicide, wherein the plant comprises a nucleic acid sequence encoding the PPO polynucleotide or a bioactive fragment thereof according to claim 1, or the PPO-inhibiting herbicide is applied in combination with one or more additional herbicides.
As discussed above, Gocal teaches the PPO mutant protein resistant to PPO-inhibiting herbicide. However, Gocal does not teach the combined application of PPO-inhibiting herbicide with one or more additional herbicides.
Sung teaches that as a positive control, Mutant AtPPO1 was used, in which amino acid replacements of Y426M (replacement of tyrosine by methionine at position 426) (Example 3). Sung teaches method of conferring herbicide resistance on a plant, the method comprising: transforming a plant with a nucleotide sequence encoding a polypeptide consisting of the amino acid sequence of SEQ ID NO: 5, wherein the herbicide is selected from the group consisting of Tiafenacil, Saflufenacil, Butfenacil, Flumioxazin, Fomesafen, Actifluorfen, Oxyfluorfen, Sulfentrazone, Pentoxazone, Pyraflufen-ethyl, Oxadiozon, Fluthiacet-methyl, Pyraclonil, and a combination thereof (Claim 1); Sung teaches wherein the plant or the alga additionally comprises a second nucleotide sequence encoding an herbicide-resistant polypeptide that confers resistance to a second herbicide; (Claim 4), applying an effective dosage of protoporphyrinogen oxidase-inhibiting herbicide to the croplands wherein the applying an effective dosage of a protoporphyrinogen oxidase-inhibiting herbicide to the cropland is performed by applying two or more combinations of protoporphyrinogen oxidase-inhibiting herbicides at an effective dosage thereof, sequentially or simultaneously (Claims 12-13).
Therefore, it would have been prima facie obvious to apply the method of Sung to the plant comprising one of the mutant PPO of Gocal, such as the positive control of Sung which has the Y-to-M mutation at the Y of the LLLNYI motif and arriving at the instantly claimed method of combined application of protoporphyrinogen oxidase-inhibiting herbicides with another herbicide. The person having ordinary skills would have been motivated to do so given the instructions of Sung and would have reasonable expectation of success.
Therefore, claims 20-21 are prima facie obvious in view of the combined teachings of the prior art.
Response to Applicant’s Remarks:
In response to the rejections above, Applicant addressed both the rejections under 102 and 103, regarding the teachings of Gocal. Applicant argued that: Gocal merely lists a huge number of mutations that may be contained in a mutated PPX protein; there is no pointer leading one of skill in the art from Gocal the introduction of mutations simultaneously at positions 3 and 5 in the motif "LLLNYI", or to the two specific mutations as recited in amended claim 1; and that the Examiner has relied on “the benefit of hindsight”. And finally, Applicant argued that the claimed PPO polypeptide shows “significant or even unexpected technical advantages.”
These arguments have been fully considered but not deemed persuasive.
Firstly, regarding the specific L-to-S/Y-to-I combination in the motif "LLLNYI", Gocal has taught, as one of the claimed embodiments, e.g., in Claim 2. Regarding the argument that the Examiner has to rely on hindsight reasoning to pick the specific combination from the “laundry list” of a large number of combinatorial mutants, it should be noted that the fact the Gocal discloses a multitude of effective combinations does not render any particular formulation less obvious. This is especially true because the claimed composition is used for the identical purpose taught by the prior art.
Secondly, regarding the argument of unexpected result, Applicant is reminded that firstly, evidence of unexpected properties may be in the form of a direct or indirect comparison of the claimed invention with the closest prior art which is commensurate in scope with the claims. In the instant case, the evidence proffered by Applicant regarding Example 4, is a test of the inhibition by “compound A” in an exotic context, i.e., E. coli. In contrast, the claimed scope is regarding a modification of endogenous plant protein in its native cellular context. To that end, Applicant has not actually shown any result, let alone unexpected result, of significant improvement of herbicide tolerance in a plant.
Moreover, it should be noted that whether the unexpected results are the result of unexpectedly improved results or a property not taught by the prior art, the "objective evidence of nonobviousness must be commensurate in scope with the claims which the evidence is offered to support." In other words, the showing of unexpected results must be reviewed to see if the results occur over the entire claimed range. In the instant case, Applicant has, at least for claims 1, 9-18, and 20-26, claimed tolerance to any PPO inhibitor herbicide in any of the many plant species, while the evidence of “unexpected results” is only for rice PPO expressed in E. coli against “compound A”. Therefore, the evidence of unexpected properties is not commensurate in scope with the claims.
At least for these reasons, the rejections are maintained.
Conclusion
No claims are allowed.
Applicant's amendment 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.
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WEIHUA . FAN
Examiner
Art Unit 1663
/WEIHUA FAN/Examiner, Art Unit 1663