DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of the Application
2. Claims 68-73 and 75-87 are pending.
3. Claims 70-73 and 86 are withdrawn.
4. Claims 68, 69, 75-85 and 87 are examined herein. 5. The objections to the specification are withdrawn in view of Applicant’s amendments to the disclosure.
6. The objections to the claims are withdrawn in view of Applicant’s amendments to the claims.
7. The rejection under 35 U.S.C. 112(b) is withdrawn in view of Applicant’s amendments to the claims.
8. The rejection of claims 68 and 69 for Improper Markush Grouping is withdrawn in view of Applicant’s amendments to the claims and argument in the Remarks. The search was extended to the previously non-examined species.
Election/Restrictions
9. Applicant’s election of Group I, claims 68, 69 and 74-85, and SEQ ID NO: 2 as species, in the reply filed on June 26, 2025 is acknowledged. 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)). Claims 70-73 and 86 remain withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on June 26, 2025. Given that new claim 87 would have been included in the elected Group, it is examined herein.
Claim Rejections - 35 USC § 112(a)
10. The following is a quotation 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 35 U.S.C. 112 (pre-AIA ), first paragraph:
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
11. Claims 68, 69, and 75-85 remain and claim 87 is 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
This rejection has been modified in view of Applicant’s amendments to the claims. Applicant’s arguments submitted on December 29, 2025 were fully considered but they are not found to be persuasive.
Applicant claims a transgenic plant expressing an exogenous fungal-derived PPO enzyme conferring resistance or tolerance to at least one PPO inhibitor herbicide, wherein the enzyme comprises “an amino acid sequence having at least 80% similarity to an amino acid sequence as denoted by any one of” the recited amino acid sequences including SEQ ID NO: 2. Applicant claims said plant, wherein the PPO further comprises a chloroplast transit peptide.
Applicant describes the full-length SEQ ID NO: 2 as a PPO protein isolated from Aspergillus sp., isolated in a screen for herbicide tolerance in plants (Example 1). Applicant describes generating a chimeric PPO comprising SEQ ID NO: 2 and a chloroplast transit peptide and evaluating the effects of the expression of said PPO on tolerance to two PPO inhibitors (Example 2; Fig. 3). Applicant describes two additional PPOs that fall within the genus of PPOs having 80% identity to SEQ ID NO: 2: SEQ ID NO: 1 that has 98.9% and SEQ ID NO: 86 that has 94.3% identity to SEQ ID NO: 2 (see Sequence Search Results for SEQ ID NO: 2 against the Published Applications Database). Applicant describes SEQ ID NO: 2-7, 86, 88-89, and 91-99 as PPOs from various species of fungi that conferred tolerance to PPO inhibitors when transformed into a plant (Fig. 3B and 3C).
Applicant does not describe the invention as broadly claimed. Applicant does not describe the genus of “fungal-derived” PPO enzymes having 80% to SEQ ID NO: 2 or any of the other recited sequences. Applicant does not describe the genus of plants expressing said PPOs.
The genus of structures encompassed by the claims is very large. For example, SEQ ID NO: 2 is 597 amino acid long. A protein having as little as 80% identity to it could comprise 119 substitutions, insertions or deletions anywhere along the length of the sequence. This would amount to the genus of 20119 species, a number that is infinite in practical terms. The two described species are not sufficiently representative of that vast genus. This is particularly true given the variability in herbicide tolerance observed with the several PPOs, including SEQ ID NO: 1 and 2, wherein the results show up to 5-fold difference in tolerance levels (see Fig. 2 and 3; Examples 2 and 4). This reasoning applies to the other recited PPOs as well.
In addition to not describing a number of species sufficiently representative of the claimed genus, Applicant has also failed to identify a structure or structures for the claims genus such that one of ordinary skill in the art would be able to recognize with members of the genus possess the recited function.
Applicant describes aligning the sequences of the isolated PPOs and states as follows: “According to some embodiments, ten motifs (motifs 1-10) were recognized in fungal-isolated PPO. The motifs are about 4 to about 30 amino acids in length. According to some embodiments, the motifs that were identified in fungal-isolated PPO advantageously share unique patterns of amino acid sequence and/or structure. According to some embodiments, motifs of fungal-derived PPO sequences may share more common amino acid sequences and/or structural features between enzymes of Aspergillus, Fusarium, Rhizopus, and Penicillium, than the corresponding sequences of the plant derived-PPO share between enzymes of Arabidopsis, Tabacum, and Soybean, for example, motifs 1, 2, 3, 4, 6, 7, and 10. Advantageously, according to some embodiments, a total of 70 motif sequences identified in fungal-isolated PPO enzymes of the genera Aspergillus sp., Fusarium sp., Rhizopus sp., and Penicillium sp., were considered distinct and distinguishable with respect to their corresponding sequences in plants PPO enzyme” (pages 65-66 of the Specification).
However, there is no indication in the disclosure that any of the motifs mentioned in the above portion of the specification are necessary and/or sufficient to confer herbicide tolerance to a plant expressing an PPO comprising any of said motifs. Similarly, while Applicant describes differences in the size of the ligand binding pocket between herbicide sensitive and fungal-derived herbicide tolerant PPOs, those differences cannot be relied upon to envision the genus of structures encompassed by the claims. For example, the specificaiton supplies no description of the conformational structure of any inhibitor resistant PPOs that is within the genus of enzymes with 80% identity to SEQ ID NO: 2 or the other recited sequences.
Moreover, claims 68 and 69, as instantly amended, recite “an amino acids sequence having at least 80% similarity ton an amino acid sequence as denoted by one of… ”(emphasis supplied). Due to the use of the second indefinite article, the phrase could be reasonably interpreted as encompassing only a partial sequence encompassed by SEQ ID NO: 2 or the other recited proteins. The genus would encompass a myriad of sequences that are not described either.
Given that Applicant has neither described a number of species sufficiently representative of the claimed genus nor set forth a structure or structures such that one of ordinary skill in the art would recognize which species have the recited function and which do not, it is unclear whether at the time of filing Applicant was in possession of the instant invention, as broadly claimed.
Scope of Enablement
12. Claims 68, 69, and 74-85 remain and claim 87 is 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 an herbicide tolerant transgenic plant expressing the fungal derived PPO enzyme of SEQ ID NO: 2, SEQ ID NO: 1 or SEQ ID NO: 86, wherein the PPO is fused to a chloroplast transit peptide, does not reasonably provide enablement for the genus of transgenic plants comprising any exogenous fungal-derived PPO comprising an amino acid sequence with 80% similarity to “an amino acid sequence as denoted by one of” the recited sequences, including SEQ ID NO: 2.
This rejection has been modified in view of Applicant’s amendments to the claims. Applicant’s arguments submitted on December 29, 2025 were fully considered but they are not found to be persuasive.
In re Wands, 858 F.2d 731 (Fed. Cir. 1988) lists the following eight factors for determining whether undue experimentation would be required to practice an invention: (1) quantity of experimentation necessary; (2) amount of direction or guidance supplied; (3) presence or absence of working examples; (4) nature of the invention; (5) state of the prior art; (6) relative skill of those in the art; (7) predictability or unpredictability or the prior art; (8) breadth of the claims.
Applicant claims a transgenic plant expressing an exogenous fungal-derived PPO enzyme conferring resistance or tolerance to at least one PPO inhibitor herbicide, wherein the enzyme comprises an amino acid sequence having at least 80% similarity to SEQ ID NO: 2 or other recited sequences. Applicant claims said plant, wherein the PPO further comprises a chloroplast transit peptide.
Applicant teaches that the full-length SEQ ID NO: 2 is a PPO protein isolated from Aspergillus sp., identified in a screen for herbicide tolerance (Example 1). Applicant teaches generating a chimeric PPO comprising SEQ ID NO: 2 and an Arabidopsis chloroplast transit peptide and evaluating the effects of the expression of said PPO on tolerance to two PPO inhibitors in plants (Example 2; Fig. 3). Applicant teaches two additional PPO that fall within the genus of PPOs having 80% identity to SEQ ID NO: 2: SEQ ID NO: 1 that has 98.9% and SEQ ID NO: 86 that has 94.3% identity to SEQ ID NO: 2 (see Sequence Search Results for SEQ ID NO: 2 against the Published Applications Database). Applicant teaches that SEQ ID NO: 2-7, 86, 88-89, and 91-99 are PPOs from various species of fungi and can confer tolerance to PPO inhibitors when transformed into a plant (Fig. 3B and 3C).
Applicant does not teach how to practice the claimed invention through the full scope of the claims. Applicant does not teach how to make or use the genus of “fungal-derived” PPO enzymes having 80% to SEQ ID NO: 2 or the other recited species. Applicant does not teach how to make or use the claimed genus of transgenic plants comprising any of said fungal-derived PPO’s.
The teachings of the specification and the state of the art indicate that it would be highly unpredictable to attempt to practice the invention through the full scope of the claims. For example, from the genus of herbicide tolerance-conferring PPOs having 80% identity to SEQ ID NO: 2, the specification reduced to practice three species – SEQ ID NO: 2 itself and SEQ ID NO: 1, which are two PPO’s isolated from Aspergillus sp. (see page 32; Example 1); and SEQ ID NO: 86, which a PPO from Trichoderma sp. (see page 66; Example 4).
However, the specificaiton has not supplied sufficient guidance that would enable one of ordinary skill in the art to identify and use a “fungal-derived PPO” that has at least 80% identity to SEQ ID NO: 2 or any of the other recited proteins, and can confer tolerance to PPO inhibitors when expressed in a plant – short of having to screen a variety of random fungal PPOs, which would require substantial further trial and error experimentation.
It is noted that even the PPOs that the specificaiton identifies as tolerant showed significant variability in resistance screens with only two PPO inhibitors (see Fig. 1-3). Given that such variability was observed with only a few fungal PPOs, it would be unpredictable to extrapolate the teachings of the specification onto the vast genus of any fungal-derived PPO having 80% identity to SEQ ID NO: 1-7, 86, 88-89, or 91-99.
The specificaiton teaches measuring physical distances between conserved amino acids within the ligand binding pocket of the wild-type herbicide tolerant fungal PPOs, including SEQ ID NO: 2, and finding that said pocket was smaller compared to that of thee known herbicide sensitive PPOs (see Example 5; Fig. 5; Table 1). However, the specification does not explain how one would be able to use that information to practice the claimed invention. Specifically, it is unclear how one of ordinary skill in the art would be able to rely on the pocket size to identify which of the fungal-derived PPOs with 80% identity to SEQ ID NO: 2 are herbicide tolerant and which are not, without having to obtain the crystal structures of candidate proteins.
Moreover, claims 68 and 69, as instantly amended, recite “an amino acids sequence having at least 80% similarity ton an amino acid sequence as denoted by one of… ”(emphasis supplied). Due to the use of the second indefinite article, the phrase could be reasonably interpreted as encompassing only a partial sequence encompassed by SEQ ID NO: 2 or the other recited proteins. Applicant has not taught how to practice this genus of said partial sequences either.
The limited teachings of the specification are consistent with the state of the art. The structure of the PPO binding pocket and the conserved amino acids it contains are well-known in the art. This includes the known role of phenylalanine 383, leucine 334 and arginine 97 (in the human numbering) in coordinating the ligand (see Hao et al, Chemistry in China (2011) 65:961-969; Fig. 1). However, while the overall folding patterns are similar among PPOs, their sequence similarity is known to be low (see, for example, Hao et al, pg. 962, middle col.). This means that one would not be able to rely merely on the amino acid sequence or the native enzymatic activity of a candidate fungal PPO to determine whether it can be used to confer herbicide tolerance to a plant – without further guidance or experimentation. Such experimentation, for example, could include obtaining its crystal structure or screening it for tolerance in vivo. Doing so would amount to undue trial and error experimentation.
Given limited guidance supplied by Applicant, the breadth of the claims and the nature of the invention, as well as the unpredictability in the art, it would have required one skilled in the art undue trial and error experimentation to practice the claimed invention through the full scope of its claims.
Response to Arguments
Applicant argues as follows: “The current application discloses a plurality of specific SEQ ID Nos. (e.g., SEQ ID NOs: 2, 86, 88, etc.) from multiple fungal genera (Aspergillus, Penicillium, Fusarium). These sequences are structurally aligned and functionally correlated, as detailed in Examples 1-5. Structural conservation in herbicide-binding motifs is discussed in pages 65-66 and Example 5 (Fig. 5), where multiple PPOs exhibit shared substrate pocket geometry and active site residues.
Thus, Applicant has disclosed both a representative number of species and the structural characteristics common across the genus, satisfying written description” (page 11 of the Remarks).
Applicant’s argument is not found to be persuasive. There is no dispute that Applicant did describe a number of fungal PPOs whose expression in a plant confers PPO inhibitor tolerance (see Fig. 3, for example). However, the claims are not limited to those species but continue to encompass a much broader genus. This genus is not adequately described. For example, with regard to SEQ ID NO: 2, the PPO of SEQ ID NO: 1 that has 98.9% and that of SEQ ID NO: 86 that has 94.3% identity to SEQ ID NO: 2 (see Sequence Search Results for SEQ ID NO: 2 against the Published Applications Database). However, Applicant has not described any species having as little as 80% sequence identity to SEQ ID NO: 2. Importantly, while Applicant does identify certain motifs and differences in the size of the ligand binding pocket between herbicide sensitive and fungal-derived herbicide tolerant PPOs, there is no evidence in the record that said structures are necessary and/or sufficient to confer herbicide tolerance to a plant expressing an PPO comprising them, such that one would be able to envision the members of the claimed genus that possess the recited function.
Applicant argues as follows with regard to the scope of enablement rejection: “The application includes step-by-step methods for identifying, cloning, and expressing fungal PPOs in transgenic plants. Detailed procedures are provided for testing herbicide tolerance (Examples 1-4), including transformation and selection protocols. … Multiple working examples describe functional PPO enzymes with different sequence identities and from different species. Example 1 uses Aspergillus protein, Example 2 uses Penicillium protein and Example 4 shows tolerance in Arabidopsis. The Office Action contends that variability in the PPO binding pocket makes herbicide resistance unpredictable. However, the specification teaches that sequence identity of over 80% correlates with functional conservation, particularly in the binding region. Figure 1 and Table 1 show multiple motifs shared across species. The teachings permit in silico selection of PPOs likely to function, reducing the need for trial and error. …
A person skilled in the art can use established methods, such as codon optimization, expression in Arabidopsis or crop plants, and standard herbicide resistance assays to test new PPOs. … The Office Action emphasizes the "infinite" number of potential variants, particularly due to 80% identity range. However, breadth of a claim is not per se unenabled. Applicant has set reasonable structural boundaries (at least 80% identity to defined SEQ ID NOs), which limit the genus and are supported by working examples and predictive features.” (page 12 of the Remarks).
Applicant’s argument is not found to be persuasive. Applicant has not taught how to use the teachings of the specification regarding the structures shared by some of the PPOs in the specification to identify those that fall within the claimed genera which encompass millions of sequences. For example, with regard to the binding pockets, the issue is not their “variability” as Applicant states above, but the fact that given the teachings of the specification, one of ordinary skill in the art would not be able to rely on their presence to predictably identify a fungal PPO that confers herbicide tolerance when expressed in a plant, without substantial further trial and error experimentation.
The Examiner notes that either limiting the claims to the described and enabled subject matter or providing factual evidence showing that the claimed genus is described and enabled, could help overcome the instant rejections.
Conclusion
13. No claims are allowed.
14. The claims appear to be free from the prior art. The closest prior art is UniProt Accession No. A0A318YKB3_ASPNB (submitted on October 10, 2018) that teaches a PPO from Aspergillus sp., having 99.5% identity to SEQ ID NO: 2. However, the prior art does not appear to suggest introducing a nucleic acid encoding a protein having 80% identity to SEQ ID NO: 2 into a plant.
15. THIS ACTION IS MADE FINAL. 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.
16. Any inquiry concerning this communication or earlier communications from the examiner should be directed to MYKOLA V KOVALENKO whose telephone number is (571)272-6921. The examiner can normally be reached Mon.-Fri. 9:00-5:30 PST.
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/MYKOLA V. KOVALENKO/Primary Examiner, Art Unit 1662