DETAILED CORRESPONDENCE
Status of the Application
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on June 1, 2026 has been entered.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 70-76 and 79-90 are pending in the application.
Applicant’s amendment to the claims, filed June 1, 2026, is acknowledged. This listing of the claims replaces all prior versions and listings of the claims.
Applicant’s remarks filed June 1, 2026 in response to the final rejection filed April 1, 2026 are acknowledged and have been fully considered.
Claim 77 is canceled by claim amendment filed June 1, 2026 and rejections previously applied to this claim are withdrawn.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Restriction/Election
In response to a requirement for restriction/election filed August 13, 2025, applicant elected without traverse in the reply filed September 4, 2025 the invention of Group I, corresponding to pending claims 70-77 and 79-90, drawn to the technical feature of a genetically modified fungal host cell, and the species of a polypeptide comprising, consisting essentially of, or consisting of an amino acid sequence corresponding to the amino acid sequence of IdtA from Epichloë var. lolii strain AR37, or corresponding to a polypeptide encoded by the idtA gene from Epichloë festucae var. lolii strain AR37, SEQ ID NO: 3, SEQ ID NO: 52, and SEQ ID NO: 53, variants and fragments thereof, a polypeptide involved in the production of one or more janthitrem compound, and a polypeptide comprising an enzymatic activity having as its substrate terpendole I or as its substrate or its product a compound of any one of formulae Ito VIII.
Claim Objections
The objection to claims 79-81 is withdrawn in view of applicant’s amendment to claim 79 to recite “A population of cells comprising one or more Epichloë cells as claimed in claim 70” and applicant’s amendments to claims 80 and 81 to recite “The population of cells as claimed in claim 79.”
Claim 71 is objected to in the recitation of “one or more gene products…wherein said idtF gene product” and in the interest of improving claim form and consistency, it is suggested that the term “product” in the phrase “said idtF gene product” be amended to recite the plural “products.”
Claim Rejections - 35 USC § 112(b)
The rejection of claims 70-77 and 79-90 under 35 U.S.C. 112(b) as being indefinite in the recitation of “idtA gene” is withdrawn in view of applicant’s amendment to claim 70 to recite “wherein said idtA gene product has acyltransferase activity and catalyses the conversion of epoxy-janthitrol to epox-janthitrem I.”
The rejection of claim 76 under 35 U.S.C. 112(b) as being indefinite in the recitation of “a compound of formula II” is withdrawn in view of applicant’s amendment to claim 76 to recite the structure of the formula II.
Claim 90 is rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claim 90 is indefinite in the recitation of “selected from the group comprising…” According to MPEP 2173.05(h), a Markush grouping is a closed group of alternatives, i.e., the selection is made from a group "consisting of" (rather than "comprising" or "including") the alternative members. If a Markush grouping requires a material selected from an open list of alternatives (e.g., selected from the group "comprising" the recited alternatives), the claim should generally be rejected under 35 U.S.C. 112(b) as indefinite because it is unclear what other alternatives are intended to be encompassed by the claim.
Claim Rejections - 35 USC § 112(a)
The rejections of claims 70, 72-76, 79-81, and 83-90 under 35 U.S.C. 112(a) as failing to comply with the written description and enablement requirements are withdrawn in view of applicant’s amendments to claim 70 to limit the fungal host cell to an Epichloë host cell, to define the enzymatic activity of the idtA gene product (i.e., acyltransferase activity catalyzing the conversion of epoxy-janthitrol to epox-janthitrem I), and to limit the one or more janthitrem compounds whose production is decreased by the at least one genetic modification in an idtA gene that reduces or prevents the production or activity of an idtA gene product (i.e., epoxy-janthitrem I and/or epoxy-janthitrem IV).
Claims 71 and 82 are rejected under 35 U.S.C. 112(a) 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 at the time the application was filed, had possession of the claimed invention. This rejection has been modified from its previous version to address applicant’s amendments to the claims.
MPEP 2163.II.A.2.(a).i) states, “Whether the specification shows that applicant was in possession of the claimed invention is not a single, simple determination, but rather is a factual determination reached by considering a number of factors. Factors to be considered in determining whether there is sufficient evidence of possession include the level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention.”
For claims drawn to a genus, MPEP § 2163 states the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406.
MPEP § 2163 further states that “[s]atisfactory disclosure of a ‘representative number’ depends on whether one of skill in the art would recognize that the applicant was in possession of the necessary common attributes or features possessed by the members of the genus in view of the species disclosed. For inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus…Instead, the disclosure must adequately reflect the structural diversity of the claimed genus, either through the disclosure of sufficient species that are ‘representative of the full variety or scope of the genus,’ or by the establishment of ‘a reasonable structure-function correlation.’ Such correlations may be established ‘by the inventor as described in the specification,’ or they may be ‘known in the art at the time of the filing date.’"
The factors considered in the Written Description requirement are (1) level of skill and knowledge in the art, (2) partial structure, (3) physical and/or chemical properties, (4) functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the (5) method of making the claimed invention. Disclosure of any combination of such identifying characteristics that distinguish the claimed invention from other materials and would lead one of skill in the art to the conclusion that the applicant was in possession of the claimed species is sufficient." MPEP § 2163.
As amended, claim 71 is drawn to a genus of genetically modified Epichloë host cell as claimed in claim 70 comprising at least one genetic modification associated with altered regulation or production of one or more gene products encoded by an idtF gene, wherein said idtF gene product has prenyl transferase activity and catalyses the conversion of epoxy-janthitriol to epoxy-janthitrem III.
The “at least one genetic modification associated with altered regulation or production of one or more gene products encoded by an idtF gene” is/are undefined and unlimited. As such, the genus of Epichloë host cells of claim 71 is considered to encompass widely variant species.
As amended, claim 82 is drawn to the genetically modified Epichloë host cell of claim 70, wherein the Epichloë host cell comprises at least one genetic modification in an idtF gene that reduces or prevents the production or activity of an idtF gene product, wherein the production or amount of one or more epoxy-janthitrem compounds is decreased when compared to an Epichloë host cell or Epichloë organism of the same species in which such a genetic modification in an idtF gene is not present.
The recited “one or more epoxy-janthitrem compounds” is undefined and unlimited and while the language of claim 82 indicates that the idtF gene product is related to production or amount of one or more undefined and unlimited epoxy-janthitrem compounds, the catalytic activity, substrate(s), and product(s) of the “idtF gene product” are undefined and unlimited. As such, the genus of Epichloë host cells of claim 82 is considered to encompass widely variant species.
The specification discloses the actual reduction to practice of the following species of claimed Epichloë host cells – an Epichloë host cell having a deletion of an idtA gene encoding the polypeptide of SEQ ID NO: 3 or 53 and transfected with an idtF polynucleotide encoding a polypeptide comprising the amino acid sequence of SEQ ID NO: 17, 19, 72, 73, or 74 and having prenyl transferase activity to catalyze the conversion of epoxy-janthitriol to epoxy-janthitrem, or an Epichloë host cell having a deletion of an idtA gene encoding the polypeptide of SEQ ID NO: 3 or 53 and a deletion of an idtF gene encoding a polypeptide comprising the amino acid sequence of SEQ ID NO: 72, 73, or 74 and having prenyl transferase activity to catalyze the conversion of epoxy-janthitriol to epoxy-janthitrem. Other than these representative species, the specification fails to provide direction or guidance regarding other Epichloë host cells with genetic modification associated with altered regulation or production of one or more gene products encoded by an idtF gene or genetic modification in an idtF gene that reduces or prevents the production or activity of an idtF gene product, wherein the production or amount of one or more epoxy-janthitrem compounds is decreased.
Regarding the level of skill and knowledge in the art, Zhou et al. (Cell Mol Life Sci 63:2260-2290, 2006; cited on the attached Form PTO-892) teach that a gene in a cell may be regulated by different transcription factors and the contribution from different transcription factors may function under different conditions (page 2283, left column, lines 12-22). Zhou et al. also teach that the relationship between transcription factors and genes may be much more complex than we imagine and states that data from mRNA expression and transcription factor-DNA interactions give only limited information that does not include post-transcriptional events or protein-protein interactions. Kozak, M. (Gene 234:187-208, 1999; cited on the attached Form PTO-892) while describing the principles of protein synthesis states that the details of translational regulation are unique to each mRNA, and thus too complicated to be included in a review of basic mechanisms (page 187, right column, last line-page 188, left column, line 4). Given the unpredictability of transcription and translation regulation in prokaryotes, one of skill in the art would have expected an even higher level of unpredictability of transcription and translation regulation in a eukaryotic cell such as an Epichloë host cell. Further regarding the genus of genetic modifications, it is noted that the field of metabolic engineering can be inherently unpredictable and advances in metabolic pathway engineering are often achieved only by empirical experimentation. According to Guo et al. (Comp Struct Biotechnol J, 15:161-167, 2017; cited on the attached Form PTO-892) “First, a lot of organisms are difficult to be engineered because of unknown regulation patterns and the lack of engineering tools for non-model organisms [16]. Even for model microorganisms like Escherichia coli and Saccharomyces cerevisiae, which are well studied and equipped with a broad spectrum of biomolecular tools to allow metabolic engineering easily, the effects of heterologous expression of pathways are often unpredictable to guarantee a high productivity…Second, a key challenge in metabolic engineering is balancing the tug-of-war that exists between the cell's physiological and evolutionary objectives on one side and the engineer's process objectives on the other [20]. Such conflict of resource allocation sometimes cannot be well addressed and toxic intermediates could be built up in the unbalanced pathway” (p. 162, column 1, middle). Thus, one of skill in the art would have recognized a high level of unpredictability regarding Epichloë host cells with genetic modification associated with altered regulation or production of one or more gene products encoded by an idtF gene or genetic modification in an idtF gene that reduces or prevents the production or activity of an idtF gene product, wherein the production or amount of one or more epoxy-janthitrem compounds is decreased.
Given the high level of unpredictability in the relevant art and given that the specification discloses only a relative few representative species among a widely variant genus, one of skill would not accept the disclosed species of an Epichloë host cell having a deletion of a gene encoding the polypeptide of SEQ ID NO: 3 or 53 and transfected with a polynucleotide encoding a polypeptide comprising the amino acid sequence of SEQ ID NO: 17, 19, 72, 73, or 74 as being representative of the entire genus of genetically modified Epichloë host cells. The claimed subject matter is not supported by an adequate written description because a representative number of species has not been described.
RESPONSE TO REMARKS: Applicant argues the rejection is obviated by amendments to claims 70 and 71 in combination with the disclosure of the specification.
Applicant’s arguments are not found persuasive. For the reasons stated above, including that there is a high level of unpredictability in the relevant art and the specification discloses only a relative few representative species among a widely variant genus, one of skill would not accept the disclosed species as being representative of the entire genus of genetically modified Epichloë host cells.
Claims 71 and 82 are rejected under 35 U.S.C. 112(a) because the specification, while being enabling for the Epichloë host cell of claim 70 transfected with a polynucleotide encoding a polypeptide comprising the amino acid sequence of SEQ ID NO: 17, 19, 72, 73, or 74 or an Epichloë host cell having a deletion of an idtA gene encoding the polypeptide of SEQ ID NO: 3 or 53 and a deletion of an idtF gene encoding a polypeptide comprising the amino acid sequence of SEQ ID NO: 72, 73, or 74 and having prenyl transferase activity to catalyze the conversion of epoxy-janthitriol to epoxy-janthitrem, does not reasonably provide enablement for all genetically modified Epichloë host cells as broadly encompassed by the claims. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
“The test of enablement is not whether any experimentation is necessary, but whether, if experimentation is necessary, it is undue.” In re Angstadt, 537 F.2d 498, 504, 190 USPQ 214, 219 (CCPA 1976). Factors to be considered in determining whether undue experimentation is required are summarized in In re Wands (858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988)) as follows: (A) The breadth of the claims; (B) The nature of the invention; (C) The state of the prior art; (D) The level of one of ordinary skill; (E) The level of predictability in the art; (F) The amount of direction provided by the inventor; (G) The existence of working examples; and (H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. See MPEP § 2164.01(a). The Factors considered to be most relevant to the instant rejection are addressed in detail below.
The nature of the invention: According to the specification, “there is a need for ways of providing one or more beneficial indole diterpene compounds, without concomitant or with reduced provision of one or more detrimental or undesirable indole diterpene compounds. It is therefore an object of the invention to provide one or more host cells capable of producing one or more epoxy-janthitrem compounds” (p. 1, line 40 to p. 2, line 2).
The breadth of the claims: As amended, claim 71 is drawn to a genus of genetically modified Epichloë host cell as claimed in claim 70 comprising at least one genetic modification associated with altered regulation or production of one or more gene products encoded by an idtF gene, wherein said idtF gene product has prenyl transferase activity and catalyses the conversion of epoxy-janthitriol to epoxy-janthitrem III.
The “at least one genetic modification associated with altered regulation or production of one or more gene products encoded by an idtF gene” is/are undefined and unlimited.
As amended, claim 82 is drawn to the genetically modified Epichloë host cell of claim 70, wherein the Epichloë host cell comprises at least one genetic modification in an idtF gene that reduces or prevents the production or activity of an idtF gene product, wherein the production or amount of one or more epoxy-janthitrem compounds is decreased when compared to an Epichloë host cell or Epichloë organism of the same species in which such a genetic modification in an idtF gene is not present.
The recited “one or more epoxy-janthitrem compounds” is undefined and unlimited and while the language of claim 82 indicates that the idtF gene product is related to production or amount of one or more undefined and unlimited epoxy-janthitrem compounds, the catalytic activity, substrate(s), and product(s) of the “idtF gene product” are undefined and unlimited.
The state of the prior art; The level of one of ordinary skill; and The level of predictability in the art: According to MPEP 2164.03, “…what is known in the art provides evidence as to the question of predictability” and “[I]f one skilled in the art cannot readily anticipate the effect of a change within the subject matter to which that claimed invention pertains, then there is lack of predictability in the art.”
As taught in the prior art, prokaryotes achieve gene transcription and translation regulation by means of a series of complex mechanisms. Zhou et al. (Cell Mol Life Sci 63:2260-2290, 2006; cited on the attached Form PTO-892) teach that a gene in a cell may be regulated by different transcription factors and the contribution from different transcription factors may function under different conditions (page 2283, left column, lines 12-22). Zhou et al. also teach that the relationship between transcription factors and genes may be much more complex than we imagine and states that data from mRNA expression and transcription factor-DNA interactions give only limited information that does not include post-transcriptional events or protein-protein interactions. Kozak, M. (Gene 234:187-208, 1999; cited on the attached Form PTO-892) while describing the principles of protein synthesis states that the details of translational regulation are unique to each mRNA, and thus too complicated to be included in a review of basic mechanisms (page 187, right column, last line-page 188, left column, line 4). Given the unpredictability of transcription and translation regulation in prokaryotes, one of skill in the art would have expected an even higher level of unpredictability of transcription and translation regulation in a eukaryotic cell such as an Epichloë host cell.
Further regarding the recited genetic modification, it is noted that the field of metabolic engineering can be inherently unpredictable and advances in metabolic pathway engineering are often achieved only by empirical experimentation. According to Guo et al. (Comp Struct Biotechnol J, 2017, 15:161; cited on the attached Form PTO-892) “First, a lot of organisms are difficult to be engineered because of unknown regulation patterns and the lack of engineering tools for non-model organisms [16]. Even for model microorganisms like Escherichia coli and Saccharomyces cerevisiae, which are well studied and equipped with a broad spectrum of biomolecular tools to allow metabolic engineering easily, the effects of heterologous expression of pathways are often unpredictable to guarantee a high productivity…Second, a key challenge in metabolic engineering is balancing the tug-of-war that exists between the cell's physiological and evolutionary objectives on one side and the engineer's process objectives on the other [20]. Such conflict of resource allocation sometimes cannot be well addressed and toxic intermediates could be built up in the unbalanced pathway” (p. 162, column 1, middle).
Thus, one of skill in the art would have recognized a high level of unpredictability for genetic modification associated with altered regulation or production of one or more gene products encoded by an idtF gene.
The amount of direction provided by the inventor and The existence of working examples: The specification discloses the following working examples of the claimed Epichloë host cell – an Epichloë host cell having a deletion of an idtA gene encoding the polypeptide of SEQ ID NO: 3 or 53 and transfected with an idtF polynucleotide encoding a polypeptide comprising the amino acid sequence of SEQ ID NO: 17, 19, 72, 73, or 74 and having prenyl transferase activity to catalyze the conversion of epoxy-janthitriol to epoxy-janthitrem, or an Epichloë host cell having a deletion of an idtA gene encoding the polypeptide of SEQ ID NO: 3 or 53 and a deletion of an idtF gene encoding a polypeptide comprising the amino acid sequence of SEQ ID NO: 72, 73, or 74 and having prenyl transferase activity to catalyze the conversion of epoxy-janthitriol to epoxy-janthitrem.
The quantity of experimentation needed to make or use the invention based on the content of the disclosure: While methods of genetic modifications to introduce heterologous genetic material into a fungal host cell or genetic modification to delete a desired gene were known at the time of the invention, it was not routine in the art to make all Epichloë host cells as broadly encompassed by the claims.
In view of the overly broad scope of the claims, the lack of guidance and working examples provided in the specification, the high level of unpredictability as evidenced by the prior art, and the amount of experimentation required to make the invention, undue experimentation would be necessary for a skilled artisan to make and use the entire scope of the claimed invention. Applicants have not provided sufficient guidance to enable one of ordinary skill in the art to make and use the claimed invention in a manner reasonably correlated with the scope of the claims. The scope of the claims must bear a reasonable correlation with the scope of enablement (In re Fisher, 166 USPQ 19 24 (CCPA 1970)). Without sufficient guidance, determination of having the desired biological characteristics is unpredictable and the experimentation left to those skilled in the art is unnecessarily, and improperly, extensive and undue. See In re Wands 858 F.2d 731, 8 USPQ2nd 1400 (Fed. Cir, 1988).
RESPONSE TO REMARKS: Applicant argues the rejection is obviated by amendments to claims 70 and 71 in combination with the disclosure of the specification.
Applicant’s arguments are not found persuasive. In view of the detailed analysis of the Factors of In re Wands above including that the “at least one genetic modification associated with altered regulation or production of one or more gene products encoded by an idtF gene” in claim 71 is/are undefined and unlimited and the recited “one or more epoxy-janthitrem compounds” in claim 82 is undefined and unlimited and while the language of claim 82 indicates that the idtF gene product is related to production or amount of one or more undefined and unlimited epoxy-janthitrem compounds, the catalytic activity, substrate(s), and product(s) of the “idtF gene product” are undefined and unlimited, the specification fails to enable the full scope of the claimed invention.
Claim Rejections - 35 USC § 103
Claims 70-76 and 79-90 are rejected under 35 U.S.C. 103 as being unpatentable over Spangenberg et al. (WO 2018/027275 A1; cited on the IDS filed November 2, 2022; hereafter “Spangenberg”) in view of
Saikia et al. (FEBS Lett. 580:1625-1630, 2006; cited on Form PTO-892 filed April 1, 2026; hereafter “Saikia”),
Scott et al. (Toxins 5:1422-1446, 2013; cited on Form PTO-892 filed April 1, 2026; hereafter “Scott”), and
Giraldo et al. (Transgenic Res. 27:397-407, 2018; cited on Form PTO-892 filed April 1, 2026; hereafter “Giraldo”), and as evidenced by
GenBank Database Accession Number DQ443465 (February 2007, 11 pages; cited on the attached Form PTO-892; hereafter “GenBank DQ443465”),
GenBank Database Accession Number QGV56749 (December 2019, 1 page; cited on Form PTO-892 filed April 1, 2026; hereafter “GenBank QGV56749”), and
UniProt Database Accession Number J7FK08 (February 2019, 1 page; cited on Form PTO-892 filed April 1, 2026; hereafter “UniProt J7FK08”).
As amended, the claims are drawn to a genetically modified Epichloë host cell capable of producing one or more indole diterpene compounds, wherein the Epichloë host cell comprises at least one genetic modification in an idtA gene that reduces or prevents the production or activity of an idtA gene product, wherein said idtA gene product has acyltransferase activity and catalyses the conversion of epoxy-janthitrol to epox-janthitrem I, and wherein the production or amount of epoxy-janthitrem I and/or epoxy-janthitrem IV is decreased when compared to an Epichloë host cell or Epichloë organism of the same species in which such a genetic modification in an idtA gene is not present.
Regarding claim 70, Spangenberg teaches janthitrems are a class of indole diterprenes produced by a subgroup of endophytes (p. 1, lines 29-30), which provide protection against pasture pests in perennial ryegrass pastures (p. 2, lines 9-10). Spangenberg teaches there is an increasing need to further understand janthitrems and their biosynthesis, as this would provide information useful in manipulating janthitrem production (p. 2, lines 21-23). Spangenberg teaches the identification of the janthitrem biosynthetic gene cluster in the Epichloë endophyte LpTG3/NEA12 genome (p. 3, lines 28-31; pp. 22-23; and Table 2), which comprises gene clusters 1, 2, 3, and 4 (p. 14, lines 11-13; p. 25, lines 17-20). Spangenberg teaches gene cluster 3 comprises a PP02 gene (p. 14, lines 11-13), which is predicted to be associated with janthitrem biosynthesis in Epichloë endophytes (p. 14, lines 19-25; p. 26, lines 17-18; Figure 20) as a membrane-bound O-acyl transferase (p. 16, line 33). Spangenberg teaches the nucleotide sequence of the PP02 gene (Figure 10) and corresponding amino acid sequence (Figure 11). Although Spangenberg does not refer to the PP02 gene as idtA and Spangenberg does not teach the PP02 gene product has acyltransferase activity and catalyses the conversion of epoxy-janthitrol to epox-janthitrem I, SEQ ID NO: 6 of Spangenberg encodes the amino acid sequence of instant SEQ ID NO: 3 (see Appendix at pp. 25-27 of the Office action mailed October 27, 2025 for sequence alignment), which is disclosed in the instant specification as the polypeptide encoded by the idtA gene from Epichloë festucae var. lolii AR37 (p. 26, lines 17-18). As such, the PP02 gene of Spangenberg is considered to be the same as the idtA gene in the claims of this application.
Spangenberg does not teach a genetic modification in an idtA gene that reduces or prevents the production or activity of an idtA gene product.
Saikia teaches the cloning and characterization of a cluster of genes from Penicillium paxillin necessary for the biosynthesis of the indole diterpene paxilline (p. 1625, column 2, top). Saikia teaches systematic gene disruption and chemical complementation studies have enabled identification of the enzymes that are needed for paxilline biosynthesis (p. 1625, column 2, top). Saikia teaches ectoptic expression of all or different subsets of paxilline biosynthetic genes in a paxilline-negative deletion mutant that lacks the entire paxilline biosynthetic gene cluster to identify the genes necessary for biosynthesis of a paxilline intermediate (p. 1627, column 1, middle).
Similar to Saikia, Scott teaches paxilline is an indole diterpene synthesized by Penicillium paxilli (p. 1422, Abstract) and teaches a complete functional analysis of the paxilline gene cluster using a combination of experiments including multiple targeted replacement of all identified genes of the paxilline gene cluster (p. 1424, last full paragraph; p. 1426, middle to bottom).
In view of the combined teachings of Spangenberg, Saikia, and Scott, it would have been obvious to one of ordinary skill in the art before the effective filing date to make an Epichloë endophyte NEA12 mutant deleted only for PP02 (idtA) and an Epichloë endophyte NEA12 mutant deleted for the entire janthitrem gene cluster including the PP02 (idtA) gene in order to identify genes necessary for biosynthesis of janthitrem. One would have been motivated to do so because, while Spangenberg teaches a need to understand janthitrems and their biosynthesis, Spangenberg predicts genes and their corresponding roles in janthitrem biosynthesis, Saikia and Scott teach experiments – including systematic gene disruption and chemical complementation studies, ectoptic expression of all or different subsets of biosynthetic genes in a deletion mutant that lacks an entire biosynthetic gene cluster, and multiple targeted replacement of all identified genes of a gene cluster – to identify the genes necessary for biosynthesis of janthitrem and intermediates. One would have expected success because Spangenberg teaches the nucleotide sequence of the PP02 (idtA) gene and Scott teaches experimental methodology for gene deletion based on the nucleotide sequence of a gene (beginning at the bottom of p. 1437).
The combination of Spangenberg, Saikia, and Scott does not teach or suggest an Epichloë endophyte NEA12 mutant deleted for PP02 (idtA) exhibits decreased production or amount of epoxy-janthitrem I and/or epoxy-janthitrem IV. However, instant Figure 1 shows that idtA converts epoxy-janthitrol to epox-janthitrem I and converts epox-janthitrem III to epox-janthitrem IV and an Epichloë endophyte NEA12 mutant deleted for PP02 (idtA) would inherently exhibit decreased production or amount of epoxy-janthitrem I and/or epoxy-janthitrem IV.
Regarding claim 71, for reasons stated above, in view of the combined teachings of Spangenberg, Saikia, and Scott, it would have been obvious to make an Epichloë endophyte NEA12 mutant deleted for the entire janthitrem gene cluster, which, according to Spangenberg, also includes a ltmF gene (p. 14, lines 11-17; Figure 4; Table 2) that encodes a polypeptide with predicted function of prenyltransferase (Table 2). Although Spangenberg does not refer to the ltmF gene as idtF and Spangenberg does not teach the ltmF gene product catalyses the conversion of epoxy-janthitrol to epox-janthitrem III, Spangenberg teaches the ltmF gene of NEA12 has the top BLAST hit of GenBank Accession Number DQ443465 with 99% sequence identity (Table 2). According to the instant specification, the gene product of idtF has a predicted amino acid sequence of SEQ ID NO: 72 (p. 17, lines 26-29) and the amino acid sequence of evidentiary reference GenBank DQ443465 is identical to SEQ ID NO: 72 of this application (see attached Appendix for sequence alignment). As such, the ltmF gene of Spangenberg is considered to be encompassed by idtF gene in instant claim 71 and an Epichloë endophyte NEA12 mutant deleted for the entire janthitrem gene cluster includes a deletion of the idtF gene.
Regarding claim 72, Spangenberg teaches the identification of the janthitrem biosynthetic gene cluster in the Epichloë endophyte LpTG3/NEA12 genome (p. 3, lines 28-31; pp. 22-23; and Table 2), which comprises gene cluster 4 containing a JtmD gene (p. 26, bottom). Evidentiary reference GenBank QGV56749 is cited to show that the amino acid sequence of JtmD is substantially identical but nonetheless distinct from the amino acid sequence of instant SEQ ID NO: 6 (see Appendix at p. 28 of the Office action filed April 1, 2026 for sequence alignment). The instant specification also discloses the idtD gene encodes SEQ ID NO: 6 (p. 26, lines 19-20), instant Figure 1 shows that idtD converts terpendole I to epoxy-janthitriol and converts terpendole J to epoxy-janthitrem III. Given that JtmD is substantially identical but distinct from the amino acid sequence of instant SEQ ID NO: 6, the JtmD of Epichloë endophyte LpTG3/NEA12 is considered to be “heterologous” to an Epichloë endophyte NEA12 mutant deleted only for PP02 (idtA) of the combination of Spangenberg, Saikia, and Scott and converts terpendole I to epoxy-janthitriol and converts terpendole J to epoxy-janthitrem III.
Regarding claims 73 and 74, for reasons stated above, in view of the combined teachings of Spangenberg, Saikia, and Scott, it would have been obvious to make an Epichloë endophyte NEA12 mutant deleted only for the PP02 (idtA) gene and as shown by instant Figures 1A and 1B, such a mutant would still express genes for the production of compounds with structures that are encompassed by formulae IV to VIII. For example, in view of instant Figure 1A, an Epichloë endophyte NEA12 mutant deleted only for the PP02 (idtA) gene would still express genes for production of paxilline, which is encompassed by Formula VII of claim 73.
Regarding claims 75 and 83-88, for reasons stated above, in view of the combined teachings of Spangenberg, Saikia, and Scott, it would have been obvious to make an Epichloë endophyte NEA12 mutant deleted only for the PP02 (idtA) gene and as shown by instant Figure 20, such a mutant would still express genes for the production of compounds with structures that are encompassed by formula II. For example, in view of instant Figure 20, an Epichloë endophyte NEA12 mutant deleted only for the PP02 (idtA) gene would still express genes for production of epoxy-janthitrem intermediates such as epoxy-janthitriol and epoxy-janthitrem III, which are encompassed by Formula II of claim 75 and formulae IIA and IID of claims 85-87, and given the deletion of PP02 (idtA), the intermediates epoxy-janthitriol and epoxy-janthitrem III would accumulate and not be converted to epoxy-janthitrem I and epoxy-janthitrem IV by idtA.
Regarding claim 76, for reasons stated above, in view of the combined teachings of Spangenberg, Saikia, and Scott, it would have been obvious to make an Epichloë endophyte NEA12 mutant deleted only for the PP02 (idtA) gene with ectoptic expression of all or different subsets of biosynthetic genes in a deletion mutant that lacks an entire biosynthetic gene cluster, and multiple targeted replacement of all identified genes of a gene cluster to identify the genes necessary for biosynthesis of janthitrem and intermediates and doing so would have resulted in expression of genes for production of epoxy-janthitrem compounds encompassed by formula II of claim 76.
Regarding claims 79-81, Spangenberg teaches that while the presence of janthitrems in perennial ryegrass pastures provides superior protection against a wide range of important pasture pests (p. 2, lines 9-10) and Epichloë endophyte-derived janthitrems have been observed to exhibit bioprotective properties that provide an advantage to pasture (p. 2, lines 17-18), janthitrems including janthitrems A and B can be tremorgenic and cause animals grazing on endophyte infected pastures develop to ataxia, tremors, and hypersensitivity to external stimuli (p. 2, lines 10-14).
Spangenberg teaches a plant inoculated with an endophyte (p. 10, lines 30-33).
Giraldo teaches that alkaloid profiles vary among different endophyte species and strains and development of endophyte strains with optimal alkaloid profiles are important in the livestock industry, noting that it is essential to deliver the specific concentration of alkaloids, to prevent insect attack on plants, but to not affect animal wellbeing (p. 399, column 1, third paragraph).
In view of the combined teachings of Spangenberg, Saikia, Scott, and Giraldo, it would have been obvious to one of ordinary skill in the art to inoculate a perennial ryegrass with the Epichloë endophyte NEA12 mutant of the combination of Spangenberg, Saikia, and Scott. One would have been motivated to do this in order to determine the effects of alkaloid production by such an Epichloë endophyte NEA12 mutant on insect attack and animal wellbeing and for development of an Epichloë endophyte strain with optimal alkaloid profiles. One would have had expected success because Spangenberg taught a plant inoculated with an endophyte.
Regarding claim 82, for reasons stated above, in view of the combined teachings of Spangenberg, Saikia, and Scott, it would have been obvious to make an Epichloë endophyte NEA12 mutant deleted for the entire janthitrem gene cluster, which, according to Spangenberg, also includes a ltmF gene (p. 14, lines 11-17; Figure 4; Table 2. Although Spangenberg does not refer to the ltmF gene as idtF, Spangenberg teaches the ltmF gene of NEA12 has the top BLAST hit of GenBank Accession Number DQ443465 with 99% sequence identity (Table 2). According to the instant specification, the gene product of idtF has a predicted amino acid sequence of SEQ ID NO: 72 (p. 17, lines 26-29) and the amino acid sequence of evidentiary reference GenBank DQ443465 is identical to SEQ ID NO: 72 of this application (see attached Appendix for sequence alignment). As such, the ltmF gene of Spangenberg is considered to be encompassed by idtF gene in instant claim 82 and an Epichloë endophyte NEA12 mutant deleted for the entire janthitrem gene cluster includes a deletion of the idtF gene.
Regarding claim 89, Spangenberg teaches the janthitrem producing endophyte is Epichloë endophyte strain NEA12 (p. 3, lines 28-31), which is an endophytic symbiont.
Regarding claim 90, for reasons stated above, in view of the combined teachings of Spangenberg, Saikia, and Scott, it would have been obvious to make an Epichloë endophyte NEA12 mutant deleted only for PP02 (idtA) and according to Spangenberg, the janthitrem gene cluster includes a ltmF gene (p. 14, lines 11-17; Figure 4; Table 2). Although Spangenberg does not refer to the ltmF gene as idtF, Spangenberg teaches the ltmF gene of NEA12 has the top BLAST hit of GenBank Accession Number DQ443465 with 99% sequence identity (Table 2). According to the instant specification, the gene product of idtF has a predicted amino acid sequence of SEQ ID NO: 72 (p. 17, lines 26-29) and the amino acid sequence of evidentiary reference GenBank DQ443465 is identical to SEQ ID NO: 72 of this application (see attached Appendix for sequence alignment). As such, the ltmF gene of Spangenberg is considered to be encompassed by idtF gene in instant claim 90 and an Epichloë endophyte NEA12 mutant deleted only for PP02 (idtA) includes a functional idtF gene.
Therefore, the invention of claims 70-76 and 82-90 would have been obvious to one of ordinary skill in the art before the effective filing date.
RESPONSE TO REMARKS: Applicant argues that because Spangenberg teaches epoxy-janthitrem biosynthesis begins with paxilide compounds, one would have been motivated to alter epoxy-janthitrem biosynthesis in Epichloë that produces paxiline, which is completely different from the claimed genetically modified Epichloë host cell. Thus, according to applicant, Spangenberg teaches away from the claimed invention. Applicant further contends that because Spangenberg teaches production of epoxy-janthitrem I is catalyzed by PP01 gene product, one would have focused on PP01 gene rather than PP02.
Applicant’s arguments are not found persuasive. As stated above, Spangenberg teaches a need to understand janthitrems and their biosynthesis, however, Spangenberg only predicts genes of Epichloë endophyte NEA12 including PP02 and their corresponding roles in janthitrem biosynthesis, while Saikia and Scott teach empirical experiments – including systematic gene disruption and chemical complementation studies, ectoptic expression of all or different subsets of biosynthetic genes in a deletion mutant that lacks an entire biosynthetic gene cluster, and multiple targeted replacement of all identified genes of a gene cluster – to identify the genes necessary for biosynthesis of janthitrem and intermediates. As such, contrary to applicant’s position, it would have been obvious to one of ordinary skill in the art before the effective filing date to apply the experimental methodology taught by Saikia and Scott to the Epichloë endophyte NEA12 of Spangenberg and make an Epichloë endophyte NEA12 mutant deleted only for PP02 (idtA) and an Epichloë endophyte NEA12 mutant deleted for the entire janthitrem gene cluster including the PP02 (idtA) gene in order to identify genes necessary for biosynthesis of janthitrem.
Applicant further argues the cited prior art does not correlate undesirable tremorgenicity with epoxy-janthitrem I and does not teach increasing production of epoxy-janthitriol to minimize tremorgenicity, and thus, according to applicant, one would not have been motivated to modify an Epichloë host cell to minimize or prevent production of epoxy-janthitrem I or to increase the production of epoxy-janthitriol without impermissible hindsight reconstruction.
Applicant’s argument is not found persuasive. The reason or motivation to modify the reference may often suggest what the inventor has done, but for a different purpose or to solve a different problem. It is not necessary that the prior art suggest the combination to achieve the same advantage or result discovered by applicant. See MPEP 2144.IV. While applicant argues the obviousness rationale relies on improper hindsight reasoning, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. In this case, the obviousness rationale relies on knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure.
For these reasons, it is the examiner’s position that the claimed invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
Conclusion
Status of the claims:
Claims 70-76 and 79-90 are pending in the application.
Claims 70-76 and 79-90 are rejected.
No claim is in condition for allowance.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DAVID J STEADMAN whose telephone number is (571)272-0942. The examiner can normally be reached Monday to Friday, 7:30 AM to 4:00 PM.
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/David Steadman/Primary Examiner, Art Unit 1656
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Prosecution Insights