XYLANASES WITH ENHANCED THERMOTOLERANCE AND USES THEREOF

§103 §112

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 of Group I, claims 1-3, in the reply filed on 09/08/2026 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)). Priority The instant application filed on 10/28/2024 is a 371 of PCT/US2023/066345 filed on 04/28/2023 and claims priority to U.S. Provisional Application 63/335,925 filed on 04/28/2022. U.S. PRO 63/335,925 finds support for the instantly claimed invention. Therefore, the effective filing date of the instant application is 04/28/2022. Information Disclosure Statement The information disclosure statement (IDS) submitted on 04/21/2025 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner. Claim Objections Claim 1 is objected to because of the following informalities: claim 1 recites “relative a second xylanase”; however, this should recite “relative to a second xylanase”. Appropriate correction is required. This is an objection, not a rejection, because this appears to be a typographical error. Claim Rejections - 35 USC § 112(b), Indefiniteness The following is a quotation of 35 U.S.C. 112(b): (b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention. Claim 3 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 (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention. Claim 3 recites “the amino acid substitution”, but then proceeds to list a set of amino acid substitutions that are joined by an “and” linking phrase signifying that all the amino acid substitutions are required. However, “the amino acid substitution” is singular, not plural. Therefore, it is unclear if the xylanase comprises one amino acid substitution from the list or all of the listed amino acid substitutions. For the purposes of applying prior art, the Examiner has interpreted this to be that the xylanase comprises one amino acid from the listed amino acids due to the language “the amino acid substitution”, with “substitution” being singular, not plural. Additionally, independent claim 1 recites a Markush listing of substitutions, which is a closed group, while dependent claim 3 recites the transitional phrase “comprises” which is an open group of substitutions. An open group of amino acid substitutions cannot follow a closed group of substitutions as it is unclear what is included and excluded from the substitutions. Claim Rejections - 35 USC § 103, Obviousness 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 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. Claims 1-2 are rejected under 35 U.S.C. 103 as being unpatentable over Berka (Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris; 2011) as evidenced by GenBank (glycoside hydrolase family 11 protein [Thermothielavioides terrestris NRRL 8126]) in view of Han (CN 109750016; Date of Publication: May 14, 2019). Berka’s general disclosure relates to describing and comparing the genomes of two thermophilic fungi, Myceliophthora thermophila and Thielavia terrestris, wherein “Examination of transcriptome data and secreted proteins suggests that the two fungi use shared approaches in the hydrolysis of cellulose and xylan but distinct mechanisms in pectin degradation. Characterization of the biomass-hydrolyzing activity of recombinant enzymes suggests that these organisms are highly efficient in biomass decomposition at both moderate and high temperatures. Furthermore, we present evidence suggesting that aside from representing a potential reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using classical and molecular genetics” (see, e.g., Berka, abstract). Regarding claim 1 pertaining to SEQ ID NO: 2, Berka teaches the complete sequence of T. terrestris NRRL 8126 chromosome 1, which comprises THITE_2107799, corresponding to GenBank AEO062969.1 and encodes an T. terrestris xylanase (see, e.g., Berka, Accession codes CP033009 & Table 2). GenBank is cited only to show that the GenBank AEO062969.1 T. terrestris xylanase taught by Berka has 100% sequence similarity to instant SEQ ID NO: 2 (see, e.g., Office Action Appendix). However, Berka does not teach: one amino acid substitution at a position selected from the group consisting of 90, 105, 114, and 115 of SEQ ID NO:2 and/or any of sets of substitutions selected from the group consisting of: (a) G48C and T206C; (b) Y123V, S125C, andN171C;(c) S114C,Y123V, S125C, and N171C; (d) Y123V, S125C, N171C, G48C, and T206C; or (e) S114C, Y123V, S125C, N171C, G48C, and T206C (claim 1); or wherein the at least one substitution is selected from the group consisting of S90T, Q105V, Q105I, S114C, S114P, and A115S (claim 2). Han’s general disclosure relates to a method of producing xylanase mutants, wherein the mutants have increased or improved thermostability therefore resulting in the mutants being suitable for industrialized large-scale production (see, e.g., Han, abstract – English Translation). Regarding claims 1-2 pertaining to the amino acid substitution, Han teaches a S90T amino acid substitution in an engineered xylanase (see, e.g., Han, abstract – English Translation). Han teaches that the S90T amino acid substitution increases the heat-resistance and thermostability of the xylanase (see, e.g., Han, abstract – English Translation). It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to produce Berka’s T. terrestris xylanase corresponding to GenBank AEO062969.1, wherein the xylanase comprises an S90T amino acid substitution, as taught by Han. One would have been motivated to do so because Han teaches that the S90T amino acid substitution increases the heat-resistance and thermostability of the xylanase (see, e.g., Han, abstract – English Translation). Moreover, Berka teaches that the T. terrestris xylanase corresponding to THITE_2107799 functions at an optimal temperature of 50oC (see, e.g., Berka, Table 2). Therefore, it would have been obvious to produce a mutant xylanase with the S90T amino acid substitution to have a xylanase that performs its inherent function of degrading biomass, as taught by Berka (see, e.g., Berka, “Enzymes for biomass degradation”, pg. 923), wherein the xylanase is also thermotolerant at temperatures higher than its optimal temperature of 50oC; therefore, allowing the enzyme to function at high temperatures. One would have expected success because Berka and Han both teach thermotolerant xylanases. Regarding claim 1 pertaining to the recitation “wherein the amino acid substitution or substitutions increases thermotolerance of the xylanase relative a second xylanase comprising the amino acid sequence SEQ ID NO:2”, this is considered inherent. The combined prior art of Berka and Han teach SEQ ID NO: 2 with an S90T amino acid substitution, and Han teaches that the S90T amino acid substitution increases the heat-resistance and thermostability of the xylanase (see, e.g., Han, abstract – English Translation). Therefore, this amino acid substitution would inherently result in increased thermotolerance of the xylanase relative a second xylanase comprising the amino acid sequence SEQ ID NO:2. Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over Berka and Han as applied to claims 1-2 above, and further in view of Johansen (WO 2018/234465; Date of Publication: December 27, 2018). The references of Berka and Han are discussed above as it pertains to a mutant xylanase with enhanced thermotolerance. However, the references do not teach: wherein the amino acid substitution comprises Y123V, S125C, N171C, G48C, and T206C (claim 3). Johansen’s general disclosure relates to xylanase variants with improved properties compared to its parent xylanase (see, e.g., Johansen, abstract & pg. 2, lines 19-20). Regarding claim 3 pertaining to the G48C amino acid substitution, Johansen teaches the G48C amino acid substitution in a xylanase (see, e.g., Johansen, pg. 16, line 16). Refer to 112(b) rejection above for claim interpretation. It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to produce Berka and Han’s T. terrestris xylanase corresponding to GenBank AEO062969.1 with an S90T amino acid substitution, wherein the xylanase also comprises a G48C amino acid substitution, as taught by Johansen. One would have been motivated to do so because Johansen teaches that the G48C amino acid substitution results in improved thermostability of the xylanase variant compared to its parent xylanase (see, e.g., Johansen, pg. 47, lines 13-15). Han teaches that the S90T amino acid substitution increases the heat-resistance and thermostability of the xylanase (see, e.g., Han, abstract – English Translation). Berka teaches that the T. terrestris xylanase corresponding to THITE_2107799 functions at an optimal temperature of 50oC (see, e.g., Berka, Table 2). Therefore, it would have been obvious to produce a mutant xylanase with the S90T and G48C amino acid substitutions to have a xylanase that performs its inherent function of degrading biomass, as taught by Berka (see, e.g., Berka, “Enzymes for biomass degradation”, pg. 923), wherein the xylanase is also thermotolerant at temperatures higher than its optimal temperature of 50oC; therefore, allowing the enzyme to function at high temperatures. One would have expected success because Berka, Han, and Johansen all teach thermotolerant xylanases. Conclusion Claims 1-3 are rejected. No claims are allowed. Correspondence Information Any inquiry concerning this communication or earlier communications from the examiner should be directed to NATALIE IANNUZO whose telephone number is (703)756-5559. The examiner can normally be reached Mon - Fri: 8:30-6:00 EST. Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Sharmila Landau can be reached at (571) 272-0614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000. /NATALIE IANNUZO/Examiner, Art Unit 1653 /SHARMILA G LANDAU/Supervisory Patent Examiner, Art Unit 1653