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 .
DETAILED ACTION
This application is a 371 of PCT/FR2020/052282.
Continued Examination Under 37 CFR 1.114
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 December 18, 2025 has been entered.
Election/Restrictions
Applicant elected with traverse of Group I with a species election of SEQ ID NO:2 as the ID78713 gene encoding SEQ ID NO:3 in the reply filed on January 23, 2025.
Claims 25-31 and 34 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on January 23, 2025.
Status of Claims
Claims 17-19, 25-31, and 33-40 are pending.
Claims 25-31 and 34 are withdrawn.
Claims 17-19, 33, and 35-40 are under examination.
Response to Arguments
Claim Rejections - 35 USC § 112(a)
Applicant’s arguments, see pages 5-6 of the Remarks, filed December 18, 2025, with respect to claims17-19, 23 and 33 have been fully considered and are persuasive. Claim 1 has been amended to narrow the genus of the claimed fungus to a Trichoderma reesei, wherein it’s ID78713 gene having 90-100% sequence identity to SEQ ID NO:2 or encoding a protein having 90-100% sequence identity to SEQ ID NO:2. Applicant's argument that the specification provides sufficient examples to support the claimed genus has been found persuasive. Therefore, the rejection of claims 17-19, 23 and 33 under 35 U.S.C. 112(a) for lack of written description has been withdrawn.
Claim Rejections - 35 USC § 102
Applicant’s arguments, see pages 6-7 of the Remarks, filed December 18, 2025, with respect to claims 17-19, 23, and 33 have been fully considered. Claim 17 has been amended to recite a Trichoderma reesei strain, wherein it’s ID78713 gene having 90-100% sequence identity to SEQ ID NO:2 or encoding a protein having 90-100% sequence identity to SEQ ID NO:2. Such T. reesei strain is not taught or suggested by Bodie (US 9,587,242 – cited previously on form PTO-892). Therefore, the rejection of claims 17-19, 23, and 33 under 35 U.S.C. 102(a)(1) as being anticipated by Bodie has been withdrawn.
Claim Rejections - 35 USC § 103
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 17-19, 33, and 35-40 is/are rejected under 35 U.S.C. 103 as being unpatentable over Bodie (US 9,587,242 – form PTO-892), GL985066 (GenBank Database. July 25, 2016 – form PTO-892), and G0RL27_HYPJQ (UniPRotKB/TrEMBL Datablase. June 7, 2017 – form PTO-892),
MPEP 2111.01 states that ''[d]uring examination, the claims must be interpreted as broadly as their terms reasonably allow.'' MPEP 2113 states that “ [P]product by process claims are not limited to the manipulations of the recited steps, only the structure implied by the steps. [E]ven though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production.”. In the instant case, the structure of the claimed Trichoderma reesei implied is the same whether the Trichoderma reesei is obtained from use of the invalidation cassette comprising a nucleotide sequence of SEQ ID NO:1 or is obtained from mutagenesis, as long as the resulting product has the structural limitations recited in the claim, a Trichoderma reesei, wherein the ID78713 gene of SEQ ID NO:2 has been invalidated. Therefore, the claims encompass a Trichoderma reesei comprising an invalidated ID78713 gene, wherein the ID78713 gene comprises the nucleotide sequence of SEQ ID NO:2 and encodes a protein having the amino acid sequence of SEQ ID NO:3.
Regarding claim 17, Bodie discloses a genetically modified fungus, Trichoderma reesei, wherein its Gas 1/Gel 1 gene encoding β-(1,3)-glucanosyltransferase of SEQ ID NO:1 has been invalidated (claims 1-2, Column 2, lines 14-21 and lines 43-50, Column 12 line 45 through Column 14, and Example 1).
Regarding claim 18, the genetically modified Trichoderma reesei of Bodie has a reduced viscosity compared to the Trichoderma reesei not comprising the invalidated Gas 1/Gel 1 gene (Column 1, lines 58-60, Column 8, lines 41-51, Column 11, lines 25-36, and Column 24 lines 36-57). Bodie discloses that filamentous fungi are well-suited for large scale production of enzymes and other protein for industrial, pharmaceutical, animal health and food and beverage application (Column 1, lines 34-44). Bodie discloses that filamentous fungi having reduced viscosity has an advantageous in large-scale production of enzymes or proteins because the higher the viscosity of the broth, the less uniform the distribution of oxygen and nutrients, and the more energy required to agitate the culture and the viscosity of the broth becomes sufficiently high to significantly interfere with the dissolution of oxygen and nutrients, thereby adversely affecting the growth of the fungi (Column 1, lines 45-54).
Regarding claims 19 and 33, the Gas 1/Gel 1 gene has been inactivated by mutagenesis in the genetically modified Trichoderma reesei of Bodie (claim 5 and Column 2, lines 14-26).
Bodie does not disclose a Trichoderma reesei comprising an invalidated gene having the nucleic acid sequence of SEQ ID NO:2 and encoding a protein having the amino acid sequence of SEQ ID NO:3.
Regarding claims 17 and 35-40, G0RL27_HYPJQ discloses a Trichoderma reesei β-(1,3)-glucanosyltransferase (ORF Name TRIREDRAFT_78713) having 100% sequence identity to SEQ ID NO:3 of the instant application (see page 2 and the sequence alignment below). Said β-(1,3)-glucanosyltransferase is encoded by a gene having the accession number GL985066. GL985066 discloses a gene having 100% sequence identity to the ID78713 gene of SEQ ID NO:2 of the instant application (see page 3 and the sequence alignment below).
Therefore, in combining the above references, it would have been obvious to one having ordinary skill in the art before the time the claimed invention was effectively filed to substitute the invalidation of the Trichoderma reesei Gas-1/Gel-1 gene encoding a β-(1,3)-glucanosyltransferase (SEQ ID NO:1) of Bodie with another Trichoderma reesei β-(1,3)-glucanosyltransferase gene. The rationale to support a conclusion that the claims would have been obvious is that the substitution of one known element (invalidation of a β-(1,3)-glucanosyltransferase in a filamentous fungi) for another yields predictable results to one of ordinary skill in the art. One having ordinary skill in the art would have been motivated to do so in order to further reduce viscosity in Trichoderma reesei. One of ordinary skill in the art would have had a reasonable expectation of success since Bodie teaches invalidating genes encoding β-(1,3)-glucanosyltransferase in Trichoderma reesei to reduce is viscosity thereby improving large-scale production of enzymes and proteins, G0RL27_HYPJQ teaches a Trichoderma reesei β-(1,3)-glucanosyltransferase, and GL985066 teaches a gene encoding said Trichoderma reesei β-(1,3)-glucanosyltransferase of G0RL27_HYPJQ.
Therefore, the above references render claims 17-19, 33, and 35-40 prima facie obvious.
Applicant's arguments filed December 18, 2025 have been fully considered but they are not persuasive.
Applicant argues that the claims are not obvious because (1) the results of Bodie are obtained with the gene and protein GAS1, which only shares a sequence identity of 32.2% with the protein of SEQ ID NO:3 of the instant application which means the gene/protein of Bodie are clearly different from the gene/protein of the invention even if they belong to the very broad family of beta-1,3-glucanosyltransferase, (2) there is no suggestion in Bodie that the invalidation of the gene of SEQ ID NO:2 of the invention would be similar to the invention of the GAS1 gene. Applicant argues that the gene/protein belonging to the same broad family does not all act similarly by citing Mouyna (form PTO-1449). Applicant argues that Mouyna describes a mutant Aspergillus fumigatus, in which the gene encoding 1,3-β-glucanosyltransferase BGT1 is invalidated and concludes that that the variant strain does not prevent a different phenotype to the parent strain.
This is not found persuasive. (1) Applicant has failed to provide a rationale as to why one reading Bodie would have required a certain sequence identity for the amino acid sequences of GAS1 proteins and GAS1 genes. With the disclosure of Bodie at hand, one of ordinary skill in the art would have recognized to invalidate other Gas-1/Gel-1 gene encoding a β-(1,3)-glucanosyltransferase in T. reesei other than those expressly disclosed by Bodie. One having ordinary skill in the art would have been motivated to do so in order to further reduce viscosity in Trichoderma reesei. (2) The disclosure of Mouyna is directed to invalidation of a 1,3-β-glucanosyltransferase in Aspergillus fumigatus and not T. reesei. The teachings of Mouyna does not criticize, discredit, or otherwise discourage the solution claimed. Further, MPEP 2143.02. II. states that “[o]bviousness does not require absolute predictability, but at least some degree of predictability is required.”. In the instant case, one of ordinary skill in the art would have had a reasonable expectation of success since Bodie teaches invalidating genes encoding β-(1,3)-glucanosyltransferase in Trichoderma reesei to reduce is viscosity thereby improving large-scale production of enzymes and proteins, G0RL27_HYPJQ teaches a Trichoderma reesei β-(1,3)-glucanosyltransferase, and GL985066 teaches a gene encoding said Trichoderma reesei β-(1,3)-glucanosyltransferase of G0RL27_HYPJQ. Therefore, it would have been obvious to one having ordinary skill in the art before the time the claimed invention was effectively filed to substitute the invalidation of the Trichoderma reesei Gas-1/Gel-1 gene encoding a β-(1,3)-glucanosyltransferase (SEQ ID NO:1) of Bodie with another Trichoderma reesei β-(1,3)-glucanosyltransferase gene.
Hence the rejection is maintained.
Conclusion
Claims 17-19, 25-31, and 33-40 are pending.
Claims 25-31 and 34 are withdrawn.
Claims 17-19, 33, and 35-40 are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to YONG D PAK whose telephone number is (571)272-0935. The examiner can normally be reached M-Th: 5:30 am - 3:30 pm.
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, Robert Mondesi can be reached on 408-918-7584. 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.
/YONG D PAK/Primary Examiner, Art Unit 1652
Sequence alignment of SEQ ID NO:3 of the instant application (“Qy”) and Trichoderma reesei β-(1,3)-glucanosyltransferase of G0RL27_HYPJQ (“Db”)
G0RL27_HYPJQ
ID G0RL27_HYPJQ Unreviewed; 374 AA.
AC G0RL27;
DT 19-OCT-2011, integrated into UniProtKB/TrEMBL.
DT 19-OCT-2011, sequence version 1.
DT 27-NOV-2024, entry version 42.
DE RecName: Full=1,3-beta-glucanosyltransferase {ECO:0000256|RuleBase:RU361209};
DE EC=2.4.1.- {ECO:0000256|RuleBase:RU361209};
DE Flags: Fragment;
GN ORFNames=TRIREDRAFT_78713 {ECO:0000313|EMBL:EGR48094.1};
OS Hypocrea jecorina (strain QM6a) (Trichoderma reesei).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes;
OC Hypocreomycetidae; Hypocreales; Hypocreaceae; Trichoderma.
OX NCBI_TaxID=431241 {ECO:0000313|Proteomes:UP000008984};
RN [1] {ECO:0000313|EMBL:EGR48094.1, ECO:0000313|Proteomes:UP000008984}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=QM6a {ECO:0000313|EMBL:EGR48094.1,
RC ECO:0000313|Proteomes:UP000008984};
RX PubMed=18454138; DOI=10.1038/nbt1403;
RA Martinez D., Berka R.M., Henrissat B., Saloheimo M., Arvas M., Baker S.E.,
RA Chapman J., Chertkov O., Coutinho P.M., Cullen D., Danchin E.G.,
RA Grigoriev I.V., Harris P., Jackson M., Kubicek C.P., Han C.S., Ho I.,
RA Larrondo L.F., de Leon A.L., Magnuson J.K., Merino S., Misra M., Nelson B.,
RA Putnam N., Robbertse B., Salamov A.A., Schmoll M., Terry A., Thayer N.,
RA Westerholm-Parvinen A., Schoch C.L., Yao J., Barabote R., Nelson M.A.,
RA Detter C., Bruce D., Kuske C.R., Xie G., Richardson P., Rokhsar D.S.,
RA Lucas S.M., Rubin E.M., Dunn-Coleman N., Ward M., Brettin T.S.;
RT "Genome sequencing and analysis of the biomass-degrading fungus Trichoderma
RT reesei (syn. Hypocrea jecorina).";
RL Nat. Biotechnol. 26:553-560(2008).
CC -!- FUNCTION: Splits internally a 1,3-beta-glucan molecule and transfers
CC the newly generated reducing end (the donor) to the non-reducing end of
CC another 1,3-beta-glucan molecule (the acceptor) forming a 1,3-beta
CC linkage, resulting in the elongation of 1,3-beta-glucan chains in the
CC cell wall. {ECO:0000256|RuleBase:RU361209}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000256|ARBA:ARBA00004609,
CC ECO:0000256|RuleBase:RU361209}; Lipid-anchor, GPI-anchor
CC {ECO:0000256|ARBA:ARBA00004609, ECO:0000256|RuleBase:RU361209}.
CC -!- SIMILARITY: Belongs to the glycosyl hydrolase 72 family.
CC {ECO:0000256|ARBA:ARBA00007528, ECO:0000256|RuleBase:RU361209}.
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DR EMBL; GL985066; EGR48094.1; -; Genomic_DNA.
DR RefSeq; XP_006966138.1; XM_006966076.1.
DR AlphaFoldDB; G0RL27; -.
DR EnsemblFungi; EGR48094; EGR48094; TRIREDRAFT_78713.
DR GeneID; 18488920; -.
DR KEGG; tre:TRIREDRAFT_78713; -.
DR VEuPathDB; FungiDB:TRIREDRAFT_78713; -.
DR eggNOG; ENOG502SHAA; Eukaryota.
DR HOGENOM; CLU_021855_0_0_1; -.
DR OrthoDB; 2783940at2759; -.
DR Proteomes; UP000008984; Unassembled WGS sequence.
DR GO; GO:0043188; C:cell septum edging; IEA:EnsemblFungi.
DR GO; GO:0051286; C:cell tip; IEA:EnsemblFungi.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0000936; C:primary cell septum; IEA:EnsemblFungi.
DR GO; GO:0098552; C:side of membrane; IEA:UniProtKB-KW.
DR GO; GO:0030427; C:site of polarized growth; IEA:EnsemblFungi.
DR GO; GO:0042124; F:1,3-beta-glucanosyltransferase activity; IEA:EnsemblFungi.
DR GO; GO:0071970; P:fungal-type cell wall (1->3)-beta-D-glucan biosynthetic process; IEA:EnsemblFungi.
DR GO; GO:0031505; P:fungal-type cell wall organization; IEA:TreeGrafter.
DR Gene3D; 3.20.20.80; Glycosidases; 1.
DR InterPro; IPR004886; Glucanosyltransferase.
DR InterPro; IPR017853; Glycoside_hydrolase_SF.
DR PANTHER; PTHR31468; 1,3-BETA-GLUCANOSYLTRANSFERASE GAS1; 1.
DR PANTHER; PTHR31468:SF8; 1,3-BETA-GLUCANOSYLTRANSFERASE GAS2; 1.
DR Pfam; PF03198; Glyco_hydro_72; 1.
DR SUPFAM; SSF51445; (Trans)glycosidases; 1.
PE 3: Inferred from homology;
KW Glycoprotein {ECO:0000256|RuleBase:RU361209};
KW GPI-anchor {ECO:0000256|RuleBase:RU361209};
KW Lipoprotein {ECO:0000256|RuleBase:RU361209};
KW Membrane {ECO:0000256|RuleBase:RU361209};
KW Reference proteome {ECO:0000313|Proteomes:UP000008984};
KW Signal {ECO:0000256|RuleBase:RU361209};
KW Transferase {ECO:0000256|RuleBase:RU361209}.
FT SIGNAL 1..19
FT /evidence="ECO:0000256|RuleBase:RU361209"
FT CHAIN 20..374
FT /note="1,3-beta-glucanosyltransferase"
FT /evidence="ECO:0000256|RuleBase:RU361209"
FT /id="PRO_5005130792"
FT NON_TER 374
FT /evidence="ECO:0000313|EMBL:EGR48094.1"
SQ SEQUENCE 374 AA; 41274 MW; F8AA26EC8A2CF10E CRC64;
Query Match 100.0%; Score 2009; Length 374;
Best Local Similarity 100.0%;
Matches 374; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MRWSSVAVALASAKSFAVALDPVSVVGNKFFNKDGSQFFIKGIAYQLVPQDPLVDTDQCK 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MRWSSVAVALASAKSFAVALDPVSVVGNKFFNKDGSQFFIKGIAYQLVPQDPLVDTDQCK 60
Qy 61 RDAKLMAELGTNTIRVYHVDPDADHDGCMSAFDDAGIYVLADLDTFDTYIIPQNNYWNKT 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 RDAKLMAELGTNTIRVYHVDPDADHDGCMSAFDDAGIYVLADLDTFDTYIIPQNNYWNKT 120
Qy 121 KFDRYAEVLDTFQKYDNLLGVFVGNENIATKDDSPTAPYLKAAARDMKAYRDAQGYREIP 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 KFDRYAEVLDTFQKYDNLLGVFVGNENIATKDDSPTAPYLKAAARDMKAYRDAQGYREIP 180
Qy 181 VGYSAADILQLRPMLQDYLTCGGNSSETVDFFALNSYSWCDPSTYKESTYDQLEAYAKKF 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 VGYSAADILQLRPMLQDYLTCGGNSSETVDFFALNSYSWCDPSTYKESTYDQLEAYAKKF 240
Qy 241 PVPIFLSETGCIVPGPRQFDDQDAIFGPEMVNDWSGAIIYEWIQEENGYGIITYAPAGQA 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 PVPIFLSETGCIVPGPRQFDDQDAIFGPEMVNDWSGAIIYEWIQEENGYGIITYAPAGQA 300
Qy 301 AGPNVEGGFLRKGTPTPKLPDFTALKSKWATNTPTGVSRDDYDAKDVSTRACPSSTAGGW 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 AGPNVEGGFLRKGTPTPKLPDFTALKSKWATNTPTGVSRDDYDAKDVSTRACPSSTAGGW 360
Qy 361 WQVDGDAKLPTLGQ 374
||||||||||||||
Db 361 WQVDGDAKLPTLGQ 374
Sequence Alignment between SEQ ID NO:2 of the instant application (“Query”) and polynucleotide encoding Trichoderma reesei β-(1,3)-glucanosyltransferase of GL985066 (“Sbjct”)
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2360
1832
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Greyscale