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 without traverse of Group I (Claims 1-7 and 14-17) in the reply filed on 5/27/2026 is acknowledged. Claims 9 and 11-13 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected inventions, there being no allowable generic or linking claim. Claims 1-7 and 14-17 will be examined on the merits.
Claim Objections
Claim 16 is objected to as to form because it recites “belongs to the specifies Trichoderma reesei,” where “specifies” appears to be a typographical error for “species.” Appropriate correction is required.
Claim Rejections - 35 USC § 112 – 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.
Claims 1-7 and 14-17 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, 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 1 (and those dependent)
Claim 1 recites “inserting several copies of a gene of interest into the genome of a fungus.” The term “several” is a term of degree that fails to provide a reasonably certain boundary as to the number of copies required. While the specification discusses “multiple copies” and states in paragraph [26] that “multiple copies” means at least two copies, the claim itself uses the different term “several”, not “multiple,” and does not define it. Thus, it is unclear whether “several” requires two copies, more than two copies, or some other quantity.
Claim 1 further recites “a TEF1 promoter identical to the endogenous TEF1 promoter of the fungus species.” The term “identical” ordinarily denotes exact sequence sameness. However, the specification states at paragraph [24] that this phrase also encompasses a TEF1 promoter sequence that “may vary at certain nucleotides.” Thus, the claim language and specification present inconsistent scope as to whether exact identity is required or whether non-identical promoter variants are included. This issue is further complicated by the apparent introduction of sequence variants in Claim 4 (see more discussion below). As a result, the metes and bounds of the claim are not reasonably certain.
Claim 1 also recites “a terminator that is not the endogenous TEF1 terminator of the fungus species.” The negative limitation itself is not inherently improper, but the claim fails to make reasonably clear what degree of difference is required. For example, it is unclear whether the limitation excludes only the exact endogenous TEF1 terminator sequence, excludes close sequence variants, or excludes any TEF1-derived terminator generally. The specification introduces embodiments using sequence identity concepts for terminators, but such boundaries are not recited in the claim. Therefore, the scope of the exclusion is not reasonably certain.
Claim 3
The phrase “the endogenous TEF1 gene” lacks proper antecedent basis, as Claim 1 does not recite an endogenous TEF1 gene. Further, the phrase “the endogenous TEFI gene under the control of the endogenous TEF1 promoter are retained” is grammatically inconsistent and unclear as to whether the claim requires retention of the gene itself, the promoter-gene arrangement, or endogenous TEF1 function/expression. Therefore, the scope of Claim 3 is not reasonably certain.
Claim 4
Claim 4 depends from Claim 1, which requires a TEF1 promoter “identical to the endogenous TEF1 promoter of the fungus species.” Claim 4, however, recites a TEF1 promoter represented by: “SEQ ID NO: 1 or a sequence having a percentage identity of at least 60% with SEQ ID NO: 1 …” A sequence having only 60% identity to SEQ ID NO: 1 is not ordinarily “identical” to the endogenous TEF1 promoter. Thus, claim 4 is internally inconsistent with claim 1 and the scope of the claimed promoter is unclear.
Claim 4 alternatively recites: “the promoter of a gene encoding a protein of SEQ ID NO: 2 or a protein having a percentage identity of at least 80% with SEQ ID NO: 2.” This language does not clearly define the promoter by structure or by a single identifiable class. Different organisms can contain different promoters for genes encoding proteins meeting that protein-identity threshold. Thus, the promoter scope is not reasonably certain.
Claim 4 includes the language “preferably at least 80%.” The use of “preferably” in a claim is improper because it renders unclear whether the recited preferred feature is a limitation of the claim or merely optional descriptive language. Therefore, this language contributes to indefiniteness.
Claim 17
Claim 17 recites: “wherein said enzyme is a cellulolytic enzyme such as a cellulase or hemicellulose.” The phrase “such as” is exemplary language and renders it unclear whether the recited items are limiting or merely illustrative examples.
Claim 17 depends from claim 7, which requires that the gene of interest encodes an enzyme. However, claim 17 recites “a cellulase or hemicellulose.” The term hemicellulose ordinarily refers to a polysaccharide substrate, not an enzyme. Therefore, one of the listed alternatives does not correspond to the required enzyme limitation, rendering the claim internally inconsistent and indefinite.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1, 4-6, and 16 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Bidard-Michelot et al. “Bidard” (WO 2017115033A1; published 7/6/2017 – Google Patents translation provided). Claim 4 as evidenced by UniProtKB accession G0RPK5_HYPJQ (https://www.uniprot.org/uniprotkb/G0RPK5/entry; accessed 6/9/2026).
Regarding Claim 1, Bidard teaches a method for producing a protein in a filamentous fungal cell by overexpressing the TrAZF1 gene or a variant thereof in the cell (see pg. 1-2, translation). Bidard further teaches that overexpression is preferably performed by introducing into the genome of the cell a cassette comprising: (a) at least one constitutive promoter, (b) the TrAZF1 gene or a variant thereof, and (c) optionally, a terminator (see pg. 2, translation). Bidard teaches that suitable constitutive promoters include the TEF1 promoter of Trichoderma reesei, the gpd promoter of T. reesei, and the gpd promoter of Aspergillus nidulans (see pg. 2, translation). Bidard further teaches that the terminator is preferably the T. reesei gpd terminator. (see pg. 2, translation). Bidard further teaches that overexpression may be performed by introducing a DNA fragment comprising the TrAZF1 gene with a constitutive promoter, a terminator, and a selection marker, and that the cassette may be introduced by a vector such as a plasmid, preferably a pRS426-type plasmid (see pg. 2-3, translation).
Bidard additionally teaches an embodiment in which the transformed strain comprises, in addition to the TrAZF1 gene already present in the genome, an additional copy of the TrAZF1 gene, such that the strain comprises at least two copies of TrAZF1, with one copy being expressed constitutively (see pg. 2, translation). Thus, Bidard teaches transforming a filamentous fungal cell with an expression cassette comprising a constitutive promoter, TrAZF1, and a terminator, and teaches embodiments in which the transformed cell contains multiple copies of the TrAZF1 gene in its genome. Accordingly, Bidard teaches the claimed method.
The Office acknowledges that the prior Restriction Requirement mailed 04/01/2026 stated that Bidard did not teach “multiple” copies of the gene of interest. However, upon further consideration of Bidard and the claim language presently under examination, the Office finds that Bidard does in fact anticipate Claim 1. In particular, Bidard teaches an embodiment in which, in addition to the endogenous TrAZF1 gene present in the genome, the transformed strain includes an additional exogenous copy of TrAZF1, such that the strain comprises at least two copies of the gene. Further, as discussed above, the term “several” is reasonably indefinite and does not reasonably exclude an arrangement in which both the endogenous and exogenous copies of the gene satisfy the claimed limitation.
Regarding Claim 4, Bidard expressly teaches use of the Trichoderma reesei TEF1 promoter as a constitutive promoter (see pg. 2, translation). Claim 4 alternatively recites that the TEF1 promoter is “the promoter of a gene encoding a protein of SEQ ID NO: 2.” UniProtKB accession G0RPK5_HYPJQ identifies the Trichoderma reesei elongation factor 1-alpha (TEF1) protein, and the sequence associated with that entry exhibits a 100% alignment with claimed SEQ ID NO: 2, as shown by the truncated alignment set forth in this Office action (full alignment available in sequence search result file: us-18-288-280-2.minpct70_szlim700_1000.rup). Therefore, the T. reesei TEF1 promoter disclosed by Bidard is the promoter of the gene encoding the protein of SEQ ID NO: 2, and Bidard anticipates claim 4.
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Regarding Claim 5, Bidard expressly discloses that the filamentous fungus may be selected from fungi belonging to classes including Orbiliomycetes, Pezizomycetes, Dothideomycetes, Eurotiomycetes, Lecanoromycetes, Leotiomycetes, Sordariomycetes, and Saccharomycetes (see translation pg. 2).
Regarding Claims 6 and 16, Bidard expressly teaches that the preferred filamentous fungus is Trichoderma reesei (see translation pg. 2).
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
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 2, 3, and 14 are rejected under 35 U.S.C. § 103 as obvious over Bidard-Michelot et al. “Bidard” (WO 2017115033A1; published 7/6/2017 – Google Patents translation provided) in view of Bouchon et al. (WO 2018/0580064 A1; published 3/29/2018).
The teachings of Bidard were outlined above.
Regarding Claims 2 and 3, Bidard does not expressly disclose that the insertion is carried out upstream of the endogenous TEF1 promoter, or that the endogenous TEF1 gene under the control of the endogenous TEF1 promoter is retained in the transformed genome.
Bouchon teaches genome editing by insertion of exogenous nucleic acid into a genomic sequence, including at, within, or near a gene or its regulatory elements (see [0007]-[0009], [0018]). More specifically, Bouchon teaches embodiments wherein the genomic sequence is “in an intergenic region that is upstream of the promoter of the endogenous WAS gene in the genome” (see [0019]) and wherein the intergenic region is “at least 500 bp upstream of the first exon of the endogenous WAS gene” (see [0020]). The same upstream-promoter insertion concept is repeated in the treatment embodiments (see [0055]-[0056]). Thus, Bouchon teaches the known insertion strategy of placing exogenous sequence upstream of an endogenous promoter rather than within the endogenous coding region. Such upstream/intergenic insertion preserves the endogenous coding sequence while allowing exogenous sequence to be introduced nearby.
It would have been prima facie obvious to one of ordinary skill in the art at the time of filing to modify Bidard’s fungal transformation method by carrying out the insertion upstream of the endogenous TEF1 promoter, as taught by Bouchon, because upstream/intergenic insertion was a known targeted insertion strategy for introducing exogenous sequence while avoiding disruption of the endogenous coding region and preserving endogenous locus context. Accordingly, claim 2 would have been obvious over Bidard-Michelot in view of Bouchon.
Regarding Claim 14, Bidard does not teach the positional limitation of Claim 14.
It would have been prima facie obvious to one of ordinary skill in the art to modify Bidard’s fungal transformation method by placing the insertion upstream of the endogenous TEF1 promoter, as taught by Bouchon, because upstream/intergenic insertion was a known targeted insertion strategy that avoided disruption of the endogenous coding region. Further, once upstream insertion was selected, the exact upstream distance from the endogenous TEF1 gene/promoter region would have been a result-effective variable subject to routine optimization. Since Bouchon teaches insertion at least 500 bp upstream of the endogenous gene region, selecting an insertion site between 750 and 1250 bp relative to the TEF1 translation initiation site would have been an obvious matter of routine optimization of a known insertion-position variable to achieve suitable targeted insertion while preserving endogenous gene context, absent a showing that the claimed range is critical or yields unexpected results. Accordingly, claim 14 would have been obvious over Bidard-Michelot in view of Bouchon.
Claims 7 and 17 are rejected under 35 U.S.C. § 103 as obvious over Bidard-Michelot et al. “Bidard” (WO 2017115033A1; published 7/6/2017 – Google Patents translation provided) in view of Udagawa (WO 2012/160093 A1; published 11/29/2012).
The teachings of Bidard were outlined above.
Regarding Claims 7 and 17, Bidard does not expressly teach the gene of interest as a cellulolytic enzyme.
Udagawa teaches site-specific multicopy integration of genes encoding enzymes in filamentous fungi, including amylase, glucoamylase, beta-glucosidase, cellulase, and xylanase (see pg. 8-10). Thus, Udagawa teaches fungal integration/expression of beta-glucosidase and other cellulase-related enzymes.
It would have been prima facie obvious to substitute Bidard’s TrAZF1 cargo with an enzyme-encoding gene, as taught by Udagawa, as a predictable use of known fungal expression cargo in a known fungal integration system.
Claim 15 is rejected under 35 U.S.C. § 103 as being unpatentable over Bidard-Michelot et al. in view of Bouchon et al. (WO 2018/0580064 A1; published 3/29/2018), and further in view of UniProtKB accession G0RPK5_HYPJQ (https://www.uniprot.org/uniprotkb/G0RPK5/entry; accessed 6/9/2026).
The teachings of Bidard and Bouchon were outlined above.
Regarding Claim 15, those references do not expressly identify the TEF1 protein by the sequence of SEQ ID NO: 2.
UniProt entry G0RPK5_HYPJQ expressly discloses an elongation factor 1 alpha-like protein / elongation factor 1-alpha from Hypocrea jecorina (Trichoderma reesei), strain QM6a, with ORF name TRIREDRAFT_65530, and provides the amino acid sequence of that TEF1 protein. Thus, G0RPK5_HYPJQ teaches the specific T. reesei TEF1 protein sequence, i.e., the sequence corresponding to SEQ ID NO: 2.
It would have been prima facie obvious to use the known TEF1 protein sequence of G0RPK5_HYPJQ to characterize the TEF1 gene/protein associated with the otherwise obvious Claim 14 method.
Prior Art Search
A prior art search did not reveal a reference disclosing SEQ ID NO: 1 as recited in Claim 4. Accordingly, on the present record, the specific TEF1 promoter sequence recited as SEQ ID NO: 1 has not been shown by the prior art located during search. The prior art rejection of Claim 4 is therefore based on the alternative limitation directed to the promoter of a gene encoding the protein of SEQ ID NO: 2, rather than on an express disclosure of SEQ ID NO: 1 itself.
The prior art made of record and not relied upon is considered pertinent to Applicant's disclosure: Uzbas et al., Applied Microbiology and Biotechnology, 93: 1601-1608 (2012). Uzbas discloses recombinant expression of cellulase genes in Trichoderma reesei under the TEF1 promoter and also teaches use of the terminator region of the respective cellulase gene, rather than the endogenous TEF1 terminator (see pg. 1602, Materials and methods).
Conclusion
No claims are allowed.
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/CHRISTOPHER M BABIC/ Supervisory Patent Examiner, Art Unit 1633
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