Detailed Action
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s election of Group I, claims 1-16, to SEQ ID NO: 2, in the reply filed on October 27, 2025 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 21-28 are canceled. Claims 17-20 have been withdrawn from further consideration by the examiner because they are drawn to non-elected inventions. Claims 1-16, to SEQ ID NO: 2, are under consideration.
Priority: This application is a 371 of PCT/US2021/026202, filed April 7, 2021, which claims benefit of provisional applications 63/008098, filed April 10, 2020, and 63/147352, filed February 9, 2021.
Claim Objections
Claims 3, 7 are objected to because of the following informalities: in claim 3, the term “UAS” should be spelled out in the full the first time that it is recited in the claims; in claim 7, the term “TEV” should be spelled out in the full the first time that it is recited in the claims. Appropriate correction is required.
Claim Rejections - 35 USC § 112
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.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 2-3 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 2 recites the promoter sequence comprises a sequence selected from the group of noted SEQ ID NOS. 1-6. Claim 2 then recites optionally wherein said promoter sequence comprises of a sequence selected from SEQ ID NO: 2, 6, optionally, wherein the promoter comprises SEQ ID NO: 1 and 2. It is not clear if the optional features are elements that are further incorporated to the selected promoter sequence, regardless of SEQ ID NO. or whether the promoter sequence is optionally that noted sequence. It is not clear how the promoter sequence is then optionally another sequence. Further clarification and/or correction is requested.
Further, a broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 2 recites the broad recitation of a sequence selected from one of SEQ ID NO: 1-6, and the claim also recites the sequence is one of SEQ ID NO: 2 and 6, which is the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims. It is not clear what is being claimed.
Claim 3 is included in this rejection because it is dependent on claim 2 and fails to cure its defects.
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.
Claims 1-2, 9, 10-16 are rejected under 35 U.S.C. 103 as being unpatentable over Dominguez et al. (1998 Internatl Microbiol 1:131-142), and evidenced by Prado-Gonzalez et al. (Sequence submission of Prado-Gonzalez et al. Thesis 1993). Dominguez et al. disclose non-conventional yeasts, including Yarrowia lipolytica (Y. lipolytica), for heterologous protein production (at least p. 131). Dominguez et al. disclose homologous promoters in the yeast Y. lipolytica for the expression of heterologous protein include XPR2 and MTP I/II (p. 133 Table 2). Dominguez et al. disclose developing vectors for Y. Lipolytica, the vector comprising a promoter and a polylinker sequence (p. 136-138, Fig. 2). Therefore, it would have been obvious to one of ordinary skill that a vector can be developed to comprise a MTP I/II promoter and a polylinker sequence.
While Dominguez et al. do not explicitly teach the nucleic acid sequence for the promoter to MTP I/II, it is noted that the MTP I/II promoter comprises a nucleic acid sequence having at least 95% sequence identity with the recited promoter sequence comprising instant SEQ ID NO: 2, as submitted in the thesis of Prado-Gonzalez et al. See below:
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Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to arrive at the claimed transcription element or a vector comprising a promoter and a polylinker, wherein the promoter comprises a nucleic acid sequence having at least 95% sequence identity to instant SEQ ID NO: 2, and wherein the polylinker is operably linked to the promoter sequence (instant claims 1-2, 9). The motivation to do so is given by the prior art. In this instance, the prior art Dominguez et al. disclose developing a vector (or transcription element) comprising a Y. lipolytica promoter and a polylinker, where known Y. lipolytica promoters include MTP I/II promoter, which appears to be the same promoter of instant SEQ ID NO: 2. One of ordinary skill would have a reasonable expectation of success because developing vectors for heterologous protein production is known and the prior art has identified known Y. lipolytica promoters, including the instant promoter sequence.
Regarding instant claim 10, as noted above, Dominguez et al. disclose the vector comprises the Y. lipolytica promoter operably linked to a polylinker sequence. MPEP 2144.04 notes that the duplication of part is obvious. Therefore, it would be obvious that the vector developed to comprise the Y. lipolytica promoter MTP I/II can be flanked on each end by a polylinker sequence as an obvious design choice.
Regarding instant claims 11, 13, Dominguez et al. disclose integrating a LEU2 region (p. 136-137).
Regarding instant claims 12, 14, Dominguez et al. disclose that the usual transforming vectors for yeast are hybrids between yeast-derived and bacterial sequences, because plasmids can be amplified and isolated with greater ease from E. coli, harbor an ori, and also have a sequence conferring resistance against a specific antibiotic (p. 133). Therefore, it would be obvious to one of ordinary skill that the vector comprising the Y. lipolytica promoter MTP I/II can further comprise an antibiotic resistance marker (instant claim 12) and/or an E. coli replication region (instant claim 14).
Regarding instant claims 15-16, as noted above, Dominguez et al. disclose Y. lipolytica is a system for heterologous protein production (p. 131). Therefore, it would be obvious to one of ordinary skill that the vector comprising the Y. lipolytica promoter MTP I/II of Dominguez et al. can be operably linked to a heterologous coding sequence (instant claim 15) and it would be further obvious that a Y. lipolytica host cell can comprise the vector (instant claim 16).
Claims 1-2, 3, 8, 9-16 are rejected under 35 U.S.C. 103 as being unpatentable over Dominguez et al. (1998 Internatl Microbiol 1:131-142) in view of Darvishi et al. (2018 Applied Microbiology and Biotechnology 102:5925-5938). The teachings of Dominguez et al. over at least instant claims 1-2, 9-16 are noted above.
Regarding instant claim 3, Darvishi et al. disclose Y. lipolytica is an important industrial host for the production of recombinant proteins and chemicals (p. 5925). Darvishi et al. disclose that promoters are the key elements in controlling gene expression and that the strength of a promoter is determined by factors including core promoter, TATA box, proximal promoter sequence, and upstream activating sequences (UAS) (p. 5926). Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to further operably link one or more UAS to the promoter MTP I/II in the vector developed to comprise promoter MTP I/II and a polylinker of Dominquez et al. noted above. The motivation to do is given by the prior art Darvishi et al., which disclose strong hybrid promoters are engineered by fusing a core promoter with a plurality of UAS (p. 5926). One of ordinary skill would have a reasonable expectation of success because elements for developing vectors and transcription elements for heterologous protein expression are known and available in the prior art.
Regarding instant claim 8, Darvishi et al. disclose that many of the genes encoding central metabolic enzymes in Y. lipolytica contain introns at the beginning of the gene, where including these introns improve expression of heterologous genes (p. 5926). Darvishi et al. disclose that an intron-containing translation elongation factor-1α (TEF1intron) promoter exhibited a 17- and 5-fold increase in gene expression over intron-less TEF1 and HP4D promoters (p. 5926). Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to further include a TEF1intron in the vector developed to comprise promoter MTP I/II and a polylinker of Dominquez et al. noted above, where the TEF1intron is positioned between the promoter and polylinker as an obvious design choice. The motivation to do so is given by the prior art Darvishi et al., which disclose including Y. lipolytica introns, such as TEF1 intron, improve expression of heterologous genes. One of ordinary skill would have a reasonable expectation of success because elements for developing vectors and transcription elements for heterologous protein expression are known and available in the prior art.
Claims 1-2, 4-6, 9-16 are rejected under 35 U.S.C. 103 as being unpatentable over Dominguez et al. (1998 Internatl Microbiol 1:131-142) in view of Szymczak et al. (2005 Expert Opin Biol Ther 5(5):627-638) and O’Shea et al. (US 20180355379). The teachings of Dominguez et al. over at least instant claims 1-2, 9-16 are noted above.
Regarding instant claim 4, Szymczak et al. disclose utilizing 2A peptides to design vectors to express multiple genes (p. 627). Szymczak et al. disclose that the advantages of using 2A peptide sequences include their small size and ability for efficient coexpression of genes that are placed between them; genes placed downstream of different 2A peptide sequences are able to induce higher levels of expression when compared with placement following IRES (p. 631). Due to their small size and divergent N-terminal sequence, multiple 2A peptide sequences can be used in vectors (p. 632). Szymczak et al. disclose functional 2A-peptide sequences used in vector construction (p. 631 Table 2). O’Shea et al. also disclose 2A peptides allows for expression of multiple proteins (paragraphs 0146-0147). O’Shea et al. disclose exemplary 2A peptides, including the 2A peptides of Szymczak et al. (paragraphs 0147-0148), where the 2A peptides are modified to include Gly-Ser-Gly at the N terminus to improve cleavage efficiency, and where modified P2A sequence GSGATNFSLLKQAGDVEENPGP (SEQ ID NO: 18) and modified T2A sequence GSGEGRGSLLTCGDVEENPGP (SEQ ID NO: 21) have 100% sequence identity with instant SEQ ID NO: 13 and 14, respectively. Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to further include a 2A peptide coding nucleic acid sequence downstream of the polylinker in the vector developed to comprise promoter MTP I/II and a polylinker of Dominquez et al. noted above. The motivation to do so is given by the prior art Szymczak et al. and/or O’Shea et al., which disclose the advantages of utilizing 2A peptides in vector design to express multiple proteins. One of ordinary skill would have a reasonable expectation of success because elements for developing vectors and transcription elements for heterologous protein expression are known and available in the prior art.
Regarding instant claim 5, since the prior art O’Shea et al. disclose 2A peptide sequences that are structurally the same as the recited 2A peptide sequences, it would be obvious to arrive at the recited nucleic acid sequence encoding the recited 2A peptide sequence(s).
Regarding instant claim 6, as noted above, Szymczak et al. and O’Shea et al. disclose utilizing more than one 2A peptide for expressing multiple proteins. Szymczak et al. disclose cleavage occurs at the end of the 2A peptide (p. 631). MPEP 2144.04 also notes that the duplication and/or rearrangement of parts is obvious. Therefore, it would have been obvious to one of ordinary skill to further include a plurality of 2A peptide coding nucleic acid sequences in the vector developed to comprise promoter MTP I/II and a polylinker of Dominquez et al. noted above, where the plurality of 2A peptide coding nucleic acid sequences are each preceded with a unique recognized cleavage site. The motivation to do so is given by the prior art Szymczak et al. and/or O’Shea et al., which disclose the advantages of utilizing 2A peptides in vector design to express multiple proteins. One of ordinary skill would have a reasonable expectation of success because elements for developing vectors and transcription elements for heterologous protein expression are known and available in the prior art.
Claims 1-2, 4-6, 7, 9-16 are rejected under 35 U.S.C. 103 as being unpatentable over Dominguez et al. (1998 Internatl Microbiol 1:131-142) in view of Szymczak et al. (2005 Expert Opin Biol Ther 5(5):627-638), O’Shea et al. (US 20180355379), and Cesaratto et al. (2016 Journal of Biotechnology 231:239-249). The teachings of Dominguez et al., Szymczak et al., and O’Shea et al. over at least instant claims 1-2, 4-6, 9-16 are noted above.
Regarding instant claim 7, Cesaratto et al. disclose Tobacco Etch Virus protease (TEVp) is an efficient and specific protease that has become a valuable biotechnological tool (p. 239). Cesaratto et al. disclose TEVp has often been used to facilitate stoichiometric expression of multiple genes in bacteria, yeast, plant, and mammalian cells (p. 244). Cesaratto et al. disclose that peptide 2A, depending on the upstream protein, may not result in 1:1 stoichiometric expression of protein subunits (p. 244). Cesaratto et al. disclose that TEVp stoichiometry, instead is 1:1 (p. 244). Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to further incorporate a nucleic acid sequence encoding a TEVp in vector developed to comprise promoter MTP I/II, a polylinker, and a plurality of 2A peptide coding nucleic acid sequences of Dominguez et al., Szymczak et al., and O’Shea et al. noted above. The motivation to do so is given by the prior art Cesaratto et al., which disclose TEVp is an efficient tool for facilitating stoichiometric expression of multiple genes in various host cells, including yeast. One of ordinary skill would have a reasonable expectation of success because elements for developing vectors and transcription elements for heterologous protein expression are known and available in the prior art.
No claim is allowed.
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/Marsha Tsay/Primary Examiner, Art Unit 1656