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 .
Specification
The disclosure is objected to because of the following informalities:
On page 2, line 27, the instant specification recites, “a MODI promoter element from Pichia methanolica”. The promoter from Pichia methanolica is the MOD1.
Appropriate correction is required.
Claim Objections
Claim 10 is objected to because of the following informalities:
Claim 10 recites “a MODI promoter element from Pichia methanolica”. The promoter from Pichia methanolica is the MOD1.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 18 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Regarding Claim 18, Claim 1 recites a yeast cell with no limitations on the type of yeast cell. Claim 18, dependent on Claim 1, recites the yeast cell of Claim 1 that is a methylotrophic yeast cell or a non-methylotrophic yeast cell, and therefore does not limit the genus of yeast cells claimed in Claim 1 as there are no categories of yeast cells excluded by Claim 18. Therefore, Claim 18 is rejected under 35 USC 112(d) for failing to further limit the subject matter of Claim 1.
Applicant may cancel the claim, amend the claim to place the claim in proper dependent form, rewrite the claim in independent form, or present a sufficient showing that the dependent claim complies with the statutory requirements.
Claim Rejections - 35 USC § 102
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 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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-3, 5, 7, 8, 18 and 19 are rejected under 35 U.S.C. 102(a)(1) and 35 U.S.C. 102(a)(2) as being anticipated by Cornish, V., WO 2021/092589 A1, published May 14, 2021.
Regarding Claim 1, Cornish teaches a yeast cell: “[T]he genetically engineered cell of the present disclosure is a species of phylum Ascomycota. In certain embodiments, the species of the phylum Ascomycota is selected from Saccharomyces cerevisiae … Komagataella (Pichia) pastoris” (p. 35, lines 14-20). Cornish teaches the yeast cell with a first exogenous nucleic acid encoding a Rtg operably linked to a first promoter element: “an additional nucleic acid can be introduced into the cells to express a transcription factor for regulation expression of the molecule encoded by the nucleic acid … examples of such transcription factors include .. Rtg1p, Rtg3p” and “a nucleic acid can include a constitutively active promoter” (p. 48, lines 16-30 and line 11). Cornish teaches the yeast cell with a second exogenous nucleic acid encoding a polypeptide operably linked to a first promoter element or second promoter element: “a nucleic acid encoding a molecule of the present disclosure, e.g., peptide and/or protein, is introduced into the yeast cell either as a construct or a plasmid in which it is operably linked to a promoter active in the yeast cell” (p. 48, lines 3-5). Therefore, Claim 1 is anticipated by Cornish.
Regarding Claim 2, Cornish teaches a yeast cell where in the Rtg is Rtg1 in Pichia pastoris or Saccharomyces cerevisiae. Therefore, Claim 2 is anticipated by Cornish.
Regarding Claim 3, Cornish teaches the polypeptide may be an enzyme (p. 49, line 11). Therefore, Claim 3 is anticipated by Cornish.
Regarding Claim 5, Cornish teaches nucleic acids may be “introduced into the cell to .. integrate into the genome” (p. 47, lines 19-20). Therefore, Claim 5 is anticipated by Cornish.
Regarding Claim 7, Cornish teaches “a nucleic acid can include a constitutively active promoter” (p. 48, line 11). Therefore, Claim 7 is anticipated by Cornish.
Regarding Claim 8, Cornish teaches “a nucleic acid can include an inducible promoter” (p. 48, line 12). Therefore, Claim 8 is anticipated by Cornish.
Regarding Claim 18, Claim 18 is rejected under 112(d) for failing to limit Claim 1. Claim 1 is anticipated by Cornish. Cornish teaches a methylotrophic yeast cell, P. pastoris, and a non-methylotrophic yeast cell, S. cerevisiae. Therefore, Claim 18 is anticipated by Cornish.
Regarding Claim 19, Cornish teaches a methylotrophic yeast cell, P. pastoris. Therefore, Claim 19 is anticipated by Cornish.
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.
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.
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 3, 4, 6, 11, 13, and 21 are rejected under 35 U.S.C. 103 as being unpatentable over Cornish, V., WO 2021/092589 A1, published May 14, 2021 as applied to Claim 1 above, and further in view of Roy-Chaudhuri, B. and Shankar, S., US 2020/0340000 A1, published October 29, 2020.
Regarding Claims 3 and 4, Claim 1 is anticipated by Cornish including a first exogenous nucleic acid encoding a Rtg operably linked to a promoter element.
Cornish does not teach the expression of a heme-binding protein.
Roy-Chaudhuri teaches a yeast cell comprising a first exogenous nucleic acid and a second exogenous nucleic acid wherein the second nucleic acid encodes a heme-binding protein (p. 1, [0006]). Roy-Chaudhuri teaches, “The heme-binding protein can be selected from the group consisting of a globin, a cytochrome, a cytochrome c oxidase, a ligninase, a catalase, and a peroxidase” (p. 1, [0007]).
Regarding Claim 3, it would have been obvious to one skilled in the art before the effective filing date to perform a simple substitution of known element for another with the yeast cell taught by Cornish and the heme-binding proteins taught by Roy-Chaudhuri to create the yeast cell of Claim 1 wherein the polypeptide is a heme-binding protein. Cornish teaches Claim 1 with a yeast cell comprising an exogenous nucleic acid encoding a polypeptide, and Roy-Chaudhuri teaches a yeast cell comprising an exogenous nucleic acid encoding a heme-binding protein, which is a polypeptide. For one skilled in the art, the substitution would have been predictable because Cornish and Roy-Chaudhuri teach the expression of proteins in yeast cells and provide examples of expression in yeast cells. Therefore, Claim 3 is obvious over Cornish in further view of Roy-Chaudhuri.
Regarding Claim 4, Roy-Chaudhuri teaches the heme-binding protein can be a globin, a cytochrome, a cytochrome c oxidase, a ligninase, a catalase, or a peroxidase. Therefore, Claim 4 is obvious over Cornish in further view of Roy-Chaudhuri.
Regarding Claim 6, Claim 1 is anticipated by Cornish. Cornish teaches “the genetic molecular components are introduced into the cell to persist as a plasmid” (p. 47, lines 19-20).
Cornish does not teach replication-competent plasmids.
Roy-Chaudhuri teaches the nucleic acids in the yeast cell “can be extrachromosomally expressed from a replication-competent plasmid” (p. 13, [0080]).
It would have been obvious to one skilled in the art before the effective filing date to perform a simple substitution of one known element for another with the teachings of Cornish and Roy-Chaudhuri to use replication-competent plasmids in the yeast cells of Cornish. Roy-Chaudhuri teaches the structure and function of replication-competent plasmids. For one skilled in the art, the results would have been predictable because Cornish suggests plasmids that persist, and Roy-Chaudhuri teaches expression in yeast cells. Therefore, Claim 6 is obvious over Cornish in further view of Roy-Chaudhuri.
Regarding Claim 11 and 13, Claim 1 is anticipated by Cornish. Cornish teaches the use of a constitutive or inducible promoter element (p. 48, lines 11-12).
Cornish does not teach a third exogenous nucleic acid encoding Mxr1 operably linked to a promoter element or the use of methanol-inducible promoters.
Roy-Chaudhuri teaches “a third nucleic acid construct comprising a nucleotide sequence encoding a third protein operably linked to the first promoter element, the second promoter element, or a third promoter element” wherein “the third protein can be a transcription factor … transcription factor can be Mxr1”. Roy-Chaudhuri also teaches methanol-inducible promoter elements: “Suitable methanol inducible promoters include pAOX1… pAOX2 promoter” (p. 11, [0072]).
Regarding Claim 11, it would have been obvious to one skilled in the art before the effective filing date to combine prior art elements according to known methods with the teachings of Cornish with the teachings of Roy-Chaudhuri to create the yeast cell of Claim 1 with a third exogenous nucleic acid encoding Mxr1 operably linked to a first, second, or a third promoter element promoter. Cornish teaches a first and second exogenous nucleic acid, Roy-Chaudhuri teaches a third exogenous nucleic acid, and each element performs the same function in combination because they are separate components. For one skilled in the art, the results would have been predictable because Cornish and Roy-Chaudhuri both teach yeast expression systems and Roy-Chaudhuri provides guidance on the use of Mxr1 in yeast cells. Therefore, Claim 11 is obvious over Cornish in further view of Roy-Chaudhuri.
Regarding Claim 13, Cornish teaches the use of a constitutive or inducible promoter element. It would have been obvious to one skilled in the art before the effective filing date to perform the simple substitution of one known element for another with the methanol-inducible promoter element for the inducible promoter element taught by Cornish because they have the same function. For one skilled in the art, the results of the substitution would have been predictable because Roy-Chaudhuri provides guidance on the use of methanol-inducible promoters. Therefore, Claim 13 is obvious over Cornish in further view of Roy-Chaudhuri.
Regarding Claim 21, Claim 1 is anticipated by Cornish.
Cornish does not teach methods for culturing cells.
Roy-Chaudhuri teaches “methods of culturing cells” (p. 12, [0079] and provides an example in Example 10 (p. 21, [0244]).
It would have been obvious to one skilled in the art to perform a simple substitution of one known element for another with the yeast cell taught by Cornish with the method taught by Roy-Chaudhuri to culture the yeast cells for conditions suitable for expression. Cornish teaches yeast cells with exogenous nucleic acids and Roy-Chaudhuri teaches culturing yeast cells with exogenous nucleic acids. For one skilled in the art the results would have been predicable because Roy-Chaudhuri teaches the methods “are known in the art” (p. 12, [0079]). Therefore Claim 21 is obvious over Cornish in further view of Roy-Chaudhuri.
Claims 9 and 10 are rejected under 35 U.S.C. 103 as being unpatentable over Cornish, V., WO 2021/092589 A1, published May 14, 2021 as applied to Claim 8 above, and further in view of Roy-Chaudhuri, B. and Shankar, S., US 2020/0340000 A1, published October 29, 2020.
Regarding Claims 9 and 10, Claim 8 is anticipated by Cornish including the use of an inducible promoter element.
Cornish does not teach a methanol-inducible promoter element.
Roy-Chaudhuri teaches methanol-inducible promoter elements: “Suitable methanol inducible promoters include pAOX1… pAOX2 promoter” as well as the MOX, MOD1 and DHAS promoter elements (p. 11, [0072]).
Regarding Claim 9, it would have been obvious to one skilled in the art before effective filing date to perform a simple substitution of one known element for another with into the yeast cell taught by Cornish the methanol inducible promoter elements taught by Roy-Chaudhuri. Cornish teaches inducible promoters, and Roy-Chaudhuri teaches methanol inducible promoters. For one skilled in the art, the results would have been predictable because Cornish teaches the use of inducible promoter elements, and Roy-Chaudhuri teaches a specific promoter element and describes its function. Therefore, Claim 9 is anticipated by Cornish and Roy-Chaudhuri.
Regarding Claim 10, Roy-Chaudhuri teaches methanol-inducible promoter elements AOX1, AOX2, and DHAS promoter elements from P. pastoris, MOX promoter element from H. polymorpha, and MOD1 promoter from P. methanolica (p. 11, [0072]). Therefore, Claim 10 is obvious over Cornish in further view of Roy-Chaudhuri.
Claims 14-17 and 24 are rejected under 35 U.S.C. 103 as being unpatentable over Cornish, V., WO 2021/092589 A1, published May 14, 2021; and Roy-Chaudhuri, B. and Shankar, S., US 2020/0340000 A1, published October 29, 2020.
Regarding Claim 14, Roy-Chaudhuri teaches a methylotrophic yeast cell comprising a first exogenous nucleic acid encoding a ALAS protein operably linked to a first promoter element and a second exogenous nucleic acid encoding a heme-binding protein operably linked to a first or second promoter element (p. 1, [0006]). Roy-Chaudhuri also teaches the cell with “a third nucleic acid construct comprising a nucleotide sequence encoding a transcription factor” operably linked to a promoter (p. 1, [0007]. Roy-Chaudhuri teaches transcription factors include Mxr1, Mit1 and Trm1 (p. 11, [0069]).
Roy-Chaudhuri does not teach the use of Rtg1.
Cornish teaches a yeast cell with am exogenous nucleic acid encoding Rtg1 operably linked to a promoter element: “an additional nucleic acid can be introduced into the cells to express a transcription factor for regulation expression of the molecule encoded by the nucleic acid … examples of such transcription factors include .. Rtg1p” and “a nucleic acid can include a constitutively active promoter” (p. 48, lines 16-30 and line 11).
It would have been obvious to one skilled in the art before the effective filing date to perform a simple substitution of one known element for another with the transcription factor Rtg1 into the yeast cell taught by Cornish. Cornish teaches the structure and function of the Rtg1 transcription factor. For one skilled in the art, the results would have been predictable because Cornish and Roy-Chaudhuri teach yeast cell expression systems and Roy-Chaudhuri teaches transcription factors in their invention. Therefore Claim 14 is obvious over Roy-Chaudhuri and Cornish.
Regarding Claim 15, Claim 14 is obvious over Roy-Chaudhuri and Cornish. Roy-Chaudhuri further teaches, “[A]ny of the cells … herein can further include a fourth nucleic acid construct comprising a nucleotide sequence encoding a fourth protein operably linked to the first promoter element, the second promoter element, the third promoter element, or a fourth promoter element … a fourth protein can be a protein involved in heme biosynthesis” (p. 12, [0074]). Therefore, Claim 15 is obvious Roy-Chaudhuri and Cornish.
Regarding Claim 16, Claim 15 is obvious over Roy-Chaudhuri and Cornish. Roy-Chaudhuri further teaches, “The protein involved in heme biosynthesis can be selected from the group consisting of ALA dehydratase, porphobilinogen deaminase, UPG III synthase, UPG III decarboxylase, CPG oxidase, PPG oxidase, and ferrochelatase” (p. 1, [0007]). Therefore, Claim 16 is obvious Roy-Chaudhuri and Cornish.
Regarding Claim 17, Claim 15 is obvious over Roy-Chaudhuri and Cornish. Roy-Chaudhuri further teaches the promoter elements for nucleic acids encoding a protein involved in heme biosynthesis may be an inducible or constitutive promoter element, including a methanol-inducible promoter element (p. 10-11, [0065]; p. 11, [0068]). Therefore, Claim 17 is obvious over Roy-Chaudhuri and Cornish.
Regarding Claim 24, Claim 14 is obvious over Roy-Chaudhuri and Cornish. Roy-Chaudhuri teaches “methods of culturing cells” (p. 12, [0079] and provides an example in Example 10 (p. 21, [0244]). Therefore, Claim 24 is obvious over Roy-Chaudhuri and Cornish.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Krishna Nuggehalli Ravindra whose telephone number is (571)272-2758. The examiner can normally be reached M-Th, alternate F, 8a-5p est.
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/K.N.R./Examiner, Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636