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 continuation of 18/049,055, abandoned, which is a continuation of 17/317,443, abandoned.
The amendment filed on October 9, 2025 has been entered.
Election/Restrictions
Applicant elected without traverse of Group I with an election of species of (1) S. cerevisiae as the yeast host cell, (2) trehalase having the amino acid sequence of SEQ ID NO:7 as the heterologous polypeptide expressed in the yeast cell, and (3) promoter from the tir1 gene having the nucleic acid sequence of SEQ ID NO:10 as the heterologous promoter in the reply filed on January 28, 2025 is acknowledged.
Claims 6-11, 14, 18, and 20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species/invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on January 28, 2025.
At page 6 of the Remarks filed on October 9, 2025, Applicant argues that the Office Action provides no explanation regarding the withdrawal of claim 14 from examination. Applicant argues that claim 14 belongs to Group I and reads on the elected species.
This is not found persuasive. The Election of Species requirement of the Requirement for Restriction mailed on January 28, 2025 required election of a species by (2) identifying all heterologous polypeptide(s) expressed in the yeast cell by its sequence identifier. Applicant elected trehalase of SEQ ID NO:7 as the heterologous polypeptide expressed in the yeast cell. Claim 14 is directed to a yeast cell expressing the hydrolase and one or more 2nd-7th heterologous polypeptides. Therefore, claim 14 is directed to a non-elected species and remains withdrawn.
Status of Claims
Claims 1-11 and 14-20 are pending.
Claims 6-11, 14, 18, and 20 are withdrawn.
Claims 1-5, 15-17, and 19 are under examination.
Response to Amendments/Arguments
Claim Rejections - 35 USC § 112(b)
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.
Withdrawn Rejections
Applicant’s arguments, see page 6 of the Remarks, filed October 9, 2025, with respect to claim 1 have been fully considered and are persuasive. Claim 1 has been amended to delete the indefinite limitations. Claims 12-13 have been cancelled. Therefore, the rejection of claim 1 and claims 2-5, 15-17, and 19 under 35 U.S.C. 112(b) has been withdrawn.
Applicant’s arguments, see pages 7-9 of the Remarks, filed October 9, 2025, with respect to claim 2 have been fully considered and are persuasive. Therefore, the rejection of claim 2 under 35 U.S.C. 112(b) has been withdrawn.
Applicant’s arguments, see page 9 of the Remarks, filed October 9, 2025, with respect to claims 12-13 have been fully considered and are persuasive. Claims 12-13 have been cancelled. Therefore, the rejection of claims 12-13 under 35 U.S.C. 112(b) has been withdrawn.
New Rejections
Claim 1 and claims 2-5, 15-17, and 19 depending therefrom 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 recites the limitation “cleavage of the substrate and/or the accumulation of the enzyme product ..is detrimental to the fermentation performance of a control yeast host cell expressing the same hydrolase under the control of a constitutive promoter when compared to the recombinant yeast host cell”. The metes and bounds of the above limitations in the context of the claim are not clear. It is unclear how the cleavage of the substrate and/or the accumulation of the enzyme product of the recombaint yeast cell is detrimental to the fermentation performance of a control yeast host cell. The specification at paragraphs [5] and ]0027] discloses that cleavage of the substrate and/or the accumulation of the enzyme product, if generated prior to the fermentation, is detrimental to the performance of the recombinant yeast host cell during fermentation. Clarification is requested.
Claim 1 and claims 2-5, 15-17, and 19 depending therefrom 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 recites the limitation “detrimental to the performance of a control yeast host cell”. The metes and bounds of the above limitation in the context of the claim are not clear. Some objective standard must be provided in order to allow the public to determine the metes and bounds of the claim. A claim that requires the exercise of subjective judgment without restriction renders the claims indefinite. In the instant case, it is unclear as to what properties of the recombinant yeast host cell are considered as “performance” and what effect on the “performance” is considered as “detrimental”. A perusal of the specification did not provide a clear definition for the above limitations. Without a clear definition, those skilled in the art would be unable to conclude a detrimental effect on the performance of a recombinant yeast cell. Clarification is requested.
The above rejection was made previously for claims 12-13. Claims 12-13 were cancelled and Applicant did not submit any rebuttal.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Withdrawn Rejections
Applicant’s arguments, see pages 9-13 of the Remarks, filed October 9, 2025, with respect to claims 1-5, 12-13, 15-17, and 19 have been fully considered and are persuasive. Claims 12-13 have been cancelled. Therefore, the rejections of claims1-5, 12-13, 15-17, and 19 under 35 U.S.C. 112(a) have been withdrawn.
New Rejection – New Matter
Claims 1-5, 15-17, and 19 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 1-5, 15-17, and 19 are drawn to a recombinant yeast host cell…wherein, cleavage of the substrate and/or the accumulation of the enzyme product ..is detrimental to the fermentation performance of a control yeast host cell expressing the same hydrolase under the control of a constitutive promoter when compared to the recombinant yeast host cell”. However, such yeast cells not described in the application as originally filed nor in any of its parent applications. The specification (paragraphs [5] and [0027]) as filed is limited to a recombinant yeast cell, wherein cleavage of the substrate and/or the accumulation of the enzyme product, if generated prior to the fermentation, is detrimental to the performance of the recombinant yeast host cell during the fermentation. Therefore, claims 1-5, 15-17, and 19contain new matter.
Given this lack of description, the specification fails to sufficiently describe the claimed invention in such full, clear, concise, and exact terms that a skilled artisan would recognize that applicants were in possession of the inventions of claims 1-5, 15-17, and 19 at the time of filing of the instant application.
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 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.
Claim(s) 1-5, 15-17, and 19 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Rice (US 2018/0265853 – form PTO-1449).
Regarding claims 1 and 3-4, Rice discloses a recombinant yeast host cell expressing a first heterologous trehalase, a glycoside hydrolase, under the control of a heterologous promoter, wherein the promoter limits the expression of the trehalase during propagation (aerobic conditions) and favors expression of the trehalase during fermentation (anaerobic conditions) and wherein the trehalase generates enzymatic product (glucose) from a substrate of a yeast cellular component (polysaccharides or trehalose) ([0003], [0008] and [0041] and [0007]-[0008]). The property of having detrimental fermentation performance due to the cleavage of the substrate generated prior to fermentation of a control yeast cell expressing the same trehalase under the control of a constitutive promoter is an inherent property of said control yeast cell. Since the trehalase is under the control of a constitutive promoter, trehalase is expressed during propagation (anaerobic conditions) and during fermentation (anaerobic conditions). The specification at paragraph [6] of the instant application discloses that the fermentation products, such as ethanol, are detrimental to the fermentation performance of a yeast host cell. Therefore, a control yeast cell constitutive expressing trehalases does not limit the expression of the trehalase prior to fermentation, resulting in cleavage of its substrates, generating glucose and thereby fermentation products, such as ethanol, which causes stress and decreases performance of the yeast during fermentation ([0004]).
Regarding claim 2, the substrate of Rice is associated to the yeast cell membrane or is an intracellular component ([0003]).
Regarding claim 5, since there is no structural limitation of the trehalase variant, any trehalase classified under EC 3.2.1.28 is a variant of the N. crassa trehalase of SEQ ID NO:7 of the instant application. Further, Rice discloses expressing variants or fragments of heterologous polypeptides [0069]-[0070].
Regarding claim 15, the promoter of Rice is an anaerobic specific promoter ([0007]-[0008]).
Regarding claim 16, the anaerobic specific promoter of Rice is the promoter from the pau5 gene or the tdh1 gene ([0008]).
Regarding claim 17, the yeast of Rice is S. cerevisiae ([0008]).
Regarding claim 19, Rice discloses a composition comprising the yeast and buffer (stabilizer) [0068].
Therefore, the reference of Rice anticipates claims 1-5, 15-17, and 19.
Applicant's arguments filed October 9, 2025 have been fully considered but they are not persuasive.
Applicant argues that Rice does not disclose that cleavage of the substrate/accumulation of enzymatic product heterologously expressed by the yeast prior to the fermentation would be detrimental to the performance of the recombinant yeast, Rice does not disclose that the specific combination of a fermentation specific promoter and a heterologous hydrolase would be a solution for such problem, and Rice does not disclose that cleavage of the substrate generated prior to fermentation causes stress and is a detriment to the performance of the yeast during fermentation.
This is not found persuasive. Claim 1 does not recite that cleavage of the substrate/accumulation of enzymatic product heterologously expressed by the yeast prior to the fermentation would be detrimental to the performance of the recombinant yeast. Instead, claim recites that cleavage of the substrate and/or the accumulation of the enzyme product is detrimental to the fermentation performance of a control yeast host cell.
The property of having detrimental fermentation performance due to the cleavage of the substrate generated prior to fermentation of a control yeast cell expressing the same trehalase under the control of a constitutive promoter is an inherent property of said control yeast cell. Since the trehalase is under the control of a constitutive promoter, trehalase is expressed during propagation (anaerobic conditions) and during fermentation (anaerobic conditions). The specification at paragraph [6] of the instant application discloses that the fermentation products, such as ethanol, are detrimental to the fermentation performance of a yeast host cell. Therefore, a control yeast cell constitutive expressing trehalases does not limit the expression of the trehalase prior to fermentation, resulting in cleavage of its substrates, generating glucose and thereby fermentation products, such as ethanol, which causes stress and decreases performance of the yeast during fermentation ([0004]).
Hence the rejection is maintained.
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 1-5, 15-17, and 19 is/are rejected under 35 U.S.C. 103 as being unpatentable over Jauert (WO 2018/204798 – form PTO-1449) and Rice (US 2018/0265853 – form PTO-1449).
Regarding claims 1, 3-5 and 17, Jauert discloses a recombinant S. cerevisiae expressing a heterologous N. crassa trehalase, a glycoside hydrolase, having the amino acid sequence of SEQ ID NO:80, which is identical to the N. crassa trehalase having the amino acid sequence of SEQ ID NO:7 of the instant application ([0004] and [0056] and see the sequence alignment below). Jauert discloses expression of a heterologous trehalase in S. cerevisiae to convert trehalose to glucose, thereby improving yield of fermentation products (abstract and [0004]).
Jauert does not disclose expressing the heterologous trehalase under the control of a heterologous promoter capable of limiting the expression of the trehalase during propagation and favoring expression of the trehalase during fermentation.
Regarding claim 1, Rice discloses a recombinant yeast host cell expressing a first heterologous trehalase under the control of a heterologous promoter, wherein the promoter limits the expression of the hydrolase during propagation (aerobic conditions) and favors expression of the hydrolase during fermentation (anaerobic conditions) and wherein the hydrolase generates enzymatic product (glucose) from a substrate of a yeast cellular component (polysaccharides or trehalose) ([0003], [0007]-[0008], and [0041]). The property of having detrimental fermentation performance due to the cleavage of the substrate generated prior to fermentation of a control yeast cell expressing the same trehalase under the control of a constitutive promoter is an inherent property of said control yeast cell. Since the trehalase is under the control of a constitutive promoter, trehalase is expressed during propagation (anaerobic conditions) and during fermentation (anaerobic conditions). The specification at paragraph [6] of the instant application discloses that the fermentation products, such as ethanol, are detrimental to the fermentation performance of a yeast host cell. Therefore, a control yeast cell constitutive expressing trehalases does not limit the expression of the trehalase prior to fermentation, resulting in cleavage of its substrates, generating glucose and thereby fermentation products, such as ethanol, which causes stress and decreases performance of the yeast during fermentation ([0004]).
Regarding claim 2, the substrate of Rice is associated to the yeast cell membrane or is an intracellular component ([0003]).
Regarding claim 15, the promoter of Rice is an anaerobic specific promoter ([0007]-[0008]).
Regarding claim 16, the anaerobic specific promoter of Rice is the promoter from the pau5 gene or the tdh1 gene ([0008]).
Regarding claim 17, the yeast of Rice is S. cerevisiae ([0008]).
Regarding claim 19, Rice discloses a composition comprising the yeast and buffer (stabilizer) [0068].
Therefore, in combing the teachings of Jauert and Rice, it would have been obvious to one having ordinary skill in the art at the time the claimed invention was effectively filed to modify the recombinant yeast/S. cerevisiae cell of Jauert by expressing the heterologous trehalase under the control of a heterologous promoter. Using the known technique of expressing heterologous trehalase under the control of a heterologous promoter to limit the expression of the trehalase during propagation and favor expression of the trehalase during fermentation would have been obvious to one of ordinary skill. The rationale supporting that the claims would have been obvious is that a method of enhancing a particular class of devices (expressing heterologous trehalase under heterologous promoters capable of limiting the expression of the trehalase during propagation and favoring expression of the trehalase during fermentation and thereby improving yield of fermentation products) has been made part of the ordinary capabilities of one skilled in the art based upon the teaching of such improvement in other situations. One of ordinary skill in the art would have been capable of applying this known method of enhancement to a “base” device (recombinant yeast/S. cerevisiae cell expressing a heterologous trehalase) in the prior art and the results would have been predictable to one of ordinary skill in the art. One having ordinary skill in the art would have been motivated to express the N. crassa trehalase of Jauert under the control of a heterologous promoter disclosed by Rice in order to limit the expression of the trehalase during propagation and favor expression of the trehalase during fermentation and thereby improving yield of fermentation products. One having ordinary skill in the art would have had a reasonable expectation of success since Jauert discloses expression of heterologous N. crassa trehalase in S. cerevisiae and Rice discloses expression of heterologous trehalase in S. cerevisiae under the control of heterologous promoters that limit the expression of the trehalase during propagation and favor expression of the trehalase during fermentation.
Therefore, the above references render claims 1-5, 15-17, and 19 prima facie obvious.
Applicant's arguments filed October 9, 2025 have been fully considered but they are not persuasive.
Applicant argues that Rice does not disclose that cleavage of the substrate/accumulation of enzymatic product heterologously expressed by the yeast prior to the fermentation would be detrimental to the performance of the recombinant yeast, Rice does not disclose that the specific combination of a fermentation specific promoter and a heterologous hydrolase would be a solution for such problem, Jauert fails to remedy the deficiency of Rice, and neither Rice nor Jauert disclose the specific combination of a fermentation specific promoter and a heterologous hydrolase would be a solution for such problem.
This is not found persuasive. Claim 1 does not recite that cleavage of the substrate/accumulation of enzymatic product heterologously expressed by the yeast prior to the fermentation would be detrimental to the performance of the recombinant yeast. Instead, claim recites that cleavage of the substrate and/or the accumulation of the enzyme product is detrimental to the fermentation performance of a control yeast host cell.
The property of having detrimental fermentation performance due to the cleavage of the substrate generated prior to fermentation of a control yeast cell expressing the same trehalase under the control of a constitutive promoter is an inherent property of said control yeast cell. Since the trehalase is under the control of a constitutive promoter, trehalase is expressed during propagation (anaerobic conditions) and during fermentation (anaerobic conditions). The specification at paragraph [6] of the instant application discloses that the fermentation products, such as ethanol, are detrimental to the fermentation performance of a yeast host cell. Therefore, a control yeast cell constitutive expressing trehalases does not limit the expression of the trehalase prior to fermentation, resulting in cleavage of its substrates, generating glucose and thereby fermentation products, such as ethanol, which causes stress and decreases performance of the yeast during fermentation ([0004]).
Applicant argues that the present application provides evidence of unexpected superior properties of the claimed recombinant yeast host cells. Applicant argues that Figures 1 to 9 and Example 1 of the application as filed demonstrate that expression of hydrolase with a fermentation-specific promoter exhibited an improved stability/viability prior to fermentation, especially during propagation and/or storage. Applicant agues that the fermentation performance was improved as compared to a control yeast host cell expressing the same hydrolase under the control of a constitutive promoter (wherein expression of the same hydrolase was detrimental to fermentation performance in the control yeast host cell).
This is not found persuasive. “Whether the unexpected results are the result of unexpectedly improved results or a property not taught by the prior art, the “objective evidence of nonobviousness must be commensurate in scope with the claims which the evidence is offered to support.”, see MPEP 716.02(d). In the instant case, Figures 1-9 and Example 1 of the instant specification are limited to recombinant Saccharomyces cerevisiae host cell expressing specific hydrolases under specific promoters, such as the trehalase of SEQ ID NO:1 under the control of a tir1 promoter. However, the instant claims are directed to any recombinant yeast cells or S. cerevisiae host cell expressing any hydrolase under the control of any fermentation-specific promoter or the tir1 promoter. Therefore, the asserted unexpected results of Figures 1-9 and Example 1 are insufficient to rebut the prima facie case because the alleged unexpected results are not commensurate in scope with the claims.
Hence the rejection is maintained.
Claims 1-5, 15-17, and 19 is/are rejected under 35 U.S.C. 103 as being unpatentable over Jauert (WO 2018/204798 – form PTO-1449), Rice (US 2018/0265853 – form PTO-1449), and Argyros (US 11,198,881– form PTO-1449 or US 2021/0292776 – form PTO-1449 or 2021/0163995 – form PTO-1449. US 11,198,881 is used for specific passages of Argyros).
Regarding claims 1, 3-5 and 17, Jauert discloses a recombinant S. cerevisiae expressing a heterologous N. crassa trehalase, a glycoside hydrolase, having the amino acid sequence of SEQ ID NO:80, which is identical to the N. crassa trehalase having the amino acid sequence of SEQ ID NO:7 of the instant application ([0004] and [0056] and see the sequence alignment below). Jauert discloses expression of heterologous trehalase in S. cerevisiae to convert treholase to glucose, thereby improving yield of fermentation products (abstract and [0004]).
Jauert does not disclose expressing the heterologous trehalase under the control of a heterologous promoter or the promoter from the tir1 gene capable of limiting the expression of the trehalase during propagation and favoring expression of the trehalase during fermentation.
Regarding claim 1, Rice discloses a recombinant yeast host cell expressing a first heterologous trehalase under the control of a heterologous promoter, wherein the promoter limits the expression of the hydrolase during propagation (aerobic conditions) and favors expression of the hydrolase during fermentation (anaerobic conditions) and wherein the hydrolase generates enzymatic product (glucose) from a substrate of a yeast cellular component (polysaccharides or trehalose) ([0003], [0007]-[0008], and [0041]). The property of having detrimental fermentation performance due to the cleavage of the substrate generated prior to fermentation of a control yeast cell expressing the same trehalase under the control of a constitutive promoter is an inherent property of said control yeast cell. Since the trehalase is under the control of a constitutive promoter, trehalase is expressed during propagation (anaerobic conditions) and during fermentation (anaerobic conditions). The specification at paragraph [6] of the instant application discloses that the fermentation products, such as ethanol, are detrimental to the fermentation performance of a yeast host cell. Therefore, a control yeast cell constitutive expressing trehalases does not limit the expression of the trehalase prior to fermentation, resulting in cleavage of its substrates, generating glucose and thereby fermentation products, such as ethanol, which causes stress and decreases performance of the yeast during fermentation ([0004]).
Regarding claim 2, the substrate of Rice is associated to the yeast cell membrane or is an intracellular component ([0003]).
Regarding claim 15, the promoter of Rice is an anaerobic specific promoter ([0007]-[0008]).
Regarding claim 17, the yeast of Rice is S. cerevisiae ([0008]).
Regarding claim 19, Rice discloses a composition comprising the yeast and buffer (stabilizer) [0068].
Regarding claim 16, Argyros discloses using the promoter from the tir1 gene to limit expression of heterologous hydrolases in S. cerevisiae during propagation and increasing fermentation yields (US 11,198,881: Column 17, line 13 through Column 18, line 34. US 2021/0292776: [0058]-[0059]. 2021/0163995: [0057]-[0059]).
Therefore, in combing the teachings of Jauert, Rice, and Argyros, it would have been obvious to one having ordinary skill in the art at the time the claimed invention was effectively filed to modify the recombinant yeast/S. cerevisiae cell of Jauert by expressing the heterologous trehalase under the control of a heterologous promoter, such as the promoter from the tir1 gene. Using the known technique of expressing heterologous trehalase under the control of a heterologous promoter to limit the expression of the trehalase during propagation and favor expression of the trehalase during fermentation would have been obvious to one of ordinary skill. The rationale supporting that the claims would have been obvious is that a method of enhancing a particular class of devices (expressing heterologous trehalase under heterologous promoters capable of limiting the expression of the trehalase during propagation and favoring expression of the trehalase during fermentation and thereby improving yield of fermentation products) has been made part of the ordinary capabilities of one skilled in the art based upon the teaching of such improvement in other situations. One of ordinary skill in the art would have been capable of applying this known method of enhancement to a “base” device (recombinant yeast/S. cerevisiae cell expressing a heterologous trehalase) in the prior art and the results would have been predictable to one of ordinary skill in the art. One having ordinary skill in the art would have been motivated to express the N. crassa trehalase of Jauert under the control of a heterologous promoter disclosed by Rice in order to limit the expression of the trehalase during propagation and favor expression of the trehalase during fermentation and thereby improving yield of fermentation products. One having ordinary skill in the art would have been motivated use the promoter of Argyros, such as the promoter from the tir1 gene, because Argyros discloses that the promoter limits expression of hydrolases during propagation and thereby increases yield of fermentation products. One having ordinary skill in the art would have had a reasonable expectation of success since Jauert discloses expression of heterologous N. crassa trehalase in S. cerevisiae, Rice discloses expression of heterologous trehalase in S. cerevisiae, and Argyros discloses promoters that limit expression of heterologous hydrolases in S. cerevisiae during propagation.
Therefore, the above references render claims 1-5, 15-17, and 19 prima facie obvious.
Applicant's arguments filed October 9, 2025 have been fully considered but they are not persuasive.
Applicant argues that neither Rice nor Jauert discloses the claimed recombinant yeast cell as discussed above and Argyros fails to remedy he deficiency of Rice and Jauer.
This is not found persuasive. As discussed above, claim 1 does not recite that cleavage of the substrate/accumulation of enzymatic product heterologously expressed by the yeast prior to the fermentation would be detrimental to the performance of the recombinant yeast. Instead, claim recites that cleavage of the substrate and/or the accumulation of the enzyme product is detrimental to the fermentation performance of a control yeast host cell.
The property of having detrimental fermentation performance due to the cleavage of the substrate generated prior to fermentation of a control yeast cell expressing the same trehalase under the control of a constitutive promoter is an inherent property of said control yeast cell. Since the trehalase is under the control of a constitutive promoter, trehalase is expressed during propagation (anaerobic conditions) and during fermentation (anaerobic conditions). The specification at paragraph [6] of the instant application discloses that the fermentation products, such as ethanol, are detrimental to the fermentation performance of a yeast host cell. Therefore, a control yeast cell constitutive expressing trehalases does not limit the expression of the trehalase prior to fermentation, resulting in cleavage of its substrates, generating glucose and thereby fermentation products, such as ethanol, which causes stress and decreases performance of the yeast during fermentation ([0004]).
Hence the rejection is maintained.
Conclusion
Claims 1-11 and 14-20 are pending.
Claims 6-11, 14, 18, and 20 are withdrawn.
Claims 1-5, 15-17, and 19 are rejected.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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.
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/YONG D PAK/Primary Examiner, Art Unit 1652
Sequence alignment between SEQ ID NO:7 (“Qy”) of the instant application (“Qy”) and SEQ ID NO:80 of Jauert )“Db”)
BFU53507
ID BFU53507 standard; protein; 692 AA.
XX
AC BFU53507;
XX
DT 27-DEC-2018 (first entry)
XX
DE Neurospora crassa trehalase polypeptide, SEQ ID 80.
XX
KW EC 3.2.1.28; Trehalase; ethanol; fermentation;
KW genetically engineered microorganism.
XX
OS Neurospora crassa.
XX
CC PN WO2018204798-A1.
XX
CC PD 08-NOV-2018.
XX
CC PF 04-MAY-2018; 2018WO-US031110.
XX
PR 04-MAY-2017; 2017US-0501288P.
PR 28-FEB-2018; 2018US-0636716P.
PR 27-MAR-2018; 2018US-0648679P.
XX
CC PA (CRGI ) CARGILL INC.
XX
CC PI Jauert PA, Poynter GM, Rush BJ;
XX
DR WPI; 2018-87809V/78.
XX
CC PT New genetically modified yeast comprise heterologous gene encoding
CC PT trehalase polypeptide, for producing ethanol when yeast is present in
CC PT fermentation medium comprising trehalose, where yeast secretes trehalase
CC PT to reduce trehalose content.
XX
CC PS Disclosure; SEQ ID NO 80; 66pp; English.
XX
CC The present invention relates to a novel genetically modified yeast,
CC useful for producing ethanol when yeast is present in a fermentation
CC medium comprising trehalose, where yeast secretes trehalase to reduce
CC trehalose content. The genetically modified yeast comprises a
CC heterologous gene encoding trehalase polypeptide having a sequence of SEQ
CC ID NO: 1-3 (see BFU53428-BFU53430) or SEQ ID NO: 87 (see BFU53514). The
CC invention further relates to a method for manufacturing ethanol, which
CC involves fermenting a medium using the genetically modified yeast. The
CC present sequence is a Neurospora crassa trehalase polypeptide, used in
CC the method for preparing the genetically modified yeast, which is useful
CC for producing ethanol.
XX
SQ Sequence 692 AA;
Query Match 100.0%; Score 3671; DB 26; Length 692;
Best Local Similarity 100.0%;
Matches 692; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MVSRFLGATVPLAAAILPGARALYVNGSVTAPCDSPIYCYGELLHQVELARPFSDSKTFV 60
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Db 1 MVSRFLGATVPLAAAILPGARALYVNGSVTAPCDSPIYCYGELLHQVELARPFSDSKTFV 60
Qy 61 DMPTIKPVDEVLEAFSKLTLPLSNNSELHEFLSTYFGPAGGELEAVPTDQLHVSPTFLDN 120
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Db 61 DMPTIKPVDEVLEAFSKLTLPLSNNSELHEFLSTYFGPAGGELEAVPTDQLHVSPTFLDN 120
Qy 121 VSDDVIKQFVDSVINIWPDLTRKYVGAGELCTGCADSFIPVNRTFVVAGGRFREPYYWDS 180
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Db 121 VSDDVIKQFVDSVINIWPDLTRKYVGAGELCTGCADSFIPVNRTFVVAGGRFREPYYWDS 180
Qy 181 FWILEGLLRTGGAFTEISKNIIENFLDLVEQIGFVPNGARLYYLDRSQPPLLTQMVRIYV 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 FWILEGLLRTGGAFTEISKNIIENFLDLVEQIGFVPNGARLYYLDRSQPPLLTQMVRIYV 240
Qy 241 EHTNDTSILERAVPVLKKEWEWWTTNRTVEVTADGKTYSLQRYHVDNNQPRPESYREDYI 300
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Db 241 EHTNDTSILERAVPVLKKEWEWWTTNRTVEVTADGKTYSLQRYHVDNNQPRPESYREDYI 300
Qy 301 TANNNSYYATSGIIYPETTPLNDTQKALLYANLASGAESGWDYSSRWLKNPGDAARDVYF 360
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Db 301 TANNNSYYATSGIIYPETTPLNDTQKALLYANLASGAESGWDYSSRWLKNPGDAARDVYF 360
Qy 361 PLRSLNVLEIVPVDLNSILYQNEVTIGKFLAQQGSKDEAEEWAKKAEERSEAMYKLMWNS 420
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Db 361 PLRSLNVLEIVPVDLNSILYQNEVTIGKFLAQQGSKDEAEEWAKKAEERSEAMYKLMWNS 420
Qy 421 TLWSYFDYNLTSSSQNIYVPADPQVFPFEQPSGTPEGYQVLFSVNQMFPFWTGAAPDQLK 480
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Db 421 TLWSYFDYNLTSSSQNIYVPADPQVFPFEQPSGTPEGYQVLFSVNQMFPFWTGAAPDQLK 480
Qy 481 GNPLAVKLAFERIKNLLDNKAGGIPATNFVTGQQWDEPNVWPPLMHVLMDGLLNTPATFG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 GNPLAVKLAFERIKNLLDNKAGGIPATNFVTGQQWDEPNVWPPLMHVLMDGLLNTPATFG 540
Qy 541 EDDPAYQETQTLALRLAQRYVDSTFCTWYATGGSTSETPKLQGLGSDLKGIMFEKYSDNS 600
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Db 541 EDDPAYQETQTLALRLAQRYVDSTFCTWYATGGSTSETPKLQGLGSDLKGIMFEKYSDNS 600
Qy 601 TNVAGSGGEYEVVEGFGWTNGVLIWAADKFGDKLKRPDCGDITPAQVGKRADITMEKRAV 660
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Db 601 TNVAGSGGEYEVVEGFGWTNGVLIWAADKFGDKLKRPDCGDITPAQVGKRADITMEKRAV 660
Qy 661 ELDVFDAKFTKKFARKGKLEKLKAKFKRRAAI 692
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Db 661 ELDVFDAKFTKKFARKGKLEKLKAKFKRRAAI 692