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 divisional of 14/911,102, issued as US Patent No. 11,753,656, which is a 371 of PCT/US2014/051355.
The response filed on May 7, 2026 has been entered.
Election/Restrictions
Applicant’s election without traverse of Group I with a species election of
(1) S. cerevisiae as the microorganism;
(2) (a) S. cerevisiae STL1 as the heterologous protein that functions to import glycerol; and (b) upregulated;
(3) (a) S. fibuligera glucoamylase as the heterologous saccharolytic enzyme; and
(b) upregulated;
(4) B. adolescentis Bifunctional acetaldehyde/alcohol dehydrogenase as the enzymes for converting acetyl-CoA to an alcohol; and
(5) B. adolescentis Pyruvate formate lyase (PFL) as the enzymes for converting pyruvate to formate
in the reply filed on May 7, 2026 is acknowledged.
Claims 15, 39, 84, and 88 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species (claims 15 and 39) and invention (claims 84 and 88), there being no allowable generic or linking claim. Election was made without traverse in the reply filed on May 7, 2026.
Status of Claims
Claims 1-4, 11-16, 22-23, 38-39, 41-42, 49, 81-82, 84, 88, and 111-112 are pending.
Claims 15, 39, 84, and 88 are withdrawn.
Claims 1-4, 11-14, 16, 22-23, 38, 41-42, 49, 81-82, and 111-112 are under examination.
Claim for Domestic Priority
Applicants' claim for domestic priority under 35 USC 119(e) to US provisional application 61/866,338 filed 08/15/2013 is acknowledged.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on April 26, 2024 and October 30, 2025 are compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner.
Claim Objections
Claims 4 and 112 are objected to due to the recitation of “STL1”. Abbreviation/acronym unless otherwise obvious and/or commonly used in the art, should not be recited in the claims without at least once reciting the entire phrase for which the abbreviation/acronym is used.
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.
Claim 42 is 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 42 recites the phrase “(glu-01111-CO)”. The phrase "(glu-01111-CO)" renders the claim indefinite because it is unclear whether the limitation(s) enclosed in the parentheses are part of the claimed invention. See MPEP § 2173.05(d).
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.
Claims 1-4, 11-14, 16, 22-23, 38, 41-42, 49, 81-82, and 111-112 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
MPEP 2111.01 states that ''[d]uring examination, the claims must be interpreted as broadly as their terms reasonably allow.'' In this case, the claims have been broadly interpreted to encompass any recombinant yeast or S. cerevisiae comprising (a) any native or heterologous proteins that functions to import glycerol into the yeast or S. cerevisiae, STL1, S. cerevisiae STL1, or STL1 having the amino acid sequence of SEQ ID NO:140, (b) deletion or downregulation of any native enzyme or gpd1, gpd2, gpp1, and/or gpp2 that functions to produce glycerol, and (c) any native or heterologous saccharolytic enzyme enzymes, any amylase, any glucoamylase, or S. fibuligera glucoamylase, and further comprising of (d) any enzyme that converts acetyl-CoA to an alcohol, any acetaldehyde dehydrogenase, any alcohol dehydrogenase, any acetaldehyde dehydrogenase or any bifunctional acetaldehyde/alcohol dehydrogenase, (e) any enzyme that converts pyruvate to acetyl-CoA or any pyruvate formate lyase, wherein the recombinant yeast or S. cerevisiae produces ethanol. Therefore, the claims are drawn to a genus of recombinant yeast or S. cerevisiae having unknown structure.
MPEP 2163 I. states that to “satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention.
MPEP 2163. II.A.3.(a) sates that “Possession may be shown in many ways. For example, possession may be shown by describing an actual reduction to practice of the claimed invention. Possession may also be shown by a clear depiction of the invention in detailed drawings or in structural chemical formulas which permit a person skilled in the art to clearly recognize that inventor had possession of the claimed invention. An adequate written description of the invention may be shown by any description of sufficient, relevant, identifying characteristics so long as a person skilled in the art would recognize that the inventor had possession of the claimed invention.
According to MPEP 2163.II.A.3.(a).ii), “Satisfactory disclosure of a ‘representative number’ depends on whether one of skill in the art would recognize that the applicant was in possession of the necessary common attributes or features possessed by the members of the genus in view of the species disclosed. For inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus…Instead, the disclosure must adequately reflect the structural diversity of the claimed genus, either through the disclosure of sufficient species that are ‘representative of the full variety or scope of the genus,’ or by the establishment of ‘a reasonable structure-function correlation.’"
The recitation of “proteins that function to import glycerol into the recombinant yeast”, “STL1”, “enzymes that function to produce glycerol”, “gpd1”, “gpd2”, “gpp1”, “gpp2”, “bifunctional acetaldehyde/alcohol dehydrogenase”, “acetaldehyde dehydrogenase”, “alcohol dehydrogenase”, “conversion of acetyl-CoA to ethanol”, “saccharolytic enzyme”, ”amylase”, and “glucoamylase” fail to provide a sufficient description of the genus of proteins/enzymes that are modified in the genus of yeast or S. cerevisiae as it merely describes the functional features of the genus without providing any definition of the structural features of the species within the genus.
The prior art discloses a recombinant S. cerevisiae comprising (a) overexpressing STL1, a glycerol importer, (b) deletion of gpd1 polynucleotide and/or gpd2 polynucleotide, which encode for an enzyme that produces glycerol, and (c) overexpression of a cellulase, a saccharolytic enzyme, see Zelle (US 2014/0256011 – form PTO-1449). The prior art also discloses a S. cerevisiae STL1 having 100% sequence identity to the STL1 of the SEQ ID NO:140 of the instant application, see Zhao (The STL1 gene of Saccharomyces cerevisiae is predicted to encode a sugar transporter-like protein. Gene. 1994 Sep 2;146(2):215-9 –form PTO-1449). However, the claimed genus of recombinant yeast or S. cerevisiae was not known.
The specification is limited to a recombinant S. cerevisiae (a) overexpressing the heterologous STL1 of SEQ ID NO:140, (b) deletion of gpd1, gpd2, gpp1, and/or gpp2, (c) overexpression of a heterologous S. fibuligera glucoamylase, (d) overexpression of Bifidobacterium adolescentis aldehyde/alcohol dehydrogenase ADHE, and (e) Bifidobacterium adolescentis pyruvate formate lyase, wherein said S. cerevisiae produces ethanol. While MPEP 2163 acknowledges that in certain situations “one species adequately supports a genus,” it also acknowledges that “[f]or inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus.” In view of the widely variant species encompassed by the genus, this one example is not enough and does not constitute a representative number of species to describe the whole genus, and there is no evidence on the record of the relationship between the above recombinant S. cerevisiae and the structure of the claimed genus of yeast. Therefore, the specification fails to describe a representative species of the claimed genus.
The claimed invention requires a defined set of (1) yeast or S. cerevisiae, (2) proteins that functions to import glycerol into the yeast or S. cerevisiae, STL1, S. cerevisiae STL1, or STL1 having the amino acid sequence of SEQ ID NO:140, (3) gpd1, gpd2, gpp1, and/or gpp2, and (4) saccharolytic enzyme enzymes, amylase, glucoamylase, or S. fibuligera glucoamylase, and further comprising of (5) enzyme that converts acetyl-CoA to an alcohol, acetaldehyde dehydrogenase, alcohol dehydrogenase, acetaldehyde dehydrogenase or bifunctional acetaldehyde/alcohol dehydrogenase, and (6) enzyme that converts pyruvate to acetyl-CoA or any pyruvate formate lyase, wherein the yeast or S. cerevisiae produces ethanol from any carbohydrate via acetyl-CoA. Although the specification discloses exemplary enzymes/proteins that can be expressed in a yeast, a “laundry list” disclosure of every possible moiety does not necessarily constitute a written description of every species in a genus because it would not “reasonably lead” those skilled in the art to any particular species, see Fujikawa v. Wattanasin, 93 F.3d 1559, 1571, 39 USPQ2d 1895, 1905 (Fed. Cir. 1996) or MPEP 2163. While the exemplary enzymes/proteins/yeast/metabolic pathways of some carbons to ethanol were known in the art and disclosed in the Examples of the instant specification, this knowledge alone would not allow one level of skill in the art to immediately envisage the claimed genus. Therefore, the level of skill and knowledge in the art is such that one of ordinary skill would not be able to identify without further testing which combination of enzymes/proteins to express or delete in any yeast or S. cerevisiae to produce alcohols from any starting material.
Given this lack of additional representative species as encompassed by the claims, applicants have failed to sufficiently describe the claimed invention in such full, clear, concise, and exact terms that a skilled artisan would recognize applicants were in possession of the claimed invention.
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.
(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.
Claim(s) 1-3, 11, 14, 16, 22-23, 49, 81-82, and 111 is/are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Zelle (US 2014/0256011 – form PTO-1449).
Regarding claims 1, 3, and 11, Zelle discloses a recombinant yeast (a) overexpressing STL1, a glycerol importer, (b) having a deletion of gpd1 polynucleotide and/or gpd2 polynucleotide, which encode for an enzyme that produces glycerol, and (c) overexpressing cellulase, a saccharolytic enzyme ([0006], [0010], [0028], [0032], [0038], [0212], and [0256]).
Regarding claim 2, since the gpd1 polynucleotide and/or gpd2 polynucleotide are deleted, the recombinant yeast of Zelle produces less glycerol.
Regarding claims 111, 14, and 16, Zelle discloses that the recombinant yeast overexpresses a bifunctional acetaldehyde/alcohol dehydrogenase ([0038] and claims 1 and 6).
Regarding claims 111 and 22-23, Zelle discloses that the recombinant yeast overexpresses a pyruvate formate lyase, which converts pyruvate to acetyl-coA and formate ([0128] and claim 1).
Regarding claim 49, Zelle discloses that the recombinant yeast produces ethanol (abstract, [0010], and claim 1).
Regarding claims 81-82, Zelle discloses that the recombinant yeast is S. cerevisiae ([0034]).
Therefore, the reference of Zelle anticipates claims 1-3, 11, 14, 16, 22-23, 49, 81-82, and 111.
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 1-4, 11-14, 16, 22-23, 38, 41-42, 49, 81-82, and 111-112 is/are rejected under 35 U.S.C. 103 as being unpatentable over Argyros (WO 2012/138942 – form PTO-1449), Zelle (US 2014/0256011 – form PTO-1449), and Zhao (The STL1 gene of Saccharomyces cerevisiae is predicted to encode a sugar transporter-like protein. Gene. 1994 Sep 2;146(2):215-9 –form PTO-1449).
Regarding claims 1 (b) and (c), 11, 38, 41-42, 49, and 81-82, Argyros discloses a recombinant yeast, S. cerevisiae strain M3465 (Δgpd2Δfdh1Δfdh2 and B. adolescentis pflA+pflB+adhE) and recombinant S. cerevisiae strain M3469 (Δgpd1Δfdh1Δfdh2 and B. adolescentis pflA+pflB+adhE) comprising a deletion of gpd2 or gpd1, which function to produce glycerol into the recombinant S. cerevisiase ([0509]-[0510]). The Bifidobacterium adolescentis AdhE expressed in strains M3465 and M3469 converts acetyl-CoA to ethanol (Figure 1 and [0123]). Argyros discloses further modifying the recombinant yeast by overexpressing a saccharolytic enzyme, S. fibuligera glucoamylase (glu-0111-CO) ([0036]).
Regarding claim 2, recombinant S. cerevisiae of Argyros has reduced glycerol formation due to the deletion of its gdp2 or gdp1 gene (([0509]-[0510]).
Regarding claims 11-12, Argyros discloses deletion of gpd1 and/or gpd2, wherein the gdp1 is operably linked to gpd2 promoter polynucleotide ([0007]).
Regarding claim 13, Argyros discloses further deletion of gpp1 and/or gpp2 ([0007]).
Regarding claims 111, 14 and 16, the Bifidobacterium adolescentis AdhE (bifunctional acetaldehyde dehydrogenase/alcohol dehydrogenase) overexpressed in strain M3465 and strain 3469 converts acetyl-CoA to ethanol ([0509]-[0510]).
Regarding claims 111 and 22-23, the Bifidobacterium adolescentis pflA/B (pyruvate formate lyase) overexpressed in strain M3465 and strain 3469 converts acetyl-CoA to formate ([0509]-[0510]).
Argyros does not disclose overexpressing STL1.
Regarding claims 1, 3, and 11, Zelle discloses a recombinant yeast (a) overexpressing STL1, a glycerol importer, (b) having a deletion of gpd1 polynucleotide and/or gpd2 polynucleotide, which encode for an enzyme that produces glycerol, and (c) overexpressing cellulase, a saccharolytic enzyme ([0006], [0010], [0028], [0032], [0038], [0212], and [0256]).
Regarding claim 2, since the gpd1 polynucleotide and/or gpd2 polynucleotide are deleted, the recombinant yeast of Zelle produces less glycerol.
Regarding claims 111, 14, and 16, Zelle discloses that the recombinant yeast overexpresses a bifunctional acetaldehyde/alcohol dehydrogenase ([0038] and claims 1 and 6).
Regarding claims 111 and 22-23, Zelle discloses that the recombinant yeast overexpresses a pyruvate formate lyase, which converts pyruvate to acetyl-coA and formate ([0128] and claim 1).
Regarding claim 49, Zelle discloses that the recombinant yeast produces ethanol (abstract, [0010], and claim 1).
Regarding claims 81-82, Zelle discloses that the recombinant yeast is S. cerevisiae ([0034]).
Regarding claims 4 and 112, Zhao discloses a S. cerevisiae STL1 having 100% sequence identity to the STL1 of the SEQ ID NO:140 of the instant application (Figure 2 on page 217).
Therefore, in combing the teachings of Argyros, Zelle, and Zhao, 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 S. cerevisiae of Argyros by overexpressing STL1 since all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination yielded nothing more than predictable results to one of ordinary skill in the art. One of ordinary skill in the art at the time the invention was made would have been motivated to overexpress STL1 in the S. cerevisiae of Argyros because Zelle teaches expressing STL1 in a yeast converting a carbohydrate to alcohol, such as ethanol. Further, the normal desire of scientists or artisans to improve upon what is already generally known provides the motivation to determine the optimum ethanol producing S. cerevisiae. Further, regarding overexpressing S. cerevisiae STL1 of Zhao, the rationale to support a conclusion that the claims would have been obvious is that the substitution of one known element (S. cerevisiae STL1) for another yields predictable results (import of glycerol) to one of ordinary skill in the art. Therefore, it would have been obvious to one of ordinary skill in the art to replace the prior art STL1 with another known and available STL1, such as the S. cerevisiae STL1, known to lead to glycerol import, because one of ordinary skill in the art would have been able to carry out such a substitution, and the results were reasonably predictable.
Therefore, the above references render claims 1-4, 11-14, 16, 22-23, 38, 41-42, 49, 81-82, and 111-112 prima facie obvious.
Claims 1-4, 11-14, 16, 22-23, 38, 41-42, 49, 81-82, and 111-112 is/are rejected under 35 U.S.C. 103 as being unpatentable over Argyros (WO 2012/138942 – form PTO-1449, Wang (Biotechnol Lett (2013) 35:1859–1864 – form PTO-1449), and Zhao (The STL1 gene of Saccharomyces cerevisiae is predicted to encode a sugar transporter-like protein. Gene. 1994 Sep 2;146(2):215-9 –form PTO-1449).
Regarding claims 1(b) and (c), 11, 38, 41-42, 49, and 81-82, Argyros discloses a recombinant yeast, S. cerevisiae strain M3465 (Δgpd2Δfdh1Δfdh2 and B. adolescentis pflA+pflB+adhE) and recombinant S. cerevisiae strain M3469 (Δgpd1Δfdh1Δfdh2 and B. adolescentis pflA+pflB+adhE) comprising a deletion of gpd2 or gpd1, which function to produce glycerol into the recombinant S. cerevisiase ([0509]-[0510]). The Bifidobacterium adolescentis AdhE expressed in strains M3465 and M3469 converts acetyl-CoA to ethanol (Figure 1 and [0123]). Argyros discloses further modifying the recombinant yeast by overexpressing a saccharolytic enzyme, S. fibuligera glucoamylase (glu-0111-CO) ([0036]).
Regarding claim 2, recombinant S. cerevisiae of Argyros has reduced glycerol formation due to the deletion of its gdp2 or gdp1 gene (([0509]-[0510]).
Regarding claims 11-12, Argyros discloses deletion of gpd1 and/or gpd2, wherein the gdp1 is operably linked to gpd2 promoter polynucleotide ([0007]).
Regarding claim 13, Argyros discloses further deletion of gpp1 and/or gpp2 ([0007]).
Regarding claims 111, 14 and 16, the Bifidobacterium adolescentis AdhE (bifunctional acetaldehyde dehydrogenase/alcohol dehydrogenase) overexpressed in strain M3465 and strain 3469 converts acetyl-CoA to ethanol ([0509]-[0510]).
Regarding claims 111 and 22-23, the Bifidobacterium adolescentis pflA/B (pyruvate formate lyase) overexpressed in strain M3465 and strain 3469 converts acetyl-CoA to formate ([0509]-[0510]).
Argyros does not disclose overexpressing STL1.
Regarding claim 1 (a), Wang discloses a recombinant S. cerevisiae overexpressing a H+/glycerol symporter (STL1), wherein ethanol production is increased in said recombinant S. cerevisiae (abstract, pages 1860-1861 and 1863). Wang discloses overcoming the growth defect of S. cerevisiae comprising Δgpd1Δgpd2 by expression of STL1 and GLT1, which results in S. cerevisiae having 8.2% increase in ethanol production (abstract and page 1863).
Zhao discloses a S. cerevisiae STL1 having 100% sequence identity to the STL1 of the SEQ ID NO:140 of the instant application (Figure 2 on page 217).
Therefore, in combing the teachings of Argyros, Wang, and Zhao, 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 S. cerevisiae of Argyros by overexpressing STL1 and GLT1. The rationale supporting that the claims would have been obvious is that a method of enhancing a particular class of devices (overcoming growth defects due to deletion of Δgpd1 and/or Δgpd2) 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 (genetically modified S. cerevisiae of Argyros) that was ready for improvement and the results would have been predictable to one of ordinary skill in the art. One of ordinary skill in the art at the time the invention was made would have been motivated to incorporate the genetic modifications of Wang to further increase ethanol production by overcoming growth defects due to deletion of Δgpd1 and/or Δgpd2. Further, the normal desire of scientists or artisans to improve upon what is already generally known provides the motivation to determine the optimum ethanol producing S. cerevisiae. Further, regarding overexpressing S. cerevisiae STL1 of Zhao, the rationale to support a conclusion that the claims would have been obvious is that the substitution of one known element (S. cerevisiae STL1) for another yields predictable results (import of glycerol) to one of ordinary skill in the art. Therefore, it would have been obvious to one of ordinary skill in the art to replace the prior art STL1 with another known and available STL1, such as the S. cerevisiae STL1, known to lead to glycerol import, because one of ordinary skill in the art would have been able to carry out such a substitution, and the results were reasonably predictable.
Therefore, the above references render claims 1-4, 11-14, 16, 22-23, 38, 41-42, 49, 81-82, and 111-112 prima facie obvious.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-4, 14, 16, 22-23, 49, and 111-112 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-25 of US Patent No. 11,753,656 (reference patent). Although the claims at issue are not identical, they are not patentably distinct from each other because the claims of the instant application and the claims of the reference patent are directed to a recombinant yeast.
Regarding claims 1, 3, 111, 14, 16, and 49 of the instant application, claims 1-2, 3, and 7 of the reference patent recite an ethanol producing recombinant yeast comprising (a) STL1, (b) deletion of a native enzyme that functions to produce glycerol, (c) a native and/or heterologous saccharolytic enzyme, and (d) a bifunctional acetaldehyde/alcohol dehydrogenase. It would have been obvious to activate STL1 and the saccharolytic enzyme in order to increase production of ethanol.
Regarding claim 2 of the instant application, claim 20 of the reference patent recites that the recombinant yeast produces less glycerol than the yeast without STL1.
Regarding claims 3-4 and 112, claims 16-17 of the reference patent recite that the STL1 is a S. cerevisiae STL1 having the amino acid sequence of SEQ ID NO:140, which is identical to the S. cerevisiae STL1 having the amino acid sequence of SEQ ID NO:140.
Regarding claims 22-23 of the instant application, claim 4 of the reference patent recites an enzyme that converts pyruvate to acetyl-CoA and formate.
Therefore, the conflicting claims are not patentably distinct from each other.
Conclusion
Claims 1-4, 11-16, 22-23, 38-39, 41-42, 49, 81-82, 84, 88, and 111-112 are pending.
Claims 15, 39, 84, and 88 are withdrawn.
Claims 1-4, 11-14, 16, 22-23, 38, 41-42, 49, 81-82, and 111-112 are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to YONG D PAK whose telephone number is (571)272-0935. The examiner can normally be reached M-Th: 5:30 am - 3:30 pm.
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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 the STL1 of SEQ ID NO:140 (“Qy”) and the STL1 of Zhao (“Db”)
STL1_YEAST
ID STL1_YEAST Reviewed; 569 AA.
AC P39932; D6VTF6; E9P950;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 2.
DT 18-JUN-2025, entry version 186.
DE RecName: Full=Sugar transporter STL1;
GN Name=STL1; OrderedLocusNames=YDR536W; ORFNames=D9719.39;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=8076821; DOI=10.1016/0378-1119(94)90295-x;
RA Zhao S., Douglas N.W., Heine M.J., Williams G.M., Winther-Larsen H.C.,
RA Meaden P.G.;
RT "The STL1 gene of Saccharomyces cerevisiae is predicted to encode a sugar
RT transporter-like protein.";
RL Gene 146:215-219(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169867; DOI=10.1038/387s075;
RA Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,
RA Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,
RA Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,
RA Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,
RA Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,
RA Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,
RA Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,
RA Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,
RA Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,
RA Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,
RA Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,
RA Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,
RA Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,
RA Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,
RA Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,
RA Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,
RA Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,
RA Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,
RA Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,
RA Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,
RA Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,
RA Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,
RA Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,
RA Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,
RA Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,
RA Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,
RA Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,
RA Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,
RA Mewes H.-W., Zollner A., Zaccaria P.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.";
RL Nature 387:75-78(1997).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP TOPOLOGY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 208353 / W303-1A;
RX PubMed=16847258; DOI=10.1073/pnas.0604075103;
RA Kim H., Melen K., Oesterberg M., von Heijne G.;
RT "A global topology map of the Saccharomyces cerevisiae membrane proteome.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:11142-11147(2006).
CC -!- SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein.
CC -!- SIMILARITY: Belongs to the major facilitator superfamily. Sugar
CC transporter (TC 2.A.1.1) family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA57229.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; L07492; AAA57229.1; ALT_FRAME; Genomic_DNA.
DR EMBL; U33057; AAB64975.1; -; Genomic_DNA.
DR EMBL; AY723796; AAU09713.1; -; Genomic_DNA.
DR EMBL; BK006938; DAA12366.1; -; Genomic_DNA.
DR PIR; S69591; S69591.
DR RefSeq; NP_010825.3; NM_001180844.3.
DR AlphaFoldDB; P39932; -.
DR SMR; P39932; -.
DR BioGRID; 32584; 120.
DR DIP; DIP-5275N; -.
DR FunCoup; P39932; 99.
DR IntAct; P39932; 2.
DR STRING; 4932.YDR536W; -.
DR TCDB; 2.A.1.1.38; the major facilitator superfamily (mfs).
DR GlyCosmos; P39932; 2 sites, No reported glycans.
DR GlyGen; P39932; 2 sites.
DR PaxDb; 4932-YDR536W; -.
DR PeptideAtlas; P39932; -.
DR EnsemblFungi; YDR536W_mRNA; YDR536W; YDR536W.
DR GeneID; 852149; -.
DR KEGG; sce:YDR536W; -.
DR AGR; SGD:S000002944; -.
DR SGD; S000002944; STL1.
DR VEuPathDB; FungiDB:YDR536W; -.
DR eggNOG; KOG0254; Eukaryota.
DR HOGENOM; CLU_001265_30_3_1; -.
DR InParanoid; P39932; -.
DR OMA; TQHFQRM; -.
DR OrthoDB; 6133115at2759; -.
DR BioCyc; YEAST:G3O-30046-MONOMER; -.
DR BioGRID-ORCS; 852149; 7 hits in 10 CRISPR screens.
DR PRO; PR:P39932; -.
DR Proteomes; UP000002311; Chromosome IV.
DR RNAct; P39932; protein.
DR GO; GO:0071944; C:cell periphery; HDA:SGD.
DR GO; GO:0000324; C:fungal-type vacuole; HDA:SGD.
DR GO; GO:0016020; C:membrane; IBA:GO_Central.
DR GO; GO:0005886; C:plasma membrane; IDA:SGD.
DR GO; GO:0005351; F:carbohydrate:proton symporter activity; IBA:GO_Central.
DR GO; GO:0015295; F:solute:proton symporter activity; IDA:SGD.
DR GO; GO:0015793; P:glycerol transmembrane transport; IMP:SGD.
DR GO; GO:0055085; P:transmembrane transport; IMP:SGD.
DR CDD; cd17356; MFS_HXT; 1.
DR FunFam; 1.20.1250.20:FF:000061; MFS sugar transporter; 1.
DR Gene3D; 1.20.1250.20; MFS general substrate transporter like domains; 1.
DR InterPro; IPR020846; MFS_dom.
DR InterPro; IPR005828; MFS_sugar_transport-like.
DR InterPro; IPR050360; MFS_Sugar_Transporters.
DR InterPro; IPR036259; MFS_trans_sf.
DR InterPro; IPR003663; Sugar/inositol_transpt.
DR InterPro; IPR005829; Sugar_transporter_CS.
DR NCBIfam; TIGR00879; SP; 1.
DR PANTHER; PTHR48022; PLASTIDIC GLUCOSE TRANSPORTER 4; 1.
DR PANTHER; PTHR48022:SF55; SUGAR TRANSPORTER STL1; 1.
DR Pfam; PF00083; Sugar_tr; 1.
DR PRINTS; PR00171; SUGRTRNSPORT.
DR SUPFAM; SSF103473; MFS general substrate transporter; 1.
DR PROSITE; PS50850; MFS; 1.
DR PROSITE; PS00216; SUGAR_TRANSPORT_1; 1.
PE 1: Evidence at protein level;
KW Glycoprotein; Membrane; Reference proteome; Repeat; Sugar transport;
KW Transmembrane; Transmembrane helix; Transport.
FT CHAIN 1..569
FT /note="Sugar transporter STL1"
FT /id="PRO_0000050461"
FT TOPO_DOM 1..29
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 30..50
FT /note="Helical; Name=1"
FT /evidence="ECO:0000255"
FT TOPO_DOM 51..79
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 80..100
FT /note="Helical; Name=2"
FT /evidence="ECO:0000255"
FT TOPO_DOM 101..107
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 108..128
FT /note="Helical; Name=3"
FT /evidence="ECO:0000255"
FT TOPO_DOM 129
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 130..150
FT /note="Helical; Name=4"
FT /evidence="ECO:0000255"
FT TOPO_DOM 151..168
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 169..189
FT /note="Helical; Name=5"
FT /evidence="ECO:0000255"
FT TOPO_DOM 190..203
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 204..224
FT /note="Helical; Name=6"
FT /evidence="ECO:0000255"
FT TOPO_DOM 225..291
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 292..312
FT /note="Helical; Name=7"
FT /evidence="ECO:0000255"
FT TOPO_DOM 313..330
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 331..351
FT /note="Helical; Name=8"
FT /evidence="ECO:0000255"
FT TOPO_DOM 352..358
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 359..379
FT /note="Helical; Name=9"
FT /evidence="ECO:0000255"
FT TOPO_DOM 380..389
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 390..410
FT /note="Helical; Name=10"
FT /evidence="ECO:0000255"
FT TOPO_DOM 411..426
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT TRANSMEM 427..447
FT /note="Helical; Name=11"
FT /evidence="ECO:0000255"
FT TOPO_DOM 448..453
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 454..474
FT /note="Helical; Name=12"
FT /evidence="ECO:0000255"
FT TOPO_DOM 475..569
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT REGION 524..569
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 524..533
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 556..569
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CARBOHYD 197
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 319
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CONFLICT 237
FT /note="E -> G (in Ref. 4; AAU09713)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 569 AA; 63532 MW; 053F3C546F84F056 CRC64;
Query Match 100.0%; Score 2961; Length 569;
Best Local Similarity 100.0%;
Matches 569; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MKDLKLSNFKGKFISRTSHWGLTGKKLRYFITIASMTGFSLFGYDQGLMASLITGKQFNY 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MKDLKLSNFKGKFISRTSHWGLTGKKLRYFITIASMTGFSLFGYDQGLMASLITGKQFNY 60
Qy 61 EFPATKENGDHDRHATVVQGATTSCYELGCFAGSLFVMFCGERIGRKPLILMGSVITIIG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 EFPATKENGDHDRHATVVQGATTSCYELGCFAGSLFVMFCGERIGRKPLILMGSVITIIG 120
Qy 121 AVISTCAFRGYWALGQFIIGRVVTGVGTGLNTSTIPVWQSEMSKAENRGLLVNLEGSTIA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 AVISTCAFRGYWALGQFIIGRVVTGVGTGLNTSTIPVWQSEMSKAENRGLLVNLEGSTIA 180
Qy 181 FGTMIAYWIDFGLSYTNSSVQWRFPVSMQIVFALFLLAFMIKLPESPRWLISQSRTEEAR 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 FGTMIAYWIDFGLSYTNSSVQWRFPVSMQIVFALFLLAFMIKLPESPRWLISQSRTEEAR 240
Qy 241 YLVGTLDDADPNDEEVITEVAMLHDAVNRTKHEKHSLSSLFSRGRSQNLQRALIAASTQF 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 YLVGTLDDADPNDEEVITEVAMLHDAVNRTKHEKHSLSSLFSRGRSQNLQRALIAASTQF 300
Qy 301 FQQFTGCNAAIYYSTVLFNKTIKLDYRLSMIIGGVFATIYALSTIGSFFLIEKLGRRKLF 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 FQQFTGCNAAIYYSTVLFNKTIKLDYRLSMIIGGVFATIYALSTIGSFFLIEKLGRRKLF 360
Qy 361 LLGATGQAVSFTITFACLVKENKENARGAAVGLFLFITFFGLSLLSLPWIYPPEIASMKV 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 LLGATGQAVSFTITFACLVKENKENARGAAVGLFLFITFFGLSLLSLPWIYPPEIASMKV 420
Qy 421 RASTNAFSTCTNWLCNFAVVMFTPIFIGQSGWGCYLFFAVMNYLYIPVIFFFYPETAGRS 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 RASTNAFSTCTNWLCNFAVVMFTPIFIGQSGWGCYLFFAVMNYLYIPVIFFFYPETAGRS 480
Qy 481 LEEIDIIFAKAYEDGTQPWRVANHLPKLSLQEVEDHANALGSYDDEMEKEDFGEDRVEDT 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 LEEIDIIFAKAYEDGTQPWRVANHLPKLSLQEVEDHANALGSYDDEMEKEDFGEDRVEDT 540
Qy 541 YNQINGDNSSSSSNIKNEDTVNDKANFEG 569
|||||||||||||||||||||||||||||
Db 541 YNQINGDNSSSSSNIKNEDTVNDKANFEG 569
Prosecution Insights