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 PCT/CN2024/108982.
Status of Claims
Claims 1-11 are pending.
Claims 1-11 are under consideration.
Foreign Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on January 30, 2025 in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Objections
Claims 1, 3, and 10 are objected to because of the following informalities: The microorganism “Bacillus subtilis” should be italicized. Appropriate correction is required.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claim 11 is rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter. The claim(s) does/do not fall within at least one of the four categories of patent eligible subject matter because the claims are directed to a process without setting forth any steps involved in the process. The recitation of “An application” for the intended use of the composite bacteria does not recite any active, positive steps delimiting how this use is actually practiced and therefore the claims are not a proper process claim. See also the 112(b) rejection below.
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 2 and claim 3 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.
The term “similar” in claim 2 is a relative term which renders the claim indefinite. The term “similar” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. It is unclear as to how much protein activity is considered as “similar” to the activity of SEQ ID NO:1 or 2. A perusal of the specification did not provide a clear definition for the above limitation. Without a clear definition in terms of numerical value, those skilled in the art would be unable to ascertain what level of protein activity is “similar” to the activity of SEQ ID NO:1 or 2. Appropriate correction is required.
Claim 11 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.
The claims are indefinite because the claims are directed to a process without setting forth any steps involved in the process. The recitation of “An application” for the intended use of the composite bacteria does not recite any active, positive steps delimiting how this use is actually practiced. Appropriate correction is required.
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 1-2 and 4-11 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.'' The claims have been broadly interpreted to encompass a method for production of D-psicose by fermenting (1) a Bacillus subtilis comprising a gene encoding any glucose isomerase derived from Thermus thermophilus, any glucose isomerase derived from Thermus thermophilus having at least 90% sequence identity to SEQ ID NO:1 or any glucose isomerase derived from Thermus thermophilus having any number of amino acid substitutions, deletion, or additions of SEQ ID NO:1 and (2) another Bacillus subtilis comprising a gene encoding any D-psicose-3-epimerase derived from Ruminococcus sp., any D-psicose-3-epimerase derived from Ruminococcus sp having at least 90% sequence identity to SEQ ID NO:2 or any D-psicose-3-epimerase derived from Ruminococcus sp. having any number of amino acid substitutions, deletion, or additions of SEQ ID NO:2. Therefore, the claims are drawn to a method of producing D-psicose by fermenting (1) B. subtilis comprising a genus of genes encoding glucose isomerase and (2) B. subtilis comprising a genus of genes encoding D-psicose-3-epimerase.
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 recitations of “glucose isomerase” and “D-psicose-3-epimerase” fail to provide a sufficient description of the genus of the enzymes used in the claimed method 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 specification does not specifically define any of the species that fall within the genus. The specification does not define any structural features commonly possessed by members of the genus that distinguish them from others. One skilled in the art therefore cannot, as one can do with a fully described genus, visualize or recognize the identity of the members of the genus.
The prior art discloses a Thermus thermophilus glucose isomerase having 100% sequence identity to the glucose isomerase of SEQ ID NO:1 of the instant application, see Loviny-Anderton (WP_244348257.1 – form PTO-1449 and the sequence alignment below). The prior art also discloses a Ruminococcus sp. D-psicose-3-epimerase having 100% sequence identity to the D-psicose-3-epimerase of SEQ ID NO:2 of the instant application, see Lou (MBS6425357.1 – form PTO-1449 and the sequence alignment below). However, D-psicose production by glucose isomerase having unknown structure and D-psicose-3-epimerase having unknown structure was not known in the prior art.
The specification is limited to a method of producing D-psicose by fermenting (1) a Bacillus subtilis comprising a gene encoding the Thermus thermophilus glucose isomerase having the amino acid sequence of SEQ ID NO:1 and (2) Bacillus subtilis comprising a gene encoding the Ruminococcus sp. D-psicose-3-epimerase having the amino acid sequence of SEQ ID NO:2, and obtaining a crude enzyme preparation comprising said glucose isomerase and D-psicose-3-epimerase. 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, the example described above is not enough and does not constitute a representative number of species to describe the whole genus. Therefore, the specification fails to describe a representative species of the claimed genus.
Regarding claim 2, one of skill in the art could identify variants of SEQ ID NO:1 or 2. However, there is no teaching regarding which amino acids of SEQ ID NO:1 and 2 can vary and result in a polypeptide having glucose isomerase activity and D-psicose-3-epimerase activity, respectively, that when reacted with glucose, D-psicose is produced.
Fransceus (J Ind Microbiol Biotechnol. 2017 May;44(4-5):687-695. – form PTO-892) reviews protein engineering techniques, such as random mutagenesis and recombination, directed evolution and iterative or combinatory saturation “hotspots”. Fransceus states that “a recurring problem, however, is choosing which amino acid positions should be targeted. Answering this question is not an easy feat and requires substantial insight in the relationship between an enzyme’s sequence or structure and its properties.” Sanavia (Computational and Structural Biotechnology Journal, Volume 18, 2020, Pages 1968-1979. – form PTO-892) discloses challenges in the prediction of protein stability in the occurrence of multiple mutations. “Multiple-point mutations are common variations of the protein sequence that may be needed in protein engineering when a single-point mutation is not enough to yield the desired stability change. Dealing with multiple-site variations adds another level of complexity beyond the prediction of the effect of a single variant on protein stability, since it requires the learning of many types of combinatorial effects”.
An important consideration is that structure is not necessarily a reliable indicator of function. In the instant case, there is no disclosure relating similarity of structure to conservation of function. Conservation of structure is not necessarily a surrogate for conservation of function.
While general knowledge in the art may have allowed one of skill in the art to identify other polypeptides expected to have the same or similar tertiary structure, there was no general knowledge in the art in the ability of any glucose isomerase and D-psicose-3-epimerase to produce D-psicose.
Given this lack of description of the representative species encompassed by the genus of the claims, 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 1-2 and 4-11.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
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 subtipoint 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 1-2 and 10-11 is/are rejected under 35 U.S.C. 103 as being unpatentable over Li (CN113980880 – form PTO-1449 and English Translation of CN113980880 (retrieved on September 15, 2026 – form PTO-892), Loviny-Anderton (WP_244348257.1 – form PTO-1449), Lou (MBS6425357.1 – form PTO-1449), and Mittermeier (Artificial microbial consortia for bioproduction processes. Eng Life Sci. 2022 Apr 14;23(1):e2100152 – form PTO-892).
Regarding claims 1 and 10-11, Li discloses a method for producing D-psicose comprising (a) co-expression of a fusion protein comprising a glucose isomerase and a Ruminococcus sp. D-psicose-3-epimerase (RUM55) in Bacillus subtilis, (b) inoculating the resulting engineered Bacillus subtilis into a fermentation medium and disrupting said Bacillus subtilis to obtain a crude enzyme preparation containing said glucose isomerase and RUM55, and (c) catalyzing glucose with said crude enzyme preparation to obtain D-psicose (abstract, Embodiment 2, Table 4, and claims 1-10). D-psicose is sugar substitute (2nd paragraph at page 2).
Regarding claim 2, MPEP 2113 states that “The patentability of a product does not depend on its method of production.”. In the instant case, the structure of the claimed glucose isomerase obtained by substituting, deleting, or adding one or more amino acids to/from SEQ ID NO:1 implied is the same whether the mutant is obtained from SEQ ID NO:1 or is obtained from any source, as long as the resulting product has the structural limitations recited in the claims (at least one amino acid different). Similarly, the structure of the claimed D-psicose-3-epimearse obtained by substituting, deleting, or adding one or more amino acids to/from SEQ ID NO:2 implied is the same whether the mutant is obtained from SEQ ID NO:2 or is obtained from any source, as long as the resulting product has the structural limitations recited in the claims (at least one amino acid different). The glucose isomerase of SEQ ID NO:2 of Li has at least one amino acid difference from the glucose isomerase of SEQ ID NO:1 of the instant application (claim 3 and see the sequence alignment below). The D-psicose-3-epimerase of SEQ ID NO:4 of Li has at least one amino acid difference from the D-psicose-3-epimerase of SEQ ID NO:2 of the instant application (claim 4 and see the sequence alignment below).
Li does not disclose separately transferring a Thermus thermophilus glucose isomerase (GI) of SEQ ID NO:1 of the instant application into B. subtilis and transferring D-psicose-3-epimerase (DPEase) having the amino acid sequence of SEQ ID NO:2 into another B. subtilis.
Regarding claims 1 and 10-11, Loviny-Anderton discloses a Thermus thermophilus glucose isomerase having 100% sequence identity to the glucose isomerase of SEQ ID NO:1 of the instant application (see pages 1-2 and the sequence alignment below).
Regarding claims 1 and 10-11, Lou discloses a Ruminococcus sp. D-psicose-3-epimerase having 100% sequence identity to the D-psicose-3-epimerase of SEQ ID NO:2 of the instant application (see pages 1-2 and the sequence alignment below).
Regarding claims 1 and 10-11, Mittermeier discloses that co-cultures used in bioproduction processes are well-defined and consist nearly exclusively of two different species or even two different strains from the same species and are specifically designed and optimized for their respective purpose (2nd paragraph at page 1 through top of page 2). Mittermeier discloses that co-cultivation may provide significant advantages as compared to the cultivation of pure cultures (1st paragraph at page 2). Mittermeier discloses that process limitations caused by the metabolic burden of gene overexpression, accumulation of toxic and inhibiting byproducts or intermediates or thermodynamic limitations can be evaded.
Therefore, in combining the teachings of the above references, it would have been obvious to one having ordinary skill in the art before the time the claimed invention was effectively filed to modify the method of Li by (1) replacing the glucose isomerase with Thermus thermophilus glucose isomerase of Loviny-Anderton and replacing the D-psicose-3-epimerase with the Ruminococcus sp. D-psicose-3-epimerase of Lou because one of ordinary skill in the art would have been able to carry out such a substitution and (2) introducing the gene encoding glucose isomerase into a B. subtilis and introducing the gene encoding D-psicose-3-epimerase in another B. subtilis. (1) The rationale to support a conclusion that the claims would have been obvious is that the substitution of one known element (glucose isomerase and D-psicose-3-epimerase) for another (Thermus thermophilus glucose isomerase and the Ruminococcus sp. D-psicose-3-epimerase) yields predictable results (conversion of glucose to D-psicose via D-fructose) to one of ordinary skill in the art. See MPEP 2143. (2) One having ordinary skill in the art would have been motivated to express glucose isomerase and D-psicose-3-epimerase in separate B. subtilis in order to evade the limitations caused by the metabolic burden of gene overexpression, accumulation of toxic and inhibiting byproducts or intermediates or thermodynamic limitations. One of ordinary skill in the art would have had a reasonable expectation of success since Li disclose a method of producing D-psicose by fermenting B. subtilis expressing glucose isomerase and D-psicose-3-epimerase, Loviny-Anderton discloses Thermus thermophilus glucose isomerase, Lou discloses Ruminococcus sp. D-psicose-3-epimerase, and Mittermeier discloses the advantages of co-cultures of two different strains from the same species that are specifically designed and optimized for their respective purpose
Therefore, the above references render claims 1-2 and 10-11 prima facie obvious.
Claim(s) claims 4-9 is/are rejected under 35 U.S.C. 103 as being unpatentable over Li (CN113980880 – form PTO-1449 and English Translation of CN113980880. Retrieved on September 15, 2026 – form PTO-892), Loviny-Anderton (WP_244348257.1 – form PTO-1449), Lou (MBS6425357.1 – form PTO-1449), and Mittermeier (Artificial microbial consortia for bioproduction processes. Eng Life Sci. 2022 Apr 14;23(1):e2100152 – form PTO-892) as applied to claims 1-2 and 10-11 above, and further in view of Wang (CN 114480359 A – form PTO-892 and the English Translation of CN 114480359 A. Retrieved on September 15, 2026 – form PTO-892), Zhang (A novel strategy for D-psicose and lipase co-production using a co-culture system of engineered Bacillus subtilis and Escherichia coli and bioprocess analysis using metabolomics. Bioresour Bioprocess. 2021 Aug 19;8(1):77. – form PTO-892), de Bruin (A method for assessing efficiency of bacterial cell disruption and DNA release. BMC Microbiol 16, 197 (2016) – form PTO-892), and Long (Separation of D-psicose and D-fructose using simulated moving bed chromatography. J Sep Sci. 2009 Jun;32(11):1987-95. – form PTO-892).
The combined teachings of Li, Loviny-Anderton, Lou, and Mittermeir do not disclose the fermentation steps recited in claims 4-8 and separately obtaining the D-psicose and D-fructose.
Regarding claim 4, Wang discloses a method of producing D-psicose by fermenting Bacillus subtilis by cultivating the Bacillus subtilis at 37°C and 200 rpm for 48 hrs (page 3).
Regarding claim 5, Wang discloses a fermentation medium comprising water, peptone (5-15 g/L), yeast extract (1-5 g/L), monopotassium phosphate (potassium dihydrogen phosphate) (0.5-5 g/L), potassium hydrogen phosphate (dipotassium hydrogen phospahte) (5-20 g/L), manganese chloride tetrahydrate (0.02-0.2 g/L), and glucose (2-10 g/L) (page 4). Zhang discloses fermentation medium for producing D-psicose by B. Bacillus comprising magnesium sulfate heptahydrate (0.71 g/L).
Regarding claim 6, Li discloses a step of preparing a seed broth with the engineered Bacillus subtilis and inoculating the engineered Bacillus subtilis into an LB seed culture medium and performing overnight cultivation at 37°C (Embodiment 2 and Table 4). Wang discloses preparing a seed broth and cultivation at 37°C and 200 rpm (bottom of page 6 through top of page 7).
Regarding claim 7, Li discloses disruption of the B. subtilis cells (Embodiment 2 and Table 4) but does not disclose mixing lysozyme and a fermentation broth. However, Bacillus subtilis cell disruption by lysozyme (reaction at 37°C for 1 hr) was known in the art, as disclose by de Bruin (“Comparison of acid/HPLC with other methods used to quantifying the amount of DNA in a sample of bacteria” at pages 4-5).
Regarding claim 8, Li discloses that the temperature of the isomerization at 50°C for 7 hours, which falls within the recited range of 2 to 24 hours (Embodiment 2 and Table 4).
Regarding claim 9, Long discloses a method of separating and isolating D-psicose and fructose by sequentially filtering, purifying, chromatographically separating, and concentrating products (abstract and “3 Experimental” at pages 1989-1991).
“[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.”, see MPEP 2144. It would have been well within the knowledge of one having ordinary skill in the art to vary and optimize the concentrations of the components of the fermentation medium, vary and optimize the temperature, shaking speed, and temperature of fermentation, and vary and optimize the temperature and time of the reaction.
Therefore, in combining the teachings of the above references, it would have been obvious to one having ordinary skill in the art before the time the claimed invention was effectively filed to modify the method of (1) by varying and optimizing the concentrations of the components of the fermentation medium, varying and optimizing the temperature, shaking speed, and temperature of fermentation, varying and optimizing the temperature and time of the reaction, (2) disrupting the engineered B. subtilis cells with lysozyme, and (3) isolating and separating the D-psicose and fructose (1) One having ordinary skill in the art would have been motivated to vary and optimize the fermentation medium, fermentation, and reaction to increase yields of D-psicose. (2) One having ordinary skill in art would have been motivated to disrupt the engineered B. subtilis with lysozyme to obtain the crude enzyme preparation comprising glucose isomerase and D-psicose-3-epimerase. (3) One having ordinary skill in the art would have been motivated to isolate and separate D-psicose from fructose to use D-psicose as a sugar substitute. One of ordinary skill in the art would have had a reasonable expectation of success since Wang and Zhang teach fermentation mediums for B. subtilis and fermentation parameters, deBruin teaches disruption of B. subtilis with lysozyme, and Long teaches isolation and separation of D-psicose and fructose.
Therefore, the above references render claims 1-2 and 4-11 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 1-11 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of copending Application No. 19/041,945 (reference application) in view of Li (CN113980880 – form PTO-1449 and English Translation of CN113980880 – form PTO-892), Mittermeier (Artificial microbial consortia for bioproduction processes. Eng Life Sci. 2022 Apr 14;23(1):e2100152 – form PTO-892), Zhang (A novel strategy for D-psicose and lipase co-production using a co-culture system of engineered Bacillus subtilis and Escherichia coli and bioprocess analysis using metabolomics. Bioresour Bioprocess. 2021 Aug 19;8(1):77. – form PTO-892), Wang (CN 114480359 A – form PTO-892 and the English Translation of CN 114480359 A. Retrieved on September 15, 2026 – form PTO-892), and de Bruin (A method for assessing efficiency of bacterial cell disruption and DNA release. BMC Microbiol 16, 197 (2016) – form PTO-892).
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 application are directed to a method of producing D-psicose by reacting glucose with a glucose isomerase having the amino acid sequence of SEQ ID NO:1 and a D-psicose-3-epimerase having the amino acid sequence of SEQ ID NO:2. The glucose isomerase having the amino acid sequence of SEQ ID NO:1 of the instant application is identical to the glucose isomerase having the amino acid sequence of SEQ ID NO:1 of the reference application. The D-psicose-3-epimerase having the amino acid sequence of SEQ ID NO:2 of the instant application is identical to the D-psicose-3-epimerase having the amino acid sequence of SEQ ID NO:2 of the reference application.
Regarding claims 1-3 and 10-11 of the instant application, claims 1-5 of the reference application recites a polynucleotide having the nucleic acid sequence of SEQ ID NO:3 encoding the Thermus thermophilus glucose isomerase having the amino acid sequence of SEQ ID NO:1 and a polynucleotide having the nucleic acid sequence of SEQ ID NO:4 encoding the Ruminococcus sp. D-psicose-3-epimerase having the amino acid sequence of SEQ ID NO:2. SEQ ID NO:1-4 of the reference application are identical to SEQ ID NO:1-4, respectively, of the instant application. Claim 10-12 of the reference application recites a method f producing D-psicose by fermenting and culturing an engineered bacteria, performing bacterial cell disruption to obtain a crude enzyme preparation comprising glucose isomerase and D-psicose-3-epimerase, and adding glucose to obtain D-psicose.
Regarding claim 9 of the instant application, claim 12 of the reference application recite filtering, purifying, chromatographically separating, and concentrating the reaction products to separate obtain the D-psicose and fructose.
The claims of the reference application do not recite separating introducing the Thermus thermophilus glucose isomerase into B. subtilis and transferring Ruminococcus sp. D-psicose-3-epimerase into another B. subtilis, fermentation parameters of claims 4-6 and 7, and disrupting the B. subtilis with lysozyme.
Regarding claim 4 of the instant application, Wang discloses a method of producing D-psicose by fermenting Bacillus subtilis by cultivating the Bacillus subtilis at 37°C and 200 rpm for 48 hrs (page 3).
Regarding claim 5 of the instant application, Wang discloses a fermentation medium comprising water, peptone (5-15 g/L), yeast extract (1-5 g/L), monopotassium phosphate (potassium dihydrogen phosphate) (0.5-5 g/L), potassium hydrogen phosphate (dipotassium hydrogen phospahte) (5-20 g/L), manganese chloride tetrahydrate (0.02-0.2 g/L), and glucose (2-10 g/L) (page 4). Zhang discloses fermentation medium for producing D-psicose by B. Bacillus comprising magnesium sulfate heptahydrate (0.71 g/L).
Regarding claim 6 of the instant application, Li discloses a step of preparing a seed broth with the engineered Bacillus subtilis and inoculating the engineered Bacillus subtilis into an LB seed culture medium and performing overnight cultivation at 37°C (Embodiment 2 and Table 4). Wang discloses preparing a seed broth and cultivation at 37°C and 200 rpm (bottom of page 6 through top of page 7).
Regarding claim 7 of the instant application, Bacillus subtilis cell disruption by lysozyme (reaction at 37°C for 1 hr) was known in the art, as disclose by de Bruin (“Comparison of acid/HPLC with other methods used to quantifying the amount of DNA in a sample of bacteria” at pages 4-5).
Regarding claim 8 of the instant application, Li discloses the temperature of the isomerization at 50°C for 7 hours, which falls within the recited range of 2 to 24 hours (Embodiment 2 and Table 4).
“[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.”, see MPEP 2144. It would have been well within the knowledge of one having ordinary skill in the art to vary and optimize the concentrations of the components of the fermentation medium, vary and optimize the temperature, shaking speed, and temperature of fermentation, and vary and optimize the temperature and time of the reaction.
Therefore, it would have been obvious to one having ordinary skill in the art to modify the claims of the reference application by (1) introducing the gene encoding glucose isomerase into a B. subtilis and introduce the gene encoding D-psicose-3-epimerase in another B. subtilis, (2) varying and optimizing the concentrations of the components of the fermentation medium, varying and optimizing the temperature, shaking speed, and temperature of fermentation, varying and optimizing the temperature and time of the reaction, and (3) disrupting the engineered B. subtilis cells with lysozyme.
(1) One having ordinary skill in the art would have been motivated to express glucose isomerase and D-psicose-3-epimerase in separate B. subtilis in order to evade the limitations caused by the metabolic burden of gene overexpression, accumulation of toxic and inhibiting byproducts or intermediates or thermodynamic limitations. (2) One having ordinary skill in the art would have been motivated to vary and optimize the fermentation medium, fermentation, and reaction to increase yields of D-psicose. (3) One having ordinary skill in art would have been motivated to disrupt the engineered B. subtilis with lysozyme to obtain the crude enzyme preparation comprising glucose isomerase and D-psicose-3-epimerase.
One of ordinary skill in the art would have had a reasonable expectation of success since the claims of the reference application disclose a method of producing D-psicose by fermenting a bacteria expressing glucose isomerase and D-psicose-3-epimerase and preparing crude enzyme preparation comprising glucose isomerase and D-psicose-3-epimerase, Li discloses a method of producing D-psicose by fermenting B. subtilis expressing glucose isomerase and D-psicose-3-epimerase, Mittermeier discloses the advantages of co-cultures of two different strains from the same species that are specifically designed and optimized for their respective purpose, Wang and Zhang teaches fermentation mediums for B. subtilis and fermentation parameters, and deBruin teaches disruption of B. subtilis with lysozyme.
Therefore, the conflicting claims are not patentably distinct from each other.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
Claims 1-11 are pending.
Claims 1-11 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 of the glucose isomerase of SEQ ID NO:1 of the instant application (“Qy”) and the glucose isomerase of Loviny-Anderton(“Db”)
Title: US-19-041-885-1
Perfect score: 2037
Sequence: 1 MYEPKPEHRFTFGLWTVGNL..........GYGLERLDQLAVEYLLGVRG 387
Scoring table: BLOSUM62
Gapop 10.0 , Gapext 0.5
Searched: 1 seqs, 387 residues
Total number of hits satisfying chosen parameters: 1
Minimum DB seq length: 0
Maximum DB seq length: inf
Post-processing: Minimum Match 0%
Maximum Match 100%
Listing first 50 summaries
Database : WP_244348257.1.fasta:*
SUMMARIES
%
Result Query
No. Score Match Length DB ID Description
----------------------------------------------------------------------------
1 2037 100.0 387 1 WP_244348257.1 xylose isomerase [
ALIGNMENTS
RESULT 1
WP_244348257.1
Query Match 100.0%; Score 2037; DB 1; Length 387;
Best Local Similarity 100.0%;
Matches 387; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MYEPKPEHRFTFGLWTVGNLGRDPFGDAVRERLDPVYVVHKLAELGAYGVNLHDEDLIPR 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MYEPKPEHRFTFGLWTVGNLGRDPFGDAVRERLDPVYVVHKLAELGAYGVNLHDEDLIPR 60
Qy 61 GTPPQERDQIVRRFKKALEETGLKVPMVTANLFSDPAFKDGAFTSPDPWVRAYALRKSLE 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 GTPPQERDQIVRRFKKALEETGLKVPMVTANLFSDPAFKDGAFTSPDPWVRAYALRKSLE 120
Qy 121 TMDLGAELGAEIYVVWPGREGAEVEATGKARKVWDWVREALNFMAAYAEDQGYGYRFALE 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 TMDLGAELGAEIYVVWPGREGAEVEATGKARKVWDWVREALNFMAAYAEDQGYGYRFALE 180
Qy 181 PKPNEPRGDIYFATVGSMLAFIHTLDRPERFGLNPEFAHETMAGLNFVHAVAQVLDAGKL 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 PKPNEPRGDIYFATVGSMLAFIHTLDRPERFGLNPEFAHETMAGLNFVHAVAQVLDAGKL 240
Qy 241 FHIDLNDQRMSRFDQDLRFGSENLKAAFFLVDLLESSGYQGPRHFDAHALRTEDEEGVWA 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 FHIDLNDQRMSRFDQDLRFGSENLKAAFFLVDLLESSGYQGPRHFDAHALRTEDEEGVWA 300
Qy 301 FARGCMRTYLILKERAEAFREDPEVKELLAAYYQQDPAALALLGPYSREKAEALKRAELP 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 FARGCMRTYLILKERAEAFREDPEVKELLAAYYQQDPAALALLGPYSREKAEALKRAELP 360
Qy 361 LEAKRRRGYGLERLDQLAVEYLLGVRG 387
|||||||||||||||||||||||||||
Db 361 LEAKRRRGYGLERLDQLAVEYLLGVRG 387
Sequence alignment of the D-psicose-3-epimerase of SEQ ID NO:2 of the instant application (“Qy”) and the D-psicose-3-epimerase of Lou (“Db”)
Title: US-19-041-885-2
Perfect score: 1563
Sequence: 1 MKYGIYYAYWEKEWNGDYKY..........VTLDMDAQSALHFVKHVFEV 291
Scoring table: BLOSUM62
Gapop 10.0 , Gapext 0.5
Searched: 1 seqs, 291 residues
Total number of hits satisfying chosen parameters: 1
Minimum DB seq length: 0
Maximum DB seq length: inf
Post-processing: Minimum Match 0%
Maximum Match 100%
Listing first 50 summaries
Database : MBS6425357.1.fasta:*
SUMMARIES
%
Result Query
No. Score Match Length DB ID Description
----------------------------------------------------------------------------
1 1563 100.0 291 1 MBS6425357.1 MAG: sugar phospha
ALIGNMENTS
RESULT 1
MBS6425357.1
Query Match 100.0%; Score 1563; DB 1; Length 291;
Best Local Similarity 100.0%;
Matches 291; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MKYGIYYAYWEKEWNGDYKYYIDKISKLGFDILEISCGAFSDYYTKDQELIDIGKYAKEK 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MKYGIYYAYWEKEWNGDYKYYIDKISKLGFDILEISCGAFSDYYTKDQELIDIGKYAKEK 60
Qy 61 GVTLTAGYGPHLNESLSSSEPNTQKQAISFWKETLRKLKLMDIHMVGGALYGYWPVDYSK 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 GVTLTAGYGPHLNESLSSSEPNTQKQAISFWKETLRKLKLMDIHMVGGALYGYWPVDYSK 120
Qy 121 PFDKKRDLENSIKNMKIISQYAEEYDIMMGMEVLNRFEGYMLNTCDEALAYVEEVGSSNV 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 PFDKKRDLENSIKNMKIISQYAEEYDIMMGMEVLNRFEGYMLNTCDEALAYVEEVGSSNV 180
Qy 181 GVMLDTFHMNIEEDNIAAAIRKAGDRLCHFHIGEGNRKVPGKGMLPWNEIGQALRDINYQ 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 GVMLDTFHMNIEEDNIAAAIRKAGDRLCHFHIGEGNRKVPGKGMLPWNEIGQALRDINYQ 240
Qy 241 HAAVMEPFVMQGGTVGHDIKIWRDIIGNCSEVTLDMDAQSALHFVKHVFEV 291
|||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 HAAVMEPFVMQGGTVGHDIKIWRDIIGNCSEVTLDMDAQSALHFVKHVFEV 291
Sequence alignment of the glucose isomerase of SEQ ID NO:1 of the instant application (“Qy”) and the glucose isomerase of Li (“Db”)
BKS06210
ID BKS06210 standard; protein; 413 AA.
XX
AC BKS06210;
XX
DT 21-JUL-2022 (first entry)
XX
DE Fervidobacterium gondwanense glucose isomerase protein, SEQ:2.
XX
KW fermentation; genetically engineered microorganism; glucose isomerase;
KW psicose.
XX
OS Fervidobacterium gondwanense.
OS Synthetic.
XX
FH Key Location/Qualifiers
FT Region 408..413
FT /note= "His-tag"
XX
CC PN CN113980880-A.
XX
CC PD 28-JAN-2022.
XX
CC PF 24-SEP-2021; 2021CN-11122002.
XX
PR 24-SEP-2021; 2021CN-11122002.
XX
CC PA (COFG ) COFCO NUTRITION & HEALTH RES INST CO LTD.
CC PA (COFG ) JILIN COFCO BIOCHEMICAL CO LTD.
XX
CC PI An T, Li F, Zhao G, Wu L, Tao J, Pan X, Tong Y, Zhang Y;
CC PI Wang X, Wang J, Li Y;
XX
DR WPI; 2022-30417M/056.
DR N-PSDB; BKS06209.
XX
CC PT Genetically engineered bacteria for producing psicose with glucose as raw
CC PT material, is co-express glucose isomerase and D-psicose-3-epimerase,
CC PT where glucose isomerase is derived from Streptomyces and
CC PT Acidothermuscellulolyticus.
XX
CC PS Claim 3; SEQ ID NO 2; 34pp; Chinese.
XX
CC The present invention relates to a genetically engineered bacteria useful
CC for producing psicose with glucose as raw material. The engineered
CC bacteria (e.g., Escherichia coli or Bacillus subtilis) comprises a D-
CC psicose-3-epimerase gene shown in (see BKS06211) derived from
CC Ruminococcus sp. CAG55 and a glucose isomerase gene shown in (see
CC BKS06209) derived from Fervidobacterium gondwanense, wherein a gene
CC encoding a linker and a self-aggregating short peptide is inserted
CC between the two genes. The invention further claims a method for
CC producing psicose by culturing the genetically engineered bacteria to co-
CC express the glucose isomerase shown in (see BKS06210) and D-psicose-3-
CC epimerase shown in (see BKS06212). The genetically engineered bacteria is
CC useful for converting glucose into psicose in a single step which reduces
CC the purification step of the intermediate product D-fructose thereby
CC reducing the production cost of D-psicose.
XX
SQ Sequence 413 AA;
Query Match 53.4%; Score 1088; Length 413;
Best Local Similarity 55.7%;
Matches 219; Conservative 51; Mismatches 113; Indels 10; Gaps 3;
Qy 4 PKPEHRFTFGLWTVGNLGRDPFGDAVRERLDPVYVVHKLAELGAYGVNLHDEDLIPRGTP 63
| | ||:||||||| |||||:| | |||| |||||||||||| ||:||:| |:
Db 16 PSKEDRFSFGLWTVGWQARDPFGEATRPPLDPVEAVHKLAELGAYGVTFHDDDLVPFGSS 75
Qy 64 PQERDQIVRRFKKALEETGLKVPMVTANLFSDPAFKDGAFTSPDPWVRAYALRKSLETMD 123
|| ::: |||||| :||| |||:| |||: | |||||||: | :| ||:|| : :|
Db 76 DAERARLIDRFKKALADTGLVVPMMTTNLFTHPIFKDGAFTANDRSIRRYAIRKVMRNLD 135
Qy 124 LGAELGAEIYVVWPGREGAEVEATGKARKVWDWVREALNFMAAYAEDQGYGYRFALEPKP 183
| ||||| || | ||||:|::| | | |||:: :| | :||||| ||||||||
Db 136 LAAELGARTYVFWGGREGSEIDAAKDIRAALDRYREAIDTLAQYVKDQGYGIRFALEPKP 195
Qy 184 NEPRGDIYFATVGSMLAFIHTLDRPERFGLNPEFAHETMAGLNFVHAVAQVLDAGKLFHI 243
|||||||: |:| ||||::|: : ||||| || |: ||||| :|| | ||||||
Db 196 NEPRGDIFLPTIGHALAFINSLEHSDIVGLNPEVGHEQMSNLNFVHGIAQALWHGKLFHI 255
Qy 244 DLNDQRMSRFDQDLRFGSENLKAAFFLVDLLESS------GYQGPRHFDAHALRTEDEEG 297
||| | ::|||| || :| :|||||||||: | |||||| :|||| :|
Db 256 DLNGQHGPKYDQDLVFGHGDLLSAFFLVDLLENGFPGGGPVYDGPRHFDYKPMRTEDIDG 315
Qy 298 VWAFARGCMRTYLILKERAEAFREDPEVKELLAAYYQQDPAALALLG---PYSREKAEAL 354
||| | |||||:||:||:||| ||||: | | : |: || |: |:
Db 316 VWASAAANMRTYLLLKQRAKAFRADPEVQAALTA-SRVPELAVPTLGEGESYADLLADRS 374
Qy 355 KRAELPLEAKRRRGYGLERLDQLAVEYLLGVRG 387
| :: :||| ||||||:|:||| ||
Db 375 AWEEFDVDRAANQGYGYARLDQLAIEHLLGARG 407
Sequence alignment of the D-psicose-3-epimerase of SEQ ID NO:2 of the instant application (“Qy”) and the D-psicose-3-epimerase of Li (“Db”)
BKS06212
ID BKS06212 standard; protein; 292 AA.
XX
AC BKS06212;
XX
DT 21-JUL-2022 (first entry)
XX
DE Ruminococcus sp. CAG55 D-psicose-3-epimerase protein, SEQ:4.
XX
KW D-psicose-3-epimerase; fermentation;
KW genetically engineered microorganism; psicose.
XX
OS Ruminococcus sp.; CAG55.
XX
CC PN CN113980880-A.
XX
CC PD 28-JAN-2022.
XX
CC PF 24-SEP-2021; 2021CN-11122002.
XX
PR 24-SEP-2021; 2021CN-11122002.
XX
CC PA (COFG ) COFCO NUTRITION & HEALTH RES INST CO LTD.
CC PA (COFG ) JILIN COFCO BIOCHEMICAL CO LTD.
XX
CC PI An T, Li F, Zhao G, Wu L, Tao J, Pan X, Tong Y, Zhang Y;
CC PI Wang X, Wang J, Li Y;
XX
DR WPI; 2022-30417M/056.
DR N-PSDB; BKS06211.
XX
CC PT Genetically engineered bacteria for producing psicose with glucose as raw
CC PT material, is co-express glucose isomerase and D-psicose-3-epimerase,
CC PT where glucose isomerase is derived from Streptomyces and
CC PT Acidothermuscellulolyticus.
XX
CC PS Claim 4; SEQ ID NO 4; 34pp; Chinese.
XX
CC The present invention relates to a genetically engineered bacteria useful
CC for producing psicose with glucose as raw material. The engineered
CC bacteria (e.g., Escherichia coli or Bacillus subtilis) comprises a D-
CC psicose-3-epimerase gene shown in (see BKS06211) derived from
CC Ruminococcus sp. CAG55 and a glucose isomerase gene shown in (see
CC BKS06209) derived from Fervidobacterium gondwanense, wherein a gene
CC encoding a linker and a self-aggregating short peptide is inserted
CC between the two genes. The invention further claims a method for
CC producing psicose by culturing the genetically engineered bacteria to co-
CC express the glucose isomerase shown in (see BKS06210) and D-psicose-3-
CC epimerase shown in (see BKS06212). The genetically engineered bacteria is
CC useful for converting glucose into psicose in a single step which reduces
CC the purification step of the intermediate product D-fructose thereby
CC reducing the production cost of D-psicose.
XX
SQ Sequence 292 AA;
Query Match 34.5%; Score 540; Length 292;
Best Local Similarity 41.3%;
Matches 116; Conservative 51; Mismatches 100; Indels 14; Gaps 6;
Qy 2 KYGIYYAYWEKEWNGDYKYYIDKISKLGFDILEISCGAFSDYYTKDQELIDIGKYAKEKG 61
| |::: |: ::|| |: |::: |:| ||||:: || | :| ||
Db 3 KIGVHFGYFNRDWNTDFIKRIEQVKKIGLDILEVAPAPLL-ALTKFQR-DEIAAAAKAND 60
Qy 62 VTLTAGYGPHLNESLSSSEPNTQKQAISFWKETLRKLKLMDIHMVGGALY-GYWPVDYSK 120
: || | |: |:| : :| | | :| : : | || | | ::|
Db 61 IELTFSVGLSANQDLASEDEEIRKNGIKFTTDTFQIMSEM-----GGKTYSGVDIAAWNK 115
Qy 121 PF-----DKKRDLENSIKNMKIISQYAEEYDIMMGMEVLNRFEGYMLNTCDEALAYVEEV 175
| || | || :| | : ||: | :||:||:| ::|| :||: ||:||
Db 116 TFMEGITDKSATWERSISAVKEIMKVAEDKGITFAVEVVNRYESSLVNTAEEAVKYVDEV 175
Qy 176 GSSNVGVMLDTFHMNIEEDNIAAAIRKAGDRLCHFHIGEGNRKVP-GKGMLPWNEIGQAL 234
|| | ::|||:|||||||: | ||: |:|| |||:|| ||: | | :||||| ||
Db 176 GSPNCKILLDTYHMNIEEDSFAGAIKLVGNRLGHFHVGESNRRPPCENGKMPWNEITNAL 235
Qy 235 RDINYQHAAVMEPFVMQGGTVGHDIKIWRDIIGNCSEVTLD 275
::|:|| | |||||: || || |||:|||| || ::
Db 236 KEIDYQGAIVMEPFIKMGGEVGRDIKVWRDISEGASESEME 276
Prosecution Insights