DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Objections
Claims 5, 9 and 11 are objected to because of the following informalities:
Claim 5 (in two instances) recites “by optimizing the codon preference of Bacillus subtilis.” The claim can only reasonably be understood as codon optimization of the recited genes (and not Bacillus subtilis) and should recite “the gene encoding the glucose isomerase (or D-psicose 3-epimerase) is codon optimized for expression in Bacillus subtilis” or similar.
Claim 9 recites “the gene of the glucose isomerase” and “the gene of the D-psicose 3-epimerase,” which are understood to have antecedent basis in a “nucleic acid combination” as recited in claim 4. However, consistent claim terminology should be used throughout the claims such that claim 9 should refer to the nucleic acid combination of claim 4 or set forth that such combination includes “a” gene of the glucose isomerase and D-psicose 3-epimerase in a manner as recited in claim 5.
Claim 11 is missing from the list of claims. Any future amendment should indicate claim 11 as cancelled.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-10 and 12 (all pending claims) 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 glucose isomerase derived from Thermus thermophilus and D-psicose 3-epimerase (DPE) derived from Ruminococcus sp. The statement “derived from” indicates that the recited enzymes are not limited to a glucose isomerase or DPE that can be directly isolated from a naturally-occurring Thermus thermophilus or Ruminococcus. Rather, claims 2 and 3 (part (2)) indicate that an unlimited degree of substituting, deleting or adding of amino acids can be performed and still fall within the scope of “derived from” T. thermophilus or Ruminococcus sp. Regardless, recitation of “derived from” Thermus thermophilus or Ruminococcus sp. is understood as limiting the scope of the claim as compared to as if the “derived from” limitation were not recited. However, it is unclear as to what degree of modification to glucose isomerase and/or DPE is tolerable or allowed while still be considered to be “derived from“ T. thermophilus or Ruminococcus sp. As such, an ordinarily skilled artisan is unable to determine how to avoid infringement of claims 1-3 and claims depending therefrom.
In claims 2 and 3, penultimate line, the claims recites protein activity “similar to that.” It is not clear as to what protein activity would be “similar.” For example, if SEQ ID NO: 1 has xylose and glucose isomerase activity, would an enzyme having only glucose isomerase activity be similar? If SEQ ID NO: 2 has activity to epimerize sugars other than D-psicose, would an enzyme lacking such extra activity be similar? That is, what activity may be “similar” is subjective such that an ordinarily skilled artisan cannot determine how to avoid infringement.
Claims 2 and 3, in parts (3) and (c), recite “at least 90% homology.” As set forth in Reeck et al. (“Homology” in Proteins and Nucleic Acids, Cell 50, 1987, 667): In its precise biological meaning, “homology” is a concept of quality. The word asserts a type of relationship between two or more things. Thus, amino acid or nucleotide sequences are either homologous or they are not. They cannot exhibit a particular “level of homology” or “percent homology.” As such, what is meant by “at least 90% homology” cannot be understood since the common meaning of “homology” in the art does not allow for a “percent homology.” As far as percent homology is intended to mean similarity, in the absence of a definition for similarity it cannot be understood if substitution of Ser to Ala amino acid residue is similar based on both being small amino acid residues or dissimilar since one is polar and the other is aliphatic. For this reason, an ordinarily skilled artisan cannot determine how to avoid infringement of “at least 90% homology.”
Claim 12 recites “The method according to claim 11.” The listing of claims does not contain a claim 11 such that an ordinarily skilled artisan cannot determine how to avoid infringement. Further due to claim 12 depending from a cancelled claim, the following claim terms do not have an explicit nor inherent antecedent basis: “the engineered bacteria” (line 2), “the glucose isomerase” (line 3), “the D-psicose 3-epimerase,” “the glucose substrate,” and “the D-psicose,” where none of these claim features have an explicit antecedent basis nor a reasonable inherent antecedent basis in claims 1 or 12.
Claim 9 recites the limitation "the Bacillus subtilis" in last line. There is insufficient antecedent basis for this limitation in the claim. Claim 9 depends from claim 7 wherein there is no prior recitation in the claims of “Bacillus subtilis” in claim 7 nor a claim term in claims 1, 4 or 6 that provides a reasonable antecedent basis for the Bacillus subtilis. As such, an ordinarily skilled artisan cannot determine how to avoid infringement of claim 9.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 10 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 10 depends from claim 7. Claim 7 recites “Engineered bacteria.” An engineered bacterium is understood to be a viable living cell that an ordinarily skilled artisan would recognize to have certain structural characteristics such as a cell membrane, cytoplasm, a chromosome and ribosomes for protein synthesis. Further dependent claim 10 recites an extract or an extracted or isolated enzyme preparation of the engineered bacteria according to claim 7.” Such an extract or isolated enzymes would appear not to be a viable engineered bacteria as recited in claim 7 such that claim 10 omits a requirement for engineered bacterial as recited in claim 7.
Claim 10 is not interpreted as reciting an active method step of using the engineered bacteria as recited in claim 7 (e.g. an active step of lysing the engineered bacteria of claim 7). Rather, at least an “isolated enzyme preparation of the engineered bacteria” is understood as a product-by-process that can be made by other means, such as isolating the appropriate enzymes directly from non-engineered T. thermophilus and Ruminococcus sp. cells. "[E]ven though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process." MPEP 2113(I).
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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.
Claim 5 is 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.
The purpose of the written description requirement is to ensure that the inventor had possession, at the time the invention was made, of the specific subject matter claimed. For a broad generic claim, the specification must provide adequate written description to identify the genus of the claim.
“A written description of an invention involving a chemical genus, like a description of a chemical species, 'requires a precise definition, such as by structure, formula, [or] chemical name,' of the claimed subject matter sufficient to distinguish it from other materials." Fiers, 984 F.2d at 1171, 25 USPQ2d 1601; In re Smythe, 480 F.2d 1376, 1383, 178 USPQ 279, 284985 (CCPA 1973) (“In other cases, particularly but not necessarily, chemical cases, where there is unpredictability in performance of certain species or subcombinations other than those specifically enumerated, one skilled in the art may be found not to have been placed in possession of a genus.”). Regents of the University of California v. Eli Lilly & Co., 119, F.3d 1559, 1568, 43 USPQ2d 1398, 1405 (Fed. Cir. 1997).
“The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice . . ., reduction to drawings . . ., or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus.” MPEP 2163(II)(3)(a).
Furthermore, a “‘representative number of species’ means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus. The disclosure of only one species encompassed within a genus adequately describes a claim directed to that genus only if the disclosure ‘indicates that the patentee has invented species sufficient to constitute the gen[us].’ See Enzo Biochem, 323 F.3d at 966, 63 USPQ2d at 1615; Noelle v. Lederman, 355 F.3d 1343, 1350, 69 USPQ2d 1508, 1514 (Fed. Cir. 2004) (Fed. Cir. 2004) (‘[A] patentee of a biotechnological invention cannot necessarily claim a genus after only describing a limited number of species because there may be unpredictability in the results obtained from species other than those specifically enumerated.’). ‘A patentee will not be deemed to have invented species sufficient to constitute the genus by virtue of having disclosed a single species when … the evidence indicates ordinary artisans could not predict the operability in the invention of any species other than the one disclosed.’ In re Curtis, 354 F.3d 1347, 1358, 69 USPQ2d 1274, 1282 (Fed. Cir. 2004).” MPEP 2163(II)(3)(a).
Claim 5 recites “a nucleotide sequence of the gene is shown in SEQ ID NO: 3” and “a nucleotide sequence of the gene is shown in SEQ ID NO: 4,” encoding glucose isomerase and DPE (D-psicose 3-epimerase), respectively. Recitation of “a nucleotide sequence” with an indefinite article is an indication of a genus of plural sequence that can be any fragment (including as few as two nucleotides) of SEQ ID NO: 3 or 4.
“The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice . . ., reduction to drawings . . ., or by disclosure of relevant, identifying characteristics.” The specification discloses a full-length gene of SEQ ID NO: 3 encoding SEQ ID NO: 1 having glucose isomerase activity and a full-length gene of SEQ ID NO: 4 encoding SEQ ID NO: 2 having DPE activity. The same is not representative of a much more structurally diverse genus of genes having any unlimited fragment of SEQ ID NO: 3 or 4 being a gene encoding glucose isomerase from T. thermophilus or DPE from Ruminococcus sp., nor does the specification discuss relevant, identifying characteristics allowing for identification of such genes. As such, the specification lacks an adequate written description for a genus of genes having any unlimited fragment of SEQ ID NO: 3 or 4 being a gene encoding glucose isomerase from T. thermophilus or DPE from Ruminococcus sp. This rejection can be obviated by amending the claims to recite “a nucleotide sequence of the gene comprises SEQ ID NO: 3” and “a nucleotide sequence of the gene comprises SEQ ID NO: 4.”
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.
Claim(s) 1-4, 6-7, and 10 is/are rejected under 35 U.S.C. 103 as being unpatentable over Men et al. (Co-expression of d-glucose isomerase and d-psicose 3-epimerase:Development of an efficient one-step production of d-psicose, Enz. Microbiol. Technol. 64-64, 2014, 1-5) further in view of Li et al. (Bioconversion of d‑glucose to d‑psicose with immobilized d‑xylose isomerase and d‑psicose 3‑epimerase on Saccharomyces cerevisiae spores, J. Ind. Microbiol. Biotechnol. 42, 2015, 1117-28), and Uniprot, Accession No. G9MBD7, 2022, www.uniprot.org, as evidenced by GenBank, Accession No. ZP_04858451, 2010, www.ncbi.nlm.nih.gov.
Men, abstract, states:
d-Psicose has been attracting attention in recent years because of its alimentary activities and is used as an ingredient in a range of foods and dietary supplements. To develop a one-step enzymatic process of d-psicose production, thermoactive d-glucose isomerase and the d-psicose 3-epimerase obtained from Bacillus sp. and Ruminococcus sp., respectively, were successfully co-expressed in Escherichia coli BL21 strain. The substrate of one-step enzymatic process was d-glucose. The co-expression system exhibited maximum activity at 65 °C and pH 7.0. Mg2+ could enhance the output of d-psicose by 2.32 fold to 1.6 g/L from 10 g/L of d-glucose. When using high-fructose corn syrup (HFCS) as substrate, 135 g/L d-psicose was produced under optimum conditions. The mass ratio of d-glucose, d-fructose, and d-psicose was almost 3.0:2.7:1.0, when the reaction reached equilibrium after an 8 h incubation time. This co-expression system approaching to produce d-psicose has potential application in food and beverage products, especially softdrinks.
“The full-length nucleotide sequence of dpe from Ruminococcus sp. 5 1 39BFAA was synthesized according to the sequence of a “conserved hypothetical protein” (ZP 04858451)” Men, sec. 2.1. GenBank ZP_04858451 evidences that the D-psicose 3-epimerase under discussion is over 98% identical to recited SEQ ID NO: 2.
The above is understood as a disclosure of an enzyme combination comprising glucose isomerase derived from Bacillus sp. and D-psicose 3-epimerse derived from Ruminococcus sp.
However, Men does not teach that the glucose isomerase is derived from Thermus thermophilus and having identity to recited SEQ ID NO: 1.
Li, abstract, teaches:
Saccharomyces cerevisiae spores are dormant cells, which can tolerate various types of environmental stress. In our previous work, we successfully developed biological and chemical methods for enzyme immobilization based on the structures of S. cerevisiae spore wall. In this study, we employed biological and chemical approaches for the immobilization of d-xylose isomerase (XI) from Thermus thermophilus and d-psicose 3-epimerase (DPEase) from Agrobacterium tumefaciens with yeast spores, respectively. The enzymatic properties of both immobilized XI and DPEase were characterized and the immobilized enzymes exhibit higher thermostability, broader pH tolerance, and good repeatability compared with free enzymes. Furthermore, we established a two-step approach for the bioconversion of d-glucose to d-psicose using immobilized enzymes. To improve the conversion yield, a multi-pot strategy was adopted for d-psicose production by repeating the two-step process continually. As a result, the yield of d-psicose was obviously improved and the highest yield reached about 12.0 %.
As shown in Scheme 1 of Li, the T. thermophilus XI catalyzes conversion of D-glucose to D-fructose as to be a glucose isomerase, and will be referenced as a glucose isomerase herein. “The xylA gene encoding XI was amplified by PCR using xylA-F1 and xylA-R2 as primers with the genomic DNA of T. thermophilus strain HB8 as the template purchased from ATCC (Manassas, VA).” Li, page 1119, left col. GenBank G9MBD7 evidences that the xylA gene from T. thermophilus strain HB8 has over 98% identity to recited SEQ ID NO: 1.
Substitution of known elements is obvious upon a finding of:
(1) a finding that the prior art contained a device (method, product, etc.) which differed from the claimed device by the substitution of some components (step, element, etc.) with other components;
(2) a finding that the substituted components and their functions were known in the art;
(3) a finding that one of ordinary skill in the art could have substituted one known element for another, and the results of the substitution would have been predictable; and
(4) whatever additional findings based on the Graham factual inquiries may be necessary, in view of the facts of the case under consideration, to explain a conclusion of obviousness. (MPEP 2143(I)(B)).
Here, (1) Men teaches an enzyme composition comprising glucose isomerase and D-psicose 3-epimerase from Ruminococcus sp. which differs from claim 1 by substitution of glucose isomerase for glucose isomerase from T. thermophilus. (2) The use of other thermophilic glucose isomerases for conversion of glucose to fructose to support further conversion to psicose are known in the prior art. In particularly, Li, as discussed above, Li teaches a xylose/glucose isomerase from T. thermophilus with over 98% identity to recited SEQ ID NO: 1 suitable for use in a system for D-psicose production. (3) An ordinarily skilled artisan could have substituted expression of such xylose/glucose isomerase from T. thermophilus with over 98% identity to recited SEQ ID NO: 1 in replacement of the glucose isomerase taught by Men with a reasonable expectation in success in obtaining an enzyme combination of glucose isomerase from T. thermophilus and D-psoicose-3-epimerase from Ruminococcus sp. (4) No other particular findings are needed to explain a conclusion of obviousness.
As such, in view of the guidance of MPEP 2143(I)(B), an ordinarily skilled artisan at time of filing would have been motivated to substitute a xylose/glucose isomerase from T. thermophilus with over 98% identity to recited SEQ ID NO: 1 as taught by Li in replacement of the glucose isomerase taught by Men to reach the features of claims 1-3.
Regarding claims 4, 6 and 7, sec. 2.1 of Men explains “The plasmid pCDFDuet-1 was used as the co-expression vector.” That is, both genes (a nucleic acid combination) encoding glucose isomerase and D-psicose-3-epimerase, respectively, are inserted cloned into the same backbone vector (pCDFDuet-1). “The recombinant plasmid pCDFDuet-1-RDPE-BGI was transformed into E. coliBL21 (DE3).” Men, sec. 2.2. That is, the backbone vector having the nucleic acid combination is transformed/inserted into engineered bacteria (a colony and LB medium culture further described in sec. 2.2 of Men being plural engineered bacteria). In employing a combination of xylose/glucose isomerase from T. thermophilus and D-psicose 3-epimerase from Ruminococcus as discussed above, an ordinarily skilled artisan at time of filing would have been motivated to utilize the same procedures (except with the nucleic acid/gene for glucose/xylose isomerase substituted as discussed above), which reaches the features of claims 4, 6 and 7.
Regarding claim 10, from Men:
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The glucose isomerase (BGI) and (RDPE) psicose-3-epimerase enzymes are an isolated enzyme preparation from engineered bacteria as discussed above. As discussed above, the cited prior art suggests an engineered bacteria expressing the combination of T. thermophilus glucose isomerase and Ruminococcus sp. D-psicose-3-epimerase. Upon formation of a purified enzyme composition produced therefrom (composition of T. thermophilus glucose isomerase and Ruminococcus sp. D-psicose-3-epimerase), Men teaches that D-psicose is advantageous obtained by catalyzing an reaction of glucose substrate using such an appropriate enzyme composition (e.g. composition of T. thermophilus glucose isomerase and Ruminococcus sp. D-psicose-3-epimerase) such that an ordinarily skilled artisan at time of filing would have been motivated to do the same to reach the features of claim 10.
Claim(s) 1-4, 6-7, 10 and 12 is/are rejected under 35 U.S.C. 103 as being unpatentable over Men et al. (Co-expression of d-glucose isomerase and d-psicose 3-epimerase:Development of an efficient one-step production of d-psicose, Enz. Microbiol. Technol. 64-64, 2014, 1-5) further in view of Li et al. (Bioconversion of d‑glucose to d‑psicose with immobilized d‑xylose isomerase and d‑psicose 3‑epimerase on Saccharomyces cerevisiae spores, J. Ind. Microbiol. Biotechnol. 42, 2015, 1117-28), and Uniprot, Accession No. G9MBD7, 2022, www.uniprot.org, and as evidenced by GenBank, Accession No. ZP_04858451, 2010, www.ncbi.nlm.nih.gov as applied to claims 1-4, 6-7, and 10 above, and further in view of Dou et al. (U.S. 2020/0062792 A1).
Regarding claim 12, Men, sec. 3.2, explains “Compared with isolated enzymes, whole cell catalysts can be much more readily and inexpensively prepared; the purification costs associated with the purchase of an enzyme are not paid for. The enzymes in cells are protected from the external environments; they are generally more stable in the long-term than free enzymes. In particular, microbial cells are most commonly used for industrial purposes because of their diversity and ease of handling.” Fig. 2 of Men appears to show cells expressing a glucose/xylose isomerase and D-psicose 3-epimerase used to produce D-psicose.
“SDS-PAGE analyses of the extracts of E. coli BL21 harboring pCDFDuet-1-RDPE-BGI indicated the presence of large amounts of two proteins approximately 34 and 42 kDa (the approximate molecular weights of RDPE and BGI).” Men, sec 3.1. Fig. 1b of Men shows “supernatant (pCDFDuet-1-RDPE-BGI).”
That is, Men teach that purified enzymes need not be used for conversion of glucose to psicose. In addition to whole cell catalysis, Men describes an extract of the recombinant cell expression the glucose isomerase and psicose 3-epimerse. Just as Men teaches that a whole cell catalyst can be employed, an ordinarily skilled artisan at the time of filing would have recognized that the “extract” (i.e. crude enzyme preparation) can be used to convert glucose to psicose as far as both contain active isomerase and epimerase enzymes having activity for the same. An ordinarily skilled artisan at time of filing would have been motivated to substitute purified enzymes for either whole cells or a crude enzyme preparation to avoid the costs of purification as taught by Men. As discussed, the prior art as cited motivates production of a recombinant bacterium expressing T. thermophilus glucose isomerase and Ruminococcus sp. D-psicose-3-epimerase as discussed extensively above.
As discussed above, any engineered bacterial cell expressing the desired enzymes (including T. thermophilus glucose isomerase and Ruminococcus sp. D-psicose-3-epimerase) is to be fermented and cultured wherein any “extract” is necessarily obtained by disruption to obtain a crude enzyme preparation containing T. thermophilus glucose isomerase and Ruminococcus sp. D-psicose-3-epimerase, see “supernatant” described in Fig. 1b of Men. Expression of enzymes by fermenting and culturing is discussed in sec. 2.2 of Men. As discussed, Men, sec. 3.1, directly discuses production of extracts that is understood as a description of disruption to obtain a crude enzyme preparation being the supernatant in Fig. 1b of Men.
As discussed above, Men, sec 2.6, appears to set forth that whatever composition contains the isomerase and epimerase enzymes is contacted with glucose substrate to obtain D-psicose. Upon substitution of a crude extract containing T. thermophilus glucose isomerase and Ruminococcus sp. D-psicose-3-epimerase, the same is adding glucose substrate to such a crude enzyme preparation to produce D-psicose. The specification, page 12, appears to describe invert syrup as containing fructose, glucose and psicose. As shown in Scheme 1 of Li, fructose is an intermediate and as far as the reaction does not go to completion a product that is a mixture of glucose, fructose and psicose (invert syrup) is expected as explicitly shown in Fig. 6 of Men.
Regarding the final paragraph of claim 12, Men, sec. 2.6, describes confirmation of D-psicose produced by HPLC analysis. Men does not discuss particular methods for preparative isolation of psicose from a reaction mixture, although the purpose of Men of D-psicose for application in food and beverage products that would necessarily require recovery of D-psicose.
Isolation of D-psicose product by action of a D-psicose 3-epimerase is well-established in the prior art. Dou, abstract, teaches:
A method for preparing high-purity D-psicose, comprising the following steps: (1) centrifuging a fermentation broth of Bacillus subtilis, and then subjecting the bacteria to homogenization to obtain a mixed solution containing D-psicose 3-epimerase; (2) preparing a fructose solution, adding the mixed solution containing D-psicose 3-epimerase to the fructose solution, adjusting the pH, adding cobalt chloride thereto, and performing the reaction at a certain temperature; and feeding the fructose solution to the reaction solution, continuing the reaction, and stopping the reaction, obtaining a crude D-psicose solution; and (3) subjecting the crude D-psicose solution to decolorization, filtration, ion exchange [i.e. purifying], chromatographic separation, concentration, and then crystallization or drying, obtaining D-psicose.
That is, Dou teaches purification of D-psicose from a fermentation broth by sequentially filtering, purifying (ion exchange), chromatographically separating and concentrating. Dou does not teach that mixture to be subject to purification contains an E. coli lysate, D-psicose 3-epimerse or specifically glucose in addition to fructose. Regardless, an ordinarily skilled artisan at time of filing would have recognized that the procedure of sequentially filtering, purifying (ion exchange), chromatographically separating and concentrating is an appropriate methodology to recovery preparative amounts of D-psicose from any complex mixture from which it is advantageous to recover D-psicose. In particular, Man, Fig. 6, shows that HPLC chromatography is sufficient to separate glycose, fructose and psicose. As such, at the time of filing an ordinarily skilled artisan at time of filing would have been motivated to apply the procedure of sequentially filtering, purifying (ion exchange), chromatographically separating and concentrating to any reaction mixture containing a mixture of glucose, fructose and psicose (i.e. invert syrup) produced by application of T. thermophilus glucose isomerase and Ruminococcus sp. D-psicose-3-epimerase (as discussed above) to a glucose substrate to achieve the benefit of recovery of D-psicose that can be applied to food and beverage products or other applications.
Regarding recitation at end of claim 12 of “to separately obtain the D-psicose and fructose,” again, Men, Fig. 6 shows separation of D-fructose and D-psicose by HPLC. As far as fructose is a valuable product wherein unreacted fructose can be applied to further psicose production, an ordinarily skilled artisan would have been motivated to separately separate and collect any unreacted D-fructose and D-psicose in the chromatography step that can then be concentrated and stored for future use. That is, the chromatographic separations as taught in the prior art are understood as being able to separate glucose, fructose and psicose into separate products.
Claim(s) 1-4, 6-10 and 12 is/are rejected under 35 U.S.C. 103 as being unpatentable over Men et al. (Co-expression of d-glucose isomerase and d-psicose 3-epimerase:Development of an efficient one-step production of d-psicose, Enz. Microbiol. Technol. 64-64, 2014, 1-5) further in view of Li et al. (Bioconversion of d‑glucose to d‑psicose with immobilized d‑xylose isomerase and d‑psicose 3‑epimerase on Saccharomyces cerevisiae spores, J. Ind. Microbiol. Biotechnol. 42, 2015, 1117-28), Uniprot, Accession No. G9MBD7, 2022, www.uniprot.org, and Dou et al. (U.S. 2020/0062792 A1) and as evidenced by GenBank, Accession No. ZP_04858451, 2010, www.ncbi.nlm.nih.gov as applied to claims 1-4, 6-7, 10 and 12 above, and further in view of Zhao et al. (Efficient biosynthesis of D-allulose in Bacillus subtilis through D-psicose 3-epimerase translation modification, Int. J. Biol. Macromol. 187, 2021, 1-8).
Regarding claim 8, as discussed, Men teaches an E. coli host for expression of glucose isomerase and D-psicose-3-epimerase. However, an ordinarily skilled artisan at time of filing would have understood that other bacterial expression system for expression of heterologous proteins are known in the prior art. For example, Dou teaches “In the invention, a recombinant expression plasmid pMA5-RDPE was reconstructed by using the D-psicose 3-epimerase gene rdpe from Ruminococcus sp. 5_1_39B_FAA, and Bacillus subtilis was transformed with the recombinant expression plasmid, thereby achieving the constitutive secretion and expression of RDPE in the Bacillus subtilis.” Dou, para. [0004]. As such, Dou teaches that B. subtilis can be used to express a Ruminococcus DPE (D-psicose 3-epimerase).
Zhao, abstract, teaches: “The combined catalysis of glucose isomerase (GI) and D-psicose 3-epimerase (DPEase) provided a convenient route for the direct synthesis of D-allulose from D-glucose, whose cost is lower than D-fructose. In the present research, the weak activity of DPEase was the key rate-limiting step and resulted in the accumulation of D-fructose in engineered Bacillus subtilis.” Zhao, sections 2.2 and 2.4, describe cloning of both DPEase and GI gene into the same plasmid pMA5-gi-dpe and transformed into B. subtilis for use as a whole cell catalyst.”
D-allulose is a synonym for D-psicose in the art.
Substitution of known elements is obvious upon a finding of:
(1) a finding that the prior art contained a device (method, product, etc.) which differed from the claimed device by the substitution of some components (step, element, etc.) with other components;
(2) a finding that the substituted components and their functions were known in the art;
(3) a finding that one of ordinary skill in the art could have substituted one known element for another, and the results of the substitution would have been predictable; and
(4) whatever additional findings based on the Graham factual inquiries may be necessary, in view of the facts of the case under consideration, to explain a conclusion of obviousness. (MPEP 2143(I)(B)).
Here, (1) at least Men generally teaches the co-expression of DPE and glucose isomerase in an E. coli host cell. (2) Dou teaches that use of a B. subtilis host cell is known for the expression of at least DPE from a Ruminococcus sp. and Zhao exemplifies both a DPE gene and a glucose isomerase gene coexpressed from the same vector in an engineered B. subtilis. Dou does not exemplify co-expression of a glucose isomerase and DPE in an engineered B. subtilis; however, the same is exemplified by Zhao. (3) As such, an ordinarily skilled artisan at time of filing would have had a reasonable expectation in success in expressing a T. thermophilus glucose isomerase and a Ruminococcus sp. DPE gene in an engineered B. subtilis. As such, an ordinarily skilled artisan at time of filing could have utilized the pMA5 plasmid described by Dou and Zhao to express genes (i.e. combination of nucleic acids) encoding a glucose isomerase from T. thermophilus and D-psoicose-3-epimerase from Ruminococcus sp., as discussed above, with a predictable expectation of expressing both of these enzymes.
As such, in view of MPEP 2143(I)(B), an ordinarily skilled artisan at time of filing would have been motivated to substitute a genetically engineered B. subtilis in replacement for a genetically engineered E. coli for expression of a glucose isomerase from T. thermophilus and D-psoicose-3-epimerase from Ruminococcus sp. as discussed above.
Regarding claim 9, in further of the above discussion, the plasmid pMA5 taught by Dou is a backbone vector. Men, Fig. 1, shows that when two genes are to be expressed (encoding a glucose isomerase and DPE) then both genes are connected to a backbone vector to obtain a recombinant vector. Further, Zhao, sec. 2.2, teaches that when DPE and xylose isomerase are to be expressed in the same B. subtilis host cell, genes/nucleic acids encoding the same are cloned into the same backbone expression vector, “pMA5-gi-dpe plasmid.” In practicing claim 8 as discussed above, in view of the teachings of Zhao and Duo, appropriate combination of nucleic acids/genes encoding a glucose isomerase from T. thermophilus and D-psicose-3-epimerase from Ruminococcus sp. would be connected to an appropriate backbone vector and transformed into a B. subtilis host to obtain engineered bacteria for expression.
Claim(s) 1-10 and 12 (all pending claims) is/are rejected under 35 U.S.C. 103 as being unpatentable over Men et al. (Co-expression of d-glucose isomerase and d-psicose 3-epimerase:Development of an efficient one-step production of d-psicose, Enz. Microbiol. Technol. 64-64, 2014, 1-5) , Li et al. (Bioconversion of d‑glucose to d‑psicose with immobilized d‑xylose isomerase and d‑psicose 3‑epimerase on Saccharomyces cerevisiae spores, J. Ind. Microbiol. Biotechnol. 42, 2015, 1117-28), Uniprot, Accession No. G9MBD7, 2022, www.uniprot.org, Dou et al. (U.S. 2020/0062792 A1) and Zhao et al. (Efficient biosynthesis of D-allulose in Bacillus subtilis through D-psicose 3-epimerase translation modification, Int. J. Biol. Macromol. 187, 2021, 1-8) as evidenced by GenBank, Accession No. ZP_04858451, 2010, www.ncbi.nlm.nih.gov as applied to claims 1-4 and 6-10 above, and further in view of Venkitasubramanian et al. (U.S. 2018/0112244 A1), GenBank, Accession No. NZ_GG696059.1, 2013, www.ncbi.nlm.gov and GenBank, Accession No. AB677526.1, 2022, www.ncbi.nlm.gov.
Regarding claim 5, Venkitasubramanian, abstract, teaches:
Disclosed herein are three genes of proteins herein established to exhibit a fructose to allulose [i.e. psicose] epimerase activity that are useful for production of allulose from fructose at high temperatures and at low pH in the range of 4.5 to 6.0.
“The P. cichorii epimerase enzyme, according to SEQ ID NO: 176 was additionally codon optimized using codon optimization software, many of which are commonly known in the art to express FA epimerase activity in the B. subtilis expression system.” Venkitasubramanian, para. [0254].
As such, it is well established in the prior art to codon optimize a gene, and a particularly a psicose epimerase gene, in order to benefit heterologous expression in a B. subtilis engineered host cell. Allulose and D-psicose are synonyms in the art. As such, at the time of filing, an ordinarily skilled artisan would have been motivated to codon optimize any heterologous gene for expression in B. subtilis engineered cell as discussed above including not only a nucleic acid encoding DPE but also any combination of nucleic acid being Ruminococcus DPE and T. thermophilus glucose isomerase in order to achieve the benefit of better protein expression in an engineered B. subtilis as discussed extensively above.
As discussed, GenBank, Accession No. ZP_04858451, 2010, www.ncbi.nlm.nih.gov, evidences the amino acid sequence of the Ruminococcus DPE enzyme discussed above. This GenBank record indicates that the encoding gene is "NZ_GG696059.1:45199..46074," wherein an alignment of the same to recited SEQ ID NO: 4 is as follows:
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Due to the extensive homology between a wild-type gene/nucleic acid sequence encoding Ruminococcus sp. DPE and SEQ ID NO: 4, any codon optimization of the same would result in a gene having a nucleotide sequence that is a fragment of SEQ ID NO: 4 including but not limiting to ATG encoding a start methionine as to be a nucleotide sequence of the gene shown in SEQ ID NO: 4.
As discussed above, the amino acid sequence of the discussed glucose/xylose isomerase from T. thermophilus strain HB8 is evidenced by Uniprot G9MBD7. The same amino acid sequence is encoded by GenBank AB677526.1:73632..74795 (AB677526.1 referenced in Uniprot G9MBD7) as the wild-type gene sequence from T. thermophilus strain HB8, having an alignment with recited SEQ ID NO: 3 as follows:
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Due to the extensive homology between a wild-type gene/nucleic acid sequence encoding T. thermophilus glucose/xylose isomerase and SEQ ID NO: 3, any codon optimization of the same would result in a gene having a nucleotide sequence that contains a fragment of SEQ ID NO: 3 as to be a nucleotide sequence of the gene shown in SEQ ID NO: 3.
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 1-10 and 12 (all pending claims) are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-11 of copending Application No. 19/041,885 in view of Men et al. (Co-expression of d-glucose isomerase and d-psicose 3-epimerase:Development of an efficient one-step production of d-psicose, Enz. Microbiol. Technol. 64-64, 2014, 1-5), Li et al. (Bioconversion of d‑glucose to d‑psicose with immobilized d‑xylose isomerase and d‑psicose 3‑epimerase on Saccharomyces cerevisiae spores, J. Ind. Microbiol. Biotechnol. 42, 2015, 1117-28), Uniprot, Accession No. G9MBD7, 2022, www.uniprot.org, Zhao et al. (Efficient biosynthesis of D-allulose in Bacillus subtilis through D-psicose 3-epimerase translation modification, Int. J. Biol. Macromol. 187, 2021, 1-8) and Dou et al. (U.S. 2020/0062792 A1) as evidenced by GenBank, Accession No. ZP_04858451, 2010, www.ncbi.nlm.nih.gov.
Copending claims 1-3 recite:
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The Sequence Identifiers between applications are the same. As such, the “crude enzyme preparation” in copending claim 1 anticipates claims 1-5 wherein the genes recited in claim 1 are a combination of nucleic acids.
Copending claim 10 recites a single composite engineered bacteria being Bacillus subtilis expressing both T. thermophilus glucose isomerase and Ruminococcus sp. DPE. The rejections under 35 U.S.C. 103 set forth above are incorporated herein by record in view of Men et al. (Co-expression of d-glucose isomerase and d-psicose 3-epimerase:Development of an efficient one-step production of d-psicose, Enz. Microbiol. Technol. 64-64, 2014, 1-5), Li et al. (Bioconversion of d‑glucose to d‑psicose with immobilized d‑xylose isomerase and d‑psicose 3‑epimerase on Saccharomyces cerevisiae spores, J. Ind. Microbiol. Biotechnol. 42, 2015, 1117-28), Uniprot, Accession No. G9MBD7, 2022, www.uniprot.org, Zhao et al. (Efficient biosynthesis of D-allulose in Bacillus subtilis through D-psicose 3-epimerase translation modification, Int. J. Biol. Macromol. 187, 2021, 1-8) and Dou et al. (U.S. 2020/0062792 A1) as evidenced by GenBank, Accession No. ZP_04858451, 2010, www.ncbi.nlm.nih.gov. The reasons one having ordinarily skill in the art at the time of filing would have produced an expression vector as recited in claim 6 and employed the same to meet the features of claims 7-10 and 12 (wherein claims 7 and 8 are an embodiment of copending claim 10) are set forth in the rejections above.
This is a provisional nonstatutory double patenting rejection.
Conclusion
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/TODD M EPSTEIN/Primary Examiner, Art Unit 1652
