DETAILED CORRESPONDENCE
Status of the Application
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 1-19 are pending.
Election
Applicant’s election with traverse of
Group I, claims 1-6, 10 and 12-16, drawn to the technical feature of a transformant obtained by introducing a cellulase gene and a cell surface protein gene into a cellulose-synthesizing microorganism, and
Species A2) an endoglucanase gene with the sequence limitations set forth in claim 14, wherein the endoglucanase gene is at least one DNA selected from the group consisting of the following (1) to (6): (1) DNA consisting of a base sequence of SEQ ID NO: 6; (2) DNA encoding a protein that has not less than 90% homology to the base sequence of SEQ ID NO: 6 and that has endoglucanase activity; (3) DNA (i) hybridizing, under a stringent condition, with a gene consisting of the base sequence of SEQ ID NO: 6 and (ii) encoding a protein that has endoglucanase activity; (4) DNA encoding a polypeptide consisting of an amino acid sequence of SEQ ID NO: 12; (5) DNA encoding a protein that has not less than 90% identity to the amino acid sequence of SEQ ID NO: 12 and that has endoglucanase activity; and (6) DNA encoding a protein (i) consisting of an amino acid sequence in which at least one amino acid is deleted, substituted, inserted, or added in the amino acid sequence of SEQ ID NO: 12 and (ii) having endoglucanase activity
in the reply filed 07/31/2026 is acknowledged. The traversal is on the grounds that restriction is only proper as the claims are independent and patentably distinct and there would be a serious burden placed on the examiner if restriction is not required as stated in MPEP 803, and that the Examiner has not provided any indication that the content of the claims interpreted in light of the description was considered in making the assertion of a lack of unity. Applicant contends there is a technical relationship among Groups I-IV that involves the same special technical feature. Applicant further contends there is no serious burden on the office.
Applicant’s arguments are considered and found not convincing. As outlined in the Office action mailed 06/10/2026, the restriction is made based on Lack of Unity, and is required under 35 USC 121 and 372, as the application contains the inventions or groups of inventions which are not so linked as to form a single general inventive concept under PCT Rule 13.1. Search burden, as cited by Applicant in MPEP 803, is not a criteria for restrictions made based on Lack of Unity. MPEP 1893.03(d) states when making a lack of unity requirement, the examiner must (1) list the different groups of claims and (2) explain why each group lacks unity with each other group (i.e., why there is no single general inventive concept) specifically describing the unique special technical feature in each group. Each group was compared in the previous Office action to state why each group lacks unity with each other, and the unique special technical feature of each group was specifically described. Groups I, III and IV were described to have the shared technical feature of a transformant obtained by introducing a cellulase gene and a cell surface protein gene into a cellulose-synthesizing microorganism, which is not a special technical feature as it is not contributing over the prior art. Group II does not recite this shared technical feature with the other Groups, as Group II does not require the introduction of a cellulase gene as stated in the section describing lack of a shared technical feature among Groups I and II.
While Applicant asserts there is a shared technical feature among Groups I-IV that is a contribution over the prior art, Applicant has not stated what this shared technical feature is. Considering Applicant’s statement that there is a shared technical feature among Groups I-IV (in other words, to include Group II into the shared technical feature analysis of Groups I and III-IV set forth in the previous Office action), the shared technical feature would be the broader feature of “a transformant obtained by introducing a cell surface protein gene”, which is not a special technical feature as it does not make a contribution over the prior art in view of Francisco et al. (Nature Biotechnol, 1993, 11:491; cited on the IDS filed 10/07/2024; herein Francisco) which discloses a microorganism containing an exoglucanase and OmpA which is a cell surface protein [abstract], wherein the exoglucanase is understood to be a cellulase. The phrase recited in the technical feature of “a transformant obtained by introducing a cell surface protein gene” is a product-by-process limitation, where the product (e.g., a transformant) is not limited to the manipulations of the steps of the process of making the product (e.g., the introduction of recited genes), but is limited by the structure implied by the steps (MPEP 2113.I). Therefore, the microorganism of Francisco is considered to satisfy all of the structural limitations of the recited transformant. As such, the shared same or corresponding technical feature among Groups I, II, III and IV is not a contribution over the prior art.
The requirement is still deemed proper and is therefore made FINAL.
Claims 7-9, 11 and 17-19 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made with traverse in the reply filed on 07/31/2026.
Claim 13 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made with traverse in the reply filed on 07/31/2026.
Claims 1-6, 10, 12 and 14-16 are being examined on the merits only to the extent they read on the elected subject matter.
Priority
The instant application is a national stage filing under 35 U.S.C. 371 of international application PCT/JP2023/003994, filed 02/07/2023, which claims foreign priority to Japanese Application No. 2022-017356 filed 02/07/2022.
Information Disclosure Statement
The Information Disclosure Statements (IDSs) submitted on 10/07/2024 and 05/29/2026 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the IDSs have been considered by the examiner.
Objections to Specification
The disclosure is objected to because of the following informalities.
The use of the terms NEBUILDER HIFI DNA ASSEMBLY, MAGEXTRACTOR, MCI GEL, PROMINENCE and AMINEX which are trade names or marks used in commerce, have been noted in this application in paragraphs 0064-0066, 0070, 0073, and 0089. The terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever they appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the terms.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code in para 0027. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Appropriate correction is required.
Claim Objections
Claims 10, 14 and 16 are objected to for the phrase “has not less than 90% homology to” in part (2). In the interest of improving claim form, Applicant should consider an amendment to recite “shares not less than 90% identity with”.
Claims 10, 14 and 16 are objected to for the phrase “base sequence” in options (1), (2) and (3) referring to nucleotide sequences. In the interest of improving claim form, Applicant should consider an amendment to recite the phrase “nucleotide sequence”.
Claim 12 is objected to for the phrase “wherein at least one selected from an endoglucanase gene and an exoglucanase gene is contained as the cellulase gene”. In the interest of improving claim form, Applicant should consider an amendment to recite “wherein the cellulase gene comprises one selected from the group consisting of an endoglucanase gene and an exoglucanase gene”.
Claim 15 is objected to for the phrase “wherein a β-galactosidase gene is further contained as the cellulase gene”. In the interest of improving claim form, Applicant should consider an amendment to recite “wherein the cellulase gene further comprises a β-galactosidase gene”.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 10, 14 and 16 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claims 10, 14 and 16 are indefinite for the recitation of “not less than 90% homology to the base sequence of SEQ ID NO” in option (2). As written, the limitation appears to require a polypeptide with 90% or more homology to the base sequence of the recited SEQ ID NO in each of claims 10, 14 and 16, wherein each of the recited SEQ ID NOs are nucleic acid sequences.
Claims 10, 14 and 16 are indefinite for the recitation of “DNA hybridizing, under a stringent condition, with a gene” in option (3), as the specification does not specifically define what conditions constitute “stringent”, but gives examples of what can be considered stringent regarding temperature in [para 0027]. What hybridization conditions are considered "stringent" varies widely in the art depending on the individual situation as well as the person making the determination. As such it is unclear how homologous to SEQ ID NO:1 (claim 10), SEQ ID NO: 6 (claim 14), or SEQ ID NO: 4 (claim 16) a gene sequence must be to be included within the scope of these claims.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
Claim Interpretation: The claims are drawn to a transformant obtained by introducing a cellulase gene and a cell surface protein into a cellulose-synthesizing microorganism. The “a transformant obtained by introducing a cellulase gene and a cell surface protein gene” is a product-by-process limitation, where the product (e.g., a transformant) is not limited to the manipulations of the steps of the process of making the product (e.g., the introduction of recited genes), but is limited by the structure implied by the steps (MPEP 2113.I). Therefore the only structural requirements of the claimed transformant are that it comprises a cellulase gene and a cell surface protein gene, which are considered to encode a cellulase enzyme and a cell surface protein, and the ability to synthesize cellulose. The genes themselves, and therefore the encoded polypeptides, are structurally unlimited. Therefore the claims are drawn to a genus of transformants that comprise a genus of genes that are considered widely variant with respect to structure.
A. Claims 1-6, 10, 12 and 14-16 are rejected under 35 U.S.C. 112(a) 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 at the time the application was filed, had possession of the claimed invention.
MPEP 2163.II.A.2.(a).i) states, “Whether the specification shows that applicant was in possession of the claimed invention is not a single, simple determination, but rather is a factual determination reached by considering a number of factors. Factors to be considered in determining whether there is sufficient evidence of possession include the level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention”.
For claims drawn to a genus, MPEP § 2163 states 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. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406.
According to MPEP 2163.II.A.3.(a).ii), [s]atisfactory 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 factors considered in the Written Description requirement are (1) level of skill and knowledge in the art, (2) partial structure, (3) physical and/or chemical properties, (4) functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the (5) method of making the claimed invention. Disclosure of any combination of such identifying characteristics that distinguish the claimed invention from other materials and would lead one of skill in the art to the conclusion that the applicant was in possession of the claimed species is sufficient." MPEP § 2163.
The claims recite (in relevant part) a genus of transformants comprising a genus of cellulase genes and a genus of cell surface protein genes. As stated above, the genes as well as the encoded cellulases and cell surface proteins are unlimited. In this case, the genus of cellulase genes and cell surface protein genes encompasses species that are considered to be widely variant with respect to sequence.
The specification discloses the following representative species of the genus of transformants comprising the genus of encoded polypeptides:
A Methylorubrum extorquens AM1 transformant comprising oprI (SEQ ID NO: 1), β-glucosidase bglC (SEQ ID NO: 4), endoglucanase cenA (SEQ ID NO: 6), and exoglucanase cex (SEQ ID NO: 5) genes as described in Example 2 [beginning at para 0069].
Regarding the level of skill and knowledge in the art of amino acid modification, the reference of Singh et al. (Curr. Protein Pept. Sci. 18:1-11, 2017; cited on the attached Form PTO-892) reviews various protein engineering methods and discloses that despite the availability of an ever-growing database of protein structures and highly sophisticated computational algorithms, protein engineering is still limited by the incomplete understanding of protein functions, folding, flexibility, and conformational changes [p 7, col 1, top]. Also, the unpredictability associated with residue substitution is exemplified by the reference of Zhang et al. (Structure 26:1474-1485, 2018; cited on the attached Form PTO-892), which discloses that even a substitution of a surface residue that was predicted to be benign caused significant structural changes and unexpected effects on the function of a polypeptide [p 1475, col 1]. Finally, the unpredictability associated with the effect of nucleotide changes in genes encoding proteins on protein structure and function is discussed by Ibrahim et al. (ACE Res J Microbiol Biotechnol. 2021, 1:66; cited on the attached Form PTO-892), which reviews the results of mutations on the DNA level that lead to numerous forms of sequence shift can result in inoperable gene products and prohibition of gene function [p 66, col 1, para 2], and describes the impact of changes in nucleic acid sequences encoding proteins, and states the earlier in the sequence a deletion or insertion in the coding DNA occurs, the more altered the protein amino sequence can be [p 67, col 2, final paragraph].
In view of the high level of unpredictability in the art of nucleic acid sequence and amino acid modification, because the genus of transformants comprising the genus of cellulase and cell surface genes is widely variant with respect to structure, and the specification discloses the actual reduction to practice of only one representative species among a widely variant genus, one of skill in the art would reasonably conclude that the disclosure fails to provide a representative number of species to describe the genus, and thus, that the applicant was not in possession of the recited genus of non-naturally occurring polypeptides. The claimed subject matter is not supported by an adequate written description because a representative number of species has not been described.
B. Claims 1-6, 10, 12 and 14-16 are rejected under 35 U.S.C. 112(a) because the specification, while being enabling for a Methylorubrum extorquens AM1 transformant comprising oprI (SEQ ID NO: 1), β-glucosidase bglC (SEQ ID NO: 4), endoglucanase cenA (SEQ ID NO: 6), and exoglucanase cex (SEQ ID NO: 5) genes, does not reasonably provide enablement for all transformants comprising all encoded polypeptides as encompassed by the claims. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
“The test of enablement is not whether any experimentation is necessary, but whether, if experimentation is necessary, it is undue.” In re Angstadt, 537 F.2d 498, 504, 190 USPQ 214, 219 (CCPA 1976). Factors to be considered in determining whether undue experimentation is required are summarized in In re Wands (858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988)) as follows: (A) The breadth of the claims; (B) The nature of the invention; (C) The state of the prior art; (D) The level of one of ordinary skill; (E) The level of predictability in the art; (F) The amount of direction provided by the inventor; (G) The existence of working examples; and (H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. See MPEP § 2164.01(a). The Factors considered to be most relevant to the instant rejection are addressed in detail below.
The nature of the invention: According to the specification at para 0008, “the inventor of the present invention and others have found that it is possible to produce glucose or cellobiose from a carbon source such as methanol by using a transformant having a cellulase gene and a gene that expresses the cellulase on a cell surface introduced thereinto or a transformant of a bacterium belonging to the family Methylobacteriaceae that has become capable of expressing cellulase on a bacterial cell surface by introduction of an oprI gene”. The object of the invention is therefore to provide a microbial platform to produce glucose or cellobiose from a carbon source such as methanol via genetic engineering to heterologously expressing cellulase on the cell surface.
The breadth of the claims: The claims recite (in relevant part) a transformant obtained by introducing a cellulase gene and a cell surface protein, which are considered to encode cellulase and cell surface protein polypeptides, into a cellulose-synthesizing microorganism. As stated above, the nucleic acid sequences of the genes introduced into the transformant and the amino acid sequences of encoded polypeptides are unlimited.
The state of the prior art; The level of one of ordinary skill; and The level of predictability in the art: According to MPEP 2164.03, “…what is known in the art provides evidence as to the question of predictability” and “[I]f one skilled in the art cannot readily anticipate the effect of a change within the subject matter to which that claimed invention pertains, then there is lack of predictability in the art.”
As stated above, the nucleic acid sequences of the genes introduced into the transformant and the amino acid sequences of the encoded polypeptides are unlimited. The reference of Singh (supra) reviews various protein engineering methods and discloses that despite the availability of an ever-growing database of protein structures and highly sophisticated computational algorithms, protein engineering is still limited by the incomplete understanding of protein functions, folding, flexibility, and conformational changes (see p. 7, column 1, top).
The unpredictability associated with amino acid modification is exemplified by the reference of Zhang (supra) which discloses that even a mutation that was predicted to be benign caused significant structural changes and unexpected effects on the function of a polypeptide (p. 1475, column 1).
The unpredictability associated with the effect of nucleotide changes in genes encoding proteins on protein structure and function is discussed by Ibrahim (supra) which reviews the results of mutations on the DNA level that lead to numerous forms of sequence shift can result in inoperable gene products and prohibition of gene function [p 66, col 1, para 2], and describes the impact of changes in nucleic acid sequences encoding proteins, and states the earlier in the sequence a deletion or insertion in the coding DNA occurs, the more altered the protein amino sequence can be [p 67, col 2, final paragraph].
As such, one of skill in the art would recognize a high level of unpredictability that all genes encoding polypeptides as encompassed by the claims would maintain the desired activity/utility.
The amount of direction provided by the inventor and The existence of working examples: The specification discloses the following working examples of the recited transformant:
A Methylorubrum extorquens AM1 transformant comprising oprI (SEQ ID NO: 1), β-glucosidase bglC (SEQ ID NO: 4), endoglucanase cenA (SEQ ID NO: 6), and exoglucanase cex (SEQ ID NO: 5) genes as described in Example 2 [beginning at para 0069].
Other than this working example, the specification fails to disclose any other transformants comprising a cellulase gene and a cell surface protein.
The quantity of experimentation needed to make or use the invention based on the content of the disclosure: While methods of generating transformant microorganisms and modifying the amino acid sequence of a polypeptide were known at the time of the invention, it was not routine in the art to make and determine a use for all transformants comprising all genes encoding all occurring polypeptides as recited by the claims.
In view of the overly broad scope of the claims, the lack of guidance and working examples provided in the specification, the high level of unpredictability, and the state of the prior art, undue experimentation would be necessary for a skilled artisan to make and use the entire scope of the claimed invention. Applicants have not provided sufficient guidance to enable one of ordinary skill in the art to make and use the claimed invention in a manner reasonably correlated with the scope of the claims. The scope of the claims must bear a reasonable correlation with the scope of enablement (In re Fisher, 166 USPQ 19 24 (CCPA 1970)). Without sufficient guidance, determination of having the desired biological characteristics is unpredictable and the experimentation left to those skilled in the art is unnecessarily, and improperly, extensive and undue. See In re Wands 858 F.2d 731, 8 USPQ2nd 1400 (Fed. Cir, 1988).
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.
Claims 1-2 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more. Applicant’s attention is directed to the "Guidance for Determining Subject Matter Eligibility Of Claims Reciting Or Involving Laws of Nature, Natural Phenomena, & Natural Products”, released on December 16, 2014.
Claim Interpretation: Claims 1-2 are drawn to a transformant obtained by introducing a cellulase gene and a cell surface protein into a cellulose-synthesizing microorganism. The phrase “a transformant obtained by introducing a cellulase gene and a cell surface protein gene” is a product-by-process limitation, where the product (e.g., a transformant) is not limited to the manipulations of the steps of the process of making the product (e.g., the introduction of recited genes), but is limited by the structure implied by the steps (MPEP 2113.I). Therefore the only structural requirements of the claimed transformant are that it comprises a cellulase gene and a cell surface protein gene, which are considered to encode a cellulase enzyme and a cell surface protein, and the ability to synthesize cellulose.
Romling (Res Microbiol, 2002, 153:205; cited on the attached Form PTO-892; herein Romling) discusses cellulose production in bacteria [title] and discloses examples of the bacteria A. tumafaciens and R. leguminosarum which are cellulose synthesizing organisms comprising genes that encode a cellulase from family 8 glucosidase) [p 206, col 2]. Therefore the microorganisms of Romling are considered to correspond to naturally occurring organisms capable of synthesizing cellulose that comprise cellulase genes, and are understood to contain cell surface proteins as evidenced by Filloux et al. (FEMS Microbiol Rev, 2016, 40:161; cited on the attached Form PTO-892; herein Filloux) which discusses bacterial cell surfaces [title], depicts the outer membranes of Gram positive and Gram negative bacteria that comprise proteins on the outer surfaces [Figure 1], and discloses broadly that bacteria assemble complex cell surface structures to achieve a broad range of functions carried out by a variety of complex protein-based structures [p 162, col 1, para 2].
Given a broadest reasonable interpretation, claims 1-2 are directed to a naturally-occurring microorganism such as the microorganism of Romling.
Patent Eligibility Analysis Step 1: The claims are drawn to a composition of matter, which is one of the statutory categories of invention.
Patent Eligibility Analysis Step 2A Prong 1: The claims recite a naturally occurring bacteria, which is considered to be a law of nature or natural phenomena (a natural product). Accordingly, claims 1-2 are directed to a judicial exception.
Patent Eligibility Analysis Step 2A Prong 2: There are no additional elements recited in the claims beyond the judicial exception.
Patent Eligibility Analysis Step 2B: The claims only recite the product of nature, without more and do not include any additional elements that could add significantly more to the judicial exception.
As such, the claims do not qualify as eligible subject matter. For these reasons the claim is rejected under section 101 as being directed to non-statutory subject matter.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1-2 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Gao et al. (Microb Cell Fact, 2015, 14:159; cited on the IDS filed 10/07/2024; herein Gao).
Claim 1 is drawn to a transformant obtained by introducing a cellulase gene and a cell surface protein into a cellulose-synthesizing microorganism.
The limitation “a transformant obtained by introducing a cellulase gene and a cell surface protein gene into a cellulose-synthesizing microorganism” is a product-by-process limitation, where the product (e.g., a transformant) is not limited to the manipulations of the steps of the process of making the product (e.g., the introduction of recited genes), but is limited by the structure implied by the steps (MPEP 2113.I), which are considered to be a transformant comprising a cellulase gene and a cell surface protein.
The term “cellulase” is not specifically defined by the specification, but is described as “not particularly limited, provided that it is capable of decomposing cellulose. Examples of the cellulase include endoglucanase, exoglucanase, β-glucosidase, and the like” [para 0036].
Claim 2 is drawn to the transformant of claim 1, wherein the cellulose-synthesizing microorganism is a cellulose-synthesizing bacterium.
Gao relates to the construction of cellulose-utilizing E. coli based on a secretable cellulase [title], and discusses the use of E. coli as a cell factory for the production of diverse chemicals because it is the best characterized model bacterium with many available expression and regulation tools [p 2, col 1, para 1].
Regarding claims 1-2, Gao discloses an E. coli strain that expresses β-glucosidases on the cell surface using an anchor protein [p 2, col 1, para 1], wherein β-glucosidase is considered to correspond to the recited cellulase gene, and the cell surface anchor protein is considered to correspond to the recited cell surface protein. Additionally, E. coli is understood to be a bacteria. As the microorganism of Gao satisfies all of the structural limitations of the recited transformant, the microorganism of Gao is considered to be a cellulose-synthesizing microorganism, as the functional activity of synthesizing cellulose is presumed to be inherent to the structure of the transformant (MPEP 2112.01.I).
For these reasons, Gao anticipates claims 1-2.
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 point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 3-5 are rejected under 35 U.S.C. 103 as being unpatentable over Gao in view of Delaney et al. (Plos One, 2013, 8:e62957; cited on the IDS filed 10/07/2024; herein Delaney) and evidentiary reference Green et al. (Int J Syst Evol Microbiol, 2018, 68:2727; cited on the attached Form PTO-892; herein Green).
Claim 3 (claims 4-5 dependent therefrom) is drawn to the transformant of claim 2, wherein the cellulose-synthesizing bacterium is a bacterium belonging to the family Methylobacteriaceae.
The teachings of Gao as applied to claims 1-2 are discussed above. Gao does not teach a bacterium belonging to the family Methylobacteriaceae.
Delaney relates to optimized strain and culturing methods for Methylobacterium extorquens [title], and discusses that M. extorquens strains are the best studied methylotrophic model system [abstract].
Regarding claims 3-5, Delaney teaches M. extorquens is a model system for studying growth on C1 compounds, for which a significant number of genetic tools have been developed and multiple genome sequences of strains have been characterized [p 1, col 1, para 1]. The M. extorquens of Delaney is understood to be from the family Methylobacteriaceae and the genus Methylorubrum as evidenced by Green which discloses members of the Methylobacterium genus including M. extorquens were reclassified into the new genus Methylorubrum [abstract].
In view of Delaney, it would have been prima facie obvious for one of ordinary skill in the art before the effective filing date to modify the cell of Gao by using M. extorquens, as taught by Delaney, to arrive at the claimed invention, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the E. coli of Gao and the M. extorquens of Delaney are both bacteria amenable to genetic modification, and as such both are capable of being modified with cellulase genes and cell surface proteins as described by Gao. Thus it would have been obvious to one of ordinary skill in the art to replace the E. coli cell of Gao with M. extorquens cell of Gao, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both Gao and Delaney discuss bacteria that are good model systems and have genetic tools available for their modification.
Therefore, the invention of claims 3-5 would have been obvious to one of ordinary skill in the art before the effective filing date.
Claims 6 and 10 are rejected under 35 U.S.C. 103 as being unpatentable over Gao in view of UniProt Accession No. A0A246FCX0_9PSED (2 pages, 02 June 2021; cited on the attached Form PTO-892; herein UNI1) and evidentiary reference De Vos et al. (J Bacteriol, 1998, 180:6551; cited on the attached Form PTO-892; herein De Vos)
Claim 6 (claim 10 dependent therefrom) is drawn to the transformant of claim 1, wherein the cell surface protein gene is an oprI gene.
The teachings of Gao as applied to claims 1-2 are discussed above. Gao does not teach the cell surface protein gene is an oprI gene.
Regarding claims 6 and 10, UNI1 teaches a protein from Pseudomonas nitroreducens annotated as OprI which shares 98.7% sequence identity with SEQ ID NO: 2 [see Appendix A], wherein OprI is understood to be a cell surface protein as evidenced by De Vos which discloses oprI is the gene coding for the major outer membrane lipoprotein I in Pseudomonads [abstract]. Option (6) of claim 10 states the oprI gene is DNA encoding a polypeptide (i) consisting of an amino acid sequence in which at least one amino acid is deleted, substituted, inserted, or added in the amino acid sequence of SEQ ID NO: 2 and (ii) being a cell surface protein. As there is no upper bound for the number of amino acids that are deleted, substituted, inserted, or added in the amino acid sequence of SEQ ID NO: 2, the protein satisfies the structural requirements of claim 10.
In view of UNI1, it would have been prima facie obvious for one of ordinary skill in the art before the effective filing date to modify the cell of Gao by using the protein of UNI1 to arrive at the claimed invention, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the cell surface anchor protein of Gao and the protein of UNI1 are both cell surface proteins, and as such both are capable of being incorporated into cells as described by Gao. Thus, it would have been obvious to one of ordinary skill in the art to replace the cell surface anchor protein of Gao with the Opr1 protein of UNI1, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because Gao and UNI1 relate to cell surface proteins.
Therefore, the invention of claims 6 and 10 would have been obvious to one of ordinary skill in the art before the effective filing date.
Claims 12 and 14-15 are rejected under 35 U.S.C. 103 as being unpatentable over Gao in view of UniProt Accession No. F4GZY2_CELFA (2 pages, 02 June 2021; cited on the attached Form PTO-892; herein UNI2).
Claim 12 (claims 14-15 dependent therefrom) is drawn to the transformant of claim 1, wherein at least one selected from an endoglucanase gene and an exoglucanase gene is contained as the cellulase gene.
The teachings of Gao as applied to claims 1-2 are discussed above. Gao does not teach at least one selected from an endoglucanase gene and an exoglucanase gene is contained as the cellulase gene.
Regarding claim 12, Gao teaches the construction of the transformant E. coli discussed in the rejection above as an attempt to develop an E. coli strain to degrade cellulose for the capability of producing chemicals and fuels at relatively low cost from plant biomass comprising cellulase [p 2, col 1, para 1]. Gao teaches that during the degradation of plant bio-mass, endo-glucanase attacks cellulose and produces shorter oligosaccharides, while exo-glucanase acts on the ends of cellulose to produce cellobiose, wherein cellobiose is degraded by β-glucosidase into glucose, and that incorporating enzyme generation, biomass degradation and product production into a single organism through engineering could potentially avoid the cost of generating enzymes in the process of using cellulose [p 1, col 2, para 1].
Regarding claim 12, UNI2 teaches a glucanase protein that shares 100% identity with SEQ ID NO: 12 [see Appendix B]. As the glucanase of UNI2 is annotated as a cellobiohydrolase, it is considered to be an endoglucanase.
In view of Gao and UNI2, it would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to modify the cell of Gao by incorporating the glucanase of UNI1 to arrive at the claimed invention. One of ordinary skill in the art would have been motivated to modify the cell of Gao because Gao teaches incorporating the generation of cellulase enzymes, biomass degradation and product production into a single organism through engineering could potentially avoid the cost of generating enzymes in the process of using cellulose to produce chemicals and fuels at a low cost. One of ordinary skill in the art would have had a reasonable expectation of success because Gao teaches a system of producing multiple cellulase enzymes in a single organism including endoglucanase, and UNI2 teaches an endoglucanase.
Regarding claim 14, option (6) of claim 14 states the endoglucanase gene is DNA encoding a polypeptide (i) consisting of an amino acid sequence in which at least one amino acid is deleted, substituted, inserted, or added in the amino acid sequence of SEQ ID NO: 12 and (ii) has endoglucanase activity. As there is no upper bound for the number of amino acids that are deleted, substituted, inserted, or added in the amino acid sequence of SEQ ID NO: 12, and the glucanase of UNI2 shares 100% identity with SEQ ID NO: 2, the glucanase of UNI2 satisfies the structural requirements of claim 14.
Regarding claim 15, Gao teaches the incorporation of β-glucosidase into E. coli [p 2, col 1, para 1]. Therefore, the invention of claims 12 and 14-15 would have been obvious to one of ordinary skill in the art before the effective filing date.
Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over Gao in view of UNI2 as applied to claims 1-2, 12 and 14-15 above, and further in view of WO 2015/030171 A1 (reference is made to a machine translation; cited on the attached Form PTO-892; herein Nagoya).
Claim 16 is drawn to the transformant of claim 15, wherein the β-glucosidase gene is at least one DNA selected from the group consisting of:
DNA consisting of a base sequence of SEQ ID NO: 4;
DNA encoding a protein that has not less than 90% homology to the base sequence of SEQ ID NO: 4 and that has β-glucosidase activity;
DNA (i) hybridizing, under a stringent condition, with a gene consisting of the base sequence of SEQ ID NO: 4 and (ii) encoding a protein that has β-glucosidase activity;
DNA encoding a polypeptide consisting of an amino acid sequence of SEQ ID NO: 10;
DNA encoding a protein that has not less than 90% identity to the amino acid sequence of SEQ ID NO: 10 and that has β-glucosidase activity;
DNA encoding a protein (i) consisting of an amino acid sequence in which at least one amino acid is deleted, substituted, inserted, or added int the amino acid sequence of SEQ ID NO: 10 and (ii) having β-glucosidase activity.
Regarding claim 16, Nagoya teaches microorganism expressing on the cell surface a functional fiber formed by fusing a functional molecule comprising a peptide, wherein the functional molecule is a β-glucosidase [p 3, final paragraph], and wherein the β-glucosidase is a β-glucosidase derived from Thermobifida fusca with a sequence of SEQ ID NO: 10 [p 6, following paragraph 1] which shares 99.8% sequence identity with SEQ ID NO: 10 of the instant application [see Appendix C]. Option (6) of claim 16 states the β-glucosidase gene is DNA encoding a polypeptide (i) consisting of an amino acid sequence in which at least one amino acid is deleted, substituted, inserted, or added in the amino acid sequence of SEQ ID NO: 10 and (ii) has β-glucosidase activity. As there is no upper bound for the number of amino acids that are deleted, substituted, inserted, or added in the amino acid sequence of SEQ ID NO: 10, the β-glucosidase of Nagoya satisfies the structural requirements of claim 16.
In view of Nagoya, it would have been prima facie obvious for one of ordinary skill in the art before the effective filing date to modify the combined cell of Gao and UNI2 by using the β-glucosidase of Nagoya to arrive at the claimed invention, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the β-glucosidase of Gao and the β-glucosidase of Nagoya are both β-glucosidase enzymes, and as such both are capable of being incorporated into cells as described by Gao. Thus it would have been obvious to one of ordinary skill in the art to replace the β-glucosidase of Gao with the β-glucosidase of Nagoya, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because Gao and Nagoya relate to cells expressing β-glucosidase.
Therefore, the invention of claim 16 would have been obvious to one of ordinary skill in the art before the effective filing date.
Conclusion
Status of the Application:
Claims 1-19 are pending.
Claims 7-9, 11, 13 and 17-19 are withdrawn.
Claims 1-6, 10, 12 and 14-16 are rejected.
No claim is in condition for allowance.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JOSEPH SPANGLER whose telephone number is (571)270-0314. The examiner can normally be reached M-F 7:30 am - 4:30 pm.
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/JOSEPH R SPANGLER/
Examiner
Art Unit 1656
/David Steadman/Primary Examiner, Art Unit 1656
APPENDIX A
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Sequence alignment of SEQ ID NO: 2 with UNI1.
APPENDIX B
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Sequence alignment of SEQ ID NO: 21 with UNI2
APPENDIX C
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Sequence alignment of instant SEQ ID NO: 10 with SEQ ID NO: 10 of WO 2015/030171
Prosecution Insights