DETAILED CORRESPONDENCE
Application Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
2. Claims 1-20 are pending.
Election/Restrictions
3. Applicant’s election without traverse of Group I, claims 1-13 in the reply filed on 08/03/2026 is acknowledged.
4. Claims 14-20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 without traverse in the reply filed on 08/03/2026.
Claims 1-13 are pending and examined on the merits.
Priority
5. Acknowledgement is made of applicants’ claimed domestic priority to U.S. Provisional Application No. 63/177088, filed on 04/20/2021.
Information Disclosure Statement
6. The IDS filed on 01/18/2024 has been considered by the examiner and a copy of the Form PTO/SB/08 is attached to the office action.
Drawings
7. The Drawings filed on 10/20/2023 are acknowledged and accepted by the examiner.
Specification
8. The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. 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. In the instant case, paragraph 0052 of the specification as filed contains an embedded hyperlink.
Claim Interpretation
9. The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
10. The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
The specification in paragraphs 0055 discloses “[t]he means for conditional expression of a heterologous protein may include for example a plasmid. However, certainly any means of providing to the microorganism the ability to conditional express a protein heterologous to the microorganism are encompassed by the invention.”
Claim Rejections - 35 USC § 112
11. 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.
12. Claims 1-13 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 limitation “means for” invokes 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. The specification recites “[t]he means for conditional expression of a heterologous protein may include for example a plasmid. However, certainly any means of providing to the microorganism the ability to conditional express a protein heterologous to the microorganism are encompassed by the invention”; however, the specification does not provide any kind of structure or elements of what is encompassed by “any means”. MPEP 2181.II.A states “[i]f there is no disclosure of structure, material or acts for performing the recited function, the claim fails to satisfy the requirements of 35 U.S.C. 112(b). The disclosure of the structure (or material or acts) may be implicit or inherent in the specification if it would have been clear to those skilled in the art what structure (or material or acts) corresponds to the means- (or step-) plus-function claim limitation. See id. at 1380, 53 USPQ2d at 1229; In re Dossel, 115 F.3d 942, 946-47, 42 USPQ2d 1881, 1885 (Fed. Cir. 1997). However, "[a] bare statement that known techniques or methods can be used does not disclose structure" in the context of a means plus function limitation. Biomedino, LLC v. Waters Technology Corp., 490 F.3d 946, 952, 83 USPQ2d 1118, 1123 (Fed. Cir. 2007) (Disclosure that an invention "may be controlled by known differential pressure, valving and control equipment" was not a disclosure of any structure corresponding to the claimed "control means for operating [a] valving " and the claim was held indefinite). See also Budde v. Harley-Davidson, Inc., 250 F.3d 1369, 1376, 58 USPQ2d 1801, 1806 (Fed. Cir. 2001); Cardiac Pacemakers, Inc. v. St. Jude Med., Inc., 296 F.3d 1106, 1115-18, 63 USPQ2d 1725, 1731-34 (Fed. Cir. 2002) (Court interpreted the language of the "third monitoring means for monitoring the ECG signal…for activating …" to require the same means to perform both functions and the only entity referenced in the specification that could possibly perform both functions is the physician. The court held that excluding the physician, no structure accomplishes the claimed dual functions. Because no structure disclosed in the embodiments of the invention actually performs the claimed dual functions, the specification lacks corresponding structure as required by 35 U.S.C. 112, sixth paragraph, and fails to comply with 35 U.S.C. 112, second paragraph.). Therefore, the claim is indefinite and is rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph.
Applicant may:
(a) Amend the claim so that the claim limitation will no longer be interpreted as a limitation under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph;
(b) Amend the written description of the specification such that it expressly recites what structure, material, or acts perform the entire claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(c) Amend the written description of the specification such that it clearly links the structure, material, or acts disclosed therein to the function recited in the claim, without introducing any new matter (35 U.S.C. 132(a)).
If applicant is of the opinion that the written description of the specification already implicitly or inherently discloses the corresponding structure, material, or acts and clearly links them to the function so that one of ordinary skill in the art would recognize what structure, material, or acts perform the claimed function, applicant should clarify the record by either:
(a) Amending the written description of the specification such that it expressly recites the corresponding structure, material, or acts for performing the claimed function and clearly links or associates the structure, material, or acts to the claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(b) Stating on the record what the corresponding structure, material, or acts, which are implicitly or inherently set forth in the written description of the specification, perform the claimed function. For more information, see 37 CFR 1.75(d) and MPEP §§ 608.01(o) and 2181.
Claim Rejections - 35 USC § 112(a)
13. 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.
A. Written Description under 112(f)
14. Claims 1-13 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The claims are drawn in relevant part to a method of expressing a heterologous protein product in a microorganism comprising providing a genetically modified microorganism, the genetically modified microorganism comprising means for conditional expression or overexpression of a heterologous protein product. The specification recites “[t]he means for conditional expression of a heterologous protein may include for example a plasmid. However, certainly any means of providing to the microorganism the ability to conditional express a protein heterologous to the microorganism are encompassed by the invention”. Thus the claims are drawn to an enormous and variable genus of “any means” of providing the microorganism the ability to conditional express a protein heterologous to the microorganism, and with the exception of a plasmid, does not have any definitive or particular structure. Rather, these “any means” are just generic suggestions to those skilled in the art as to what might be capable of conditional expression or overexpression of a heterologous protein. This disclosure is insufficient in terms of written description. See MPEP 2181(II)(A): The invocation of 35 U.S.C. 112(f) does not exempt an applicant from compliance with 35 U.S.C. 112(a) and 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, first and second paragraphs. See Donaldson, 16 F.3d at 1195, 29 USPQ2d at 1850; In re Knowlton, 481 F.2d 1357, 1366, 178 USPQ 486, 493 (CCPA 1973) ("[The sixth paragraph of section 112] cannot be read as creating an exception either to the description requirement of the first paragraph or to the definiteness requirement found in the second paragraph of section 112. Means-plus-function language can be used in the claims, but the claims must still accurately define the invention."). While one skilled in the art might be able to envisage some of the components encompassed in the claims and any means for conditional expression or overexpression of a heterologous protein product, this is insufficient in terms of written description because it is not up to a skilled artisan to come-up or finish the invention that Applicants’ are claiming.
The MPEP in section 2163(I) states that the purpose of the written description requirement is to ensure that the inventor had possession, at the time the invention was made/filed, of the specific subject matter claimed: To satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonable conclude the inventor had possession of the claimed invention. See, e.g., Moba, B.V. v. Diamond Automation, Inc., 325 F.3d 1306, 1319, 66 USPQ2d 1429, 1438 (Fed. Cir. 2003); Vas- Cath, Inc. V. Mahurkar, 935 F.2d at 1563, 19 USPQ2d at 1116. However, a showing of possession alone does not cure the lack of a written description. Enzo Biochem, Inc. v. Gen-Probe, Inc., 323 F.3d 956, 969-70, 63 USPQ2d 1609, 1617 (Fed. Cir. 2002). For example, it is now well accepted that a satisfactory description may be found in originally-filed claims or any other portion of the originally-filed specification. See In re Koller, 613 F.2d 819, 204 USPQ 702 (CCPA 1980); In re Gardner, 475 F.2d 1389, 177 USPQ 396 (CCPA 1973); In re Wertheim, 541 F.2d 257, 191 USPQ 90 (CCPA 1976). However, that does not mean that all originally-filed claims have adequate written support. The specification must still be examined to assess whether an originally-filed claim has adequate support in the written disclosure and/or the drawings. An applicant shows that the inventor was in possession of the claimed invention by describing the claimed invention with all of its limitations using such descriptive means as words, structures, figures, diagrams, and formulas that fully set forth the claimed invention. Lockwood V. Amer. Airlines, Inc., 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966 (Fed. Cir. 1997)".
Further, for a broad generic claim, the specification must provide adequate written description to identify the genus of the claim. In Regents of the University of California V. Eli Lilly & Co. the court stated:
"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., 43 USPQ2d 1398 (Fed. Circ. 1997).”
The courts have also held that possession may not be shown by merely describing how to obtain possession of members of the claimed genus or how to identify their common structural features. See University of Rochester, 358 F.3d at 927, 69 USPQ2d at 1895.
B. Written Description
15. Claims 1-13 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
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.
MPEP § 2163 further states that “[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.’ Such correlations may be established ‘by the inventor as described in the specification,’ or they may be ‘known in the art at the time of the filing date.’"
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.
Claims 1-13 are drawn in relevant part to a method of expressing a heterologous protein product in a microorganism, the protein requiring at least one disulfide bond for proper folding of the protein, the method comprising: (a) providing a genetically modified microorganism, the genetically modified microorganism comprising: means for conditional expression or overexpression of a heterologous protein product; a synthetic metabolic valve(s) comprising: a gene expression-silencing synthetic metabolic valve characterized by silencing gene expression of one or more genes encoding one or more enzymes; or an enzymatic degradation synthetic metabolic valve characterized by inducing enzymatic degradation of one or more enzymes, or a combination thereof, wherein reducing expression of at least one of the enzymes of a synthetic metabolic valve is effective for altering the redox characteristics of the cytosolic environment of the genetically modified microorganism. The modifications to any microorganism that results in the altering of the redox characteristics of the cytosolic environment of the genetically modified microorganism is unlimited.
In the instant case, the specification discloses an actual reduction to practice of the following representative species of the genus of modifications to any microorganism that results in the altering of the redox characteristics of the cytosolic environment as encompassed by the claims (i.e. an E. coli cell that has the gor, trxB or gshA gene targeted for inducible expression by nutrient limitation via a phosphate controlled promoter). Other than the above disclosed species, there are no other drawings or other structural formulas of microorganisms that results in the altering of the redox characteristics of the cytosolic environment as encompassed by the claims. While an E. coli comprising a gor gene deletion was known in the prior art as evidenced by Oganesyan et al. (WO 2015/117093 A1; examiner cited) and E. coli comprising deletion of thioredoxin reductase, disulfide reductase and gor as evidenced by Chang et al. (WO 2021/188379 A1, priority to 03/16/2020; examiner cited), there is no other prior art or disclosed teaching regarding which modifications to any microorganism that results in the altering of the redox characteristics of the cytosolic environment. The breadth of the claims encompass any modification to the any microorganism by mutation, substitution, or inhibitor of the gene encoding any enzyme or genes encoding proteins and transcription factors involved in the expression of said enzymes. Given what is known in the art about the likely outcome of substitutions on structure, conservation of structure is not necessarily a surrogate for conservation of function. In this case, there is no disclosed correlation between structure and function. Accordingly, one of skill in the art would not accept the disclosure of an E. coli cell that has the gor, trxB or gshA gene targeted for inducible expression by nutrient limitation via a phosphate controlled promoter disclosed above as being representative of all modifications to any microorganism that results in the altering of the redox characteristics of the cytosolic environment as encompassed by the claims. As such, the specification, taken with the pre-existing knowledge in the art of genetic modification, fails to satisfy the written description requirement of 35 U.S.C. 112(a), or first paragraph.
C. Scope of Enablement
16. Claims 1-13 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while enabling for an an E. coli cell that has the gor, trxB or gshA gene targeted for inducible expression by nutrient limitation via a phosphate controlled promoter, does not reasonably provide enablement for all modifications to any microorganism that results in the altering of the redox characteristics of the cytosolic environment 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 breadth of the claims: Claims 1-13 are drawn in relevant part to a method of expressing a heterologous protein product in a microorganism, the protein requiring at least one disulfide bond for proper folding of the protein, the method comprising: (a) providing a genetically modified microorganism, the genetically modified microorganism comprising: means for conditional expression or overexpression of a heterologous protein product; a synthetic metabolic valve(s) comprising: a gene expression-silencing synthetic metabolic valve characterized by silencing gene expression of one or more genes encoding one or more enzymes; or an enzymatic degradation synthetic metabolic valve characterized by inducing enzymatic degradation of one or more enzymes, or a combination thereof, wherein reducing expression of at least one of the enzymes of a synthetic metabolic valve is effective for altering the redox characteristics of the cytosolic environment of the genetically modified microorganism. The modifications to any microorganism that results in the altering of the redox characteristics of the cytosolic environment of the genetically modified microorganism is unlimited.
The state of the prior art; The level of one of ordinary skill; and The level of predictability in the art: As noted above, the structure and function of the claimed modifications to any microorganism that results in the altering of the redox characteristics of the cytosolic environment of the genetically modified microorganism is unlimited.
Oganesyan et al. (WO 2015/117093 A1; examiner cited) discloses an E. coli strain comprising reduced activity of one or more disulfide reductase enzymes comprising a deletion of a gor gene.
Chang et al. (WO 2021/188379 A1, priority to 03/16/2020; examiner cited) discloses an E. coli comprising deletion of thioredoxin reductase, disulfide reductase and gor
The breadth of the claims encompass and modification to the recombinant cell by mutation, substitution, or inhibitor of the gene encoding disulfide reductase enzymes or genes encoding proteins and transcription factors involved in the expression of said enzymes. To this end, it is well-known in the prior art that the amino acid sequence of a polypeptide determines the polypeptide’s functional properties. The positions within a protein's sequence where modifications can be made with a reasonable expectation of success in obtaining a polypeptide having the desired activity/utility are limited in any protein and the result of such modifications is highly unpredictable. In addition, one skilled in the art would expect any tolerance to modification for a given protein to diminish with each further and additional modification, e.g., multiple substitutions.
It is well-known in the art that even a single amino acid alteration can alter the folding of a polypeptide. See, e.g., MPEP 2144.08.II.A.4.(c), which states, “[i]n the area of biotechnology, an exemplified species may differ from a claimed species by a conservative substitution (“the replacement in a protein of one amino acid by another, chemically similar, amino acid... [which] is generally expected to lead to either no change or only a small change in the properties of the protein.” Dictionary of Biochemistry and Molecular Biology 97 (John Wiley & Sons, 2d ed. 1989)). The effect of a conservative substitution on protein function depends on the nature of the substitution and its location in the chain. Although at some locations a conservative substitution may be benign, in some proteins only one amino acid is allowed at a given position. For example, the gain or loss of even one methyl group can destabilize the structure if close packing is required in the interior of domains. James Darnell et al., Molecular Cell Biology 51 (2d ed. 1990).”
(F) The amount of direction provided by the inventor and (G) The existence of working examples: The specification discloses the following working examples of a microorganism that results in the altering of the redox characteristics of the cytosolic environment, i.e. an E. coli cell that has the gor, trxB or gshA gene targeted for inducible expression by nutrient limitation via a phosphate controlled promoter.
Other than this working example, the specification fails to disclose any other working examples of modifications to any microorganism that results in in the altering of the redox characteristics of the cytosolic environment. Moreover, the specification fails to provide guidance regarding modification(s) to said microorganisms that maintain the desired activity.
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 § 103
17. 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.
18. Claim(s) 1-5 and 8-12 is/are rejected under 35 U.S.C. 103 as being unpatentable over Lynch et al. (WO 2016/053397 A2; examiner cited) in view of Chang et al. (WO 2021/188379 A2; examiner cited).
19. With respect to claim 1, Lynch et al. teach a method for expressing a heterologous protein product in a microorganism, comprising providing a genetically modified microorganism comprising a means for conditional expression or overexpression of a heterologous protein product; a synthetic metabolic valve comprising a gene expression-silencing metabolic valve characterized by silencing gene expression of one or more genes encoding one or more enzymes or an enzymatic degradation synthetic metabolic valve characterized by inducing enzymatic degradation of one or more enzymes or a combination thereof, growing the genetically modified microorganism in a growth media comprising a limiting nutrient, transitioning from a growth phase to a stationary and protein product producing phase, the transition comprising stopping the growth of the microorganism, inducing the synthetic metabolic valve, and inducing expression or overexpression of the heterologous protein product [see Abstract; paragraphs 0008-0012, 0046-0051, 0101].
With respect to claim 5, Lynch et al. teach the method wherein the silencing synthetic metabolic valve encodes a gene operatively linked to a phoB, pstS, ugpB, and ydfH promoter [see paragraph 0119].
With respect to claim 9, Lynch et al. teach the method wherein the microorganism growth is stopped in the transition phase by phosphate depletion of the growth media [see paragraph 0036].
With respect to claim 10, Lynch et al. teach the method wherein the genetically modified microorganism is an E. coli microorganism [see paragraphs 0012-0013].
With respect to claim 11, Lynch et al. teach the method wherein the silencing synthetic metabolic valve silences or the enzyme of the enzymatic degradation synthetic metabolic valve is a fabI, gltA, udhA, zwf, and lpd [see paragraph 0086].
With respect to claim 12, Lynch et al. teach the method wherein the silencing synthetic metabolic valve encodes a soluble transhydrogenase (udhA) gene operatively linked to [see paragraphs 0086, 0116] operatively linked to a phoB, pstS, ugpB, and ydfH promoter [see paragraph 0119].
However, Lynch et al. does not teach the method of claim 1, wherein reducing expression of at least one of the enzymes of a synthetic metabolic valve is effective for altering the redox characteristics of the cytosolic environment of the genetically modified microorganism; the method of claim 2, wherein the genetically modified microorganism further comprises a chromosomal deletion of a gor, trxB, or gsh A gene; the method of claim 3, wherein the synthetic metabolic valve of the genetically modified microorganism are configured to reduce the activity of glutathione reductase, a thioredoxin reductase and a glutamate-cysteine ligase by transcriptional silencing of the glutathione reductase, a thioredoxin reductase or a glutamate-cysteine ligase, reducing the amount of glutathione reductase, thioredoxin reductase or glutamate-cysteine ligase enzyme by selective proteolysis or both; the method of claim 4, wherein the synthetic metabolic valve of the genetically modified microorganism are configured to regulate gor, trxB and gshA by transcriptional silencing of gor, trxB or gshA gene, reducing the amount of gor, trxB and gshA enzyme by selective proteolysis, or combinations thereof; the method of claim 5, wherein a synthetic metabolic valve that, when induced causes the selective degradation of trxB; and the method of claim 8, wherein the heterologous protein product is a human protein, antibody, an antibody fragment, a single chain variable fragment of an antibody, a nanobody, a protein that is approximately 14 kDa in size, a hyaluronidase-I, or a tissue plasminogen activator.
Chang et al. teach methods for the expression and purification of proteins expressed in microorganisms wherein the redox state of the cytoplasm has been modified in order to allow proper protein folding, site-directed cleavage of the protein [see Abstract]. Chang et al. further teach that E. coli is a widely used host to produce recombinant proteins; however, the reducing environment of the E. coli cytoplasm affects proteins containing disulfide bonds [see p. 2]. Chang et al. teach methods for the heterologous expression of proteins such as antibody fragments and nanobodies wherein the activity of glutathione reductase and thioredoxin reductase is reduced and trxB and gor genes are deleted [see p. 2; p. 5].
Before the effective filing date of the claimed invention, it would have been obvious for one of ordinary skill in the art to combine the teachings of Lynch et al. and Chang et al. to incorporate a synthetic metabolic valve controlling the expression and presence of enzymes involved in the redox state of an E. coli expressing a heterologous protein because Lynch et al. teach methods for the heterologous expression of recombinant proteins in E. coli under control of synthetic metabolic valves. Chang et al. teach that the reducing environment of the E. coli cytoplasm affects proteins containing disulfide bonds and reducing the activity of reducing enzymes encoded by genes such as gor and trxB increases the expression of soluble proteins containing disulfides. One of ordinary skill in the art would have had a reasonable expectation of success, a reasonable level of predictability and would have been motivated to combine the teachings of Lynch et al. and Chang et al. because Chang et al. acknowledges that the reducing the activity of enzymes contributing to the reducing environment of E. coli cytoplasm improves the production of heterologously expressed proteins. Therefore, the above invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
20. Claims 6 and 7 are rejected under 35 U.S.C. 103 as being unpatentable over Lynch et al. (WO 2016/053397 A2; examiner cited) in view of Chang et al. (WO 2021/188379 A2; examiner cited) as applied to claims 1-5 and 8-12 above, and further in view of Schlapschy et al. (Protein Engineering, Design & Selection, 2006; examiner cited).
21. The relevant teachings of Lynch et al. and Chang et al. as applied to claims 1-5 and 8-12 are set forth above.
With respect to claims 6 and 7, Chang et al. teach that in the bacterial periplasm, proteins are kept in an oxidation state by combined action of the DsbB-DsbA and DsbD-DsbC/DsbE/DsbG [see p. 10, top].
However, the combination of Lynch et al. and Chang et al. do not teach the method of claim 6 wherein the genetically modified microorganism is configured to conditionally overexpress a thiol-disulfide interchange protein, a thiol oxidase, or a combination thereof in a stationary phase and the method of claim 7, wherein the genetically modified microorganism is configured to conditionally overexpress a dsbC gene, a evr1 gene, or a combination thereof in stationary phase.
Schlapschy et al. teach that DsbA constitutes the dithiol oxidase in the periplasm of E. coli [see p. 385, column 2], and further teach the overexpression of DsbA, DsbC, FkpA and SurA as a helper plasmid in the expression of recombinant proteins in E. coli prevents inefficient disulfide formation, raises the yield of correctly folded soluble recombinant protein and abolishes toxic effects of heterologous protein secretion on the bacterial host cell [see Abstract; p. 389, column 1, bottom to column 2].
Before the effective filing date of the claimed invention, it would have been obvious for one of ordinary skill in the art to combine the teachings of Lynch et al., Chang et al. and Schlapschy et al. according to the teachings of Schlapschy et al. to include the conditional overexpression of thiol oxidases and interchange proteins such as DsbA and DsbC in the methods of Lynch et al. and Chang et al. because Lynch et al. and Chang et al. teach a synthetic metabolic valve controlling the expression and presence of enzymes involved in the redox state of an E. coli expressing a heterologous protein. Schlapschy et al. teach the overexpression of DsbA, DsbC, FkpA and SurA as a helper plasmid in the expression of recombinant proteins in E. coli prevents inefficient disulfide formation, raises the yield of correctly folded soluble recombinant protein and abolishes toxic effects of heterologous protein secretion on the bacterial host cell. One of ordinary skill in the art would have had a reasonable expectation of success, a reasonable level of predictability and would have been motivated to combine the teachings of Lynch et al., Chang et al. and Schlapschy et al. because Schlapschy et al. acknowledges the overexpression of DsbA, DsbC, FkpA and SurA as a helper plasmid in the expression of recombinant proteins in E. coli prevents inefficient disulfide formation, raises the yield of correctly folded soluble recombinant protein and abolishes toxic effects of heterologous protein secretion on the bacterial host cell. Therefore, the above invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
22. Claim 13 is rejected under under 35 U.S.C. 103 as being unpatentable over Lynch et al. (WO 2016/053397 A2; examiner cited) in view of Chang et al. (WO 2021/188379 A2; examiner cited) as applied to claims 1-5 and 8-12 above, and further in view of Zhang et al. (US Patent Application Publication 2024/0318165 A1, priority to 12/30/2020; examiner cited).
23. The relevant teachings of Lynch et al. and Chang et al. as applied to claims 1-5 and 8-12 are set forth above.
With respect to claim 13, Lynch et al. teach the method wherein the synthetic metabolic valve comprises: a gene encoding at least one small guide RNA specific for targeting more than one gene, a Cascade protein complex wherein the gene and Cascade protein complex are inhibited or suppressed when inorganic phosphate is available to the microorganism, but are activated in the absence of inorganic phosphate [see paragraphs 0008, 0032 p. 63].
However, the combination of Lynch et al. and Chang et al. do not teach the method of claim 13, wherein cas3 is absent or cas3 is modified to form part of Cascade protein complex but also lacks enzyme activity.
Zhang et al. teach Cascade protein complexes comprising catalytically inactive Cas3 for targeted genetic modification of cells [see Abstract; paragraph 0192].
Before the effective filing date of the claimed invention, it would have been obvious for one of ordinary skill in the art to combine the teachings of Lynch et al., Chang et al. and Zhang et al. to include a catalytically inactive Cas3 in the methods of Lynch et al. and Chang et al. because Lynch et al. and Chang et al. teach a synthetic metabolic valve controlling the expression and presence of enzymes involved in the redox state of an E. coli expressing a heterologous protein by targeted regulation of a synthetic metabolic valve by a Cascade protein complex. Zhang et al. teach Cascade protein complexes comprising catalytically inactive Cas3 for targeted genetic modification. One of ordinary skill in the art would have had a reasonable expectation of success and a reasonable level of predictability to combine the teachings of Lynch et al., Chang et al. and Zhang et al. because Zhang et al. acknowledges Cascade protein complexes comprising catalytically inactive Cas3 can be used for targeted genetic modification. Therefore, the above invention would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Conclusion
24. Status of the claims:
Claims 1-20 are pending.
Claims 14-20 stand withdrawn pursuant to 37 CFR 1.142(b).
Claims 1-13 are rejected.
No claims are in condition for an allowance.
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/PAUL J HOLLAND/Primary Examiner, Art Unit 1656
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