The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 9-34, 36, 38-53, 58-104, 106-131, 133, 135-146, 149-162 are canceled. Claims 1-8, 35, 37, 54-57, 105, 132, 134, 147-148, 163 are pending and under consideration.
Priority: This application is a CON of U.S. Application 16990424, filed August 11, 2020, abandoned, which is a CON of U.S. Application 15754105, filed February 21, 2018, now U.S. Patent 10774314, which is a 371 of PCT/US2016/047692, filed August 19, 2016, which claims benefit of provisional application 62/208166, filed August 21, 2015.
Failure to Comply with Sequence Rules
Where the description of a patent application discusses a sequence of 4 or more amino acids or a sequence of 10 or more nucleic acids, reference must be made to the sequence by use of the sequence identifier preceded by “SEQ ID NO:” in the text of the description even if the sequence is also embedded in the text of the description of the patent application (see 37 CFR 1.821, especially paragraphs (a)-(d)). The sequence identifier may be used in either the drawing or the Brief Description of Drawings (see MPEP 2422).
Objection to the Specification:
The specification is objected to for failure to comply with the sequence rules for the reasons as given above. The specification refers to sequences without identifiers at: see at least pages 6, 27 (of the specification filed June 9, 2023).
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code: see at least pages 11, 13, 18, 19 (of the specification filed June 9, 2023). 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.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-8, 35, 37, 54-57, 105, 132, 134, 147-148, 163 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 enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
The disclosure does not enable one of ordinary skill in the art to practice the invention without:
1) biochemical pathways to produce the one or more chemical species,
2) specific substrates that are substrates for P450 enzymes to produce the one or more chemical species, or
3) a teaching of substrates that will produce the final products/chemical species produced by P450 enzymes,
which is/are critical or essential to the practice of the invention but not included in the claim(s). See In re Mayhew, 527 F.2d 1229, 188 USPQ 356 (CCPA 1976).
This rejection has at least two main issues. While “chemical species” are produced, the focus will be terpenoids as a culture substrate for P450 enzymes, and then the product of any substrates in culture to the E. coli as an intended substrate for the P450 enzymes because the specification discloses terpenoids as a P450 oxygenated product or as a substrate for P450 chemistry and is also produced in claim 54.
The first issue is that the specification (filed June 9, 2023) teaches that the E coli cells may be fed desired P450 enzyme substrates for chemical transformation, or biochemical pathways may be expressed in the E. coli cells to generate substrates in vivo.
At Page 18, line 21+:
The E. coli cells may be fed the desired P450 substrate for chemical transformation,5 or biochemical pathways may be expressed in the host cell to generate the substrate in vivo.
At page 9, line 22+
Exemplary substrates for P450 chemistry include various secondary metabolites such asMAN-006C1 /107590-5006, without limitation, terpenoids, alkaloids, cannabinoids, steroids, saponins, glycosides, stilbenoids, polyphenols, antibiotics, polyketides, fatty acids, and non-ribosomal peptides.
Yet, the specification does not teach to feed these secondary metabolites to the E. coli cells. Rather, these secondary metabolites are synthesized by biochemical pathways that are expressed in the E. coli host cell to generate the substrate in vivo.
At page 4, line 10+:
Figure 3 shows the total terpenoid flux and oxygenated terpenoid formation upon
expression in E. coli of Valencene Oxidase (VO) enzymes truncated at residue 30 and having various E. coli anchors. The E. coli cells express a valencene synthesis pathway, producing the valencene substrate.
Page 23, line 12+:
Where the chemical species is a terpenoid, the host cell will generally contain a
recombinant downstream pathway that produces the terpenoid from IPP and DMAPP23 precursors. Terpenes such as Monoterpenes (C10), Sesquiterpenes (C15) and Diterpenes (C20) are derived from the prenyl diphosphate substrates, geranyl diphosphate (GPP), farnesyl diphosphate (FPP) and geranylgeranyl diphosphate (GGPP) respectively through the action of a very large group of enzymes called the terpene (terpenoid) synthases. ‘
IPP, which is the acronym for isopentenyl pyrophosphate, is produced through the mevalonate pathway followed by isomerization via isopentenyl-pyrophosphate delta isomerase to form DMAPP, which is the acronym for dimethylallyl pyrophosphate. Both IPP and DMAPP can be formed through the MEP pathway. Thus, when the terpenoid is the END PRODUCT, or the chemical species produced in E. coli in accordance to the method claimed, the precursors or substrates are not in the culture feed to the E. coli but produced in the E. coli, having the E. coli being transformed to express terpene synthases.
The IPP/DMAPP are not substrates for P450 enzymes for the production of terpenoids, and nor are the geranyl diphosphate (GPP), farnesyl diphosphate (FPP), and geranylgeranyl diphosphate (GGPP) substrates for the P450 enzymes.
The second issue is the chemical species produced even if terpenoids were part of the culture feed to the E. coli as a substrate for P450 enzymes, are not produced by the P450 enzymes.
At page 23, line 3+:
In an embodiment, the E. coli host cell produces a terpenoid selected from a monoterpenoid, a sesquiterpenoid, diterpenoid, a sesterpenoid, or a triterpenoid.
Page 25, line 5+:
In various embodiments, E. coli cell is cultured to produce the one or more
chemical species. For example, the E. coli cell may be cultured to produce one or more
terpenoid compounds.
At page 10, line 12+:
Exemplary terpenoid products that may be produced …: alpha-sinensal, beta-Thujone, Camphor, Carveol, Carvone, Cineole, Citral, citronellal, Cubebol, Geraniol, Limonene, Menthol, Menthone, Nootkatone, Nootkatol, Patchouli, Piperitone, Sabinene, Steviol, Steviol glycoside, Taxadiene, and Thymol.
MAN-006C1 /107590-5006
For example, Camphor is a substrate for P450cam (camphor-5-monooxygenase) which hydroxylates the camphor to 5-exo-hydroxycamphor. Thus, Camphor is not the product of P450. See Kamachi et al. 2003; A theoretical study on the mechanism of camphor hydroxylation by compound I of cytochrome P450. J. Am. Chem. 125: 4652-4661; at page 4652, para. 2.
Beta-Thujone is a substrate for P450cam and P450 BM3 for the production of 4-hydroxy-beta- thujone, for example. Thus, beta-Thujone is not the product of P450. See He et al. 2004; Radical rebound mechanism in cytochrome P-450-catalyzed hydroxylation of the multifaceted radical clocks alpha- and beta-Thujone. J. Biol. Chem. 279(38): 39479-39484; at page 39481, left col., para. 2.
Thymol and carvacrol are converted to thymohydroquinone by CYP76S40 or CYP736A300. Thus, thymol and carvacrol are not the product of P450. See Krause et al. 2021; The biosynthesis of thyol, carvacrol, and thmyohydroquinone in Lamiaceae proceeds via cytochrome P450s and a short-chain dehydrogenase. Proc. Natl. Acad. Sci. 118(52), e2110092118, pages 1-10; at Figure 4 with legend.
Limonene (the terpenoid product) is the substrate for cytochrome P450 limonene-3-hydroxylase, methone is the product of pulegone reductase (PR) and the substrate for methone reductase which produces menthol. Piperitone is the product of pulegone reductase (PR). See Mahmoud et al. 2003; Menthofuran regulates essential oil biosynthesis in peppermint by controlling a downstream monoterpene reductase. Proc. Natl. Acad. Sci. 100(24): 14481-14486; at Fig. 1 with legend.
At page 24, para. 3:
In an embodiment, the E. coli cell produces steviol or steviol glycoside (e.g.,5 RebM). Steviol is produced from kaurene by the action of two P450 enzymes, kaurene oxidase (KO) and kaurenoic acid hydroxylase (KAH). After production of steviol, various steviol glycoside products may be produced through a series of glycosylation reactions, which can take place in vitro or in vivo.
While steviol may be a product of P450 enzymes but it is not a substrate for the P450 enzymes, the steviol glycosides require an exogenous synthetic pathway in E. coli.
The rejection provides 4 references and recitations from the specification teaching that the terpenoid products which are chemical species encompassed and produced by the method claimed, are either the direct substrate of the P450 in question to produce a different product, or chemical species that is not a product of P450.
Therefore, the disclosure does not enable one of ordinary skill in the art to practice the invention without:
1) biochemical pathways to produce the one or more chemical species,
2) specific substrates that are substrates for P450 enzymes to produce the one or more chemical species, or
3) a teaching of substrates that will produce the final products/chemical species produced by P450 enzymes,
which is/are critical or essential to the practice of the invention but not taught in the specification and are not included in the claim(s).
Further, the disclosure does not enable one of ordinary skill in the art to practice the invention without biosynthetic pathways and the requisite enzymes that must be expressed in the E. coli to produce each claimed secondary metabolite which is/are critical or essential to the practice of the invention but not included in the claim(s).
The specification and claims list many metabolites produced in the E. coli such as set forth in the method of Claim 1. Yet, the specification does not provide pathways in which to make nearly all of the metabolites listed therein and in the claims. For example, which enzymes must the heterologous biosynthetic pathway comprise to make saponin? Or cannabinoid? Non-ribosomal peptides? Sabinene? If the pathways are not provided in the disclosure, then one cannot look to the disclosure to practice the invention.
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 1-8, 35, 37, 54-57, 105, 132, 134, 147-148 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
The term “substantially” in claim 2 is a relative term which renders the claim indefinite. The term “substantially” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention.
Claims 3-5 lack antecedent basis in Claim 1 because Claim 1 does not refer to recombinant enzymes and it is not clear if the recombinant enzymes are the P450 enzymes or enzymes of the biosynthetic pathway or are there for another purpose altogether.
Claim 7 is indefinite because it is not clear if the MEP pathway is the biosynthetic pathway, or why the pathway would be incomplete if only one of the many enzymes (see page 20, for example) of the MEP pathway were expressed.
Claim 8 recites wherein “at least one gene” is expressed by a strong promoter. It is not clear if the at least one gene is referring to the E. coli genes recited earlier (in claim 6).
The single pass transmembrane domain of Claim 35 lacks antecedent basis in Claim 1, that is, Claim 35 should read that the transmembrane domain derived from E. coli inner membrane cytoplasmic C-terminus protein is a single pass transmembrane domain selected from….
Claims 37, 134 recite “the P450 enzyme”. Claims 37, 134 are dependent on claims 1 and 105, respectively, which recites “membrane-anchored P450 enzyme”. It is not clear if the same P450 enzyme is being recited or referred to.
Claim 54 is drawn to a method for producing a product comprising terpenoid compounds yet the method of making terpenoid compounds is included in the method. These are two patentably distinct methods and each method should have their own claims.
The term “substantially” in claim 55 is a relative term which renders the claim indefinite. The term “substantially” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention.
Claims 56-57 lack antecedent basis in Claim 54 because Claim 54 does not refer to recombinant enzymes and it is not clear if the recombinant enzymes are the P450 enzymes or enzymes of the biosynthetic pathway or are there for another purpose altogether.
The single pass transmembrane domain of Claim 132 lacks antecedent basis in Claim 105, that is, Claim 132 should read that the transmembrane domain derived from E. coli inner membrane cytoplasmic C-terminus protein is a single pass transmembrane domain selected from….
Claim 148 recites the limitation "the membrane-anchored P450" in the claim. There is insufficient antecedent basis for this limitation in the claim.
Finally, throughout the claims, “E. coli” should be written as – Escherichia coli – to avoid stray periods within the claims, i.e. see at least claims 1, 2, 3, etc.
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 1-8, 35, 37, 54-57, 105, 132, 134, 147-148, 163 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of U.S. Patent No. 10774314 (‘314). Although the claims at issue are not identical, they are not patentably distinct from each other because both the instant claims and the ‘314 patent claims are drawn to a method for biosynthesis of one or more chemical species in E. coli, comprising: expressing one or more biosynthetic pathways in E. coli, the one or more biosynthetic pathways comprising at least one membrane-anchored P450 enzyme having a transmembrane domain derived from an E. coli inner membrane cytoplasmic C-terminus protein, and culturing the E. coli to produce the one or more chemical species from the biosynthetic pathway(s); an Escherichia coli host cell expressing one or more recombinant biosynthetic pathways that produce one or more chemical species, where the biosynthetic pathways comprise at least one membrane-anchored P450 protein; a plant P450 enzyme comprising an N-terminal truncation and a single-pass transmembrane region derived from an Escherichia coli inner membrane cytoplasmic C-terminus protein; and a polynucleotide encoding the noted P450 enzyme.
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Marsha Tsay whose telephone number is (571)272-2938. The examiner can normally be reached M-F.
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/Marsha Tsay/Primary Examiner, Art Unit 1656