Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
DETAILED ACTION
Applicant’s amendment filed on 10 July 2025 is entered. Claims 1, 6-7, 9, 16, 19-20, 22, 25-26, 28, 35, 38-41, and 48-51 are amended, claims 3, 10-15, 17-18, 21, 29-34, 36-37, 42-47, and 52 are cancelled. Claims 1-2, 4-9, 16, 19-20, 22-28, 35, 38-41, and 48-51 are pending.
Claims 1-2, 4-9, 16, 19-20, 22-28, and 35 are under examination.
The previous 112b rejections of the claims (except for the rejections of claims 1 and 22, and claims 9 and 28), and the previous 101, 102, and 103 rejections are withdrawn in light of Applicant’s amendment.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency - This application contains sequence disclosures in accordance with the definitions for nucleotide and/or amino acid sequences set forth in 37 CFR 1.821(a)(1) and (a)(2). However, this application fails to comply with the requirements of 37 CFR 1.821 - 1.825.
The sequence disclosures are located in claims 9 and 28, and in the specification pgs. 9-13, 16-18, 20-24, and 33. Many protein sequence accession numbers are provided, but no sequences corresponding to these accession numbers are provided in the sequence disclosure. The deficient disclosed protein sequence accession numbers/identifiers include esterases SC00713 (NP_625018.1), SCO1265 (NP_625552.1), SCO1735 (NP_626008.1), SC03219 (NP_627433.1), SCO4368 (NP_628538.1), SCO4746 (NP_628904.1), SC04799 (NP_628956.1), SCO6966 (NP_631032.1), SCO7131 (NP_631192.1), SBI_00115 (WP_014172715.1), SBI_00631 (WP_014173231.1), SBI_01149 (WP_014173749.1), SBI_01728 (WP_014174328.1), SAVERM_RS02860 (WP_010981907.1), SAVERM_RS4345 (WP 010036168.1), SAVERM RS04550 (WP 107083239.1), SAVERM RS23405(WP 010985956.1), SLNWT_RS18180 (WP_078845043.1), SLNWT_RS12910 (WP_040249758.1), SLNWT_RS12900 (WP_040249752.1), BSU_08350 (NP_388716.1), BSU_24510 (NP_390331.1), and BSU_21740 (NP_390057.1); acyl coenzyme A synthetases SCO1330, SCO2131, SCO2444, SCO2561, SCO2720, SCO3436, SC04006, SCO4503, SC05983, SCO6196, SCO6552, SCO6790, SCO6968, SCO7244, SCO7329, SC04383, SLNWT_0050, SLNWT_0304, SLNWT_0327, SLNWT_0598, SLNWT_0621, SLNWT_3453, SLNWT_4291, SLNWT_6199, SLNWT_6951, SVEN_0294, SVEN_0876, SVEN_2231, SVEN_3097, SVEN_4199, SVEN_6078, SVEN_6188, SVEN_6773, SVEN_6774, SVEN_7224, SLIV_03075, SLIV_04410, SLIV_07155, SLIV_16515, SLIV_25480, SLIV_36365, SAVERM_1258, SAVERM_1346, SAVERM_1603, SAVERM_2030, SAVERM_2279, SAVERM_377, SAVERM_3806, SAVERM_3864, SAVERM_5723, SAVERM_605 ,SAVERM_6612, WP_053803359.1, ELQ77730.1, WP_033034442.1, KOT44666.1, WP_033033106.1, SBI_00524, SBI_02958, SBI_03178, SBI_04546, SBI_04871, SBI_06310, SBI_07635, SBI_08381, SBI_08662, and SBI_09123; acyl-coenzyme A dehydrogenases SCO 1690, SCO2774, SCO6787, SLNWT_4686, SVEN_0520, SVEN_1293, SLIV_29290, SAVERM_1381, SAVERM_5280, SAVERM_6614, WP_125057199.1, WP_033031914.1, WP_030661846.1, WP_030634872.1, WP_030370993.1, SBI_08383, and SBI_09842; and acyl-coenzyme A hydratases SCO4384, SCO6732, SLNWT_0723, SLNWT_0850, SLNWT_4292, SLNWT_6769, SLNWT_6771, SVEN_0030, SVEN_0204, SVEN_0279, SVEN_1657, SVEN_4200, SVEN_5574, SVEN_5576, SVEN_6413, SLIV_16510, SLIV_36115, SAVERM_1245, SAVERM_1680, SAVERM_3863, SAVERM_6203, SAVERM_717, SAVERM_7216, WP_030669923.1, WP_125053679.1, SBI_01088, SBI_01673, SBI_01731, SBI_02642, and SBI_04870. Additionally, the sequences for pGCymRP21 and pCu-SCO6196 in pg. 34 last paragraph are also not disclosed.
Required response – Applicant must provide:
A "Sequence Listing" part of the disclosure, as described above in item 1); as well as
An amendment specifically directing entry of the "Sequence Listing" part of the disclosure into the application in accordance with 1.825(b)(2);
A statement that the "Sequence Listing" includes no new matter in accordance with 1.825(b)(5); and
A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.825(b)(4).
If the "Sequence Listing" part of the disclosure is submitted according to item 1) a) or b) above, Applicant must also provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter;
If the "Sequence Listing" part of the disclosure is submitted according to item 1) b), c), or d) above, Applicant must also provide:
A replacement CRF in accordance with 1.825(b)(6); and
Statement according to item 2) a) or b) above.
Claim Objections
Claims 1, 6, 9, 22, and 28 are objected to because of the following informalities:
Claims 1 and 6 recite incorrect bacterial nomenclature. All genus names need to be capitalized; and all genus and species names should be italicized to conform to standard microbial nomenclature in the art.
Claim 1 misspelled the word “obtain” on line 4 of the claim, and the word “genomes” on line 9 should be in its singular form “genome”.
Claims 9 and 28 are missing the word “and” in front of “the acyl coenzyme A synthetase” on line 2 of the claims.
Claim 22 recites the phrase comprising the steps in the method according to claim 1. The steps from claim 1 should be directly incorporated into claim 22 in order to emphasize that claim 22 is an independent claim, and to put the claim in a form that is easier to read and interpret without having to unnecessarily refer back to claim 1.
Appropriate correction is required.
Specification
The disclosure is objected to because of the following informalities:
The specification discloses bacteria names using incorrect nomenclature. All genus names need to be capitalized; and all genus and species names should be italicized to conform to standard microbial nomenclature in the art.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
(New rejection necessitated by amendment) Claims 1-2, 4-9, 16, 19-20, 22-28, and 35 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.
Regarding claims 1 and 22, it is unclear whether the contents of the parenthetical phrases on lines 3-6 and 8 of claim 1 are part of the claim limitations and intended to be limiting, or if the contents of the parenthetical phrases are merely exemplary and thus not required. Claim 22 refers to the steps recited in claim 1, so is unclear for the same reasons.
It is also unclear how the instant methods of improving production of a polyketide compound in a Streptomyces, and switching a primary metabolism to a secondary metabolism in a Streptomyces may be practiced without any active application step or step of adding cumate to induce the cumate-inducible promoter to express the Streptomyces gene. The cumate promoter must be induced for the expression can begin, and it is that expression which leads to the improved production of a polyketide compound in a Streptomyces, and switching a primary metabolism to a secondary metabolism in a Streptomyces.
Furthermore, it is unclear if the term “strengthening” is intended to convey that the triacylglycerol decomposition is increased, enhanced, somehow reinforced, somehow protected from regulation, or if genes associated with triacylglycerol decomposition are overexpressed. Examiner notes that no special definition is provided within the instant specification, and the plain meaning of the term “make or become stronger” does not elucidate the required method steps.
Regarding claims 9 and 28, it is unclear what is the structural limitation corresponding to each of the acyl coenzyme A synthetases, SCO6196, SCO6968, SCO7244, and SCO4383. There is no sequence disclosure for these gene or protein identifiers in the instant disclosure. Other than being grouped into the generic enzyme class acyl coenzyme A synthetase, no distinguishing characteristics between these gene or protein identifiers are provided in the disclosure. Therefore, these claims lack structural limitations for the required enzymes.
Claims 2, 4-9, 16, and 19-20 are dependent on claim 1, and claims 23-28 and 35 are dependent on claim 22, and so those dependent claims are indefinite for the same reasons.
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
(New rejection necessitated by amendment) Claims 1-2, 4-9, 16, 19-20, 22-28, and 35 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Wang et al. (Harnessing the intracellular triacylglycerols for titer improvement of polyketides in Streptomyces, Nature Biotechnology, vol 38, January 2020, 76–83).
In the broadest reasonable interpretation, the limitation “…for strengthening a triacylglycerol decomposition pathway in a streptomyces during a stationary phase” recited in claim 1 is an intended result or effect of practicing the method, but does not recite an active step to be performed in order to execute the method for improving the production of a polyketide compound in a Streptomyces. The method of claim 1 lacks an active method step. As such, where the prior art teaches a method of improving the production of a polyketide compound in a Streptomyces, the limitation is considered to be necessarily met.
Regarding claim 1, Wang teaches a method of improving polyketide production in Streptomyces; the method is referred to therein as dynamic degradation of TAG, or ddTAG (Wang abstract). Wang teaches amplifying a cumate inducible promoter fragment using primers CuF and CuR, amplifying the sco6196 gene of Streptomyces coelicolor M145 using primers 6196F and 6196R, and assembling the cumate inducible promoter fragment and the sco6196 fragment with linear pSET152 (100% identical to SEQ ID NO: 29) fragment using Gibson assembly to generate a plasmid pCu-SCO6196, which is then integrated into the genomes of Streptomyces coelicolor, Streptomyces venezuelae, Streptomyces rimosus, and Streptomyces avermitilis (Wang pg. 84 para. 4). The sequences of Wang’s CuF, CuR, 6196F, and 6196R primers are 100% identical to the sequences of SEQ ID Nos: 1, 2, 3, and 4 respectively (Wang Supplementary table 14).
Regarding claim 22, Wang teaches that polyketides are secondary metabolites synthesized in the secondary metabolism during the stationary phase of the Streptomyces (Wang Abstract and Fig. 1a), and that the switch between primary metabolism and secondary metabolism in Streptomyces is characterized by the switch from TAG biosynthesis to TAG degradation (Wang figs.1a, 1e, 2c, and 2e-f). Wang’s method switches the primary metabolism of Streptomyces to its secondary metabolism by inducing expression of acyl coenzyme A synthetase SCO6196, which enables selective control of the timing and strength of TAG degradation (Wang pg. 81 left col. para. 3), thereby redirecting more carbon flux toward the biosynthesis of polyketides (Wang fig. 1 and pg. 81 left col. para. 3 through right col. para. 1). Therefore, Wang’s method of improving the production of polyketides in a Streptomyces switches the primary metabolism of a Streptomyces to its secondary metabolism.
Regarding claims 2 and 23, Wang teaches the beta-oxidation pathway is activated (strengthened) by acyl-CoA synthetases, including SCO6196 (Wang pg. 80 right col. para. 3, pg. 81 left col. para. 1, and Fig. 4).
Regarding claim 4, Wang teaches their method improved production of polyketides jadomycin, oxytetracycline, and avermectin (Wang abstract).
Regarding claims 6 and 25, Wang improved the polyketide production in Streptomyces coelicolor, Streptomyces venezuelae, Streptomyces rimosus, and Streptomyces avermitilis (Wang abstract).
Regarding claims 7-9 and 26-28, Wang teaches that the expression level of acyl coenzyme A synthetase SCO6196 in Streptomyces coelicolor was enhanced, and catalyzes reactions in the beta-oxidation pathway (Wang Fig. 4).
Regarding claims 5, 16, 19, 24, and 35, these claims further limit the phrase “for strengthening a triacylglycerol decomposition pathway in the streptomyces” recited in claim 1. This phrase is an intended result or effect of practicing the method, and not an active step to be performed in order to execute the method. Since Wang teaches all of the steps in the claimed method for improving the production of polyketide compounds in engineered Streptomyces, the limitations of claims 5, 16, 19, 24, and 35 are considered anticipated by Wang.
Regarding claim 20, Wang teaches their method increased the NADH/NAD+ ratio in the Streptomyces (Wang Fig. 3c).
Claim Rejections - 35 USC § 103
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.
(New necessitated by amendment) Claims 1-2, 4-8, 16, 19, 22-27, and 35 are rejected under 35 U.S.C. 103 as being unpatentable over Hu et al. (CN 104513840 A published 15 April 2015), Horbal et al. (Dual control system – A novel scaffolding architecture of an inducible regulatory device for the precise regulation of gene expression, Metabolic Engineering 37 (2016) 11–23), and Banchio et al. (A Stationary-Phase Acyl-Coenzyme A Synthetase of Streptomyces coelicolor A3(2) Is Necessary for the Normal Onset of Antibiotic Production, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Sept. 2002, p. 4240–4246, Vol. 68, No. 9), and as evidenced by LibreTexts (Oxidation of Fatty Acids, https://chem.libretexts.org/@go/page/234043, accessed on 01 April 2025), Yang et al. (Enhancement of acyl-CoA precursor supply for increased avermectin B1a production by engineering meilingmycin polyketide synthase and key primary metabolic pathway genes, Microbial Biotechnology. 2024;17:e14470.), and Gibson et al. (Enzymatic Assembly of Overlapping DNA Fragments, Methods in Enzymology, Volume 498, 2011).
The limitation “…for strengthening a triacylglycerol decomposition pathway in a streptomyces during a stationary phase” recited in claim 1 is an intended result or effect of practicing the method, but does not recite an active step to execute the method for improving the production of a polyketide compound in a Streptomyces. As such, where the prior art teaches all of the steps of claim 1, the limitation is considered to be necessarily met.
Regarding claim 1, Hu teaches a method for improving yield of polyketide compounds in engineered Streptomyces hygroscopius (Hu Absract and pg. 3 para. 6) comprising the steps of amplifying a promoter ERM*E using primers P3 and P4 to obtain a fragment containing the ERM*E promoter and amplifying acyl coenzyme A DPTE using primers P1 and P2 to obtain a fragment containing the complete DPTE gene (Hu pg. 4 Embodiment 2 steps 1 and 2). The ERM*E promoter and DPTE fragments were assembled into plasmid pSET152 using the Gibson assembly method of digesting the ERM*E fragment with restriction enzymes BamHI and NdeI, digesting the DPTE fragment with NdeI and XbaI, digesting the pSET152 plasmid with BamHI and XbaI, and the ligating all of the fragments together using T4 DNA ligase to obtain a plasmid pSET152erm*E-DPTEF (Hu fig. 1 and pg. 4 last para. through pg. 5 para. 1). The pSET152erm*E-DPTEF plasmid was then integrated into the genome of actinomycete Streptomyces hygroscopicus by intergenic conjugation through E. coli (Hu pg. 3 para. 6 and pg. 5 Example 3).
Hu does not teach amplifying a cumate inducible promoter using primers CuF and CuR or amplifying a gene of Streptomyces using primers 6196F and 6196R.
Horbal teaches a library of cumate inducible promoters which can be used to modulate gene expression of secondary metabolite gene clusters (Horbal pg. 14 Results section 3.1).
Banchio teaches Streptomyces coelicolor acyl coenzyme A synthetase encoded by the fadD1 gene, also called the sco6196 gene, as evidenced by Yang (Yang pg. 8 right col. para. 1), modulates the activation of polyketide actinorhodin synthesis (Banchio discussion).
Hu, Horbal, and Banchio do not teach the primers CuF, CuR, 6196F, and 6196R. However, it would have been a matter of routine optimization by one of ordinary skill in the art to determine adequate primer sequences in order to amplify Horbal’s cumate inducible promoter and Banchio’s fadD1 (sco6196) acyl coenzyme A synthetase gene.
In depth instructions on how to design effective primers for amplifying DNA fragments for use in Gibson assembly are readily available and well known in the art, as evidenced by Gibson (Gibson pgs. 352-353 sec. 2 and Fig. 15.1). By referencing the DNA sequences of the cumate inducible promoter as disclosed by Horbal and fadD1 (sco6196) acyl coenzyme A synthetase gene as disclosed by Bachio, one of ordinary skill in the art would use the readily available guidance of Gibson Assembly method as disclosed by Hu to construct PCR primers that would predictably amplify the cumate inducible promoter and fadD1 (sco6196) acyl coenzyme A synthetase gene fragments, and prepare those fragments for Gibson assembly.
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the present invention to modify Hu’s method of improving polyketide production in a Streptomyces by substituting the ERM*E promoter used in Hu’s method with Horbal’s cumate inducible promoter, and Hu’s Streptomyces gene DPTE with Banchio’s Streptomyces gene fadD1 (sco6196).
One of ordinary skill in the art would have been motivated to substitute Hu’s ERM*E promoter with Horbal’s cumate inducible promoter in order to selectively control the transcription of the acyl coenzyme A synthetase gene using cumate. one of ordinary skill in the art would have a reasonable expectation of success because Horbal taught the effectiveness of a cumate inducible promoter controlling expression of downstream genes upon addition of cumate (Horbal fig. 2b).
One of ordinary skill in the art would have been motivated to substitute Hu’s acyl coenzyme A synthetase gene DPTE with Banchio’s acyl coenzyme A synthetase gene fadD1 (sco6196) in order to overexpress the transcription levels of FadD1 (SCO6196) in the Streptomyces to improve its polyketide production. One of ordinary skill in the art would have a reasonable expectation of success because Hu’s method is taught to improve the production of polyketides in a Streptomyces species by overproducing the expression of an acyl coenzyme A synthetase, and Hu’s DPTE and Banchio’s FadD1 (SCO6196) are both acyl coenzyme A synthetases produced by Streptomyces species.
Regarding claim 22, Hu teaches that polyketides are secondary metabolites (Hu pg. 2 Background), and Banchio teaches that the polyketides are synthesized during the stationary phase of the Streptomyces (Banchio Fig. 6). The obvious method of Hu in view of Horbal and Banchio improves the production of polyketides by inducing selective control over the expression of acyl coenzyme A synthetase SCO6196, which is normally expressed in the stationary phase when the secondary metabolism naturally begins and is correlated with SCO6196 levels (Banchio Figs. 3A and 6). Inducing the expression of acyl coenzyme A synthetase SCO6196 leads to increased secondary metabolites like polyketides, thereby switching the primary metabolism of Streptomyces to its secondary metabolism where the polyketides are synthesized. Therefore, performing the obvious method of Hu in view of Horbal and Banchio switches the primary metabolism of a Streptomyces to its secondary metabolism.
Regarding claims 2 and 23, acyl-coenzyme A synthetase is an enzymatic component that is part of the fatty acid (such as triacylglycerol) catabolism through β-oxidation, as evidenced by LibreTexts (Pg. 1 para. 2 and chemical equation).
Regarding claim 4, Hu teaches their method can improve the yield of polyketide avermectin (Hu pg. 2 Background).
Regarding claims 6 and 25, Hu teaches a method for improving yield of polyketide compounds in engineered Streptomyces hygroscopius (Hu Absract and pg. 3 para. 6).
Regarding claims 5, 7-8, 16, 19, 24, 26-27, and 35, these claims further limit the phrase “for strengthening a triacylglycerol decomposition pathway in the streptomyces” recited in claim 1. This phrase is an intended result or effect of practicing the method, and not an active step to be performed in order to execute the method. Since Hu teaches a method for improving yield of polyketide compounds in engineered Streptomyces hygroscopius comprising the steps of claims 1 and 22, the limitations of these claims are considered necessarily met.
(New necessitated by amendment) Claims 9 and 28 is rejected under 35 U.S.C. 103 as being unpatentable over Hu in view of Horbal and Banchio as applied to claims 1-2, 4-8, 16, 19, 22-27, and 35 above, and further in view of Risdian et al. (Biosynthesis of Polyketides in Streptomyces, Microorganisms 2019, 7, 124; doi:10.3390/microorganisms70501 24).
The obvious method of Hu in view of Horbal and Banchio enhances the expression level of the acyl coenzyme A synthetase enzyme SCO6196. However, Hu, Horbal, and Banchio do not teach the improvement in yield of polyketide compounds in the species Streptomyces coelicolor.
Risdian teaches that Streptomyces coelicolor produces polyketides actinorhodin (Risdian pg. 2-3 bridging para.) and germicidin A (Risdian pg. 11 sec. 4.1 para. 1). Risdian teaches that germicidin A is known to inhibit spore germination and be antibacterial against various Gram-positive bacteria (Risdian pg. 11 sec. 4.1 para. 1).
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the present invention to apply the obvious method of Hu in view of Horbal and Banchio to the Risdian’s Streptomycin coelicolor in order to advantageously enhance production of antibacterial and anti-spore polyketide compound germicidin A produced by Risdian’s Streptomyces coelicolor. One of ordinary skill in the art would have a reasonable expectation of success because Hu taught their method of improving polyketide yield to be useful in engineered Streptomyces cells, and so one of ordinary skill in the art would reasonably expect the method of Hu in view of Horbal and Banchio to successfully work in Streptomyces coelicolor.
Claim 20 is rejected under 35 U.S.C. 103 as being unpatentable over Hu in view of Horbal and Banchio as applied to claims 1-2, 4-8, 16, 19, 22-27, and 35 above, and further in view of Zhang et al. (Suitable extracellular oxidoreduction potential inhibit rex regulation and effect central carbon and energy metabolism in Saccharopolyspora spinosa, Microbial Cell Factories 2014, 13:98).
Hu, Horbal, and Banchio do not teach a step of increasing a NADH/NAD+ ratio in the Streptomyces.
Zhang teaches that polyketides are synthesized in the stationary growth phase of fermentation, and that the ratio of NADH/NAD+ has significant influence on polyketide production (Zhang Abstract). Zhang also teaches that the NADH/NAD+ ratio is significantly higher in stationary growth phase than in either lag or exponential growth phases under normal conditions (Zhang Fig. 2 control group). Therefore, Zhang teaches that a high NADH/NAD+ ratio is present in stationary growth phase, which allows for the production of polyketides secondary metabolites.
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the present invention to increase the ratio of NADH/NAD+ of the Streptomyces of Hu in view of Horbal and Banchio. One of ordinary skill in the art would have been motivated to do so in order to advantageously promote the secondary metabolism conditions which positively impact therapeutic polyketide production under normal growth conditions, such as a high NADH/NAD+ ratio. One of ordinary skill in the art would have had reasonable expectations of success in this endeavor because Zhang teaches that polyketides are synthesized in the stationary growth phase, the ratio of NADH/NAD+ has significant influence on polyketide production, and the NADH/NAD+ ratio is significantly higher in stationary growth phase than in either lag or exponential growth phases under normal conditions. Thus, a high NADH/NAD+ ratio is present in stationary growth phase, which enhances the production of therapeutic polyketides secondary metabolites.
Response to Arguments
Applicant's arguments filed 10 July 2025 have been fully considered but they are not persuasive.
Applicant’s argument that the sequences that lacked proper sequence disclosures as mentioned on pgs. 5-7 of the previous Office Action were canceled from the claims and specification (Remarks 10 July 2025 pg. 15) is not convincing because the sequences still need to be disclosed as the previous Office Action stated. Deleting the sequence references in the claims does not obviate the requirement for a proper sequence disclosure, and furthermore the sequence references have not been deleted from the specification.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Alexander M Duryee whose telephone number is (571)272-9377. The examiner can normally be reached Monday - Friday 9:00 am - 5:00 pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Louise Humphrey can be reached on (571)-272-5543. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/Alexander M Duryee/Examiner, Art Unit 1657