DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Application Status
The Preliminary Amendment filed November 18, 2022 is acknowledged. Claims 1-11 are pending and under examination.
Specification
The disclosure is objected to because of the following informalities: Table 1 and Table 2 on pages 23-24 of the Specification are illegible.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 8 and 9 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 8 recites A method of preparing a gene cluster construct… where the step (A1) and the step (B1) are performed by selecting a plurality of the plasmids obtained by the preparation method according to claim 7 and using the selected plasmids as the plasmids in the step (A1). 35 CFR 1.75 states “One or more claims may be presented in dependent form, referring back to and further limiting another claim or claims in the same application.” Because claim 8 refers back claim 7, it is a dependent claim of claim 7. However, “the plasmids obtained by the preparation method according to claim 7” is a product-by-process limitation. Product-by-process limitations are examined according to the structure of the product that is produced by process. In this case the product of “the preparation methods according to claim 7” is a plasmid comprising a gene cluster, which could be produced using a variety of methods including chemical synthesis, in vitro ligation, or produced in E. coli cells. Therefore, the method of claim 8 fails to require all of the steps/limitations of claim 7, from which it depends.
Claim 9 recites “A combinatorial library of plasmids obtained by the preparation method according to claim 7. 35 CFR 1.75 states “One or more claims may be presented in dependent form, referring back to and further limiting another claim or claims in the same application.” Because claim 9 refers back claim 7, it is a dependent claim of claim 7. Claim 9 is a product-by-process and will be examined according to the structure of the host cell that is produced by the method of claim 7. According to the steps in the method of claim 7, claim 9 is two or more plasmids (i.e., a library) each comprising at least a gene cluster. MPEP 608.01(n) states "The fact that the independent and dependent claims are in different statutory classes does not, in itself, render the latter improper . . . if claim 1 recites a method of making a product, a claim for a product made by the method of claim 1 could be a proper dependent claim. On the other hand, if claim 1 recites a method of making a specified product, a claim to the product set forth in claim 1 would not be a proper dependent claim if the product can be made by a method other than that recited in the base method claim, and thus, does not include the limitations of the base claim." The library of plasmids of claim 9 could be made by chemical synthesis, in vitro ligation and/or production in E. coli. Thus, the product of claim 9 does not include all the limitations of the method of claim 7.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 102 - Hutchinson
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.
Claims 1-3, 5-6 and 9-11 are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Hutchinson (US 20040203015 A1). Claim 2 is evidenced by Taylor (Cosmids, taylorandfrancis.com/ knowledge/Engineering_and_technology/Biomedical_engineering/Cosmids/ [retrieved August 28, 2025]). Claim 6 is evidenced by Bioquest (Restriction Enzymes Cut Sites Reference Table, https://www.aatbio.com/data-sets/restriction-enzymes-cut-sites-reference-table [retrieved August 28, 2025]).
Regarding claims 1, Hutchinson teaches the cloning of the megAI-III genes, which code for the biosynthetic enzyme complex responsible for producing megalomicin (i.e., a preparing a gene cluster construct encoding a multi-modal biosynthetic enzyme) ([0169]; FIGs 1-2). Regarding step (A), Hutchinson teaches isolating 1) a DNA fragment comprising megAI-II genes flanked with EcoRI-BglII recognition sequences, and 2) a DNA fragment comprising megAIII gene flanked by BglII-XbaI recognition sequences (i.e., preparing a plurality of DNA fragments which are capable of reconstructing the gene cluster construct and have structures that can be ligated to each other) ([0169]). Regarding step (B), Hutchinson teachings ligating the DNA fragments with megAI-II and megAIII together (i.e., a step of ligating the plurality of DNA fragments by mixing them in a solution to obtain the gene cluster construct) ([0169]).
Regarding claim 2, Hutchinson teaches that the DNA fragments with megAI-II and megAIII were isolated from cosmids ([0169]). Taylor teaches that a cosmid is a type of plasmid that can carry larger amounts of DNA. Therefore, Hutchinson’s cloning method inherently included preparing the DNA fragments from plasmids.
Regarding claim 3, Hutchinson teaches the cloning of the megAI-III genes, which codes for the biosynthetic enzyme complex responsible for producing megalomicin (i.e., a preparing a gene cluster construct encoding a multi-modal biosynthetic enzyme) ([0169]; FIGs 1-2). Regarding step (P), Hutchinson teaches 1) cloning a DNA fragment comprising megAI-II genes flanked with EcoRI-BglII recognition sequences to generate pKOS020-84, and 2) cloning a DNA fragment comprising megAIII gene flanked by BglII-BbvC1recognition sequences to generate pKOS070-93A (i.e., preparing a plurality of plasmids containing a plurality of DNA fragments) ([0169]). Because each DNA fragment has a 5’ end and a 3’ end they are capable of being ligated together. Regarding step (A1), Hutchinson teaches excising the megAIII fragment using BglII-XbaI restriction enzymes and subcloning it into the BglII-XbaI sites of pKOS020-84, which would require treating pKOS020 with the BglII-XbaI restriction enzymes ([0169]). Regarding step (B1), Hutchinson teaches ligating the megAI-II fragments together with the megAIII fragment (i.e., reaccumulating the DNA fragments obtained in step A1), to form pKOS1O8-06 (i.e., to obtain the gene cluster) ([0169]).
Regarding claim 5, Hutchinson teaches that the megAI-III genes encode a polyketide synthase ([0005]-[0006], [0166]).
Regarding claim 6, Hutchinson is silent on whether BglII, XbaI and BbvC1 are type II restriction enzymes. Bioquest teaches that type II restriction enzymes cleave within their restriction site (page 2). Bioquest teaches the recognition sequence and cleave site of BglII, XbaI and BbvCI, all of which cut within their recognition sequence. Therefore, the method of preparing the megAI-III gene cluster construct taught in Hutchinson inherently used type II restriction enzymes to prepare the DNA fragments.
Regarding claim 9, “a combinatorial library of plasmids obtained by the preparation method according to claim 7” is interpreted as a product-by-process claim. Therefore, the claim does not require the steps of claim 7. Rather this product-by-process will be examined according to the structure of the library of plasmids that is produced by the method of claim 7. See. MPEP 2113. The specification indicates that the product of the method is one or more plasmids that comprise gene clusters (FIGs 4-6). Therefore, claim 9 is interpreted as two or more plasmids (i.e., a library) each comprising a gene cluster. Hutchinson teaches pKOS1O8-06 comprising megAI-III and pKOS97-42 comprising megR, megK, megCV, megCIV and megBVI ([0169]-[0170]).
Regarding claims 10-11, Hutchinson teaches introducing the plasmids comprising the megAI-III genes, megB genes, megC genes and megD genes into a Streptomyces coelicolor host ([0174]).
Claim Rejections - 35 USC § 102 - Itaya
Claims 1, 7 and 9-10 are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Itaya (Itaya et al. (2014). Efficient and accurate production of de novo designed large-size gene clusters by a novel bacillus subtilis-based system. In Microbial Production: From Genome Design to Cell Engineering (pp. 35-52). Tokyo: Springer Japan).
Regarding claim 1, Itaya teaches preparing a cluster of genes encoding a nonribosomal peptide synthase (NRPS) (i.e., a multi-modular biosynthetic enzyme) (Fig 4.4). Regarding step (A), Itaya teaches PCR-amplifying the DNA fragments with SfiI recognition sequences on the 5’ and 3’ ends (i.e., having structures that can be ligated to each other) (Fig 4.4, legend). Regarding step (B), Itaya teaches mixing the fragments together and introducing them in B. subtilis for assembly by OGAB (Fig 4.4). Itaya teaches that OGAB stands for Ordered Gene Assembly in B. subtilis (Section 4.3.1 heading), and involves the ligation of the DNA fragments via the endogenous T4 ligase (i.e., a step of ligating) (page 41, ¶3).
Regarding claims 7 and 9-10, Itaya teaches a library of plasmids comprising gene clusters of the Carotenoid biosynthesis pathway (Fig 4.5). Itaya teaches the library was prepared by the OGAB (page 45, ¶2). Itaya teaches the OGAB method involves preparing DNA fragments (Step A1) and assembling them via ligation in B. subtilis (step B1) (page 41, ¶3). Itaya teaches recovering the plasmids and delivering them to E. coli (i.e., a host cell).
Claim Rejections - 35 USC § 103 - Itaya
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 2-4, 6 and 8 are rejected under 35 U.S.C. 103 as being unpatentable over Itaya (Itaya et al. (2014). Efficient and accurate production of de novo designed large-size gene clusters by a novel bacillus subtilis-based system. In Microbial Production: From Genome Design to Cell Engineering (pp. 35-52). Tokyo: Springer Japan). Claim 6 is evidenced by Pfam (Type II restriction enzyme SfiI, https://www.ebi.ac.uk/interpro/entry/pfam/PF11487/, [retrieved August 29, 2025]).
The teachings of Itaya are recited above as for claims 1, 7 and 9-10 and incorporated here. Briefly, Itaya teaches preparing a cluster of genes encoding a NRPS (i.e., a multi-modular biosynthetic enzyme) (Fig 4.4).
Regarding claim 2 and step (P) of claim 3, Itaya teaches 5 of the NRPS genes are organized in an operon and were prepared via the BReT method (Fig 4.4), which involves subcloning operons/genes into a B. subtilis plasmid (i.e., preparing plasmids containing DNA fragments having structures that can be ligated together) (page 43, ¶3). Regarding step (A1), Itaya teaches PCR-amplifying the DNA fragments with SfiI recognition sequences on the 5’ and 3’ ends (i.e., having structures that can be ligated to each other) (Fig 4.4, legend). Regarding step (B1), Itaya teaches mixing the fragments together and introducing them in B. subtilis for assembly by OGAB (Fig 4.4). Itaya teaches that OGAB stands for Ordered Gene Assembly in B. subtilis (Section 4.3.1 heading), and involves the ligation of the DNA fragments via the endogenous T4 ligase (i.e., a step of ligating) (page 41, ¶3).
In the method of preparing the NPRS gene cluster, Itaya does not teach a plurality of plasmids in step (P), since only the large ppsABCDE operon was first cloned into a plasmid before preparing the DNA fragments by treating the DNA with the SfiI restriction enzyme.
However, Itaya also teaches assembling a plasmid library of genes involved in the Carotenoid metabolic pathway (page 45, ¶2). Itaya teaches subcloning each of the five genes in the carotenoid pathway separately before assembling them via OGAB via ligation in B. subtilis (page 45, ¶2).
It would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have subcloned the degQ and sfp genes with flanking SfiI sites into plasmids and excising the genes with SfiI before assembly via OGAB. It would have amounted to the simple substitution of ones means of generating DNA fragments with flanking restriction enzyme sites for another my known means to yield predictable results. The skilled artisan would have predicted that the degQ and sfpQ fragments could be subcloned because subcloning is a standard method in the art of molecular cloning as evidence in Itaya. One would have been motivated to do so for long term storage of the degQ and sfp genes as plasmids and to check for PCR-generated mutations before assembly of the DNA fragments into large plasmids.
Regarding claim 4 and 8, Itaya also teaches that B. subtilis is well-studied and that cloning in the bacteria does not require cyclization before transformation (page 41, ¶2). It would also have been obvious to produce the degQ and sfp-containing plasmids in B. subtilis because as evidenced by Itaya, cloning and plasmid production in B. subtilis is routine. One would have been motivated to do so to avoid having to circularize the plasmid backbone and degQ and sfp genes before transformation, saving time and the cost of ligation enzymes.
Regarding claim 6, as evidenced by Pfam, SfiI is a type II restriction enzyme.
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, 5, 7, 9-11 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-11 of copending Application No. 17926204. Claims 7 and 9-11 are rejected in view of Itaya (Itaya et al. (2014). Efficient and accurate production of de novo designed large-size gene clusters by a novel bacillus subtilis-based system. In Microbial Production: From Genome Design to Cell Engineering (pp. 35-52). Tokyo: Springer Japan).
Copending claim 1 recites a method for preparing a plasmid containing DNA that encodes a Type I polyketide synthase (PKS) (i.e., a multi-modal biosynthetic enzyme), the method comprising a step of introducing a DNA construct containing tandem repeats of DNA that encodes a PKS into a Bacillus subtilis competent cell. Copending claim 2 recites the method further comprising: a step of preparing a plurality of DNA fragments having sticky ends at both ends (i.e., having structures that can be ligated to each other) by cleaving a plurality of DNA fragment precursors with a Type II restriction enzyme; and a step of preparing the DNA construct by linking the plurality of DNA fragments (i.e., ligating the fragments together). Copending claims 5 and 6 recites wherein the step of introducing the DNA construct is a step of co-culturing the DNA construct and the Bacillus subtilis competent cell and further comprising a step of recovering plasmid DNA from Bacillus subtilis into which the DNA construct is introduced. Thus, the copending claims anticipate examined claims 1 and 5. Copending claims 8 and 9 recites a method for producing a Type I polyketide synthase (PKS), the method comprising: a step of transforming a host cell with a plasmid; and a step of culturing the transformed host cell, including a bacterium of the genus Streptomyces, wherein the plasmid is the plasmid containing DNA that encodes a PKS obtained by the method according to any one of claim1.
The copending claims do not recite a combinatorial library of plasmids.
Regarding claims 7 and 9-11, Itaya teaches a method of creating a library of plasmids comprising gene clusters in B. subtilis. It would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have modified the copending method and plasmids by creating a plurality of plasmids. The copending method encompasses the OGAB method taught in Itaya. Itaya teaches that such a method can be used to create plasmids in which the order of the genes in the gene cluster is varied, thereby producing a combinatorial library of plasmids. Thus, it would have been entirely predictable that the copending method could be used to create a plasmid library. The skilled artisan would have been motivated to do so to use the copending method to make and test gene order combinations in a single step.
This is a provisional nonstatutory double patenting rejection.
Conclusion
No claims are allowable.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CATHERINE KONOPKA whose telephone number is (571)272-0330. The examiner can normally be reached Mon - Fri 7- 4.
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, Ram Shukla can be reached at (571)272-0735. 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.
/CATHERINE KONOPKA/Examiner, Art Unit 1635