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
Claim Status
The amendment on November 10, 2025 is acknowledged. Claims 1-2, 4-6, 8, 14, 19-20, 23-29, 32-35, 37-38, 42-43, 46, 51, 56-57, 59, 63, 70-71, 74-75, 78, 82 and 85 are pending. Claims 3, 7, 9-13, 15-18, 21-22, 30-31, 36, 39-41, 44-45, 47-50, 52-55, 58, 60-62, 64-69, 72-73, 76-77, 79-81, 83-84, 86-96, and 98-106 are canceled. There are no new claims. Claim 97 and its dependent claims 56-57 are withdrawn. Claims 1-2, 4-6, 8, 14, 19-20, 23-29, 32-35, 37-38, 42-43, 46, 51, 59, 63, 70-71, 74-75, 78, 82 and 85 will be examined on the merits herein.
Election/Restrictions
Applicant’s election without traverse of Group I (1-2, 4-6, 8, 14, 19-20, 23-29, 32-35, 37-38, 42-43, 46, 51, 56-57, 59, 63, 70-71, 74-75, 78, 82 and 85) in reply filed on November 10, 2025 is acknowledged. Claim 97 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 November 10, 2025.
Information Disclosure Statement (IDS)
The information disclosure statement (IDS) submitted on 04/27/2023 and 10/30/2024 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
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.
Claim 1-2, 4-6, 8, 14, 19-20, 23-29, 32-35, 37-38, 42-43, 46, 51, 56-57 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 1 is generally narrative and indefinite, falling to conform with the current U.S. practice.
Claim 1 recites “A genome-modified bacterial strain comprising deletions or inactivations of at least ten non-essential genes coding for two or more of: flagella components or transcriptional regulators thereof, chemotaxis proteins and regulators thereof, inhibitors of DNA replication, and proteins involved in active transport of sugars other than glucose”. However, the claim is indefinite because it is unclear whether it requires at least 10 deletions from each of the gene categories, or if it only requires at least 10 gene deletions total. For example, it can be 5 deletions in flagella components and 5 deletions in chemotaxis proteins or it can be at least 10 deletions of any of the categories or 10 deletions in each of the categories.
Claim 1 also recites “large scale conditions”. While this term is defined by some examples in claim 5 and in the specifications (page 2), it is unclear what is the definition of “large scale” in claim 1. For example, it’s unclear if volumes such as 750 liters, 500 liters or 100 liters are “large scale” in claim 1.
Therefore, the boundary of claim 1 is unclear.
Claim 2 recites “wherein the bacterial strain is a species of Escherichia, Bacillus, Corynebacterium, Pseudomonas, Rhodobacter, Zymomonas, Lactococcus, and Streptomyces. It is unclear how the strain can be all of the strains recited in the claim. Therefore, claim 2 is indefinite.
Claims 1-2, 4-6, 8, 14, 19-20, 23-29, 32-35, 37-38, 42-43, 46, 51, 56-57 recite the bacterial strain the strain exhibiting advantages in maintenance and biosynthesis performance under “large-scale conditions”. Because, claim 4 is dependent of claim 2, and claims 2, 6, 8, 14, 19-20, 23-29, 32-35, 37-38, 42-43, 46, 51, 56-57 are dependent of claim 1, therefore all the dependent claims mentioned above are indefinite.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1-2, 4-6, 8, 14, 19-20, 23-29, 34-35, 42, 59, 63, 70-71, 78 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Posfai et al. (Published April 27, 2006; hereafter Posfai; PTO-892).
As claims 1-2, 4-6, 8, 14, 19-20, 23-29, 34-35, 42, 59, 63, 70-71, 78, Posfai teaches serial/accumulative deletions in Escherichia coli MG1655 intended to reduce the bacterial genome by deleting nonessential genes and sequences, while preserving good growth profiles and protein production. Posfai also teaches that Escherichia coli strains MDS41, MDS42 and MDS43 have a total of 703, 704 and 743 genes deleted, respectively. Posfai also teaches that strain MDS41 contains del-MD1 through del-MD41, MDS42 also contains del-MD42, and MDS43 also contains del-MD43. See supporting material; table S1, page 13 and Table S4, pages 17-32.
Posfai teaches that strain MDS43 contains the flagellar component mutations/deletions, FliA, FliC, flgBCDEGHIJ, fliEFGHIJKLMNOPQR, and flhEAB of strain MD-28, the accumulative mutations/deletions of chemotaxis genes cheR, cheB, cheY, cheZ, cheW, and cheA from MD-27, and also mutations/deletions of proteins involved in active transport of sugars other than glucose, such as gatA, gatB, gatC, gatD and gatR from strain MD-37. See supporting material; Table S4, page 21, page 25, page 26 and page 28.
Posfai teaches the genes of the fliFGHIJK operon are deleted or inactivated and/or the genes of the fliMNOPQR operon are deleted or inactivated. See supporting material; Table S4, page 21 and 25.
Posfai teaches the genes of the flgBCDEGHIJ and/or flgKL operons are deleted or inactivated.
Posfai also teaches deleted genes motA, motB and chemotaxis proteins, cheR, cheB, cheY, cheZ, cheW, and cheA. Posfai teaches deletion of genes FliA and tar, tap, cheR, cheB, cheY, cheZ, cheW, and cheA. See supporting material; Table S4, page 26.
Posfai also teaches the strain containing deletions of genes gatA, gatB, gatC, gatD and gatR involved in active transport of sugars. See supporting material; Table 4, page 28.
Posfai teaches that strain MDS43 has 743 genes deleted, including the genes fliA, fliC, flgA, flgB, flgC, flgD, flgE, flgG, flgH, flgL, flgJ, flgK, flgL, fliE, fliF, fliG, fliH, fliI, fliJ, fliK, fliL, fliM, fliN, fliO, fliP, fliQ, fliR, fhE, flhA, flhB, cheZ, cheY, cheB, cheR, tap, tar, cheW, cheA, motB, motA, gatA, gatB, gatC, gatD, gatR, yahK, yahO, prpR and mhpR. See supporting material; Table S4, pages 19, 21, 25-26, 28.
Posfai teaches the growth and protein production in strain MDS41 (contains del-MD1 through del-MD41; 703 genes total) in minimal medium compared to MG1655 (parental strain) and the three growth phases: batch and two fed-batch controlled growth rate. See for example Posfai et al.; Figure 2.
Regarding the limitation "the strain exhibiting advantages in maintenance and biosynthesis performance under large-scale conditions as compared to a parent strain that does not contain said deletions", the claim teaches all structural features from the claim, so it is presumed to be capable of the claimed intended use. See MPEP 2112.01: "Where the claimed and prior art products are identical or substantially identical in structure or composition, or are produced by identical or substantially identical processes, a prima facie case of either anticipation or obviousness has been established. In re Best, 562 F.2d 1252, 1255, 195 USPQ 430, 433 (CCPA 1977). "When the PTO shows a sound basis for believing that the products of the applicant and the prior art are the same, the applicant has the burden of showing that they are not." In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990). Therefore, the prima facie case can be rebutted by evidence showing that the prior art products do not necessarily possess the characteristics of the claimed product. In re Best, 562 F.2d at 1255, 195 USPQ at 433." See also MPEP 2111.02: "To satisfy an intended use limitation which is limiting, a prior art structure which is capable of performing the intended use as recited in the preamble meets the claim. See, e.g., In re Schreiber, 128 F.3d 1473, 1477, 44 USPQ2d 1429, 1431 (Fed. Cir. 1997)"
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.
Claims 32-33, 37-38 are rejected under 35 U.S.C. 103 as being unpatentable over Posfai et. (Published April 27, 2006; hereafter Posfai; PTO-892) in the view of Loffler et al. (Published April 13, 2017; hereafter Loffler; PTO-892) as to applied to claims 1-2, 4-6, 8, 14, 19-20, 23-29, 34, 42, 59, 63, 70-71, 78 above.
The reasons why claims 1-2, 4-6, 8, 14, 19-20, 23-29, 34, 42, 59, 63, 70-71, 78 would have been obvious over Posfai in the view of Loffler are set forth above.
However, neither reference teaches deletions of the genes: cspD and aldA as in claims 32-33 and 37-38, respectively.
Loffler teaches that the E. coli genome may be reduced selectively by those genes that demand high switching on/off energy. Loffler also teaches top energy-consuming genes in E. coli, including cpsD (DNA replicator), which is pertinent to claims 32-33 and aldA (Aldehyde dehydrogenase A, NAD-linked), which is pertinent to claims 37 and 38.
It would be obvious to one of skill in the art to modify the teachings of Posfai and Loffler, thereby arriving at the invention of claims 32-33, 37-38. Since the E. coli genome reduction used to improve metabolic performance of Posfai was shown to be effective for production of desirable products in E. coli, it would have been obvious to substitute these known equivalents; see MPEP 2144.06.
Claims 43, 46, 82, 85 are rejected under 35 U.S.C. 103 as being unpatentable over Posfai et. (Published April 27, 2006; hereafter Posfai; PTO-892) in the view of Loffler et al. (Published April 13, 2017; hereafter Loffler; PTO-892) as to applied to claims 1-2, 4-6, 8, 14, 19-20, 23-29, 34, 42, 59, 63, 70-71, 78 above, and further in view of Michalowski et al. (Published January 18, 2017; hereafter Michalowski; PTO-892).
The reasons why claims 1-2, 4-6, 8, 14, 19-20, 23-29, 34, 42, 59, 63, 70-71, 78 would have been obvious over Posfai in the view of Loffler are set forth above.
However, neither reference teaches deletion of inactivation of relA as in claims 43, 82 or overexpression /complementation of a gene that increases glucose uptake as in claims 42, 85.
Michalowski also teaches the engineering and kinetic characterization of E. coli HGT (high glucose throughput), a novel chassis for exploiting additional glucose uptake to fuel product formation even under non- or slow-growth conditions. Michalowski also teaches E. coli HGT comprises a deletion of relA (which is pertinent to claims 43, 82) to suppress the main ppGpp synthesis and modulation of SpoT by integrating the ExDD motif, which is pertinent to claims 46, 85.
Michalowski teaches that the studies on pyruvate production by Zhu et al. (2008) have shown that reducing the activity of AceE (E1 component of pyruvate dehydrogenase complex, PDHC) is essentially beneficial for achieving high glucose uptake rates.
Michalowski also teaches that AceE mutants show increased glucose uptake rates (Zhu et al., 2008), therefore, this approach was also taken into consideration in the present metabolic engineering study. As such, the aceE[G267C] mutation, which affects the E1 protein component of the pyruvate dehydrogenase complex, was integrated, which is pertinent to claims 46, 85. In addition, low specific growth rates of aceE[G267C]-containing mutants are in agreement with published data for PDHC-disruptive mutations (Tran et al., 2014). The single G267C amino acid exchange within E1p of PDHC led to a drastic overproduction of pyruvate, which was associated with increased glucose consumption in the E coli ACE mutants compared to E coli WT and the stringent response mutant, which is pertinent to claims 46, 85. Michalowski teaches also that the combination of aceE modulation with an engineered stringent response in E. coli HGT achieved maximum glucose uptake rates.
It would have been obvious to one of the ordinary skill in the art to modify the teachings of Posfai and Michalowski, thereby arriving at the invention of claims 43, 46, 82, 85. Since Posfai’s reduced genome E. coli strain was shown to be effective in improving metabolic performance in E. coli. Also, since glucose is a source of energy for bacteria, the deletion of relA and the drastic overproduction of pyruvate, which is associated with increased glucose consumption in the ace mutants would be desired and beneficial to maximize the production of target proteins in E. coli, it would been obvious to substitute these known equivalents; MPEP 2144.06.
Claim 51 is rejected under 35 U.S.C. 103 as being unpatentable over Posfai et. (Published April 27, 2006; hereafter Posfai; PTO-892) in the view of Loffler et al. (Published April 13, 2017; hereafter Loffler; PTO-892) as to applied to claims 1-2, 4, 6, 8, 14, 19-20, 23-29, 34, 42, 59, 63, 70-71, 78 above, and further in view of Wu et al. Published April 24, 2020; hereafter Wu; PTO-892).
The reasons why claims 1-2, 4, 6, 8, 14, 19-20, 23-29, 34, 42, 59, 63, 70-71, 78 would have been obvious over Posfai in the view of Loffler are set forth above.
However, neither prior art teaches a secondary metabolite selected from a terpenoid, flavonoid, alkaloid, cannabinoid, polyketide, stilbenoid, and polyphenol.
Wu teaches the biosynthesis of sabinene, a bicyclic monoterpene, has been accomplished in engineered microorganisms by introducing heterologous pathways and using renewable sugar as a carbon source. However, the efficiency and titers of this method are limited by the low host tolerance to sabinene (in both eukaryotes and prokaryotes). Wu also teaches the overexpression of ybcK, ygiZ or scpA could partially rescue cell morphology under sabinene stress and overexpression of ygiZ or scpA could increase sabinene production in Escherichia coli. Wu also teaches a sabinene-tolerant strain for microbial production of sabinene and also potential regulatory mechanisms that are important for sabinene tolerance. In addition, for the first time, ybcK, ygiZ, and scpA were identified to be important for terpene tolerance in E. coli BL21(DE3).
It would have been obvious to one of ordinary skill in the art to modify the teachings of Posfai and Loffler, thereby arriving at the invention of claim 51. Since the production of terpene in E. coli was taught by Wu, it would be desired and beneficial to maximize the production of terpenes, such as sabinene because the E. coli strain of Posfai and Loffler were both shown to have an improved metabolic performance, which makes it very desirable for achieving high yields of target products, it would been obvious to substitute these known equivalents; MPEP 2144.06.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that combining prior art elements according to known methods to yield predictable results, is obvious unless its application is beyond that person's skill. KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) also discloses that the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results. In the instant case, all elements (i.e., Escherichia coli, genome reduction, the genes deleted, large-scale production and targeted products) were known in the art. In addition, combining these elements yields a method/composition wherein each element merely performs the same function as it does separately; thus, the results of the combination would be recognized as predictable to one of ordinary skill in the art. Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
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Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PRICILA HAUK TEODORO whose telephone number is (571)272-2784. The examiner can normally be reached M-F 6:15AM-3:15PM.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Daniel Kolker can be reached at (571) 272-3181. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/PRICILA NMN HAUK TEODORO/ Examiner, Art Unit 1645
/DANIEL E KOLKER/Supervisory Patent Examiner, Art Unit 1645