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 .
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
Claims 1-14 are currently pending. There are no new, amended or canceled claims. Claims 1-14 will be examined on the merits.
Priority
Acknowledgement is made of applicant’s claim for foreign priority based on an application filed on December 29, 2023. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement (IDS)
The information disclosure statement (IDS) 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 § 103
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 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 1-14 are rejected under 35 U.S.C. 103 as being unpatentable over Lim et al. 2019 (Published in 2019; hereafter Lim; PTO-892) in view of Atsumi et al. (Published in 2008; hereafter Atsumi; PTO-892) and further view of Wu et al. (Published in 2022; hereafter Wu; PTO-892).
Lim teaches Vibrio sp. Dhg strain can be used as a platform for the efficient conversion of brown macroalgae sugars into diverse value-added biochemicals, which is pertinent to claims 1, 7-14.
Lim teaches gene expression control in Vibrio sp. dhg at the translational level, prediction of translation efficiency in bacteria, a biophysical model of the translation initiation process, the 16S rDNA of Vibrio sp. dhg has a high similarity (90%) and the same anti-Shine-Dalgarno sequence (ACCTCCTTA) to the 16 S rDNA of E. coli, the biophysical model still requires validation in Vibrio sp. Dhg, a 5′-UTR library covering a broad range of sgfp expression levels using UTR Library Designer, which is pertinent to claims 2. See for example, Supplementary Data 3; Supplementary Table 6.
Lim teaches codon usage of Vibrio sp. Dhg., which is pertinent to claim 1. See Supplementary claim 1.
Lim teaches endogenous exo and beta in Vibrio sp. Dhg expressed under the control of the Ptac promoter and a synthetic 5′-UTR, which is pertinent to claim 2. See for example, Supplementary Table 7.
Lim teaches the promoter regions of ribosomal genes are highly expressed in Vibrio sp. dhg, and have similar sequences (TTGANN and TATAAT) to the bacterial −35 and −10 boxes (TTGACA and TATAAT, respectively), the common promoters used for E. coli would also be compatible with Vibrio sp. Dhg, plasmids encoding the sgfp (super-folding green fluorescence protein) gene under the control of the conventional promoters PJ23119, Plac, Ptac, Ptet, and Para, endogenous exo and beta in Vibrio sp. dhg, expressed under the control of the Ptac promoter and a synthetic 5′-UTR which is pertinent to claim 2. See for example, Supplementary Table 7.
Lim teaches pACYC and P15A replication origin, which is pertinent to claim 3. See for example, Supplementary Data 1 (List of strains and plasmids).
SEQ ID NO: 3 is the tac promoter sequence is well-known to one of skill in the art, which is pertinent to claim 2.
SEQ ID NO: 4 was searched. SEQ ID NO: 4 has 100% match (24 out 25 nucleotides total) with SEQ ID NO: 7 of Meijrink et al. (US Pat. US 11396665; hereafter Meijrink; PTO-892), which is pertinent to claim 2. See figure below.
It is noted that US Pat. US 11396665 teaches a “CRISPR-CAS system for a filamentous fungal host cell”, and “SEQ ID NO: 7 sets out the genome of Mortierella alpina ATCC 32222”. See column 4; line 27.
PNG
media_image1.png
264
733
media_image1.png
Greyscale
Lim teaches “minimize by-product formation”, deletion of the endogenous ldhA (lactate dehydrogenase), frdABCD (fumarate reductase) and pflB (pyruvate-formate lyase) genes, the VDHG411 strain, which is pertinent to claim 5-6. See for example, Supplementary Figure 8b; Supplementary Figure 12.
Lim teaches Vibrio sp. dhg simultaneously consume alginate and mannitol, these two sugars have different oxidation states, this property is highly advantageous for biochemical production (e.g., ethanol) in an oxygen-limited environment, Vibrio sp. dhg is highly suited to using an alginate mannitol mixture, which is pertinent to claim 13. See for example Figure. 1e; Supplementary Note 2.
Lim teaches that “the use of brown macroalgae as a feedstock has been limited due to the difficulties of alginate assimilation, and the use of Vibrio sp. dhg strain as a microbial platform could overcome this issue”, which is pertinent to claim 14.
However, Lim does not teach cimA3.7 as claim 1.
Lim does not teach leuCD deletion as claims 5-6.
Lim does not teach a method of producing citramalate as claims 7-12.
Atsumi teaches that “an alternative route to 2-ketobutyrate from pyruvate and acetyl coenzyme A (acetyl-CoA) via citramalate synthase (CimA) has been reported in some organisms (e.g., Leptospira interrogans and Methanococcus jannaschii), which is pertinent to claim 1, 7-14.
Atsumi teaches that “this pathway (designated the citramalate pathway is the most direct route to synthesize 2-ketobutyrate and does not involve transamination followed by deamination, which is pertinent to claim 5-6. See for example Figure 1.
Atsumi teaches the that “(R)-Citramalate synthesized from pyruvate and acetyl-CoA by CimA is then converted to 2-ketobutyrate via LeuCD- and LeuB-mediated reactions, parallel to the similar reactions in leucine biosynthesis. To take advantage of this short keto acid pathway, we expressed (R)-citramalate synthase (CimA) of M. jannaschii in E. coli. However, heterologous proteins are not always active in foreign hosts and thermophilic enzymes often lose activities at moderate temperatures. To improve the activity of CimA, we employed a directed evolution strategy”, which is pertinent to claim 5-6. See for example, Figure 1.
Atsumi teaches directed evolution of Methnococcus jannaschii citramalate synthase. Directed evolution of CimA enhanced the specific activity over a wide temperature range (30 to 70°C), which is pertinent to claim 1. See for example, Figures 3-4. See Figure below.
Atsumi teaches “pSA142 (p15A ori; Kanr; PLlacO1::cimA3.7-leuABCD). CimA is a homologue of LeuA”. “The activities of CimA and LeuA are regulated by the corresponding amino acid end product l-isoleucine or l-leucine, respectively”. “l-leucine binds to the C-terminal domain in LeuA”. “CimA3.7 is missing this C-terminal domain shown by homology alignment to be involved in feedback inhibition, suggesting that CimA3.7 may be insensitive to feedback inhibition by l-isoleucine”. which is pertinent to claims 3-6. See for example, Figure 7.
Atsumi teaches that “mutations in CimA3.7 increase both its activity and stability at moderate temperatures. However, the relative superiority of CimA3.7 decreases with increasing temperature, presumably because CimA mutants were screened solely for improvements in activity in E. coli at 30°C, which is pertinent to claims 3-6. See for example, Figure 2. See Figure below.
Atsumi teaches the plasmid, pCS27 (without cimA and leuABCD), which is pertinent to claims 1, 3, 5-12.
Atsumi teaches the citramalate pathway, which is pertinent to claims 7-12. See for example, Figure 1.
The SEQ ID NO: 1 encodes a polypeptide sequence that has 99% match with CimA of Methanocaldococcus jannaschii, which is pertinent to claim 1. See Figure below.
Atsumi teaches sequence analysis of CimA3.7 (SEQ ID NO: 1), structure of Mycobacterium LeuA, and CimA (M. jannaschii), CimA (E. coli) and CimA (M. tuberculosis), which is pertinent to claim 1. See Figure below.
PNG
media_image2.png
850
613
media_image2.png
Greyscale
PNG
media_image3.png
575
784
media_image3.png
Greyscale
PNG
media_image4.png
957
943
media_image4.png
Greyscale
Neither Lim nor Atsumi explicitly teach the expression cassette is introduced into a plasmid pJUMP24-1 A of a pRO 1 600/ColE I mixed replication origin as claim 4.
Lim and Atsumi also do not teach “an ackA-pta operon deletion and also do not explicitly teach a leuCD operon is deleted” as claim 5.
Wu teaches the pZElac_mjCimA plasmid has a replication origin (initiation of replication) from ColE1, pLlacO1 promoter (drives transcription of the target gene), lac repressor LacI (inhibits the metabolism of lactose), and ampicillin resistant marker (antibiotic selectable marker) and carries the gene CimA encoding the citramalate synthase, which is pertinent to claim 4. See for example Figure 1. See Figure below.
***specifications, paragraph [00381; 0064] teaches “A Vibrio sp. DHG strain introduced with a plasmid pJUMP24-1A of a pRO1600/ColE1 mixed replication origin including the cimA3.7 gene cassette was named VHC”.
Wu teaches that “Acetate is an undesirable byproduct potentially formed from acetyl-CoA in an aerobic fermentation environment. Acetal-CoA is also the key substrate for citramalate production”. The leuC and leuD knockout strains along with P1 phage of ackA were obtained from the Keio collection. The pta, ackA, and poxB gene deletions were found to be critical to reducing acetate accumulation during aerobic growth, which is pertinent to claims 5-6.
Wu teaches metabolic pathway design for maximizing the yield of (R)-citramalate, the novo production of (R)-citramalate from glucose in E. coli, which is pertinent to claims 7-14. See for example, Figure 2
SEQ ID NOs: 6-13 were searched. All searched SEQ IDs have 100% match with genome sequences from Vibrio sp. dgh, which is pertinent to claims 5-6.
PNG
media_image5.png
751
1219
media_image5.png
Greyscale
It would be obvious to one of skill in the art to combine the teachings of Lim, Atsumi and Wu thereby arriving at the invention of claims 1-14, because the same strain engineering rationale and elements used to create a De novo production of (R)-citramalate in E. coli, which was based on the biosynthetic pathway of M. jannaschii can be also transferred/adapted to Vibrio sp. dhg strain as taught by Lim, Atsumi and Wu. Thus, it would be highly desirable and beneficial to apply the successful genetic modifications made in E. coli to a platform that utilizes Vibrio sp dhg for the efficient conversion of brown macroalgae sugars into diverse value-added biochemicals with high productivities and yields, such as citramalate, especially due Vibrio sp. dhg being highly suited to use alginate mannitol mixture as taught by Wu, it would have been obvious to substitute these known equivalents; MPEP 2144.06.
See MPEP 2144(II): “The strongest rationale for combining references is a recognition, expressly or impliedly in the prior art … that some advantage or expected beneficial result would have been produced by their combination.
Also, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that the simple substitution of one known element for another to obtain 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".
Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Conclusion
No claim is 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-3:00PM.
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, Heather Calamita can be reached at (571) 272-2876. 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.
/PRICILA NMN HAUK TEODORO/ Examiner, Art Unit 1645
/HEATHER CALAMITA/ Supervisory Patent Examiner, Art Unit 1684
Prosecution Insights