Lim HG, Kwak DH, Park S, Woo S, Yang JS, Kang CW, et al. Vibrio Sp. dhg as a platform for the biorefinery of brown macroalgae. Nat Commun. 2019;10:2486.
Shin HJ, Woo S, Jung GY, Park JM. Indole-3-acetic acid production from alginate by Vibrio Sp. dhg: physiology and characteristics. Biotechnol Bioprocess Eng. 2023.
Moon JH, Woo S, Shin HJ, Lee HK, Jung GY, Lim HG. Direct Itaconate production from brown macroalgae using engineered Vibrio Sp. dhg. J Agric Food Chem. 2024;72:16860–6.
Lee HK, Woo S, Baek D, Min M, Jung GY, Lim HG. Direct and robust citramalate production from brown macroalgae using fast-growing Vibrio Sp. dhg. Bioresour Technol. 2024;394:130304.
Banno S, Nishida K, Arazoe T, Mitsunobu H, Kondo A. Deaminase-mediated multiplex genome editing in Escherichia coli. Nat Microbiol. 2018;3:423–9.
Wang Y, Liu Y, Liu J, Guo Y, Fan L, Ni X, et al. MACBETH: multiplex automated Corynebacterium glutamicum base editing method. Metab Eng. 2018;47:200–10.
Hao W, Cui W, Suo F, Han L, Cheng Z, Zhou Z. Construction and application of an efficient dual-base editing platform for Bacillus subtilis evolution employing programmable base conversion. Chem Sci. 2022;13:14395–409.
Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016;533:420–4.
Nishida K, Arazoe T, Yachie N, Banno S, Kakimoto M, Tabata M et al. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science. 2016;353.
Yue S-J, Huang P, Li S, Cai Y-Y, Wang W, Zhang X-H, et al. Developing a CRISPR-assisted base-editing system for genome engineering of Pseudomonas chlororaphis. Microb Biotechnol. 2022;15:2324–36.
Yu S, Price MA, Wang Y, Liu Y, Guo Y, Ni X, et al. CRISPR-dCas9 mediated cytosine deaminase base editing in Bacillus subtilis. ACS Synth Biol. 2020;9:1781–9.
Wang Y, Liu Y, Li J, Yang Y, Ni X, Cheng H, et al. Expanding targeting scope, editing window, and base transition capability of base editing in Corynebacterium glutamicum. Biotechnol Bioeng. 2019;116:3016–29.
Hao W, Cui W, Cheng Z, Han L, Suo F, Liu Z, et al. Development of a base editor for protein evolution via in situ mutation in vivo. Nucleic Acids Res. 2021;49:9594–605.
Wang Y, Cheng H, Liu Y, Liu Y, Wen X, Zhang K, et al. In-situ generation of large numbers of genetic combinations for metabolic reprogramming via CRISPR-guided base editing. Nat Commun. 2021;12:678.
Hao W, Cui W, Liu Z, Suo F, Wu Y, Han L, et al. A New-Generation base editor with an expanded editing window for microbial cell evolution in vivo based on CRISPR–Cas12b engineering. Adv Sci (Weinh). 2024;11:e2309767.
Xia P-F, Casini I, Schulz S, Klask C-M, Angenent LT, Molitor B. Reprogramming acetogenic bacteria with CRISPR-Targeted base editing via deamination. ACS Synth Biol. 2020;9:2162–71.
Tong Y, Whitford CM, Robertsen HL, Blin K, Jørgensen TS, Klitgaard AK, et al. Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST. Proc Natl Acad Sci USA. 2019;116:20366–75.
Wei Y, Feng L-J, Yuan X-Z, Wang S-G, Xia P-F. Developing a base editing system for marine Roseobacter clade bacteria. ACS Synth Biol. 2023;12:2178–86.
Stukenberg D, Hoff J, Faber A, Becker A. NT-CRISPR, combining natural transformation and CRISPR-Cas9 counterselection for markerless and scarless genome editing in Vibrio natriegens. Commun Biol. 2022;5:265.
Weber E, Engler C, Gruetzner R, Werner S, Marillonnet S. A modular cloning system for standardized assembly of multigene constructs. PLoS ONE. 2011;6:e16765.
Hwang G-H, Bae S. Web-Based computational tools for base editors. Methods Mol Biol. 2023;2606:13–22.
Weinstock MT, Hesek ED, Wilson CM, Gibson DG. Vibrio natriegens as a fast-growing host for molecular biology. Nat Methods. 2016;13:849–51.
Sayers EW, Bolton EE, Brister JR, Canese K, Chan J, Comeau DC, et al. Database resources of the National center for biotechnology information in 2023. Nucleic Acids Res. 2023;51:D29–38.
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75.
Liu Z, Dong H, Cui Y, Cong L, Zhang D. Application of different types of CRISPR/Cas-based systems in bacteria. Microb Cell Fact. 2020;19:172.
Lee J, Lim K, Kim A, Mok YG, Chung E, Cho S-I, et al. Prime editing with genuine Cas9 Nickases minimizes unwanted indels. Nat Commun. 2023;14:1786.
Lee HH, Ostrov N, Wong BG, Gold MA, Khalil AS, Church GM. Functional genomics of the rapidly replicating bacterium vibrio natriegens by CRISPRi. Nat Microbiol. 2019;4:1105–13.
Wang P, Du X, Zhao Y, Wang W, Cai T, Tang K, et al. Combining CRISPR/Cas9 and natural excision for the precise and complete removal of mobile genetic elements in bacteria. Appl Environ Microbiol. 2024;90:e0009524.
Anzalone AV, Koblan LW, Liu DR. Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors. Nat Biotechnol. 2020;38:824–44.
Wang X, Li J, Wang Y, Yang B, Wei J, Wu J, et al. Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion. Nat Biotechnol. 2018;36:946–9.
Zong Y, Song Q, Li C, Jin S, Zhang D, Wang Y et al. Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A. Nat Biotechnol. 2018.
Wang ZG, Smith DG, Mosbaugh DW. Overproduction and characterization of the uracil-DNA glycosylase inhibitor of bacteriophage PBS2. Gene. 1991;99:31–7.
Wang L, Xue W, Yan L, Li X, Wei J, Chen M, et al. Enhanced base editing by co-expression of free uracil DNA glycosylase inhibitor. Cell Res. 2017;27:1289–92.
Guzman LM, Belin D, Carson MJ, Beckwith J. Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J Bacteriol. 1995;177:4121–30.
Andersen JB, Sternberg C, Poulsen LK, Bjorn SP, Givskov M, Molin S. New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl Environ Microbiol. 1998;64:2240–6.
Purcell O, Grierson CS, di Bernardo M, Savery NJ. Temperature dependence of ssrA-tag mediated protein degradation. J Biol Eng. 2012;6:10.
Cutugno L, Mc Cafferty J, Pané-Farré J, O’Byrne C, Boyd A. RpoB mutations conferring rifampicin-resistance affect growth, stress response and motility in Vibrio vulnificus. Microbiol (Reading Engl). 2020;166:1160–70.
Jin DJ, Walter WA, Gross CA. Characterization of the termination phenotypes of rifampicin-resistant mutants. J Mol Biol. 1988;202:245–53.
Tripathi SA, Olson DG, Argyros DA, Miller BB, Barrett TF, Murphy DM, et al. Development of pyrF-based genetic system for targeted gene deletion in clostridium thermocellum and creation of a Pta mutant. Appl Environ Microbiol. 2010;76:6591–9.
Boeke JD, Trueheart J, Natsoulis G, Fink GR. [10] 5-Fluoroorotic acid as a selective agent in yeast molecular genetics. Recombinant DNA part E. Elsevier; 1987. pp. 164–75.
Chung D, Farkas J, Westpheling J. Overcoming restriction as a barrier to DNA transformation in Caldicellulosiruptor species results in efficient marker replacement. Biotechnol Biofuels. 2013;6:82.
Dong H, Zhang Y, Dai Z, Li Y. Engineering clostridium strain to accept unmethylated DNA. PLoS ONE. 2010;5:e9038.
Vasu K, Nagaraja V. Diverse functions of restriction-modification systems in addition to cellular defense. Microbiol Mol Biol Rev. 2013;77:53–72.
Johnston CD, Cotton SL, Rittling SR, Starr JR, Borisy GG, Dewhirst FE, et al. Systematic evasion of the restriction-modification barrier in bacteria. Proc Natl Acad Sci USA. 2019;116:11454–9.
Roberts RJ, Vincze T, Posfai J, Macelis D. REBASE: a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res. 2023;51:D629–30.
Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, et al. EggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 2019;47:D309–14.
Walton RT, Christie KA, Whittaker MN, Kleinstiver BP. Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants. Science. 2020;368:290–6.
Kim YB, Komor AC, Levy JM, Packer MS, Zhao KT, Liu DR. Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions. Nat Biotechnol. 2017;35:371–6.
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