CRISPR base editor-based targeted random mutagenesis (BE-TRM) toolbox for directed evolution
1
조회
0
다운로드
0
인용
0
참고문헌
키워드
초록
Directed evolution (DE) of desired locus by targeted randommutagenesis (TRM) tools is a powerful approach for generatinggenetic variations with novel or improved functions, particularlyin complex genomes. TRM-based DE involves developing amutant library of targeted DNA sequences and screening thevariants for the desired properties. However, DE methods havefor a long time been confined to bacteria and yeasts. Lately,CRISPR/Cas and DNA deaminase-based tools that circumventenduring barriers such as longer life cycle, small library sizes,and low mutation rates have been developed to facilitate DE innative genetic environments of multicellular organisms. Notably,deaminase-based base editing-TRM (BE-TRM) tools havegreatly expanded the scope and efficiency of DE schemes byenabling base substitutions and randomization of targeted DNAsequences. BE-TRM tools provide a robust platform for thecontinuous molecular evolution of desired proteins, metabolicpathway engineering, creation of a mutant library of desiredlocus to evolve novel functions, and other applications, suchas predicting mutants conferring antibiotic resistance. This reviewprovides timely updates on the recent advances in BE-TRMtools for DE, their applications in biology, and future directionsfor further improvements.
Abstract
Directed evolution (DE) of desired locus by targeted randommutagenesis (TRM) tools is a powerful approach for generatinggenetic variations with novel or improved functions, particularlyin complex genomes. TRM-based DE involves developing amutant library of targeted DNA sequences and screening thevariants for the desired properties. However, DE methods havefor a long time been confined to bacteria and yeasts. Lately,CRISPR/Cas and DNA deaminase-based tools that circumventenduring barriers such as longer life cycle, small library sizes,and low mutation rates have been developed to facilitate DE innative genetic environments of multicellular organisms. Notably,deaminase-based base editing-TRM (BE-TRM) tools havegreatly expanded the scope and efficiency of DE schemes byenabling base substitutions and randomization of targeted DNAsequences. BE-TRM tools provide a robust platform for thecontinuous molecular evolution of desired proteins, metabolicpathway engineering, creation of a mutant library of desiredlocus to evolve novel functions, and other applications, suchas predicting mutants conferring antibiotic resistance. This reviewprovides timely updates on the recent advances in BE-TRMtools for DE, their applications in biology, and future directionsfor further improvements.
참고문헌 (59)
- Wang Y, "Directed evolution : methodologies and applications", Chem Rev, 121, pp.12384~12444 (2021)
- Shelake RM, "Evolution of plant mutagenesis tools : a shifting paradigm from random to targeted genome editing", Plant Biotechnol Rep, 13, pp.423~445 (2019)
- Rao GS, "Synthetic directed evolution in plants: unlocking trait engineering and improvement", Synth Biol, 6, pp.ysab025~ (2021)
- McLure RJ, "Highthroughput directed evolution : a golden era for protein science", Trends Chem, 4, pp.378~391 (2022)
- Wang H, "Base editing-mediated targeted evolution of ACCase for herbicide-resistant rice mutants", J Integr Plant Biol, 64, pp.2029~2032 (2022)
- Molina RS, "In vivo hypermutation and continuous evolution", Nat Rev Methods Primers, 2, pp.37~ (2022)
- Álvarez B, "In vivo diversification of target genomic sites using processive base deaminase fusions blocked by dCas9", Nat Commun, 11, pp.6436~ (2020)
- Chen H, "Efficient, continuous mutagenesis in human cells using a pseudo-random DNA editor", Nat Biotechnol, 38, pp.165~168 (2020)
- Esvelt KM, "A system for the continuous directed evolution of biomolecules", Nature, 472, pp.499~503 (2011)
- Rees HA, "Base editing : precision chemistry on the genome and transcriptome of living cells", Nat Rev Genet, 19, pp.770~788 (2018)
- Lee HK, "Development of CRISPR technology for precise single-base genome editing : a brief review", BMB Rep, 54, pp.98~105 (2021)
- Nishida K, "Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems", Science, 353, pp.6436~ (2016)
- Komor AC, "Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage", Nature, 533, pp.420~424 (2016)
- Gaudelli NM, "Programmable base editing of T to G C in genomic DNA without DNA cleavage", Nature, 551, pp.464~471 (2017)
- Shelake RM, "In vivo rapid investigation of CRISPR-based base editing components in Escherichia coli(IRI-CCE) : a platform for evaluating base editing tools and their components", Int J Mol Sci, 23, pp.1145~ (2022)
- Pramanik D, "CRISPR-mediated engineering across the central dogma in plant biology for basic research and crop improvement", Mol Plant, 14, pp.127~150 (2021)
- Hess GT, "Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells", Nat Methods, 13, pp.1036~1042 (2016)
- Halperin SO, "CRISPRguided DNA polymerases enable diversification of all nucleotides in a tunable window", Nature, 560, pp.248~252 (2018)
- Nishida K, "Method for modifying genome sequence to introduce specific mutation to targeted DNA sequence by base-removal reaction, and molecular complex used therein", U.S. Patent Appl. No. 15, 2021
- Kim JY, "Method for inducing reactive oxygen species-mediated base mutation of target gene", KR Patent Appl. No. 1020180096931, ~ (2021)
- Klompe SE, "Transposon-encoded CRISPR-Cas systems direct RNA-guided DNA integration", Nature, 571, pp.219~225 (2019)
- Strecker J, "RNA-guided DNA insertion with CRISPR-associated transposases", Science, 365, pp.48~53 (2019)
- Anzalone AV, "Searchand-replace genome editing without double-strand breaks or donor DNA", Nature, 576, pp.149~157 (2019)
- Packer MS, "Methods for the directed evolution of proteins", Nat Rev Genet, 16, pp.379~394 (2015)
- Ma Y, "Targeted AID-mediated mutagenesis(TAM)enables efficient genomic diversification in mammalian cells", Nat Methods, 13, pp.1029~1035 (2016)
- Kurt IC, "CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells", Nat Biotechnol, 39, pp.41~46 (2021)
- Zhao D, "Glycosylase base editors enable C-to-A and C-to-G base changes", Nat Biotechnol, 39, pp.35~40 (2021)
- Chen S, "Efficient C-To-G base editing with improved target compatibility using engineered deaminase-nCas9 fusions", CRISPR J, 5, pp.389~396 (2022)
- Sun N, "Reconstructed glycosylase base editors GBE2. 0 with enhanced C-to-G base editing efficiency and purity", Mol Ther, 30, pp.2452~2463 (2022)
- Koblan LW, "Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning", Nat Biotechnol, 39, pp.1414~1425 (2021)
- Chen L, "Programmable C : G to G : C genome editing with CRISPR-Cas9-directed base excision repair proteins", Nat Commun, 12, pp.1384~ (2021)
- Yuan T, "Optimization of C-to-G base editors with sequence context preference predictable by machine learning methods", Nat Commun, 12, pp.4902~ (2021)
- Richter MF, "Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity", Nat Biotechnol, 38, pp.883~891 (2020)
- Anzalone AV, "Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors", Nat Biotechnol, 38, pp.824~844 (2020)
- Gaudelli NM, "Directed evolution of adenine base editors with increased activity and therapeutic application", Nat Biotechnol, 38, pp.892~900 (2020)
- Tong H, "Programmable A-to-Y base editing by fusing an adenine base editor with an N-methylpurine DNA glycosylase", Nat Biotechnol, 41, pp.1080~1084 (2023)
- Li C, "Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors", Nat Biotechnol, 38, pp.875~882 (2020)
- Xie J, "ACBE, a new base editor for simultaneous C-to-T and A-to-G substitutions in mammalian systems", BMC Biol, 18, pp.131~ (2020)
- Sakata RC, "Base editors for simultaneous introduction of C-to-T and A-to-G mutations", Nat Biotechnol, 38, pp.865~869 (2020)
- Zhang X, "Dual base editor catalyzes both cytosine and adenine base conversions in human cells", Nat Biotechnol, 38, pp.856~860 (2020)
- Grünewald J, "A dualdeaminase CRISPR base editor enables concurrent adenine and cytosine editing", Nat Biotechnol, 38, pp.861~864 (2020)
- Shelake RM, "Improved dual base editor systems(iACBEs)for simultaneous conversion of adenine and cytosine in the bacterium Escherichia coli", mBio, 14, pp.e0229622~ (2023)
- Hao W, "Construction and application of an efficient dual-base editing platform for Bacillus subtilis evolution employing programmable base conversion", Chem Sci, 13, pp.14395~14409 (2022)
- Tao W, "CABE-RY : a PAMflexible dual-mutation base editor for reliable modeling of multi-nucleotide variants", Mol Ther Nucleic Acids, 26, pp.114~121 (2021)
- Xiong X, "A cytosine base editor toolkit with varying activity windows and target scopes for versatile gene manipulation in plants", Nucleic Acids Res, 50, pp.3565~3580 (2022)
- Xue N, "Improving adenine and dual base editors through introduction of TadA-8e and Rad51DBD", Nat Commun, 14, pp.1224~ (2023)
- Liang Y, "AGBE : a dual deaminase-mediated base editor by fusing CGBE with ABE for creating a saturated mutant population with multiple editing patterns", Nucleic Acids Res, 50, pp.5384~5399 (2022)
- Moore CL, "A processive protein chimera introduces Mutations across defined DNA regions in vivo", J Am Chem Soc, 140, pp.11560~11564 (2018)
- Cravens A, "Polymeraseguided base editing enables in vivo mutagenesis and rapid protein engineering", Nat Commun, 12, pp.1579~ (2021)
- Butt H, "Synthetic evolution of herbicide resistance using a T7 RNAP-based random DNA base editor", Life Sci Alliance, 5, pp.e202201538~ (2022)
- Park H, "Gene-specific mutagenesis enables rapid continuous evolution of enzymes in vivo", Nucleic Acids Res, 49, pp.E32~E32 (2021)
- Eom GE, "Development of a genome-targeting mutator for the adaptive evolution of microbial cells", Nucleic Acids Res, 50, pp.E38~ (2022)
- Mengiste AA, "Expanded MutaT7 toolkit efficiently and simultaneously accesses all possible transition mutations in bacteria", Nucleic Acids Res, 51, pp.E31~ (2023)
- Seo D, "A dual gene-specific mutator system installs all transition mutations at similar frequencies in vivo", Nucleic Acids Res, 51, pp.e59~ (2023)
- Shelake RM, "Engineering drought and salinity tolerance traits in crops through CRISPR-mediated genome editing : targets, tools, challenges, and perspectives", Plant Commun, 3, pp.100417~ (2022)
- Xu R, "Development of an efficient plant dual cytosine and adenine editor", J Integr Plant Biol, 63, pp.1600~1605 (2021)
- Leong BJ, "Continuous directed evolution of a feedback-resistant Arabidopsis arogenate dehydratase in plantized Escherichia coli", ACS Synth Biol, 12, pp.43~50 (2023)
- "Activation-induced cytidine deaminase-based in vivo continuous evolution system enables rapid protein engineering" (2023)[URL]
- Liu Z, "Advances in ultrahighthroughput screening technologies for protein evolution", Trends Biotechnol, 41, pp.1168~1181 (2023)
