碱基编辑技术及其在微生物合成生物学中的应用

doi:10.12211/2096-8280.2022-053

摘要/Abstract

摘要：

CRISPR/Cas系统的发现与发展对生命科学领域产生了革命性的影响，借助CRISPR/Cas系统研发出的一系列工具为相关领域的研究带来了极大的便利。碱基编辑器便是其中一类基于CRISPR/Cas系统开发的可实现碱基转换和颠换的基因编辑工具，其通过将胞苷或腺苷脱氨酶以及其他功能元件与失去双链切割活性的Cas蛋白相融合，由sgRNA引导，实现对基因组上目标位置胞嘧啶或腺嘌呤的碱基转换。碱基编辑器一经开发便在生物学、医学等领域展现出巨大的应用潜力，虽然经过不断优化，但目前在使用时仍然存在着许多制约因素。本文简述了几种主要碱基编辑器的发展，并介绍了碱基编辑器存在的靶向范围受限和脱靶编辑的问题以及现有的优化措施。同时列举了我国部分科研工作者将碱基编辑技术运用于微生物合成生物学领域的进展，并展望了碱基编辑技术的发展及其在微生物合成生物学领域的应用前景。

关键词: 碱基编辑器, 特异性优化, 靶向范围拓展, 微生物, 合成生物学

Abstract:

The discovery and development of the CRISPR/Cas system have a revolutionary influence on life sciences. A series of tools derived from the CRISPR/Cas system have brought great convenience to research in the field of life sciences. The base editors developed based on the CRISPR/Cas system are gene editing tools that can achieve base conversions and transversion on target. The base editors are constructed by fusing cytosine or adenosine deaminase, and other functional elements to Cas proteins with abolished double strand DNA cleavage activity to convert cytidine or adenine into other bases at genome on-target sites guided by sgRNAs. Base editors have shown great potential in biology, medicine and related fields. Although they have already been continuously optimized, there are still problems affecting further application of base editors. In this review, we briefly describe the development of DNA base editors. Furthermore, we introduce in detail the problems of the limited editing range of base editors as well as the corresponding optimization strategies by increasing the target sites recognized by the locator moiety and expanding or narrowing the editing window of the effector moiety. At the same time, we introduce several off-target editing detection methods specially developed for base editing. Based on usual and developed detection methods, multiple and frequent off-target editing caused by base editors were found at both DNA and RNA levels. We also introduced various effective optimization strategies to improve the editing specificity of the base editors in every respect. Most of these strategies are based on protein modification, but also on optimization of sgRNA and spatio-temporal regulation of base editing systems. These measures greatly enrich the application scenarios of the base editors. Then, we discuss the progress on applying base editors to the field of microbial synthetic biology, including revealing the metabolic pathway and synthesis mechanism of natural products as well as improving the production of target compounds in multiple species. Finally, we envisage the promising development of base editing in synthetic biology in the future. {L-End}

Key words: base editors, improvement of specificity, expansion of target range, microorganism, synthetic biology

中图分类号:

Q812

王雁南, 孙宇辉. 碱基编辑技术及其在微生物合成生物学中的应用[J]. 合成生物学, 2023, 4(4): 720-737.

Yannan WANG, Yuhui SUN. Base editing technology and its application in microbial synthetic biology[J]. Synthetic Biology Journal, 2023, 4(4): 720-737.

图/表 1

参考文献 131

1	JANSEN R, VAN EMBDEN J D A, GAASTRA W, et al. Identification of genes that are associated with DNA repeats in prokaryotes[J]. Molecular Microbiology, 2002, 43(6): 1565-1575.
2	CONG L, RAN F A, COX D, et al. Multiplex genome engineering using CRISPR/Cas systems[J]. Science, 2013, 339(6121): 819-823.
3	MALI P, YANG L H, ESVELT K M, et al. RNA-guided human genome engineering via Cas9[J]. Science, 2013, 339(6121): 823-826.
4	LANDRUM M J, LEE J M, BENSON M, et al. ClinVar: public archive of interpretations of clinically relevant variants[J]. Nucleic Acids Research, 2016, 44(D1): D862-D868.
5	HAAPANIEMI E, BOTLA S, PERSSON J, et al. CRISPR-Cas9 genome editing induces a p53-mediated DNA damage response[J]. Nature Medicine, 2018, 24(7): 927-930.
6	IHRY R J, WORRINGER K A, SALICK M R, et al. p53 Inhibits CRISPR-Cas9 engineering in human pluripotent stem cells[J]. Nature Medicine, 2018, 24(7): 939-946.
7	KOMOR A C, KIM Y B, PACKER M S, et al. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage[J]. Nature, 2016, 533(7603): 420-424.
8	NISHIDA K, ARAZOE T, YACHIE N, et al. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems[J]. Science, 2016, 353(6305): aaf8729.
9	WANG X, LI J N, WANG Y, et al. Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion[J]. Nature Biotechnology, 2018, 36(10): 946-949.
10	KOBLAN L W, DOMAN J L, WILSON C, et al. Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction[J]. Nature Biotechnology, 2018, 36(9): 843-846.
11	LI X S, WANG Y, LIU Y J, et al. Base editing with a Cpf1-cytidine deaminase fusion[J]. Nature Biotechnology, 2018, 36(4): 324-327.
12	NISHIMASU H, SHI X, ISHIGURO S, et al. Engineered CRISPR-Cas9 nuclease with expanded targeting space[J]. Science, 2018, 361(6408): 1259-1262.
13	ZONG Y, SONG Q N, LI C, et al. Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A[J]. Nature Biotechnology, 2018, 36(10): 950–953.
14	JIANG W, FENG S J, HUANG S S, et al. BE-PLUS: a new base editing tool with broadened editing window and enhanced fidelity[J]. Cell Research, 2018, 28(8): 855-861.
15	LEE S S, DING N, SUN Y D, et al. Single C-to-T substitution using engineered APOBEC3G-nCas9 base editors with minimum genome- and transcriptome-wide off-target effects[J]. Science Advances, 2020, 6(29): eaba1773.
16	TAN J J, ZHANG F, KARCHER D, et al. Engineering of high-precision base editors for site-specific single nucleotide replacement[J]. Nature Communications, 2019, 10: 439.
17	REES H A, KOMOR A C, YEH W H, et al. Improving the DNA specificity and applicability of base editing through protein engineering and protein delivery[J]. Nature Communications, 2017, 8: 15790.
18	DOMAN J L, RAGURAM A, NEWBY G A, et al. Evaluation and minimization of Cas9-independent off-target DNA editing by cytosine base editors[J]. Nature Biotechnology, 2020, 38(5): 620-628.
19	GRÜNEWALD J, ZHOU R H, GARCIA S P, et al. Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors[J]. Nature, 2019, 569(7756): 433-437.
20	MOK B Y, DE MORAES M H, ZENG J, et al. A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing[J]. Nature, 2020, 583(7817): 631-637.
21	LIM K, CHO S I, KIM J S. Nuclear and mitochondrial DNA editing in human cells with zinc finger deaminases[J]. Nature Communications, 2022, 13(1): 366.
22	GAUDELLI N M, KOMOR A C, REES H A, et al. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage[J]. Nature, 2017, 551(7681): 464-471.
23	RICHTER M F, ZHAO K T, ETON E, et al. Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity[J]. Nature Biotechnology, 2020, 38(7): 883-891.
24	LIU Y, ZHOU J Z, LAN T, et al. Elimination of Cas9-dependent off-targeting of adenine base editor by using TALE to separately guide deaminase to target sites[J]. Cell Discovery, 2022, 8: 28.
25	LI S, YUAN B, CAO J X, et al. Docking sites inside Cas9 for adenine base editing diversification and RNA off-target elimination[J]. Nature Communications, 2020, 11: 5827.
26	ZHANG X H, ZHU B Y, CHEN L, et al. Dual base editor catalyzes both cytosine and adenine base conversions in human cells[J]. Nature Biotechnology, 2020, 38(7): 856-860.
27	WANG Y H, ZHOU L F, TAO R, et al. sgBE: a structure-guided design of sgRNA architecture specifies base editing window and enables simultaneous conversion of cytosine and adenosine[J]. Genome Biology, 2020, 21(1): 222.
28	KURT I C, ZHOU R H, IYER S, et al. CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells[J]. Nature Biotechnology, 2021, 39(1): 41-46.
29	CHEN L W, PARK J E, PAA P, et al. Programmable C∶G to G∶C genome editing with CRISPR-Cas9-directed base excision repair proteins[J]. Nature Communications, 2021, 12: 1384.
30	KOMOR A C, ZHAO K T, PACKER M S, et al. Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C: G-to-T: A base editors with higher efficiency and product purity[J]. Science Advances, 2017, 3(8): eaao4774.
31	GRÜNEWALD J, ZHOU R H, LAREAU C A, et al. A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing[J]. Nature Biotechnology, 2020, 38(7): 861-864.
32	LI C, ZHANG R, MENG X B, et al. Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors[J]. Nature Biotechnology, 2020, 38(7): 875-882.
33	SAKATA R C, ISHIGURO S, MORI H, et al. Base editors for simultaneous introduction of C-to-T and A-to-G mutations[J]. Nature Biotechnology, 2020, 38(7): 865-869.
34	TAO W Y, LIU Q, HUANG S S, et al. CABE-RY: a PAM-flexible dual-mutation base editor for reliable modeling of multi-nucleotide variants[J]. Molecular Therapy-Nucleic Acids, 2021, 26: 114-121.
35	XIE J K, HUANG X Y, WANG X, et al. ACBE, a new base editor for simultaneous C-to-T and A-to-G substitutions in mammalian systems[J]. BMC Biology, 2020, 18(1): 131.
36	ARBAB M, SHEN M W, MOK B, et al. Determinants of base editing outcomes from target library analysis and machine learning[J]. Cell, 2020, 182(2): 463-480.e30.
37	KIM H S, JEONG Y K, HUR J K, et al. Adenine base editors catalyze cytosine conversions in human cells[J]. Nature Biotechnology, 2019, 37(10): 1145-1148.
38	MA Y Q, ZHANG J Y, YIN W J, et al. Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells[J]. Nature Methods, 2016, 13(12): 1029-1035.
39	ZHAO D D, LI J, LI S W, et al. Glycosylase base editors enable C-to-A and C-to-G base changes[J]. Nature Biotechnology, 2021, 39(1): 35-40.
40	KOBLAN L W, ARBAB M, SHEN M W, et al. Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning[J]. Nature Biotechnology, 2021, 39(11): 1414-1425.
41	YUAN T L, YAN N N, FEI T Y, et al. Optimization of C-to-G base editors with sequence context preference predictable by machine learning methods[J]. Nature Communications, 2021, 12: 4902.
42	LI R Q, CHAR S N, LIU B, et al. High-efficiency plastome base editing in rice with TAL cytosine deaminase[J]. Molecular Plant, 2021, 14(9): 1412-1414.
43	WEI Y H, LI Z F, XU K, et al. Mitochondrial base editor DdCBE causes substantial DNA off-target editing in nuclear genome of embryos[J]. Cell Discovery, 2022, 8: 27.
44	CHO S I, LEE S H, MOK Y G, et al. Targeted A-to-G base editing in human mitochondrial DNA with programmable deaminases[J]. Cell, 2022, 185(10): 1764-1776.e12.
45	BASS B L. RNA editing by adenosine deaminases that act on RNA[J]. Annual Review of Biochemistry, 2002, 71: 817-846.
46	BAZAK L, HAVIV A, BARAK M, et al. A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes[J]. Genome Research, 2014, 24(3): 365-376.
47	MONTIEL-GONZALEZ M F, VALLECILLO-VIEJO I, YUDOWSKI G A, et al. Correction of mutations within the cystic fibrosis transmembrane conductance regulator by site-directed RNA editing[J]. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110(45): 18285-18290.
48	MONTIEL-GONZÁLEZ M F, VALLECILLO-VIEJO I C, ROSENTHAL J J C. An efficient system for selectively altering genetic information within mRNAs[J]. Nucleic Acids Research, 2016, 44(21): e157.
49	SCHNEIDER M F, WETTENGEL J, HOFFMANN P C, et al. Optimal guideRNAs for re-directing deaminase activity of hADAR1 and hADAR2 in trans[J]. Nucleic Acids Research, 2014, 42(10): e87.
50	STAFFORST T, SCHNEIDER M F. An RNA-deaminase conjugate selectively repairs point mutations[J]. Angewandte Chemie International Edition, 2012, 51(44): 11166-11169.
51	VOGEL P, MOSCHREF M, LI Q, et al. Efficient and precise editing of endogenous transcripts with SNAP-tagged ADARs[J]. Nature Methods, 2018, 15(7): 535-538.
52	VOGEL P, SCHNEIDER M F, WETTENGEL J, et al. Improving site-directed RNA editing in vitro and in cell culture by chemical modification of the guideRNA[J]. Angewandte Chemie International Edition, 2014, 53(24): 6267-6271.
53	WETTENGEL J, REAUTSCHNIG P, GEISLER S, et al. Harnessing human ADAR2 for RNA repair-recoding a PINK₁ mutation rescues mitophagy[J]. Nucleic Acids Research, 2017, 45(5): 2797-2808.
54	QU L, YI Z Y, ZHU S Y, et al. Programmable RNA editing by recruiting endogenous ADAR using engineered RNAs[J]. Nature Biotechnology, 2019, 37(9): 1059-1069.
55	COX D B T, GOOTENBERG J S, ABUDAYYEH O O, et al. RNA editing with CRISPR-Cas13[J]. Science, 2017, 358(6366): 1019-1027.
56	ABUDAYYEH O O, GOOTENBERG J S, FRANKLIN B, et al. A cytosine deaminase for programmable single-base RNA editing[J]. Science, 2019, 365(6451): 382-386.
57	HUANG X X, LV J J, LI Y Q, et al. Programmable C-to-U RNA editing using the human APOBEC3A deaminase [J]. The EMBO Journal, 2020, 39(22): e104741.
58	TANG G Y, XIE B R, HONG X N, et al. Creating RNA specific C-to-U editase from APOBEC3A by separation of its activities on DNA and RNA substrates[J]. ACS Synthetic Biology, 2021, 10(5): 1106-1115.
59	KIM Y B, KOMOR A C, LEVY J M, et al. Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions[J]. Nature Biotechnology, 2017, 35(4): 371-376.
60	HU J H, MILLER S M, GEURTS M H, et al. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity[J]. Nature, 2018, 556(7699): 57-63.
61	MILLER S M, WANG T N, RANDOLPH P B, et al. Continuous evolution of SpCas9 variants compatible with non-G PAMs[J]. Nature Biotechnology, 2020, 38(4): 471-481.
62	WALTON R T, CHRISTIE K A, WHITTAKER M N, et al. Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants[J]. Science, 2020, 368(6488): 290-296.
63	CHATTERJEE P, JAKIMO N, JACOBSON J M. Minimal PAM specificity of a highly similar SpCas9 ortholog[J]. Science Advances, 2018, 4(10): eaau0766.
64	CHATTERJEE P, LEE J, NIP L, et al. A Cas9 with PAM recognition for adenine dinucleotides[J]. Nature Communications, 2020, 11(1): 2474.
65	LIU Z Q, SHAN H H, CHEN S Y, et al. Efficient base editing with expanded targeting scope using an engineered Spy-mac Cas9 variant[J]. Cell Discovery, 2019, 5: 58.
66	KLEINSTIVER B P, SOUSA A A, WALTON R T, et al. Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing[J]. Nature Biotechnology, 2019, 37(3): 276-282.
67	GAUDELLI N M, LAM D K, REES H A, et al. Directed evolution of adenine base editors with increased activity and therapeutic application[J]. Nature Biotechnology, 2020, 38(7): 892-900.
68	HUANG T P, ZHAO K T, MILLER S M, et al. Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors[J]. Nature Biotechnology, 2019, 37(6): 626-631.
69	OAKES B L, FELLMANN C, RISHI H, et al. CRISPR-Cas9 circular permutants as programmable scaffolds for genome modification[J]. Cell, 2019, 176(1/2): 254-267.e16.
70	THURONYI B W, KOBLAN L W, LEVY J M, et al. Continuous evolution of base editors with expanded target compatibility and improved activity[J]. Nature Biotechnology, 2019, 37(9): 1070-1079.
71	YU W X, LI J N, HUANG S S, et al. Harnessing A3G for efficient and selective C-to-T conversion at C-rich sequences[J]. BMC Biology, 2021, 19(1): 34.
72	LIU Z Q, SHAN H H, CHEN S Y, et al. Improved base editor for efficient editing in GC contexts in rabbits with an optimized AID-Cas9 fusion[J]. FASEB Journal, 2019, 33(8): 9210-9219.
73	CHENG T L, LI S, YUAN B, et al. Expanding C-T base editing toolkit with diversified cytidine deaminases[J]. Nature Communications, 2019, 10: 3612.
74	TANENBAUM M E, GILBERT L A, QI L S, et al. A protein-tagging system for signal amplification in gene expression and fluorescence imaging[J]. Cell, 2014, 159(3): 635-646.
75	GEHRKE J M, CERVANTES O, CLEMENT M K, et al. An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities[J]. Nature Biotechnology, 2018, 36(10): 977-982.
76	ZHANG X H, CHEN L, ZHU B Y, et al. Increasing the efficiency and targeting range of cytidine base editors through fusion of a single-stranded DNA-binding protein domain[J]. Nature Cell Biology, 2020, 22(6): 740-750.
77	WANG Y H, ZHOU L F, LIU N, et al. BE-PIGS: a base-editing tool with deaminases inlaid into Cas9 PI domain significantly expanded the editing scope[J]. Signal Transduction and Targeted Therapy, 2019, 4: 36.
78	VILLIGER L, SCHMIDHEINI L, MATHIS N, et al. Replacing the SpCas9 HNH domain by deaminases generates compact base editors with an alternative targeting scope[J]. Molecular Therapy Nucleic Acids, 2021, 26: 502-510.
79	RYU S M, KOO T, KIM K, et al. Adenine base editing in mouse embryos and an adult mouse model of Duchenne muscular dystrophy[J]. Nature Biotechnology, 2018, 36(6): 536-539.
80	BANNO S, NISHIDA K, ARAZOE T, et al. Deaminase-mediated multiplex genome editing in Escherichia coli [J]. Nature Microbiology, 2018, 3(4): 423-429.
81	HAO W L, CUI W J, CHENG Z Y, et al. Development of a base editor for protein evolution via in situ mutation in vivo [J]. Nucleic Acids Research, 2021, 49(16): 9594-9605.
82	WANG Y, LIU Y, LI J W, et al. Expanding targeting scope, editing window, and base transition capability of base editing in Corynebacterium glutamicum [J]. Biotechnology and Bioengineering, 2019, 116(11): 3016-3029.
83	LIU Z Q, CHEN S Y, SHAN H H, et al. Efficient base editing with high precision in rabbits using YFE-BE4max[J]. Cell Death & Disease, 2020, 11: 36.
84	TAN J J, ZHANG F, KARCHER D, et al. Expanding the genome-targeting scope and the site selectivity of high-precision base editors[J]. Nature Communications, 2020, 11: 629.
85	ZHAO D D, JIANG G, LI J, et al. Imperfect guide-RNA (igRNA) enables CRISPR single-base editing with ABE and CBE[J]. Nucleic Acids Research, 2022, 50(7): 4161-4170.
86	KIM D, LIM K, KIM S T, et al. Genome-wide target specificities of CRISPR RNA-guided programmable deaminases[J]. Nature Biotechnology, 2017, 35(5): 475-480.
87	KIM D, KIM D E, LEE G, et al. Genome-wide target specificity of CRISPR RNA-guided adenine base editors[J]. Nature Biotechnology, 2019, 37(4): 430-435.
88	LIANG P P, XIE X W, ZHI S Y, et al. Genome-wide profiling of adenine base editor specificity by EndoV-seq[J]. Nature Communications, 2019, 10(1): 67.
89	JIN S, ZONG Y, GAO Q, et al. Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice[J]. Science, 2019, 364(6437): 292-295.
90	ZUO E W, SUN Y D, WEI W, et al. Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos[J]. Science, 2019, 364(6437): 289-292.
91	YU Y, LEETE T C, BORN D A, et al. Cytosine base editors with minimized unguided DNA and RNA off-target events and high on-target activity[J]. Nature Communications, 2020, 11(1): 2052.
92	LEI Z X, MENG H W, LV Z C, et al. Detect-seq reveals out-of-protospacer editing and target-strand editing by cytosine base editors[J]. Nature Methods, 2021, 18(6): 643-651.
93	LEI L Q, CHEN H Q, XUE W, et al. APOBEC3 induces mutations during repair of CRISPR-Cas9-generated DNA breaks[J]. Nature Structural & Molecular Biology, 2018, 25(1): 45-52.
94	JEONG Y K, LEE S, HWANG G H, et al. Adenine base editor engineering reduces editing of bystander cytosines[J]. Nature Biotechnology, 2021, 39(11): 1426-1433.
95	WANG Q, YANG J, ZHONG Z C, et al. A general theoretical framework to design base editors with reduced bystander effects[J]. Nature Communications, 2021, 12: 6529.
96	LEE J K, JEONG E, LEE J, et al. Directed evolution of CRISPR-Cas9 to increase its specificity[J]. Nature Communications, 2018, 9: 3048.
97	ZHOU J Z, LIU Y, WEI Y H, et al. Eliminating predictable DNA off-target effects of cytosine base editor by using dual guiders including sgRNA and TALE[J]. Molecular Therapy, 2022, 30(7): 2443-2451.
98	FU Y F, SANDER J D, REYON D, et al. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs[J]. Nature Biotechnology, 2014, 32(3): 279-284.
99	HU Z W, WANG Y N, LIU Q, et al. Improving the precision of base editing by bubble hairpin single guide RNA[J]. mBio, 2021, 12(2): e00342-21.
100	MCGRATH E, SHIN H, ZHANG L Y, et al. Targeting specificity of APOBEC-based cytosine base editor in human iPSCs determined by whole genome sequencing[J]. Nature Communications, 2019, 10: 5353.
101	ZUO E W, SUN Y D, YUAN T L, et al. A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects[J]. Nature Methods, 2020, 17(6): 600-604.
102	GRÜNEWALD J, ZHOU R H, IYER S, et al. CRISPR DNA base editors with reduced RNA off-target and self-editing activities[J]. Nature Biotechnology, 2019, 37(9): 1041-1048.
103	REES H A, WILSON C, DOMAN J L, et al. Analysis and minimization of cellular RNA editing by DNA adenine base editors[J]. Science Advances, 2019, 5(5): eaax5717.
104	ZHOU C Y, SUN Y D, YAN R, et al. Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis[J]. Nature, 2019, 571(7764): 275-278.
105	JANG H K, JO D H, LEE S N, et al. High-purity production and precise editing of DNA base editing ribonucleoproteins[J]. Science Advances, 2021, 7(35): eabg2661.
106	YEH W H, CHIANG H, REES H A, et al. In vivo base editing of post-mitotic sensory cells[J]. Nature Communications, 2018, 9: 2184.
107	JIANG T T, HENDERSON J M, COOTE K, et al. Chemical modifications of adenine base editor mRNA and guide RNA expand its application scope[J]. Nature Communications, 2020, 11(1): 1979.
108	BANSKOTA S, RAGURAM A, SUH S, et al. Engineered virus-like particles for efficient in vivo delivery of therapeutic proteins[J]. Cell, 2022, 185(2): 250-265.
109	LIANG M M, SUI T T, LIU Z Q, et al. AcrⅡA5 suppresses base editors and reduces their off-target effects[J]. Cells, 2020, 9(8): 1786.
110	LIU Z Q, CHEN S Y, LAI L X, et al. Inhibition of base editors with anti-deaminases derived from viruses[J]. Nature Communications, 2022, 13: 597.
111	COLLANTES J C, TAN V M, XU H T, et al. Development and characterization of a modular CRISPR and RNA aptamer mediated base editing system[J]. The CRISPR Journal, 2021, 4(1): 58-68.
112	GANGOPADHYAY S A, COX K J, MANNA D, et al. Precision control of CRISPR-Cas9 using small molecules and light[J]. Biochemistry, 2019, 58(4): 234-244.
113	ZETSCHE B, VOLZ S E, ZHANG F. A split-Cas9 architecture for inducible genome editing and transcription modulation[J]. Nature Biotechnology, 2015, 33(2): 139-142.
114	BERRÍOS K N, EVITT N H, DEWEERD R A, et al. Controllable genome editing with split-engineered base editors[J]. Nature Chemical Biology, 2021, 17(12): 1262-1270.
115	WANG L J, XUE W, ZHANG H X, et al. Eliminating base-editor-induced genome-wide and transcriptome-wide off-target mutations[J]. Nature Cell Biology, 2021, 23(5): 552-563.
116	BILLON P, BRYANT E E, JOSEPH S A, et al. CRISPR-mediated base editing enables efficient disruption of eukaryotic genes through induction of STOP codons[J]. Molecular Cell, 2017, 67(6): 1068-1079.
117	KUSCU C, PARLAK M, TUFAN T R, et al. CRISPR-STOP: gene silencing through base-editing-induced nonsense mutations[J]. Nature Methods, 2017, 14(7): 710-712.
118	WANG X J, LIU Z W, LI G L, et al. Efficient gene silencing by adenine base editor-mediated start codon mutation[J]. Molecular Therapy, 2020, 28(2): 431-440.
119	LEE C I, JO D H, HWANG G H, et al. CRISPR-Pass: gene rescue of nonsense mutations using adenine base editors[J]. Molecular Therapy, 2019, 27(8): 1364-1371.
120	LI Q, SEYS F M, MINTON N P, et al. CRISPR-Cas9^D10A nickase-assisted base editing in the solvent producer Clostridium beijerinckii [J]. Biotechnology and Bioengineering, 2019, 116(6): 1475-1483.
121	LUO Y F, GE M, WANG B L, et al. CRISPR/Cas9-deaminase enables robust base editing in Rhodobacter sphaeroides 2.4.1[J]. Microbial Cell Factories, 2020, 19(1): 93.
122	ZHONG Z Y, GUO J H, DENG L, et al. Base editing in Streptomyces with Cas9-deaminase fusions[EB/OL]. bioRxiv, 2019[2022-09-01]. .
123	LI S C, LIU Q, ZHONG Z Y, et al. Exploration of hygromycin B biosynthesis utilizing CRISPR-Cas9-associated base editing[J]. ACS Chemical Biology, 2020, 15(6): 1417-1423.
124	CHENG L, MIN D, HE R L, et al. Developing a base-editing system to expand the carbon source utilization spectra of Shewanella oneidensis MR-1 for enhanced pollutant degradation[J]. Biotechnology and Bioengineering, 2020, 117(8): 2389-2400.
125	ABDULLAH, WANG P J, HAN T R, et al. Adenine base editing system for Pseudomonas and prediction workflow for protein dysfunction via ABE[J]. ACS Synthetic Biology, 2022, 11(4): 1650-1657.
126	ZHAO Y W, TIAN J Z, ZHENG G S, et al. Multiplex genome editing using a dCas9-cytidine deaminase fusion in Streptomyces [J]. Science China Life Sciences, 2020, 63(7): 1053-1062.
127	SUN J, LU L B, LIANG T X, et al. CRISPR-assisted multiplex base editing system in Pseudomonas putida KT2440[J]. Frontiers in Bioengineering and Biotechnology, 2020, 8: 905.
128	WANG Y, LIU Y, LIU J, et al. MACBETH: multiplex automated Corynebacterium glutamicum base editing method[J]. Metabolic Engineering, 2018, 47: 200-210.
129	WANG Y, CHENG H J, LIU Y, et al. In-situ generation of large numbers of genetic combinations for metabolic reprogramming via CRISPR-guided base editing[J]. Nature Communications, 2021, 12: 678.
130	PAN Y J, XIA S Y, DONG C, et al. Random base editing for genome evolution in Saccharomyces cerevisiae [J]. ACS Synthetic Biology, 2021, 10(10): 2440-2446.
131	WANG J, ZHAO D D, LI J, et al. Helicase-AID: a novel molecular device for base editing at random genomic loci[J]. Metabolic Engineering, 2021, 67: 396-402.

碱基编辑器	版本	组成	PAM (5′-3′)	特点	参考文献
CBE	BE3	rAPOBEC1-SpnCas9-UGI	NGG	初代碱基编辑器，TC基序偏好性	[7]
	Target-AID	SpnCas9-CDA1-UGI	NGG	初代碱基编辑器	[8]
	hA3A-BE3	hAPOBEC3A-SpnCas9-UGI	NGG	可编辑甲基化的C及GC基序的C	[9]
	BE4-Max	rAPOBEC1-SpnCas9-UGI-UGI	NGG	密码子优化，高活性	[10]
	dCpf1-BE	rAPOBEC1-dLbCpf1-UGI	TTTV	识别富含T的PAM	[11]
	Target-AID-NG	SpnCas9 (NG)-CDA1-UGI	NG	识别NG PAM	[12]
	A3A-PBE	hAPOBEC3A-SpnCas9-UGI	NGG	1～17号位编辑窗口，几乎无基序偏好性	[13]
	BE-PLUS	SunTag-SpnCas9-scFv-rAPOBEC1-UGI	NGG	4～16号位编辑窗口，高保真	[14]
	A3G-BEs	hAPOBEC3G-SpnCas9-UGI-UGI	NGG	编辑CC基序中的第二个C	[15]
	BE-PAPAPAP	rAPOBEC1-SpnCas9-UGI	NGG	5～6号位编辑窗口，PAPAPAP替换XTEN linker	[16]
	HF-BE3	rAPOBEC1-HFnCas9-UGI	NGG	减少sgRNA依赖的脱靶编辑	[17]
	YE1-BE4	rAPOBEC1 (W90Y, R126E)-SpnCas9-UGI-UGI	NGG	缩小编辑窗口，减少非sgRNA依赖的脱靶编辑	[18]
	SECURE BE3	rAPOBEC1 (R33A, K34A)-SpnCas9-UGI	NGG	减少RNA层面的脱靶编辑，缩小编辑窗口	[19]
	DdCBEs	TALE-split DddAtox-UGI	None	同时编辑DNA双链，可编辑线粒体、叶绿体基因组	[20]
	ZFDs	ZFP-split DddAtox-UGI	None	同时编辑DNA双链，可编辑线粒体、叶绿体基因组	[21]
ABE	ABE7.10	ecTadA-ecTadA*-SpnCas9	NGG	初代碱基编辑器	[22]
	ABEmax	ecTadA-ecTadA*-SpnCas9	NGG	密码子优化，高活性	[10]
	ABE8e	ecTadA-ecTadA*-SpnCas9	NGG	高活性，TadA-8e	[23]
	TaC9-ABE	ecTadA-ecTadA*-TALE,SpnCas9	NGG	消除sgRNA依赖的脱靶编辑	[24]
	ABE-nSpCas9-DS	ecTadA-ecTadA-SpnCas9 (DS)	NGG	拓宽编辑窗口，减少RNA层面的脱靶编辑	[25]
ACBE	A&C-BEmax	rAPOBEC1/hAID-ecTadA-ecTadA*-SpnCas9-UGI-UGI	NGG	可同时编辑A或C	[26]
	sgBE	SpnCas9, MCP-cytosine/adenosine deaminase	NGG	可同时编辑A或C	[27]
GBE	CGBE1	eUNG-rAPOBEC1 (R33A)-SpnCas9-UGI-UGI	NGG	可实现C变G的碱基颠换	[28]
	CGBE	rAPOBEC1-SpnCas9-rXRCC1	NGG	利用碱基切除修复通路实现C变G的碱基颠换	[29]

碱基编辑器	版本	组成	PAM (5′-3′)	特点	参考文献
CBE	BE3	rAPOBEC1-SpnCas9-UGI	NGG	初代碱基编辑器，TC基序偏好性	[7]
	Target-AID	SpnCas9-CDA1-UGI	NGG	初代碱基编辑器	[8]
	hA3A-BE3	hAPOBEC3A-SpnCas9-UGI	NGG	可编辑甲基化的C及GC基序的C	[9]
	BE4-Max	rAPOBEC1-SpnCas9-UGI-UGI	NGG	密码子优化，高活性	[10]
	dCpf1-BE	rAPOBEC1-dLbCpf1-UGI	TTTV	识别富含T的PAM	[11]
	Target-AID-NG	SpnCas9 (NG)-CDA1-UGI	NG	识别NG PAM	[12]
	A3A-PBE	hAPOBEC3A-SpnCas9-UGI	NGG	1～17号位编辑窗口，几乎无基序偏好性	[13]
	BE-PLUS	SunTag-SpnCas9-scFv-rAPOBEC1-UGI	NGG	4～16号位编辑窗口，高保真	[14]
	A3G-BEs	hAPOBEC3G-SpnCas9-UGI-UGI	NGG	编辑CC基序中的第二个C	[15]
	BE-PAPAPAP	rAPOBEC1-SpnCas9-UGI	NGG	5～6号位编辑窗口，PAPAPAP替换XTEN linker	[16]
	HF-BE3	rAPOBEC1-HFnCas9-UGI	NGG	减少sgRNA依赖的脱靶编辑	[17]
	YE1-BE4	rAPOBEC1 (W90Y, R126E)-SpnCas9-UGI-UGI	NGG	缩小编辑窗口，减少非sgRNA依赖的脱靶编辑	[18]
	SECURE BE3	rAPOBEC1 (R33A, K34A)-SpnCas9-UGI	NGG	减少RNA层面的脱靶编辑，缩小编辑窗口	[19]
	DdCBEs	TALE-split DddAtox-UGI	None	同时编辑DNA双链，可编辑线粒体、叶绿体基因组	[20]
	ZFDs	ZFP-split DddAtox-UGI	None	同时编辑DNA双链，可编辑线粒体、叶绿体基因组	[21]
ABE	ABE7.10	ecTadA-ecTadA*-SpnCas9	NGG	初代碱基编辑器	[22]
	ABEmax	ecTadA-ecTadA*-SpnCas9	NGG	密码子优化，高活性	[10]
	ABE8e	ecTadA-ecTadA*-SpnCas9	NGG	高活性，TadA-8e	[23]
	TaC9-ABE	ecTadA-ecTadA*-TALE,SpnCas9	NGG	消除sgRNA依赖的脱靶编辑	[24]
	ABE-nSpCas9-DS	ecTadA-ecTadA-SpnCas9 (DS)	NGG	拓宽编辑窗口，减少RNA层面的脱靶编辑	[25]
ACBE	A&C-BEmax	rAPOBEC1/hAID-ecTadA-ecTadA*-SpnCas9-UGI-UGI	NGG	可同时编辑A或C	[26]
	sgBE	SpnCas9, MCP-cytosine/adenosine deaminase	NGG	可同时编辑A或C	[27]
GBE	CGBE1	eUNG-rAPOBEC1 (R33A)-SpnCas9-UGI-UGI	NGG	可实现C变G的碱基颠换	[28]
	CGBE	rAPOBEC1-SpnCas9-rXRCC1	NGG	利用碱基切除修复通路实现C变G的碱基颠换	[29]

[1]	赵国淼, 杨鑫, 张媛, 王靖, 谭剑, 魏超, 周娜娜, 李凡, 王小艳. 生物设施平台及其工业应用[J]. 合成生物学, 2023, 4(5): 892-903.
[2]	孙梦楚, 陆亮宇, 申晓林, 孙新晓, 王佳, 袁其朋. 基于荧光检测的高通量筛选技术和装备助力细胞工厂构建[J]. 合成生物学, 2023, 4(5): 947-965.
[3]	刁志钿, 王喜先, 孙晴, 徐健, 马波. 单细胞拉曼光谱测试分选装备研制及应用进展[J]. 合成生物学, 2023, 4(5): 1020-1035.
[4]	卢挥, 张芳丽, 黄磊. 合成生物学自动化装置iBioFoundry的构建与应用[J]. 合成生物学, 2023, 4(5): 877-891.
[5]	白仲虎, 任和, 聂简琪, 孙杨. 高通量平行发酵技术的发展与应用[J]. 合成生物学, 2023, 4(5): 904-915.
[6]	吴玉洁, 刘欣欣, 刘健慧, 杨开广, 随志刚, 张丽华, 张玉奎. 基于高通量液相色谱质谱技术的菌株筛选与关键分子定量分析研究进展[J]. 合成生物学, 2023, 4(5): 1000-1019.
[7]	胡哲辉, 徐娟, 卞光凯. 自动化高通量技术在天然产物生物合成中的应用[J]. 合成生物学, 2023, 4(5): 932-946.
[8]	刘欢, 崔球. 原位电离质谱技术在微生物菌株筛选中的应用进展[J]. 合成生物学, 2023, 4(5): 980-999.
[9]	刘晚秋, 季向阳, 许慧玲, 卢屹聪, 李健. 限制性内切酶的无细胞快速制备研究[J]. 合成生物学, 2023, 4(4): 840-851.
[10]	孙美莉, 王凯峰, 陆然, 纪晓俊. 解脂耶氏酵母底盘细胞的工程改造及应用[J]. 合成生物学, 2023, 4(4): 779-807.
[11]	程真真, 张健, 高聪, 刘立明, 陈修来. 代谢工程改造微生物利用甲酸研究进展[J]. 合成生物学, 2023, 4(4): 756-778.
[12]	孙智, 杨宁, 娄春波, 汤超, 杨晓静. 功能拓扑的理性设计及其在合成生物学中的应用[J]. 合成生物学, 2023, 4(3): 444-463.
[13]	赖奇龙, 姚帅, 查毓国, 白虹, 宁康. 微生物组生物合成基因簇发掘方法及应用前景[J]. 合成生物学, 2023, 4(3): 611-627.
[14]	孟巧珍, 郭菲. “可折叠性”在酶智能设计改造中的应用研究——以AlphaFold2为例[J]. 合成生物学, 2023, 4(3): 571-589.
[15]	王晟, 王泽琛, 陈威华, 陈珂, 彭向达, 欧发芬, 郑良振, 孙瑨原, 沈涛, 赵国屏. 基于人工智能和计算生物学的合成生物学元件设计[J]. 合成生物学, 2023, 4(3): 422-443.