Classification and Research Status of CRISPR/Cas Systems

doi:10.19586/j.2095-2341.2021.0198

Current Biotechnology ›› 2022, Vol. 12 ›› Issue (4): 532-538.DOI: 10.19586/j.2095-2341.2021.0198

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Classification and Research Status of CRISPR/Cas Systems

Weisong GAO(), Jinping DOU, Shuang WEI, Xingjian LIU, Zhifang ZHANG, Yinyu LI()

Biotechnology Research Institute，Chinese Academy of Agricultural Sciences，Beijing 100081，China

Received:2021-12-23 Accepted:2022-01-27 Online:2022-07-25 Published:2022-08-10
Contact: Yinyu LI

CRISPR/Cas系统的分类及研究现状

高维崧(), 窦金萍, 韦双, 刘兴健, 张志芳, 李轶女()

中国农业科学院生物技术研究所，北京 100081

通讯作者: 李轶女
作者简介:高维崧 E-mail：caasgaows@163.com；
基金资助:
国家自然科学基金项目(32072796);宁夏回族自治区重点研发计划项目(2020BFG02017)

Abstract

Abstract:

Clustered regularly interspaced short palindromic repeats（CRISPR）is a rapid developed gene editing technology which is widely used in microorganisms， animals and plants. In this article， the origin and classification characteristics of CRISPR/Cas systems was explained， and we focused on the development process of CRISPR/Cas system classification， and introduced the action mechanism of different types of CRISPR/Cas system， the action characteristics， application and development of different internal proteins according to the latest classification methods. This paper aimed to explore more CRISPR/Cas systems and expand the application of this system.

Key words: CRISPR/Cas systems, gene editing, classification

摘要：

CRISPR技术作为一种新型的基因编辑技术，被广泛应用于微生物、动物和植物领域。对CRISPR/Cas系统的起源、分类特点等进行了阐述，重点梳理了CRISPR/Cas系统分类的发展历程，并根据最新分类方法，介绍了不同类型的CRISPR/Cas系统的作用机制、内部不同蛋白的作用特点及应用与发展，以期探寻更多的CRISPR/Cas系统，扩大该系统的应用领域。

关键词: CRISPR/Cas系统, 基因编辑, 分类

CLC Number:

Weisong GAO, Jinping DOU, Shuang WEI, Xingjian LIU, Zhifang ZHANG, Yinyu LI. Classification and Research Status of CRISPR/Cas Systems[J]. Current Biotechnology, 2022, 12(4): 532-538.

高维崧, 窦金萍, 韦双, 刘兴健, 张志芳, 李轶女. CRISPR/Cas系统的分类及研究现状[J]. 生物技术进展, 2022, 12(4): 532-538.

Figures/Tables 1

References 50

1	ISHINO Y, SHINAGAWA H, MAKINO K, et al.. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product[J]. J. Bacteriol., 1987, 169(12): 5429-5433.
2	MOJICA F J, DIEZ-VILLASENOR C, SORIA E, et al.. Biological significance of a family of regularly spaced repeats in the genomes of archaea, bacteria and mitochondria[J]. Mol. Microbiol., 2000, 36(1): 244-246.
3	SHE Q, SINGH R K, CONFALONIERI F, et al.. The complete genome of the crenarchaeon Sulfolobus solfataricus P2[J]. Proc. Natl. Acad. Sci. USA, 2001, 98(14): 7835-7840.
4	JANSEN R, EMBDEN J D, GAASTRA W, et al.. Identification of a novel family of sequence repeats among prokaryotes[J]. OMICS, 2002, 6(1): 23-33.
5	JANSEN R, EMBDEN J D A, GAASTRA W, et al.. Identification of genes that are associated with DNA repeats in prokaryotes[J]. Mol. Microbiol., 2002, 43(6): 1565-1575.
6	JINEK M, CHYLINSKI K, FONFARA I, et al.. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity[J]. Science, 2012, 337(6096): 816-821.
7	CONG L, RAN F A, COX D, et al.. Multiplex genome engineering using CRISPR/Cas systems[J]. Science, 2013, 339(6121): 819-823.
8	KOBLAN L W, ERDOS M R, WILSON C, et al.. In vivo base editing rescues Hutchinson-Gilford progeria syndrome in mice[J]. Nature, 2021, 589(7843): 608-614.
9	MAKAROVA K S, GRISHIN N V, SHABALINA S A, et al. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action[J/OL]. Biol. Direct., 2006, 1: 7[2022-04-18]. .
10	HAFT D H, SELENGUT J, MONGODIN E F, et al.. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes[J/OL]. PLoS Comput. Biol., 2005, 1(6): e60[2022-04-18]. .
11	MAKAROVA K S, HAFT D H, BARRANGOU R, et al.. Evolution and classification of the CRISPR-Cas systems[J]. Nat. Rev. Microbiol., 2011, 9(6): 467-477.
12	MAKAROVA K S, WOLF Y I, ALKHNBASHI O S, et al.. An updated evolutionary classification of CRISPR-Cas systems[J]. Nat. Rev. Microbiol., 2015, 13(11): 722-736.
13	MAKAROVA K S, WOLF Y I, IRANZO J, et al.. Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants[J]. Nat. Rev. Microbiol., 2019, 18(2): 67-83.
14	BURSTEIN D, HARRINGTON L B, STRUTT S C, et al.. New CRISPR-Cas systems from uncultivated microbes[J]. Nature, 2017, 542(7640): 237-241.
15	YAN W X, HUNNEWELL P, ALFONSE L E, et al.. Functionally diverse type V CRISPR-Cas systems[J]. Science, 2019, 363(6422): 88-91.
16	ABUDAYYEH O O, GOOTENBERG J S, KONERMANN S, et al.. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector[J/OL]. Science, 2016, 353(6299): aaf5573[2022-04-18]. .
17	KOONIN E V, MAKAROVA K S. Origins and evolution of CRISPR-Cas systems[J/OL]. Philos. Trans. R Soc. Lond. B Biol. Sci., 2019, 374(1772): 20180087[2022-04-18]. .
18	NUNEZ J K, KRANZUSCH P J, NOESKE J, et al.. Cas1-Cas2 complex formation mediates spacer acquisition during CRISPR-Cas adaptive immunity[J]. Nat. Struct. Mol. Biol., 2014, 21(6): 528-534.
19	MAKAROVA K S, WOLF Y I, KOONIN E V. The basic building blocks and evolution of CRISPR-CAS systems[J]. Biochem. Soc. Trans., 2013, 41(6): 1392-1400.
20	SINKUNAS T, GASIUNAS G, FREMAUX C, et al.. Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system[J]. EMBO J., 2011, 30(7): 1335-1342.
21	KIEPER S N, ALMENDROS C, HAAGSMA A C, et al.. Cas4-Cas1 is a protospacer adjacent motif-processing factor mediating half-site spacer integration during CRISPR adaptation[J]. CRISPR J., 2021, 4(4): 536-548.
22	LI M, WANG R, ZHAO D, et al.. Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process[J]. Nucl. Acids Res., 2014, 42(4): 2483-2492.
23	PLAGENS A, TJADEN B, HAGEMANN A, et al.. Characterization of the CRISPR/Cas subtype I-A system of the hyperthermophilic crenarchaeon Thermoproteus tenax [J]. J. Bacteriol., 2012, 194(10): 2491-500.
24	NAM K H, HAITJEMA C, LIU X, et al.. Cas5d protein processes pre-crRNA and assembles into a cascade-like interference complex in subtype I-C/Dvulg CRISPR-Cas system[J]. Structure, 2012, 20(9): 1574-84.
25	BROUNS S J J, JORE M M, LUNDGREN M, et al.. Small CRISPR RNAs guide antiviral defense in prokaryotes[J]. Science, 2008, 321(5891): 960-964.
26	CATCHPOLE R J, TERNS M P. New Type Ⅲ CRISPR variant and programmable RNA targeting tool: Oh, thank heaven for Cas7-11[J]. Mol. Cell, 2021, 81(21): 4354-4356.
27	MAKAROVA K S, KARAMYCHEVA S, SHAH S A, et al.. Predicted highly derived class 1 CRISPR-Cas system in Haloarchaea containing diverged Cas5 and Cas7 homologs but no CRISPR array[J/OL]. FEMS Microbiol. Lett., 2019, 366(7): fnz079[2022-04-18]. .
28	OZCAN A, PAUSCH P, LINDEN A, et al.. Type Ⅳ CRISPR RNA processing and effector complex formation in Aromatoleum aromaticum[J]. Nat. Microbiol., 2019, 4(1): 89-96.
29	KOSLOVA A, TREFIL P, MUCKSOVA J, et al.. Precise CRISPR/Cas9 editing of the NHE1 gene renders chickens resistant to the J subgroup of avian leukosis virus[J]. Proc. Natl. Acad. Sci. USA, 2020, 117(4): 2108-2112.
30	DOUGLAS C, MACIULYTE V, ZOHREN J, et al.. CRISPR-Cas9 effectors facilitate generation of single-sex litters and sex-specific phenotypes[J/OL]. Nat. Commun., 2021, 12(1): 6926[2022-04-18]. .
31	曹巧,史占良,张国丛,等.CRISPR/Cas9技术在小麦育种中的应用进展[J].生物技术进展,2021,11(6):661-667.
32	VOSS-FELS K P, STAHL A, HICKEY L T. Q&A: modern crop breeding for future food security[J/OL]. BMC Biol., 2019, 17(1): 18[2022-04-18]. .
33	MIAO C, XIAO L, HUA K, et al.. Mutations in a subfamily of abscisic acid receptor genes promote rice growth and productivity[J]. Proc. Natl. Acad. Sci. USA, 2018, 115(23): 6058-6063.
34	MONTE D F M, NETHERY M A, BARRANGOU R, et al.. Whole-genome sequencing analysis and CRISPR genotyping of rare antibiotic-resistant Salmonella enterica serovars isolated from food and related sources[J/OL]. Food Microbiol., 2021, 93: 103601[2022-04-18]. .
35	FUJITA T, FUJII H. Efficient isolation of specific genomic regions and identification of associated proteins by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR[J]. Biochem. Biophys. Res. Commun., 2013, 439(1): 132-136.
36	BIKARD D, JIANG W, SAMAI P, et al.. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system[J]. Nucl. Acids Res., 2013, 41(15): 7429-7437.
37	HSU P D, LANDER E S, ZHANG F. Development and applications of CRISPR-Cas9 for genome engineering[J]. Cell, 2014, 157(6): 1262-1278.
38	ZETSCHE B, GOOTENBERG J S, ABUDAYYEH O O, et al.. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system[J]. Cell, 2015, 163(3): 759-771.
39	李树磊,徐妙云,郑红艳,王磊.CRISPR/Cpf1单碱基编辑系统的构建及应用[J].生物技术进展,2021,11(6):732-740.
40	GAO P, YANG H, RAJASHANKAR K R, et al.. Type V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition[J]. Cell Res., 2016, 26(8): 901-913.
41	JIAO J, KONG K, HAN J, et al. Field detection of multiple RNA viruses/viroids in apple using a CRISPR/Cas12a-based visual assay[J]. Plant Biotechnol. J., 2021, 19(2): 394-405.
42	LIU H, WANG J, ZENG H, et al.. RPA-Cas12a-FS: A frontline nucleic acid rapid detection system for food safety based on CRISPR-Cas12a combined with recombinase polymerase amplification[J/OL]. Food Chem., 2021, 334: 127608[2022-04-18]. .
43	MAYURAMART O, NIMSAMER P, RATTANABURI S, et al.. Detection of severe acute respiratory syndrome coronavirus 2 and influenza viruses based on CRISPR-Cas12a[J]. Exp. Biol. Med., 2021, 246(4): 400-405.
44	HE C, LIN C, MO G, et al.. Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform[J/OL]. Biosens. Bioelectron., 2021, 198: 113857[2022-04-18]. .
45	WU Y, BATTALAPALLI D, HAKEEM M J, et al.. Engineered CRISPR-Cas systems for the detection and control of antibiotic-resistant infections[J/OL]. J. Nanobiotechnol., 2021, 19(1): 401[2022-04-18]. .
46	ZHANG B, YE W, YE Y, et al.. Structural insights into Cas13b-guided CRISPR RNA maturation and recognition[J]. Cell Res., 2018, 28(12): 1198-1201.
47	谢宇宙,付伟,闫超杰,等.基于CRISPR/Cas原理的转基因产品检测技术研究进展[J].生物技术进展,2021,11(4):430-437.
48	KANNAN S, ALTAE-TRAN H, JIN X, et al.. Compact RNA editors with small Cas13 proteins[J]. Nat. Biotechnol., 2021:40(2):194-197.
49	KHAN W A, BARNEY R E, TSONGALIS G J. CRISPR-cas13 enzymology rapidly detects SARS-CoV-2 fragments in a clinical setting[J/OL]. J. Clin. Virol., 2021, 145: 105019[2022-04-18]. .
50	LI S, ZHANG H, ZHANG L, et al.. LinearTurboFold: Linear-time global prediction of conserved structures for RNA homologs with applications to SARS-CoV-2[J/OL]. Proc. Natl. Acad. Sci. USA, 2021, 118(52):e2116269118[2022-04-18]. .

大类	型	亚型	包含的Cas蛋白
第一大类	Ⅰ型	Ⅰ⁃A、Ⅰ⁃B、Ⅰ⁃C、Ⅰ⁃D、Ⅰ⁃E、Ⅰ⁃F1、Ⅰ⁃F2、Ⅰ⁃F3	Cas1、Cas2、Cas3、Cas4、Cas5、Cas6、Cas7、Cas8
	Ⅲ型	Ⅲ⁃A、Ⅲ⁃B、Ⅲ⁃C、Ⅲ⁃D、Ⅲ⁃E、Ⅲ⁃F	Cas1、Cas2、Cas5、Cas6、Cas7、Cas10、Cas11
	Ⅳ型	Ⅳ⁃A、Ⅳ⁃B、Ⅳ⁃C	Cas1、Cas2、Cas5、Cas6、Cas7
第二大类	Ⅱ型	Ⅱ⁃A、Ⅱ⁃B、Ⅱ⁃C1、Ⅱ⁃C2	Cas1、Cas2、Cas4、Cas9
	Ⅴ型	Ⅴ⁃A、Ⅴ⁃B1、Ⅴ⁃B2、Ⅴ⁃C、Ⅴ⁃D、Ⅴ⁃E、Ⅴ⁃F1、Ⅴ⁃F1（Ⅴ⁃U3）、Ⅴ⁃F2、Ⅴ⁃F3、Ⅴ⁃G、Ⅴ⁃U1、Ⅴ⁃U2、Ⅴ⁃U4、Ⅴ⁃K（Ⅴ⁃U5）	Cas1、Cas2、Cas4、Cas12
	Ⅵ型	Ⅵ⁃A、Ⅵ⁃B1、Ⅵ⁃B2、Ⅵ⁃C、Ⅵ⁃D	Cas1、Cas2、Cas13

大类	型	亚型	包含的Cas蛋白
第一大类	Ⅰ型	Ⅰ⁃A、Ⅰ⁃B、Ⅰ⁃C、Ⅰ⁃D、Ⅰ⁃E、Ⅰ⁃F1、Ⅰ⁃F2、Ⅰ⁃F3	Cas1、Cas2、Cas3、Cas4、Cas5、Cas6、Cas7、Cas8
	Ⅲ型	Ⅲ⁃A、Ⅲ⁃B、Ⅲ⁃C、Ⅲ⁃D、Ⅲ⁃E、Ⅲ⁃F	Cas1、Cas2、Cas5、Cas6、Cas7、Cas10、Cas11
	Ⅳ型	Ⅳ⁃A、Ⅳ⁃B、Ⅳ⁃C	Cas1、Cas2、Cas5、Cas6、Cas7
第二大类	Ⅱ型	Ⅱ⁃A、Ⅱ⁃B、Ⅱ⁃C1、Ⅱ⁃C2	Cas1、Cas2、Cas4、Cas9
	Ⅴ型	Ⅴ⁃A、Ⅴ⁃B1、Ⅴ⁃B2、Ⅴ⁃C、Ⅴ⁃D、Ⅴ⁃E、Ⅴ⁃F1、Ⅴ⁃F1（Ⅴ⁃U3）、Ⅴ⁃F2、Ⅴ⁃F3、Ⅴ⁃G、Ⅴ⁃U1、Ⅴ⁃U2、Ⅴ⁃U4、Ⅴ⁃K（Ⅴ⁃U5）	Cas1、Cas2、Cas4、Cas12
	Ⅵ型	Ⅵ⁃A、Ⅵ⁃B1、Ⅵ⁃B2、Ⅵ⁃C、Ⅵ⁃D	Cas1、Cas2、Cas13

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Classification and Research Status of CRISPR/Cas Systems

CRISPR/Cas系统的分类及研究现状

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