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Abstract
The number and diversity of known CRISPR–Cas systems have substantially increased in recent years. Here, we provide an updated evolutionary classification of CRISPR–Cas systems and cas genes, with an emphasis on the major developments that have occurred since the publication of the latest classification, in 2015. The new classification includes 2 classes, 6 types and 33 subtypes, compared with 5 types and 16 subtypes in 2015. A key development is the ongoing discovery of multiple, novel class 2 CRISPR–Cas systems, which now include 3 types and 17 subtypes. A second major novelty is the discovery of numerous derived CRISPR–Cas variants, often associated with mobile genetic elements that lack the nucleases required for interference. Some of these variants are involved in RNA-guided transposition, whereas others are predicted to perform functions distinct from adaptive immunity that remain to be characterized experimentally. The third highlight is the discovery of numerous families of ancillary CRISPR-linked genes, often implicated in signal transduction. Together, these findings substantially clarify the functional diversity and evolutionary history of CRISPR–Cas.
The number and diversity of known CRISPR–Cas systems have substantially increased in recent years. In this Review, Koonin and colleagues provide an updated evolutionary classification of CRISPR–Cas systems and cas genes, with an emphasis on major developments, and outline a complete scenario for the origins and evolution of CRISPR–Cas systems.
Details
; Wolf, Yuri I 1
; Iranzo Jaime 1 ; Shmakov, Sergey A 1 ; Alkhnbashi, Omer S 2 ; Brouns Stan J J 3 ; Charpentier Emmanuelle 4 ; Cheng, David 5 ; Haft, Daniel H 1 ; Horvath, Philippe 6 ; Moineau Sylvain 7
; Mojica Francisco J M 8
; Scott, David 9 ; Shah, Shiraz A 10 ; Siksnys Virginijus 11 ; Terns, Michael P 12 ; Česlovas, Venclovas 11
; White, Malcolm F 13
; Yakunin, Alexander F 14
; Yan, Winston 15 ; Zhang, Feng 16 ; Garrett, Roger A 17 ; Backofen Rolf 18 ; van der Oost John 19
; Barrangou Rodolphe 20
; Koonin, Eugene V 1
1 National Library of Medicine, National Center for Biotechnology Information, Bethesda, USA (GRID:grid.280285.5) (ISNI:0000 0004 0507 7840)
2 University of Freiberg, Bioinformatics group, Department of Computer Science, Freiberg, Germany (GRID:grid.280285.5)
3 Delft University of Technology, Kavli Institute of Nanoscience, Department of Bionanoscience, Delft, The Netherlands (GRID:grid.5292.c) (ISNI:0000 0001 2097 4740)
4 Humboldt University, Max Planck Unit for the Science of Pathogens, Berlin, Germany (GRID:grid.7468.d) (ISNI:0000 0001 2248 7639)
5 Arbor Biotechnologies, Cambridge, USA (GRID:grid.7468.d)
6 DuPont Nutrition and Health, Dangé–Saint–Romain, France (GRID:grid.280285.5)
7 Université Laval, Québec City, Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Félix d’Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Québec, Canada (GRID:grid.23856.3a) (ISNI:0000 0004 1936 8390)
8 Universidad de Alicante, Departamento de Fisiología, Genética y Microbiología, Alicante, Spain (GRID:grid.5268.9) (ISNI:0000 0001 2168 1800)
9 Arbor Biotechnologies, Cambridge, USA (GRID:grid.5268.9)
10 University of Copenhagen, COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, Gentofte, Denmark (GRID:grid.5254.6) (ISNI:0000 0001 0674 042X)
11 Vilnius University, Institute of Biotechnology, Life Sciences Center, Vilnius, Lithuania (GRID:grid.6441.7) (ISNI:0000 0001 2243 2806)
12 University of Georgia, Biochemistry and Molecular Biology, Genetics and Microbiology, Athens, USA (GRID:grid.213876.9) (ISNI:0000 0004 1936 738X)
13 University of St. Andrews, Biomedical Sciences Research Complex, St. Andrews, UK (GRID:grid.11914.3c) (ISNI:0000 0001 0721 1626)
14 University of Toronto, Department of Chemical Engineering and Applied Chemistry, Toronto, Canada (GRID:grid.17063.33) (ISNI:0000 0001 2157 2938) ; Bangor University, Bangor, Centre for Environmental Biotechnology, School of Natural Sciences, Gwynedd, UK (GRID:grid.7362.0) (ISNI:0000000118820937)
15 Arbor Biotechnologies, Cambridge, USA (GRID:grid.7362.0)
16 Broad Institute of MIT and Harvard, Cambridge, USA (GRID:grid.66859.34) ; McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, USA (GRID:grid.116068.8) (ISNI:0000 0001 2341 2786) ; Howard Hughes Medical Institute, Cambridge, USA (GRID:grid.413575.1) (ISNI:0000 0001 2167 1581) ; Massachusetts Institute of Technology, Department of Brain and Cognitive Sciences and Department of Biological Engineering, Cambridge, USA (GRID:grid.116068.8) (ISNI:0000 0001 2341 2786)
17 Copenhagen University, Archaea Centre, Department of Biology, Copenhagen, Denmark (GRID:grid.5254.6) (ISNI:0000 0001 0674 042X)
18 University of Freiberg, Bioinformatics group, Department of Computer Science, Freiberg, Germany (GRID:grid.5254.6) ; University of Freiburg, BIOSS Centre for Biological Signaling Studies, Cluster of Excellence, Freiburg, Germany (GRID:grid.5963.9)
19 Wageningen University, Laboratory of Microbiology, Wageningen, The Netherlands (GRID:grid.4818.5) (ISNI:0000 0001 0791 5666)
20 North Carolina State University, Department of Food, Bioprocessing, and Nutrition Sciences, Raleigh, USA (GRID:grid.40803.3f) (ISNI:0000 0001 2173 6074)