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Nat Rev Microbiol. 2020 Feb;18(2):67-83. doi: 10.1038/s41579-019-0299-x. Epub 2019 Dec 19.

Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants.

Author information

1
National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA.
2
Bioinformatics group, Department of Computer Science, University of Freiberg, Freiberg, Germany.
3
Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands.
4
Max Planck Unit for the Science of Pathogens, Humboldt University, Berlin, Germany.
5
Arbor Biotechnologies, Cambridge, MA, USA.
6
DuPont Nutrition and Health, Dangé-Saint-Romain, France.
7
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, Université Laval, Québec City, Québec, Canada.
8
Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain.
9
COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Gentofte, Denmark.
10
Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
11
Biochemistry and Molecular Biology, Genetics and Microbiology, University of Georgia, Athens, GA, USA.
12
Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, UK.
13
Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada.
14
Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, UK.
15
Broad Institute of MIT and Harvard, Cambridge, MA, USA.
16
McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
17
Howard Hughes Medical Institute, Cambridge, MA, USA.
18
Department of Brain and Cognitive Sciences and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
19
Archaea Centre, Department of Biology, Copenhagen University, Copenhagen, Denmark.
20
BIOSS Centre for Biological Signaling Studies, Cluster of Excellence, University of Freiburg, Freiburg, Germany.
21
Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
22
Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA.
23
National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA. koonin@ncbi.nlm.nih.gov.

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.

PMID:
31857715
DOI:
10.1038/s41579-019-0299-x

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