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

被引:1449
作者
Makarova, Kira S. [1 ]
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 [5 ]
Shah, Shiraz A. [9 ]
Siksnys, Virginijus [10 ]
Terns, Michael P. [11 ]
Venclovas, Ceslovas [10 ]
White, Malcolm F. [12 ]
Yakunin, Alexander F. [13 ,14 ]
Yan, Winston [5 ]
Zhang, Feng [5 ,15 ,16 ,17 ,18 ,19 ]
Garrett, Roger A. [20 ]
Backofen, Rolf [2 ,21 ]
van der Oost, John [22 ]
Barrangou, Rodolphe [23 ]
Koonin, Eugene, V [1 ]
机构
[1] Natl Lib Med, Natl Ctr Biotechnol Informat, Bethesda, MD 20894 USA
[2] Univ Freiberg, Dept Comp Sci, Bioinformat Grp, Freiberg, Germany
[3] Delft Univ Technol, Kavli Inst Nanosci, Dept Bionanosci, Delft, Netherlands
[4] Humboldt Univ, Max Planck Unit Sci Pathogens, Berlin, Germany
[5] Arbor Biotechnol, Cambridge, MA USA
[6] DuPont Nutr & Hlth, Dange St Romain, France
[7] Univ Laval, Dept Biochim Microbiol & Bioinformat, Fac Sci & Genie,Fac Med Dent, Grp Rech Ecol Buccale,Felix dHerelle Reference Ct, Quebec City, PQ, Canada
[8] Univ Alicante, Dept Fisiol Genet & Microbiol, Alicante, Spain
[9] Univ Copenhagen, Herlev & Gentofte Hosp, Copenhagen Prospect Studies Asthma Childhood, COPSAC, Gentofte, Denmark
[10] Vilnius Univ, Life Sci Ctr, Inst Biotechnol, Vilnius, Lithuania
[11] Univ Georgia, Genet & Microbiol, Biochem & Mol Biol, Athens, GA 30602 USA
[12] Univ St Andrews, Biomed Sci Res Complex, St Andrews, Fife, Scotland
[13] Univ Toronto, Dept Chem Engn & Appl Chem, Toronto, ON, Canada
[14] Bangor Univ, Ctr Environm Biotechnol, Sch Nat Sci, Bangor, Gwynedd, Wales
[15] Broad Inst MIT & Harvard, Cambridge, MA 02142 USA
[16] MIT, McGovern Inst Brain Res, 77 Massachusetts Ave, Cambridge, MA 02139 USA
[17] Howard Hughes Med Inst, Cambridge, MA USA
[18] MIT, Dept Brain & Cognit Sci, E25-618, Cambridge, MA 02139 USA
[19] MIT, Dept Biol Engn, 77 Massachusetts Ave, Cambridge, MA 02139 USA
[20] Univ Copenhagen, Archaea Ctr, Dept Biol, Copenhagen, Denmark
[21] Univ Freiburg, BIOSS Ctr Biol Signaling Studies, Cluster Excellence, Freiburg, Germany
[22] Wageningen Univ, Lab Microbiol, Wageningen, Netherlands
[23] North Carolina State Univ, Dept Food Bioproc & Nutr Sci, Raleigh, NC USA
关键词
ADAPTIVE IMMUNITY; DIVERSITY; BACTERIAL; ARCHAEAL; DISCOVERY; ELEMENTS; PAM;
D O I
10.1038/s41579-019-0299-x
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
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.
引用
收藏
页码:67 / 83
页数:17
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