Diversity and evolution of class 2 CRISPR-Cas systems

Sergey Shmakov; Aaron Smargon; David Scott; David Cox; Neena Pyzocha; Winston Yan; Omar O Abudayyeh; Jonathan S Gootenberg; Kira S Makarova; Yuri I Wolf; Konstantin Severinov; Feng Zhang; Eugene V Koonin

doi:10.1038/nrmicro.2016.184

Diversity and evolution of class 2 CRISPR-Cas systems

Nat Rev Microbiol. 2017 Mar;15(3):169-182. doi: 10.1038/nrmicro.2016.184. Epub 2017 Jan 23.

Authors

Sergey Shmakov^{1

2}, Aaron Smargon^{3

4}, David Scott³, David Cox³, Neena Pyzocha^{3

5}, Winston Yan³, Omar O Abudayyeh^{3

6}, Jonathan S Gootenberg^{3

7}, Kira S Makarova², Yuri I Wolf², Konstantin Severinov^{1

8

9}, Feng Zhang^{3

6

7

10

11}, Eugene V Koonin²

Affiliations

¹ Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Skolkovo 143025, Russia.
² National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.
³ Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts 02142, USA.
⁴ Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.
⁵ Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.
⁶ Department of Health Sciences and Technology, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.
⁷ McGovern Institute for Brain Research at Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.
⁸ Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA.
⁹ Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.
¹⁰ Department of Brain and Cognitive Science, Massachusetts Institute of Technology Cambridge (MIT), Massachusetts 02139, USA.
¹¹ Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA.

Abstract

Class 2 CRISPR-Cas systems are characterized by effector modules that consist of a single multidomain protein, such as Cas9 or Cpf1. We designed a computational pipeline for the discovery of novel class 2 variants and used it to identify six new CRISPR-Cas subtypes. The diverse properties of these new systems provide potential for the development of versatile tools for genome editing and regulation. In this Analysis article, we present a comprehensive census of class 2 types and class 2 subtypes in complete and draft bacterial and archaeal genomes, outline evolutionary scenarios for the independent origin of different class 2 CRISPR-Cas systems from mobile genetic elements, and propose an amended classification and nomenclature of CRISPR-Cas.

MeSH terms

Archaea / genetics
Bacteria / genetics
CRISPR-Associated Proteins / genetics*
CRISPR-Cas Systems / genetics*
Gene Editing / methods*
Genome, Archaeal / genetics*
Genome, Bacterial / genetics*
Protein Domains / genetics*

Substances

CRISPR-Associated Proteins

Abstract

MeSH terms

Substances

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