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Nucleic Acids Res. 2014 Jun;42(10):6091-105. doi: 10.1093/nar/gku241. Epub 2014 Apr 11.

Classification and evolution of type II CRISPR-Cas systems.

Author information

1
The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden Max F. Perutz Laboratories, University of Vienna, Vienna 1030, Austria.
2
National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA.
3
The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå 90187, Sweden Helmholtz Centre for Infection Research, Department of Regulation in Infection Biology, Braunschweig 38124, Germany Hannover Medical School, Hannover 30625, Germany.
4
National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA koonin@ncbi.nlm.nih.gov.

Abstract

The CRISPR-Cas systems of archaeal and bacterial adaptive immunity are classified into three types that differ by the repertoires of CRISPR-associated (cas) genes, the organization of cas operons and the structure of repeats in the CRISPR arrays. The simplest among the CRISPR-Cas systems is type II in which the endonuclease activities required for the interference with foreign deoxyribonucleic acid (DNA) are concentrated in a single multidomain protein, Cas9, and are guided by a co-processed dual-tracrRNA:crRNA molecule. This compact enzymatic machinery and readily programmable site-specific DNA targeting make type II systems top candidates for a new generation of powerful tools for genomic engineering. Here we report an updated census of CRISPR-Cas systems in bacterial and archaeal genomes. Type II systems are the rarest, missing in archaea, and represented in ∼ 5% of bacterial genomes, with an over-representation among pathogens and commensals. Phylogenomic analysis suggests that at least three cas genes, cas1, cas2 and cas4, and the CRISPR repeats of the type II-B system were acquired via recombination with a type I CRISPR-Cas locus. Distant homologs of Cas9 were identified among proteins encoded by diverse transposons, suggesting that type II CRISPR-Cas evolved via recombination of mobile nuclease genes with type I loci.

PMID:
24728998
PMCID:
PMC4041416
DOI:
10.1093/nar/gku241
[Indexed for MEDLINE]
Free PMC Article

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