title: Classification and evolution of type II CRISPR-Cas systems.
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.
authors.affiliation: 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.
authors.forename: Krzysztof
authors.initials: K
authors.lastname: Chylinski
authors.affiliation: National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA.
authors.forename: Kira S
authors.initials: KS
authors.lastname: Makarova
authors.affiliation: 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.
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Charpentier
authors.affiliation: National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA koonin@ncbi.nlm.nih.gov.
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Koonin
mesh_terms: D064130:CRISPR-Associated Proteins / Q000737:chemistry / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D064113:CRISPR-Cas Systems; D004720:Endonucleases / Q000378:metabolism; D019143:Evolution, Molecular; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D010802:Phylogeny
chemical_list: D064130:CRISPR-Associated Proteins; D004720:Endonucleases
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