title: Evolution and classification of the CRISPR-Cas systems.
abstract: The CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) modules are adaptive immunity systems that are present in many archaea and bacteria. These defence systems are encoded by operons that have an extraordinarily diverse architecture and a high rate of evolution for both the cas genes and the unique spacer content. Here, we provide an updated analysis of the evolutionary relationships between CRISPR-Cas systems and Cas proteins. Three major types of CRISPR-Cas system are delineated, with a further division into several subtypes and a few chimeric variants. Given the complexity of the genomic architectures and the extremely dynamic evolution of the CRISPR-Cas systems, a unified classification of these systems should be based on multiple criteria. Accordingly, we propose a 'polythetic' classification that integrates the phylogenies of the most common cas genes, the sequence and organization of the CRISPR repeats and the architecture of the CRISPR-cas loci.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, USA.
authors.forename: Kira S
authors.initials: KS
authors.lastname: Makarova
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Haft
authors.forename: Rodolphe
authors.initials: R
authors.lastname: Barrangou
authors.forename: Stan J J
authors.initials: SJ
authors.lastname: Brouns
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Charpentier
authors.forename: Philippe
authors.initials: P
authors.lastname: Horvath
authors.forename: Sylvain
authors.initials: S
authors.lastname: Moineau
authors.forename: Francisco J M
authors.initials: FJ
authors.lastname: Mojica
authors.forename: Yuri I
authors.initials: YI
authors.lastname: Wolf
authors.forename: Alexander F
authors.initials: AF
authors.lastname: Yakunin
authors.forename: John
authors.initials: J
authors.lastname: van der Oost
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Koonin
mesh_terms: D056704:Adaptive Immunity / Q000235:genetics*; D001105:Archaea / Q000235:genetics; D019843:Archaeal Proteins / Q000145:classification / Q000235:genetics; D001426:Bacterial Proteins / Q000145:classification / Q000235:genetics; D016680:Genome, Bacterial; D010802:Phylogeny; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins