CRISPR–Cas systems provide archaea and bacteria with adaptive immunity against viruses and plasmids.
CRISPR–Cas genomic loci show extreme diversity in sequence and gene arrangement.
We developed a computational approach for CRISPR–Cas classification, combining comparisons of Cas protein sequences and locus architectures.
Two classes, five types and 16 subtypes of CRISPR–Cas systems were identified based on this approach.
An automated classifier was developed for assigning CRISPR–Cas loci from sequenced genomes to specific subtypes.
The evolution of CRISPR–Cas systems is marked by extensive horizontal transfer and recombination of functional modules.
The evolution of CRISPR–cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR–cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR–Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized.
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K.S.M., Y.I.W., D.H. and E.V.K. are supported by the National Institutes of Health (NIH) Intramural Research Program at the National Library of Medicine, US Department of Health and Human Services. R.M.T. and M.P.T. are supported by NIH grants RO1 GM54682 and RO1 GM99876. J.v.d.O. was partly supported by SIAM Gravitation Grant 024.002.002 from the Netherlands Organization for Scientific Research (N.W.O.). S.J.J.B. was financially supported by an NWO Vidi grant (864.11.005) and European Research Council (ERC) Stg (639707). A.F.Y. is supported by the Natural Sciences and Engineering Research Council (NSERC) Strategic Network Grant IBN and NSERC Discovery grant. S.M. acknowledges funding from Natural Sciences and Engineering Research Council of Canada (Discovery program) and holds a Tier 1 Canada Research Chair in Bacteriophages. F.J.M.M. is supported by the Ministerio de Economía y Competitividad (BIO2014-53029). R.B. is supported by the Deutsche Forschungsgemeinschaft (DFG) grant (BA 2168/5-2). S.A.S. and R.A.G. were funded primarily by the Danish Natural Science Research Council. O.S.A., F.C., S.J.S., R.B., S.A.S and R.A.G. are grateful to all members of the FOR1680 for helpful discussions.
The authors declare no competing financial interests.
The core proteins of CRISPR-Cas systems (PDF 257 kb)
The list of all Cas profiles with assigned gene names, system types and subtypes and a role in CRISPR-Cas function (XLSX 23 kb)
Methods (PDF 444 kb)
The classes, types and subtypes of CRISPR-Cas systems, their signature proteins and key features (PDF 254 kb)
Cas1 phylogenetic tree in the Newick format (DOCX 48 kb)
Cas3 phylogenetic tree in the Newick format (DOCX 177 kb)
The list of all cas loci, profiles and cas gene names assigned for each gene in the locus (XLSX 1239 kb)
Distribution of different types and subtypes of CRISPR-Cas in archaeal and bacterial phyla (PDF 169 kb)
Cas10 phylogenetic trees in the Newick format (DOCX 164 kb)
Distribution of array to loci distances. (XLSX 123 kb)
Comparison of different classifications of CRISPR-Cas systems (PDF 137 kb)
Locus architecture phylogentic tree in the Newick format (DOCX 46 kb)
Sequence similarity-based dendrogram of the crRNA-effector complexes in the Newick format (DOCX 179 kb)
Sequence similarity-based dendrogram of the adaptation cas genes in the Newick format (DOCX 56 kb)
Performance of an automated classifier for annotation of CRISPR–cas loci (PDF 112 kb)
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Makarova, K., Wolf, Y., Alkhnbashi, O. et al. An updated evolutionary classification of CRISPR–Cas systems. Nat Rev Microbiol 13, 722–736 (2015). https://doi.org/10.1038/nrmicro3569
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