Nature Reviews Microbiology 9, 467-477 (June 2011) | doi:10.1038/nrmicro2577

OpinionEvolution and classification of the CRISPR–Cas systems

Kira S. Makarova1, Daniel H. Haft2, Rodolphe Barrangou3, Stan J. J. Brouns4, Emmanuelle Charpentier5, Philippe Horvath6, Sylvain Moineau7, Francisco J. M. Mojica8, Yuri I. Wolf1, Alexander F. Yakunin9, John van der Oost4 & Eugene V. Koonin1  About the authors


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.

Author affiliations

  1. Kira S. Makarova, Yuri I. Wolf & Eugene V. Koonin are at the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894, USA.
  2. Daniel H. Haft is at The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland 20850, USA.
  3. Rodolphe Barrangou is at Danisco USA Inc., 3329 Agriculture Drive, Madison, Wisconsin 53716, USA.
  4. Stan J. J. Brouns and John van der Oost are at the Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.
  5. Emmanuelle Charpentier is at the Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden.
  6. Philippe Horvath is at Danisco France SAS, BP10, 86220 Dangé-Saint-Romain, France.
  7. Sylvain Moineau is at the Département de Biochimie, Microbiologie et Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, Quebec G1V 0A6, Canada.
  8. Francisco J. M. Mojica is at the Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, 03080-Alicante, Spain.
  9. Alexander F. Yakunin is at the Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada.

Correspondence to: Eugene V. Koonin1 Email:

Published online 9 May 2011