BACKGROUND: Clustered regularly interspaced short palindromic repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in approximately 40% of bacterial and most archaeal genomes analyzed to date. More than 40 gene families, called CRISPR-associated sequences (CASs), appear in conjunction with these repeats and are thought to be involved in the propagation and functioning of CRISPRs. It has been recently shown that CRISPR provides acquired resistance against viruses in prokaryotes. RESULTS: Here we analyze CRISPR repeats identified in 195 microbial genomes and show that they can be organized into multiple clusters based on sequence similarity. Some of the clusters present stable, highly conserved RNA secondary structures, while others lack detectable structures. Stable secondary structures exhibit multiple compensatory base changes in the stem region, indicating evolutionary and functional conservation. CONCLUSION: We show that the repeat-based classification corresponds to, and expands upon, a previously reported CAS gene-based classification, including specific relationships between CRISPR and CAS subtypes.
BACKGROUND: Clustered regularly interspaced short palindromic repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present in approximately 40% of bacterial and most archaeal genomes analyzed to date. More than 40 gene families, called CRISPR-associated sequences (CASs), appear in conjunction with these repeats and are thought to be involved in the propagation and functioning of CRISPRs. It has been recently shown that CRISPR provides acquired resistance against viruses in prokaryotes. RESULTS: Here we analyze CRISPR repeats identified in 195 microbial genomes and show that they can be organized into multiple clusters based on sequence similarity. Some of the clusters present stable, highly conserved RNA secondary structures, while others lack detectable structures. Stable secondary structures exhibit multiple compensatory base changes in the stem region, indicating evolutionary and functional conservation. CONCLUSION: We show that the repeat-based classification corresponds to, and expands upon, a previously reported CAS gene-based classification, including specific relationships between CRISPR and CAS subtypes.
Authors: Thean-Hock Tang; Norbert Polacek; Marek Zywicki; Harald Huber; Kim Brugger; Roger Garrett; Jean Pierre Bachellerie; Alexander Hüttenhofer Journal: Mol Microbiol Date: 2005-01 Impact factor: 3.501
Authors: Mohammed Sebaihia; Brendan W Wren; Peter Mullany; Neil F Fairweather; Nigel Minton; Richard Stabler; Nicholas R Thomson; Adam P Roberts; Ana M Cerdeño-Tárraga; Hongmei Wang; Matthew T G Holden; Anne Wright; Carol Churcher; Michael A Quail; Stephen Baker; Nathalie Bason; Karen Brooks; Tracey Chillingworth; Ann Cronin; Paul Davis; Linda Dowd; Audrey Fraser; Theresa Feltwell; Zahra Hance; Simon Holroyd; Kay Jagels; Sharon Moule; Karen Mungall; Claire Price; Ester Rabbinowitsch; Sarah Sharp; Mark Simmonds; Kim Stevens; Louise Unwin; Sally Whithead; Bruno Dupuy; Gordon Dougan; Bart Barrell; Julian Parkhill Journal: Nat Genet Date: 2006-06-25 Impact factor: 38.330
Authors: Benjamin Bolduc; Daniel P Shaughnessy; Yuri I Wolf; Eugene V Koonin; Francisco F Roberto; Mark Young Journal: J Virol Date: 2012-02-29 Impact factor: 5.103