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Evolutionary conservation of sequence and secondary structures in CRISPR repeats

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7 pages
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.
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2eKVt0uoal0nlu7i.nme8,Issue4,ArticleR61Open Access Research Evolutionary conservation of sequence and secondary structures in CRISPR repeats ¤ ¤ Victor Kunin, Rotem Sorekand Philip Hugenholtz
Address: DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.
¤ These authors contributed equally to this work.
Correspondence: Victor Kunin. Email: vkunin@lbl.gov
Published: 18 April 2007 GenomeBiology2007,8:R61 (doi:10.1186/gb-2007-8-4-r61) The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2007/8/4/R61
Received: 9 October 2006 Revised: 24 January 2007 Accepted: 18 April 2007
© 2007 Kuninet al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 1pC<9rlpou5>sntTmoehiurcenrdctabierodeasgglltueasynidlrrocaoneoimaonretnysesrpsurtndsohwaetacctrephtratdurahrousciruwsetlehpamlasyfnrotsseniinalopmodcrdmfsoictoleCvartusbsyeepeoarechs.s<naegyncainagdsmesguRterllanI>pet/gberieRepasimilaroerstuqPnaeleicsnaddreoomicnuposbedecaphSdtmeyg,roaunpdsC(tIhRaPtSssoRsahevmorfsecneuqes)
Abstract
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 repetitive structures in Bacteria and Archaea composed of exact repeat sequences 24 to 48 bases long (herein called repeats) separated by unique spacers of similar length (herein called spacers) [1,2]. The CRISPR sequences appear to be among the most rapidly evolving elements in the genome, to the point that closely related species and strains, sometimes more than 99% identical at the DNA level, differ in their CRISPR composition [3,4].
Up to 45 gene families, called CRISPR-associated sequences (CASs), appear in conjunction with these repeats and are hypothesized to be responsible for CRISPR propagation and functioning [2,5,6]. It has been proposed that CASs can be divided into seven or eight subtypes, according to their operon organization and gene phylogeny [5,6]. Phylogenetic analysis additionally indicates that CASs have undergone extensive horizontal gene transfer, as very similar CAS genes are found in distantly related organisms [6,7]. CRISPRs and CASs have been found on mobile genetic elements, such as
GenomeBiology2007,8:R61
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