Evolutionary conservation of sequence and secondary structures in CRISPR repeats.
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.


CONCLUSIONS
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.
Kunin
Victor
V
DOE Joint Genome Institute, Walnut Creek, CA 94598, USA. vkunin@lbl.gov
Sorek
Rotem
R
Hugenholtz
Philip
P
D001105:Archaea / Q000235:genetics*; D001419:Bacteria / Q000235:genetics*; D001483:Base Sequence; D016000:Cluster Analysis; D017124:Conserved Sequence; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D005810:Multigene Family; D009690:Nucleic Acid Conformation; D019642:RNA, Archaeal / Q000737:chemistry*; D012329:RNA, Bacterial / Q000737:chemistry*; D012091:Repetitive Sequences, Nucleic Acid; D017423:Sequence Analysis, RNA; D012984:Software
D019642:RNA, Archaeal; D012329:RNA, Bacterial