There I was waffling about the delights of CRISPRs – and here they come again. This new genomic analysis indicates that CRISPRs can be classified and clustered using the presence/absence of putative RNA secondary structure.
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 (CAS), 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.
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 presented stable, highly conserved RNA secondary structures, while others lacked detectable structures. Stable secondary structures exhibited multiple compensatory base changes in the stem region, indicating evolutionary and functional conservation.