Distribution of CRISPR spacer matches in viruses and plasmids of crenarchaeal acidothermophiles and implications for their inhibitory mechanism

Transcripts from spacer sequences within chromosomal repeat clusters [CRISPRs (clusters of regularly intersparced palindromic repeats)] from archaea have been implicated in inhibiting or regulating the propagation of archaeal viruses and plasmids. For the crenarchaeal thermoaciclophiles, the chromosomal spacers show a high level of matches (similar to 30%) with viral or plasmid genomes. Moreover, their distribution along the virus/plasmid genomes, as well as their DNA strand specificity, appear to be random. This is consistent with the hypothesis that chromosomal spacers are taken up directly and randomly from virus and plasmid DNA and that the spacer transcripts target the genomic DNA of the extrachromosomal elements and not their transcripts.