Cyanobacterial CRISPR-Cas systems, an archaeal-bacterial hybrid?

The CRISPR system is a highly adaptive and heritable resistance mechanism in prokaryotes against bacteriophages and other invading DNA elements. CRISPRs incorporate spacer sequences derived from foreign DNA into their repertoire and following transcription, CRISPR-derived sRNAs act as guide RNAs programming enzymatic cleavage of invading DNA sequences. However, many aspects are only poorly understood and profound differences have been found between archaea and bacterial CRISPR systems. We have characterized the primary transcriptome of the cyanobacterium Synechocystis PCC6803^[1] and found the precursors and small RNAs deriving from 3 CRISPR loci, all located on the megaplasmid pSYSA, as among the most highly accumulating RNA molecules in the cell. For each of the 3 CRISPR regions long precursor RNAs are processed by a unique mechanism, leading to the accumulation of very distinct sRNAs. Comparison to the homologous region in Synechocystis PCC6714 provided insight into the evolutionary past shared by the two strains. Mutants were generated for each of the 3 CRISPRs and for 8 different CRISPR-associated proteins, indicating processing by specific Cas6-type RNA endonucleases and at least one alternative activity. The unique effects mediated by proteins Slr7010-Slr7016 suggest CRISPR1 as an archetypical copy, whereas the other two are quite different and CRISPR2 responds to environmental stimuli. The cyanobacterial CRISPRs as represented on plasmid pSYSA are unique in combining features known from archaea with an otherwise bacterial CRISPR system. Altogether, about two thirds of the coding capacity of pSYSA are involved in these mechanisms, characterizing it as the defense plasmid of Synechocystis.