Kira Makarova and other members of a group led by Eugene Koonin, from the National Institutes of Health, Bethesda, USA, carried out a comparative genomic analysis of CRISPR and cas genes in archaeal and bacterial genome sequences retrieved from National Center for Biotechnology Information (NCBI) databases.
Makarova et al. identified a number of cas genes that are always located close to CRISPR clusters and encode proteins potentially involved in RNA-processing mechanisms such as unwinding and cleaving. These proteins might be functionally similar to eukaryotic enzymes involved in the RNA-interference system – Makarova et al. identify an analog to the eukaryotic RNAi protein Dicer and several potential analogs to the eukaryotic RNAi protein Slicer. But they are not homologous to Dicer and Slicer as they have no sequence similarity with them.
It has been shown that a proportion of inserts in CRISPR units are similar to fragments of viral or plasmid genomes. Makarova et al. extend these observations and propose that all CRISPR inserts are derived from viruses or plasmids but this is not immediately obvious because most of these agents are still unknown. They speculate that the inserts are transcribed and silence phage or plasmid sequences via the formation of a duplex, which is then cleaved by Cas proteins to destroy the foreign RNA.
Article:
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action
Kira S Makarova, Nick V Grishin, Svetlana A Shabalina, Yuri I Wolf and Eugene V Koonin
Biology Direct 2006, (in press)
Biology Direct