Prediction of a prokaryotic RNA-silencing system

Researchers have used computational methods to predict what could be a prokaryotic RNA-silencing mechanism similar to the eukaryotic RNA- interference system. A study published today in the open access journal with a novel system of peer review, Biology Direct, provides the first strong evidence that a type of tandem repeats found in archaea and bacteria, the Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR), might act in conjunction with the CRISPR-associated (cas) family of genes as a defence mechanism against phage and plasmid RNA. A number of Cas proteins are shown to contain domains that suggest a functional similarity to eukaryotic proteins involved in the eukaryotic RNA-interference system.

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.