BACKGROUND: All archaeal and many bacterial genomes contain Clustered Regularly 
Interspaced Short Palindrome Repeats (CRISPR) and variable arrays of the 
CRISPR-associated (cas) genes that have been previously implicated in a novel 
form of DNA repair on the basis of comparative analysis of their protein product 
sequences. However, the proximity of CRISPR and cas genes strongly suggests that 
they have related functions which is hard to reconcile with the repair 
hypothesis.
RESULTS: The protein sequences of the numerous cas gene products were classified 
into approximately 25 distinct protein families; several new functional and 
structural predictions are described. Comparative-genomic analysis of CRISPR and 
cas genes leads to the hypothesis that the CRISPR-Cas system (CASS) is a 
mechanism of defense against invading phages and plasmids that functions 
analogously to the eukaryotic RNA interference (RNAi) systems. Specific 
functional analogies are drawn between several components of CASS and proteins 
involved in eukaryotic RNAi, including the double-stranded RNA-specific 
helicase-nuclease (dicer), the endonuclease cleaving target mRNAs (slicer), and 
the RNA-dependent RNA polymerase. However, none of the CASS components is 
orthologous to its apparent eukaryotic functional counterpart. It is proposed 
that unique inserts of CRISPR, some of which are homologous to fragments of 
bacteriophage and plasmid genes, function as prokaryotic siRNAs (psiRNA), by 
base-pairing with the target mRNAs and promoting their degradation or 
translation shutdown. Specific hypothetical schemes are developed for the 
functioning of the predicted prokaryotic siRNA system and for the formation of 
new CRISPR units with unique inserts encoding psiRNA conferring immunity to the 
respective newly encountered phages or plasmids. The unique inserts in CRISPR 
show virtually no similarity even between closely related bacterial strains 
which suggests their rapid turnover, on evolutionary scale. Corollaries of this 
finding are that, even among closely related prokaryotes, the most commonly 
encountered phages and plasmids are different and/or that the dominant phages 
and plasmids turn over rapidly.
CONCLUSION: We proposed previously that Cas proteins comprise a novel DNA repair 
system. The association of the cas genes with CRISPR and, especially, the 
presence, in CRISPR units, of unique inserts homologous to phage and plasmid 
genes make us abandon this hypothesis. It appears most likely that CASS is a 
prokaryotic system of defense against phages and plasmids that functions via the 
RNAi mechanism. The functioning of this system seems to involve integration of 
fragments of foreign genes into archaeal and bacterial chromosomes yielding 
heritable immunity to the respective agents. However, it appears that this 
inheritance is extremely unstable on the evolutionary scale such that the 
repertoires of unique psiRNAs are completely replaced even in closely related 
prokaryotes, presumably, in response to rapidly changing repertoires of dominant 
phages and plasmids.