Small RNA-Based Prokaryotic Immunity via the CRISPR-Cas system

The CRISPR-Cas system protects prokaryotes from viruses and other potential genome invaders. This adaptive RNA-based prokaryotic immune system arises from clustered regularly interspaced short palindromic repeats (CRISPRs), which harbor short invader-derived sequences, and the CRISPR-associated (Cas) protein-coding genes found in prokaryotic genomes. Using the hyperthermophile Pyrococcus furiosus, we have delineated several key steps in the CRISPR-Cas genome defense pathway. Small RNAs from the CRISPR loci target effector complexes to silence invaders. The Cas6 protein “dices” CRISPR transcripts to generate the individual invader-targeting RNAs. The mature RNAs include a signature sequence element derived from the CRISPR repeat. We have also identified a CRISPR-Cas effector complex comprised of mature CRISPR RNAs and the RAMP module (or Cmr) Cas proteins. The complexes cleave complementary target RNAs at a fixed distance from the 3' end of the integral guide RNAs. Our results indicate that prokaryotes possess a unique RNA silencing system that functions by homology-dependent cleavage of invader RNAs.