RNA-Guided RNA Cleavage by a CRISPR RNA-Cas Protein Complex

Summary Compelling evidence indicates that the CRISPR-Cas system protects prokaryotes from viruses and other potential genome invaders. This adaptive prokaryotic immune system arises from the c lustered r egularly i nterspaced s hort p alindromic r epeats (CRISPRs) found in prokaryotic genomes, which harbor short invader-derived sequences, and the C RISPR- as sociated (Cas) protein-coding genes. Here, we have identified a CRISPR-Cas effector complex that is comprised of small invader-targeting RNAs from the CRISPR loci (termed p rokaryotic si lencing (psi)RNAs) and the RAMP module (or Cmr) Cas proteins. The psiRNA-Cmr protein complexes cleave complementary target RNAs at a fixed distance from the 3′ end of the integral psiRNAs. In Pyrococcus furiosus , psiRNAs occur in two size forms that share a common 5′ sequence tag but have distinct 3′ ends that direct cleavage of a given target RNA at two distinct sites. Our results indicate that prokaryotes possess a unique RNA silencing system that functions by homology-dependent cleavage of invader RNAs.