Occurrence, Diversity of CRISPR-Cas Systems and Genotyping Implications

Abstract

The CRISPR-Cas modules are adaptive antivirus immunity systems that are present in most archaea and many bacteria. These systems function by incorporating fragments of alien genomes into specific genomic loci, transcribing the inserts and using the transcripts as guide RNAs to destroy the genome of the cognate virus or plasmid. This RNA interference-like immune response is medi-ated by numerous, highly diverse Cas (CRISPR-associated) proteins, several of which form the Cascade complex involved in the processing of CRISPR loci transcripts and cleavage of the target DNA. Comparative analysis of the CRISPR-Cas modules led to the classification of the CRISPR-Cas systems into three types (I, II and III) that are characterized by distinct sets of cas genes. Classification of Cas proteins into families and superfamilies is a non-trivial task because of the fast evolution of many cas genes. Exhaustive sequence comparison aided by analysis of the available crystal structures led to the delineation of approximately 30 protein families that can be further classified into several superfamilies. By far the most common domain in Cas proteins is the RNA Recognition Motif (RRM). The RRM domains show remarkable diversity within the CRISPR-Cas systems and in particular comprise the scaffold of the Cascade complex. In addition to the numerous RRM domains, including a distinct polymerase-cyclase domain, the Cas proteins contain a distinct Superfamily II helicase domain, and several diverse nuclease domains. Detailed comparative analysis of the sequences and structures of Cas proteins structures shed light on the deep relationships between Type I and Type III systems and allowed us to propose a simple evolutionary scenario for the