Conserved accessory proteins encoded with archaeal and bacterial Type III CRISPR-Cas gene cassettes that may specifically modulate, complement or extend interference activity

A study was undertaken to identify conserved proteins that are encoded either within, or directly adjacent to, cas gene cassettes of Type III CRISPR-Cas interference modules. These Type III modules are especially versatile functionally and have been shown to target and degrade dsDNA, ssDNA and ssRNA. In addition, the interference gene cassettes are frequently intertwined with other accessory genes, including genes encoding CARF domains, some of which are likely to be cofunctional. Using a comparative genomics approach, and defining a Type III association score accounting for coevolution and specificity of flanking genes, we identified and classified 39 new Type III associated gene families. Most archaeal and bacterial Type III modules were seen to be flanked by several accessory genes, around half of which did not encode CARF domains and remain of unknown function. Non-CARF accessory genes were found to be more diverse than their CARF counterparts, encoding nuclease, helicase, protease, ATPase, transporter and transmembrane domains and including a considerable fraction that encoded no known domains. The diversity of non-CARF Type III accessory genes found in this study suggests that additional families exist which remain undetected because of the limited number of annotated genomes currently available. The method employed is scalable for potential application on metagenomic data once automated pipelines for annotation of CRISPR-Cas systems have been developed. All accessory genes found in this study are presented online in a readily accessible and searchable format for researchers to audit their model organism of choice: http://accessory.crispr.dk.