CoCoNuTs: A diverse subclass of Type IV restriction systems predicted to target RNA

Abstract

A comprehensive census of McrBC systems, a major form of prokaryotic Type IV restriction-modification (RM), followed by phylogenetic analysis, reveals their enormous abundance in diverse bacteria and archaea and a plethora of genomic associations. We focus on a previously uncharacterized branch, which we denote CoCoNuTs (coiled-coil nuclease tandems) for their salient features, the presence of extensive coiled-coil structures and tandem nucleases. The CoCoNuTs alone show extraordinary variety, with 3 distinct types and multiple subtypes. All CoCoNuTs contain domains predicted to interact with translation system components, such as OB-folds resembling the SmpB protein that binds bacterial tmRNA, YTH-like domains that might recognize methylated tmRNA, tRNA, or rRNA, and RNA-binding Hsp70 chaperone homologs, along with RNases, such as HEPN domains, all suggesting that the CoCoNuTs target RNA. Many CoCoNuTs may also target DNA, via McrC nuclease homologs. Additional restriction systems, such as Type I RM and Druantia Type III, are frequently encoded in the same predicted superoperons. In many of these superoperons, CoCoNuTs are likely regulated by cyclic nucleotides, possibly, RNA fragments with cyclic termini, that bind associated CARF (CRISPR-Associated Rossmann Fold) domains. We experimentally demonstrate the ability of Type II CoCoNuTs to protect E. coli against specific phages and plasmids.