A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems

Zhang, Dapeng; Iyer, Lakshminarayan M.; Aravind, L.

Potential evolutionary processes in diversification of toxins and immunity proteins. Imprints of the evolutionary arms race arising from the above processes are readily observed in our systems. The toxin proteins appear to show a rather peculiar pattern of diversification. The N-termini, which are typically associated with trafficking, tend to be relatively conserved while C-terminal nuclease domains show major diversity ( Figure 5 ). This is consistent with a recent study on the diversification of RHS proteins in enterobacteria which showed that the RHS proteins undergo C-terminal polymorphism due to rampant recombination with invading cassettes that encode alternative C-terminal modules (94) . This type of recombination or gene-conversion with polymorphic C-terminal cassettes might explain the presence of smaller loci found in the gene-neighborhoods characterized here that encode just a nuclease domain by itself or with an additional small N-terminal extension (Figures 2 and 5) . Hence, we extend the original proposal for RHS diversification to suggest that, more generally, recombination with cassettes with distinct C-terminal modules is the primary proximal mechanism for diversification of the toxin proteins across all bacterial lineages ( Figure 5) . Furthermore, the presence of nuclease and nucleic acid deaminase domains as the primary toxin modules of these systems raises the possibility that their nucleic acid cleaving or mutating activity is involved in triggering recombination events. This appears plausible given the observations that most of these nucleases are likely to be endonucleases, which like their counterparts in the restriction-modification systems could cleave at specific sequences. Similarly, deaminase-induced mutations have been implicated in the triggering of class-switching recombination events in vertebrates (95) . More generally, this ties in with earlier studies which have demonstrated the role for both recombination and positive selection in the evolution of plasmid-borne bacteriocins (96) . It has been proposed that pore-forming versions have predominantly utilized recombination for diversification whereas nucleases have mainly evolved through positive selection. In our systems, the evidence points to both these forces being active at different levels in the evolution of the toxin proteins (96) . While the basic architectures evolve through recombination generating C-terminal polymorphism, the C-terminal nucleases themselves show evidence for considerable sequence diversification within each family. Indeed, much of the diversification of the HNH/EndoVII fold appears to have happened within the context of these systems, with several structurally distinct forms evolving amidst the nuclease toxins ( Figure 3 ).