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.

certain domains related to adhesion and the two-partner secretory (TPS) system N-terminal to the repetitive region, such as PAAR (PFAM: PF05488) and the TpsA-secretion domain (TpsA-SD, also known as the filamentous hemagglutinin FhaB secretory domain; PFAM: PF05860) with a pectate lyase-like fold (53) (54) (55) . Some of these proteins with repetitive domains, which were recovered in our analysis of SUKH superfamily neighborhoods, are representatives of toxins of the CDI systems ( Figure 2 ) that were reported even as this study was being prepared for submission (24, 25) . Like the above proteins, the CDI toxins are characterized by multiple N-terminal TpsA-SD domains and hemagglutinin-repeats combined with polymorphic C-terminal domains that vary greatly between different CDI toxins. In all these CDI proteins the polymorphic C-terminal domain is separated from the repetitive region by either or both of two small a-helical domains annotated as domains of unknown function in the PFAM database (DUF638 or DUF637). Furthermore, it was shown that the protein encoded by the gene following the CDI toxin was an immunity gene, whose product provided resistance against the toxin to the cell that was producing it (25) . By this criterion it became clear that the SUKH superfamily genes in the CDI operons were actually immunity proteins for the toxins encoded by the upstream genes. However, in contrast to the pan-bacterial distribution of the SUKH superfamily, the CDI operons were only observed in proteobacteria (25) . Furthermore, we observed that polymorphic C-terminal domains of the CDI toxins, which are found linked to the SUKH superfamily immunity proteins in CDI systems, are also seen in bacterial lineages outside of proteobacteria, where too they are linked to SUKH superfamily genes. In these cases they are linked to other N-terminal domains that are distinct from the TpsA-SD and hemagglutinin repeat domains. Studies on CDI systems indicated that the toxin function resides in the polymorphic C-terminal domains and at least two of these domains are nuclease toxins that cleave both tRNAs and DNA (25) . Our above observations indicate that outside of CDI systems, the SUKH superfamily genes are linked to genes encoding the HNH and NucA nucleases; hence, it is likely that even these nucleases function as distinct but analogous toxins that cleave nucleic acids in target cells. Together, the above observations raised the possibility that the SUKH superfamily protein might serve as immunity proteins, not just in certain proteobacterial CDI systems, but also more generally function, across all major bacterial lineages, to protect against linked genes, which are predicted to act as toxins.