Toxic anti-phage defense proteins inhibited by intragenic antitoxin proteins.

Unlabelled: Recombination-promoting nuclease (Rpn) proteins are broadly distributed across bacterial phyla, yet their functions remain unclear. Here we report these proteins are new toxin-antitoxin systems, comprised of genes-within-genes, that combat phage infection. We show the small, highly variable Rpn -terminal domains (Rpn ), which are translated separately from the full-length proteins (Rpn ), directly block the activities of the toxic full-length proteins. The crystal structure of RpnA revealed a dimerization interface encompassing a helix that can have four amino acid repeats whose number varies widely among strains of the same species. Consistent with strong selection for the variation, we document plasmid-encoded RpnP2 protects against certain phages. We propose many more intragenic-encoded proteins that serve regulatory roles remain to be discovered in all organisms.

Significance: Here we document the function of small genes-within-genes, showing they encode antitoxin proteins that block the functions of the toxic DNA endonuclease proteins encoded by the longer genes. Intriguingly, a sequence present in both long and short protein shows extensive variation in the number of four amino acid repeats. Consistent with a strong selection for the variation, we provide evidence that the Rpn proteins represent a phage defense system.