Structural evolution of an ancient nucleotidyltransferase underlies divergence of AbiE antitoxins

Type VII toxin-antitoxin (TA) systems neutralize toxins through antitoxin-mediated post-translational modification (PTM), with the oligoAMPylation-based HepT/MntA and phosphorylation-based AbiE systems representing the most prevalent families. Although the AbiE TA system from Mycobacterium tuberculosis is known to employ antitoxin-dependent phosphorylation to antagonize its toxin, the overall distribution and regulatory diversity of AbiE-like systems remain obscure. A comprehensive search of the IMG/M database revealed that AbiE TA systems comprise a conserved toxin family paired with six distinct groups of antitoxins, including four newly identified antitoxin groups. Despite extensive sequence divergence, structural predictions indicate that most of these antitoxins share a conserved winged helix-turn-helix (wHTH) domain and a C-terminal structurally homologous domain (CTD). We further demonstrate a unifying antagonistic mechanism across these diverse systems: cognate antitoxins induce the phosphorylation of conserved serine or threonine residues in their partner toxins, resulting in toxin inactivation in a CTD-dependent manner. Structural analyses reveal that the antitoxin CTD exhibits homology to nucleotidyltransferases (NTases), including the AbiE toxin itself and the MntA antitoxins, suggesting that type VII antitoxins may have evolved from an ancestral NTase superfamily. Moreover, their DNA-binding capabilities are also diverse, with some functioning as transcriptional regulators and others lacking detectable DNA-binding activity. Collectively, this study expands the recognized diversity of type VII TA systems that rely on PTM for antagonism and provides new insights into their evolutionary trajectories.