Widespread repurposing of the human CD38 ADP-ribosyl cyclase fold for toxicity in antibacterial and anti-eukaryotic bacterial polymorphic toxins

Abstract

Bacterial polymorphic toxins are modular weapons that mediate inter-microbial competition and host interactions by delivering diverse cytotoxic domains through specialized secretion systems. Here, we identify and characterize a novel toxin domain in Pantoea ananatis that displays remarkable structural and functional conservation with the human enzyme CD38. This bacterial toxin, fused to the type VI secretion system (T6SS) PAAR domain, harbors a C-terminal ADP-ribosyl cyclase (ARC) domain that hydrolyzes NAD+ and NADP+ in vitro and in vivo, leading to growth inhibition in both bacterial and eukaryotic cells. The 1.6-[A] resolution structure of ARC reveals that it adopts a globular fold nearly identical to the human CD38 ADP ribosyl cyclase, with key catalytic residues conserved. ARC toxicity is neutralized in P. ananatis by a dedicated immunity protein. Comparative genomics reveals that CD38-like ARC domains are widespread in bacteria, fused to diverse delivery modules including T6SS, T7SS, and CDI systems. Functional assays demonstrate that these domains act as NAD-depleting toxins, with cross-immunity observed between non-cognate toxin-immunity pairs. Taken together, our findings reveal that a eukaryotic-like NAD+ hydrolase fold has been adapted in bacteria to generate a novel class of metabolic toxins, expanding the functional scope of polymorphic effectors and illustrating how conserved host-like enzymes can be co-opted for microbial warfare.