Nucleotide synthesizing enzymes in antiviral immunity

Abstract

Nucleotidyltransferase (NTase) enzymes control major cellular processes such as genome replication, DNA repair, and nucleotide-based DNA/RNA end modification. In bacteria and animal cells, a specialized family of NTases have also adapted to function as enzymes involved in antiviral immunity, where they synthesize chemically distinct nucleotide signals that couple pathogen detection to activation of downstream immune responses. Here we characterize Hailong, a family of bacterial defense systems organized around a diverse polymerase β-like NTase HalB that synthesizes a unique nucleotide signal to control the activity of a DNA-gated ion channel during phage infection. Using structural biology and biochemistry, we define the mechanism of synthesis and show how the inhibitory DNA signal suppress the HalA membrane effector, which is activated by viral exonuclease to trigger host cell growth arrest and antiphage defense. Additional phylogenetic analyses reveal Hailong diversity that extends beyond this founding pathway: distinct HalB enzymes are distributed across six system types that produce different DNA products coupled to diverse accessory proteins and effectors, mediated by negative regulation, positive activation, and transcriptional control by the nucleotide immune signal. Extending these principles beyond bacterial immunity, structural studies of HSV-1 and MPXV helicase–primase complexes show that NTases regulates viral replisome assembly, where interactions with the DNA polymerase remodel the helicase–primase architecture to control primer synthesis during viral replication. Together, these studies establish NTase nucleotide synthesizing enzymes as versatile regulators of antiviral immunity across the tree of life.