Structural modeling reveals phage proteins that manipulate bacterial immune signaling

Immune systems in animals, plants, and bacteria often rely on intracellular nucleotide signaling, which viruses can block by sequestering or degrading these signals. We identified structural and biophysical traits shared by diverse viral antidefense proteins and used these traits to develop a computational pipeline that predicts phage proteins whose role is to manipulate bacterial immune signaling. Experimental validation revealed three previously uncharacterized protein families—Sequestin, Lockin, and Acb5—that inhibit the Thoeris system and the cyclic oligonucleotide–based antiphage signaling system (CBASS). Sequestin and Lockin act as nucleotide “sponges,” binding 1″–3′ glycocyclic adenosine diphosphate–ribose (3′cADPR) and histidine conjugated to ADPR (His- ADPR), whereas Acb5 cleaves cyclic guanosine monophosphate–adenosine monosphosphate (3′3′-cGAMP) and related molecules. Structural and mutational analyses explain their binding and catalytic mechanisms. Thousands of homologs occur in phage genomes, highlighting the abundance and diversity of viral strategies to subvert nucleotide-based immunity.