Diverse bacterial pattern recognition receptors sense the conserved phage proteome

Recognition of foreign molecules inside cells is critical for immunity in all domains of life. Proteins of the STAND NTPase super-family, including eukaryotic nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs), play a central role in this process. In bacteria and archaea, although several STAND NTPase families have been reported to sense phage proteins, their functional diversity remains largely unexplored. Here, we conducted a systematic phylogenetic analysis of prokaryotic STAND NTPases and identified at least 90 structurally distinct families associated with antiviral defense. We first show that the uncharacterized Avs7 family recognizes the major capsid protein (MCP) of tailed phages. Three cryo-EM structures of Salmonella enterica Avs7 reveal an asymmetric, butterfly-shaped tetramer that assembles stepwise via large, MCP-induced conformational changes, incorporating bacterial translation elongation factor Tu (EF-Tu) as a scaffold that is required for full defense activity. Using highly parallel genetic screens, we further show that 13 additional STAND families sense 12 conserved phage protein folds, encompassing most of the core structural and replicative components of tailed phages. These include two structurally distinct families--Avs8 (PD-{lambda}-4) and Avs10 (Erebus/Hypnos/bNACHT64)--that also recognize MCP, as well as 11 other families (Avs11-21) that recognize the portal, portal adaptor, tail nozzle, head-tail connector, tail terminator, tail tube protein, tail assembly chaperone, tape measure protein, DNA polymerase, helicase/RecA-type ATPase, and single-stranded DNA annealing protein (SSAP), respectively. Together, our findings highlight structure-based pattern recognition and host factor repurposing as fundamental strategies of bacterial immunity.