Tetramerization and RNA-guided filament assembly control Schlafen–Argonaute antiphage defense

Two deeply conserved protein families, Argonaute (Ago) and Schlafen (SLFN), play defense roles in diverse prokaryotes and eukaryotes, including humans. Here, we identify a monophyletic group of proteins broadly distributed across bacteria and archaea that fuse a SLFN domain with an Ago core and a GHKL-family ATPase. Using SLFN-pAgo from Runella zeae as a model, we show that these proteins protect bacterial cells against bacteriophages by employing the Ago core as a guide-dependent sensor and the SLFN domain as a nuclease effector to induce abortive infection via tRNAs cleavage. Structural and biochemical analyses reveal that ATP binding by the GHKL domain drives tetramerization of SLFN-pAgo, reconstituting the canonical SLFN nuclease architecture found in mammalian proteins. Prior to target detection, non-canonical guide RNA binding induces the formation of long helical filaments, locking the SLFN domains in an inactive configuration. Guide-dependent recognition of complementary target DNA triggers massive structural rearrangements leading to filament disassembly and the induction of SLFN nuclease activity. Together, our findings uncover a new antiphage system that employs reversible guide- and ATP-mediated oligomerization to strictly regulate cooperation between an Ago sensor and a SLFN RNAse effector.