Structural mechanism of the type IX Retron-Kva2 anti-phage defense system

Retrons are prokaryotic genetic elements that protect bacterial cells from invading phages. The type IX retron comprises a non-coding RNA, a reverse transcriptase (RT), and dual effectors: a putative HEPN nuclease and a winged helix-turn-helix (WH) protein. Here, we show that the type IX retron system from Klebsiella variicola cleaves host rRNAs and tRNAs upon phage infection, mediating anti-phage defense via an abortive-infection mechanism. Cryo-electron microscopy analysis reveals that the RT, HEPN, and WH proteins, along with multicopy single-stranded DNA (msDNA), form a unique, sheet-like supermolecular complex. Notably, the HEPN active site is encircled by the WH and msDNA within the complex, suppressing the nuclease activity prior to phage infection. A phage-encoded exonuclease cleaves the msDNA, likely releasing the HEPN nuclease to cleave host RNAs and induce growth arrest in infected cells. Overall, these findings highlight the structural and functional diversity of prokaryotic anti-phage defense systems.