Bacterial Schlafens mediate anti-phage defense [3'-end RNA-seq]
Human Schlafen proteins restrict viral replication by cleaving tRNA and suppressing protein synthesis. The ribonuclease domain of Schlafen proteins is highly conserved and found in all three domains of life. However, its function in prokaryotes has not been determined experimentally. Here, we demonstrate that Schlafen nucleases are widespread in bacteria and mediate anti-phage defense. Bacterial Schlafen nucleases are frequently fused to a variety of domains that we predict to sense phage infection. We show that single-component phage defense, consisting of Schlafen nuclease fused to an immunoglobulin-like domain, recognizes T5-like phage tail assembly chaperones and cleaves bacterial and viral tRNA, triggering abortive infection. This work demonstrates that the Schlafen nuclease domain is an ancient, functionally and mechanistically conserved immune effector leveraged for antiviral defense across the tree of life. Overall design: to determine RNA cleaved by phage-activated bacterial Schlafen nuclease, we extracted total RNA from infected cells expressing active Schlafen nuclease or its catalytically inactive mutant. RNA was polyadenylated, sheared with ultrasound, reverse-transcribed with a polyT primer, and PCR amplified. Resulting amplicons were sequenced with Oxford Nanopore.