RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease

Abstract

The type III-E CRISPR–Cas7-11 effector binds a CRISPR RNA (crRNA) and the putative protease Csx29and catalyzes crRNA-guided RNA cleavage. We report cryo–electron microscopy structures of theCas7-11–crRNA–Csx29 complex with and without target RNA (tgRNA), and demonstrate that tgRNAbinding induces conformational changes in Csx29. Biochemical experiments revealed tgRNA-dependentcleavage of the accessory protein Csx30 by Csx29. Reconstitution of the system in bacteria showedthat Csx30 cleavage yields toxic protein fragments that cause growth arrest, which is regulated byCsx31. Csx30 binds Csx31 and the associated sigma factor RpoE (RNA polymerase, extracytoplasmic E),suggesting that Csx30-mediated RpoE inhibition modulates the cellular response to infection. Weengineered the Cas7-11–Csx29–Csx30 system for programmable RNA sensing in mammalian cells.Overall, the Cas7-11–Csx29 effector is an RNA-dependent nuclease-protease