LAUSR

In prokaryotes, CRISPR-Cas systems provide adaptive immune responses against foreign genetic elements through RNA-guided nuclease activity. Recently, additional genes with non-nuclease functions have been found in genetic association with CRISPR systems, suggesting that there may be other RNA-guided non-nucleolytic enzymes. One such gene from Desulfonema ishimotonii encodes the TPR-CHAT protease Csx29, which is associated with the CRISPR effector Cas7-11. Here, we demonstrate that this CRISPR-associated protease (CASP) exhibits programmable RNA-activated endopeptidase activity against a sigma factor inhibitor to regulate a transcriptional response. Cryo–electron microscopy of an active and substrate-bound CASP complex reveals an allosteric activation mechanism that reorganizes Csx29 catalytic residues upon target RNA binding. This work reveals an RNA-guided function in nature that can be leveraged for RNA-sensing applications in vitro and in human cells. Description RNA-activated protein cleavage CRISPR-Cas systems typically function as RNA-guided nucleases to protect bacteria against foreign genetic material; however, diverse associated genes have been identified within CRISPR-Cas systems, raising the possibility that new RNA-guided enzymatic functions exist in nature. One example is a CHAT family protease found next to the RNA-targeting CRISPR effector gRAMP. Strecker et al. found that this CRISPR-associated protease performs RNA-activated protein cleavage of a sigma factor inhibitor to activate a transcriptional response after infection. Characterization and engineering of this natural system allows for new possibilities in biology, including RNA-sensing applications in human cells. —DJ A CRISPR-associated protease cleaves a sigma factor inhibitor in response to specific RNA sequences.