Antiviral signalling by a cyclic nucleotide activated CRISPR protease

CRISPR defence systems such as the well-known DNA-targeting Cas9 and the RNA-targeting type III systems are widespread in prokaryotes(1,2). The latter orchestrates a complex antiviral response that is initiated through the synthesis of cyclic oligoadenylates after recognition of foreign RNA(3-5). Among the large set of proteins that are linked to type III systems and predicted to bind cyclic oligoadenylates(6,7), a CRISPR-associated Lon protease (CalpL) stood out to us. CalpL contains a sensor domain of the SAVED family(7) fused to a Lon protease effector domain. However, the mode of action of this effector is unknown. Here we report the structure and function of CalpL and show that this soluble protein forms a stable tripartite complex with two other proteins, CalpT and CalpS, that are encoded on the same operon. After activation by cyclic tetra-adenylate (cA(4)), CalpL oligomerizes and specifically cleaves the MazF homologue CalpT, which releases the extracytoplasmic function sigma factor CalpS from the complex. Our data provide a direct connection between CRISPR-based detection of foreign nucleic acids and transcriptional regulation. Furthermore, the presence of a SAVED domain that binds cyclic tetra-adenylate in a CRISPR effector reveals a link to the cyclic-oligonucleotide-based antiphage signalling system.

Automated summary

CRISPR defence systems are widespread in prokaryotes, and the type III systems initiate a complex antiviral response through the synthesis of cyclic oligoadenylates after recognition of foreign RNA. The CRISPR-associated Lon protease (CalpL) is linked to type III systems and binds cyclic oligoadenylates. This study reveals that CalpL forms a stable complex with two other proteins, CalpT and CalpS, and specifically cleaves CalpT to release CalpS, connecting CRISPR-based detection of foreign nucleic acids and transcriptional regulation.