Type III-B CRISPR-Cas signaling-based cascade of proteolytic cleavages

Abstract

Type III CRISPR-Cas systems provide a sequence-specific adaptive immune response that protects prokaryotic hosts against viruses and other foreign genetic invaders. These crRNA-guided Cas effector complexes bind and cleave complementary RNA targets. Specific target binding stimulates the Cas10 subunit to generate cyclic oligoadenylate (cOA) signaling molecules, that in turn allosterically activate proteins carrying cognate sensory domains: CARF or SAVED. Here, we characterize an elaborate set of genes associated with the type III-B CRISPR-Cas system from Haliangium ochraceum, which includes a signal transduction module of a CBASS defense system with two caspase-like proteases, SAVED-CHAT and PCaspase (Prokaryotic Caspase). We show that binding of a 3-nucleotide cOA (cA3) to the SAVED domain of SAVED-CHAT induces its oligomerization into long filaments that activate the proteolytic activity of the CHAT domain. Surprisingly, we find that activated SAVED-CHAT specifically cleaves and activates the second protease, PCaspase. In turn, activated PCaspase cleaves a multitude of other proteins, including a putative sigma factor and a PCaspase-inhibitor. We expressed the type III-B system and its associated genes in E. coli and observed a strong abortive phenotype when offering a complementary target RNA, but only in the presence of both SAVED-CHAT and PCaspase. Together, our findings show an intriguing cascade of proteolytic activities (conceptually similar to eukaryotic caspases) in this bacterial immune system that reveals yet another strategy to effectively defend against mobile genetic elements.