Dynamics of Cas10 Govern Discrimination between Self and Nonself in Type III CRISPR-Cas Immunity

ABSTRACT Adaptive immune systems are required to accurately distinguish between self and nonself in order to defend against invading pathogens while avoiding autoimmunity. Type III CRISPR-Cas systems employ guide RNAs that recognize complementary RNA molecules to trigger the degradation of both the target transcript and its template DNA. These systems can broadly eliminate foreign targets with multiple mutations, but still effectively curb immunity against the host. The molecular basis for these unique features remains unknown. Here we use single-molecule fluorescence microscopy to study the interaction between a type III-A ribonucleoprotein complex and various RNA substrates. We find that Cas10—the DNase effector of the complex—displays rapid conformational fluctuations on foreign RNA targets, but is locked in a static configuration on self RNA. Single-stranded DNA promotes Cas10’s occupancy at a selected set of conformational states, which is also sensitively modulated by target mutations and predictive of CRISPR interference activity. These findings highlight the central role of the internal dynamics of CRISPR-Cas complexes in self/nonself discrimination and target specificity.