Ba Cas12a3 represents a new subtype of type V CRISPR effector with collateral activity toward tRNA

Abstract The CRISPR-Cas12 family encompasses diverse RNA-guided nucleases with both DNA-targeting and RNA-targeting subtypes. They can trigger antiviral activities mainly through either direct elimination invading nucleic acids, or activating broad collateral cleavage to induce abortive infection. Here, we report a novel type V CRISPR effector Ba Cas12a3 that causes growth inhibition through a unique tRNA-cleavage mechanism. Plasmid interference assays indicated that Ba Cas12a3 inhibits host growth arrest without invoking the DNA damage response, suggesting that the immune responses may not involve double strand breaks of DNA. Indeed, biochemical characterization of the Ba Cas12a3-crRNA ribonucleoprotein (RNP) unraveled that the effector is an RNA-activating nuclease that cleaves 3′ terminus of tRNAs. Cryo-EM structures of Ba Cas12a3 reveal a conserved bilobed architecture featuring a unique nucleic acid-loading (NL) domain adjacent to the RuvC catalytic center. Structural and mutagenesis analyses show that the NL domain, together with a zinc ribbon domain, form a gated substrate groove. Target RNA binding induces conformational changes that open this groove and expose the RuvC active site, enabling specific tRNA cleavage while preventing other non-specific degradation. Our findings identified the NL domain aside the RuvC active site responsible for the tRNA recognition in Ba Cas12a3, expanding the functional diversity of CRISPR immunity.