Anti-CRISPR protein AcrIIIA1 mitigates collateral cleavage by core Cas and accessory nucleases
CRISPR-Cas systems protect bacteria and archaea from their viruses, and Anti-CRISPRs (Acrs) are small virus-encoded proteins that inhibit CRISPR-Cas immunity. Over 80 distinct families of Acrs have been described to date; however only three of these subvert Type III CRISPR-Cas immunity. Type III systems employ a complex network of CRISPR-associated (Cas) and cellular/accessory nucleases to degrade viral nucleic acids. Here, we discover and characterize AcrIIIA1, the first Type III-A specific anti-CRISPR protein. We show that AcrIIIA1 binds to the Cas effector complex and attenuates its DNase activity and second messenger production. Additionally, AcrIIIA1 associates with fragmented tRNAs (acrRNAs) that undergo further degradation during phage infection. Our results support a two-pronged model in which AcrIIIA1 directly antagonizes core Cas machinery while acrRNAs absorb collateral damage dealt by accessory nucleases. This clever strategy remains agnostic to source(s) of indiscriminate cleavage and provides robust protection against Type III CRISPR-Cas immunity.