Bacteriophages suppress CRISPR–Cas immunity using RNA-based anti-CRISPRs
Sarah Camara-Wilpert, David Mayo-Muñoz, Jakob Russel, Robert D. Fagerlund, Jonas Stenløkke Madsen, Peter C. Fineran, Søren J. Sørensen, Rafael Pinilla‐Redondo
Abstract
Abstract Many bacteria use CRISPR–Cas systems to combat mobile genetic elements, such as bacteriophages and plasmids 1 . In turn, these invasive elements have evolved anti-CRISPR proteins to block host immunity 2,3 . Here we unveil a distinct type of CRISPR–Cas Inhibition strategy that is based on small non-coding R NA a nti- CR ISPRs (Racrs). Racrs mimic the repeats found in CRISPR arrays and are encoded in viral genomes as solitary repeat units 4 . We show that a prophage-encoded Racr strongly inhibits the type I-F CRISPR–Cas system by interacting specifically with Cas6f and Cas7f, resulting in the formation of an aberrant Cas subcomplex. We identified Racr candidates for almost all CRISPR–Cas types encoded by a diverse range of viruses and plasmids, often in the genetic context of other anti-CRISPR genes 5 . Functional testing of nine candidates spanning the two CRISPR–Cas classes confirmed their strong immune inhibitory function. Our results demonstrate that molecular mimicry of CRISPR repeats is a widespread anti-CRISPR strategy, which opens the door to potential biotechnological applications 6 .