Bacteriophages suppress CRISPR–Cas immunity using RNA-based anti-CRISPRs

Sarah Camara-Wilpert, David Mayo-Muñoz, Jakob Russel, Robert D. Fagerlund, Jonas S. Madsen, Peter C. Fineran (), Søren J. Sørensen and Rafael Pinilla-Redondo ()
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Sarah Camara-Wilpert: University of Copenhagen
David Mayo-Muñoz: University of Otago
Jakob Russel: University of Copenhagen
Robert D. Fagerlund: University of Otago
Jonas S. Madsen: University of Copenhagen
Peter C. Fineran: University of Otago
Søren J. Sørensen: University of Copenhagen
Rafael Pinilla-Redondo: University of Copenhagen

Nature, 2023, vol. 623, issue 7987, 601-607

Abstract: Abstract Many bacteria use CRISPR–Cas systems to combat mobile genetic elements, such as bacteriophages and plasmids1. In turn, these invasive elements have evolved anti-CRISPR proteins to block host immunity2,3. Here we unveil a distinct type of CRISPR–Cas Inhibition strategy that is based on small non-coding RNA anti-CRISPRs (Racrs). Racrs mimic the repeats found in CRISPR arrays and are encoded in viral genomes as solitary repeat units4. 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 genes5. 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 applications6.

Date: 2023
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DOI: 10.1038/s41586-023-06612-5

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