Discovery of multiple anti-CRISPRs highlights anti-defense gene clustering in mobile genetic elements

Rafael Pinilla-Redondo, Saadlee Shehreen, Nicole D. Marino, Robert D. Fagerlund, Chris M. Brown, Søren J. Sørensen, Peter C. Fineran () and Joseph Bondy-Denomy ()
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Rafael Pinilla-Redondo: University of Copenhagen
Saadlee Shehreen: University of Otago
Nicole D. Marino: University of California
Robert D. Fagerlund: University of Otago
Chris M. Brown: University of Otago
Søren J. Sørensen: University of Copenhagen
Peter C. Fineran: University of Otago
Joseph Bondy-Denomy: University of California

Nature Communications, 2020, vol. 11, issue 1, 1-11

Abstract: Abstract Many prokaryotes employ CRISPR–Cas systems to combat invading mobile genetic elements (MGEs). In response, some MGEs have developed strategies to bypass immunity, including anti-CRISPR (Acr) proteins; yet the diversity, distribution and spectrum of activity of this immune evasion strategy remain largely unknown. Here, we report the discovery of new Acrs by assaying candidate genes adjacent to a conserved Acr-associated (Aca) gene, aca5, against a panel of six type I systems: I–F (Pseudomonas, Pectobacterium, and Serratia), I–E (Pseudomonas and Serratia), and I–C (Pseudomonas). We uncover 11 type I–F and/or I–E anti-CRISPR genes encoded on chromosomal and extrachromosomal MGEs within Enterobacteriaceae and Pseudomonas, and an additional Aca (aca9). The acr genes not only associate with other acr genes, but also with genes encoding inhibitors of distinct bacterial defense systems. Thus, our findings highlight the potential exploitation of acr loci neighborhoods for the identification of previously undescribed anti-defense systems.

Date: 2020
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DOI: 10.1038/s41467-020-19415-3

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