Virus-borne mini-CRISPR arrays are involved in interviral conflicts

Sofia Medvedeva, Ying Liu, Eugene V. Koonin, Konstantin Severinov, David Prangishvili and Mart Krupovic ()
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Sofia Medvedeva: Institut Pasteur, Department of Microbiology
Ying Liu: Institut Pasteur, Department of Microbiology
Eugene V. Koonin: National Library of Medicine
Konstantin Severinov: Skolkovo Institute of Science and Technology
David Prangishvili: Institut Pasteur, Department of Microbiology
Mart Krupovic: Institut Pasteur, Department of Microbiology

Nature Communications, 2019, vol. 10, issue 1, 1-10

Abstract: Abstract CRISPR-Cas immunity is at the forefront of antivirus defense in bacteria and archaea and specifically targets viruses carrying protospacers matching the spacers catalogued in the CRISPR arrays. Here, we perform deep sequencing of the CRISPRome—all spacers contained in a microbiome—associated with hyperthermophilic archaea of the order Sulfolobales recovered directly from an environmental sample and from enrichment cultures established in the laboratory. The 25 million CRISPR spacers sequenced from a single sampling site dwarf the diversity of spacers from all available Sulfolobales isolates and display complex temporal dynamics. Comparison of closely related virus strains shows that CRISPR targeting drives virus genome evolution. Furthermore, we show that some archaeal viruses carry mini-CRISPR arrays with 1–2 spacers and preceded by leader sequences but devoid of cas genes. Closely related viruses present in the same population carry spacers against each other. Targeting by these virus-borne spacers represents a distinct mechanism of heterotypic superinfection exclusion and appears to promote archaeal virus speciation.

Date: 2019
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DOI: 10.1038/s41467-019-13205-2

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