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Nat Microbiol. 2018 Apr;3(4):461-469. doi: 10.1038/s41564-018-0120-z. Epub 2018 Mar 5.

Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity.

Author information

1
Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
2
Centre for Bacterial Stress Response and Persistence, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
3
National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA.
4
Danish Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark. peng@bio.ku.dk.

Abstract

Viruses employ a range of strategies to counteract the prokaryotic adaptive immune system, clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas), including mutational escape and physical blocking of enzymatic function using anti-CRISPR proteins (Acrs). Acrs have been found in many bacteriophages but so far not in archaeal viruses, despite the near ubiquity of CRISPR-Cas systems in archaea. Here, we report the functional and structural characterization of two archaeal Acrs from the lytic rudiviruses, SIRV2 and SIRV3. We show that a 4 kb deletion in the SIRV2 genome dramatically reduces infectivity in Sulfolobus islandicus LAL14/1 that carries functional CRISPR-Cas subtypes I-A, I-D and III-B. Subsequent insertion of a single gene from SIRV3, gp02 (AcrID1), which is conserved in the deleted fragment, successfully restored infectivity. We demonstrate that AcrID1 protein inhibits the CRISPR-Cas subtype I-D system by interacting directly with Cas10d protein, which is required for the interference stage. Sequence and structural analysis of AcrID1 show that it belongs to a conserved family of compact, dimeric αβ-sandwich proteins characterized by extreme pH and temperature stability and a tendency to form protein fibres. We identify about 50 homologues of AcrID1 in four archaeal viral families demonstrating the broad distribution of this group of anti-CRISPR proteins.

PMID:
29507349
DOI:
10.1038/s41564-018-0120-z
[Indexed for MEDLINE]

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