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

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  • Anti-CRISPR

    Accepteret manuskript, 19,5 MB, PDF-dokument


  • Fei He, Københavns Universitet
  • ,
  • Yuvaraj Bhoobalan-Chitty, Københavns Universitet
  • ,
  • Lan B Van
  • Anders L Kjeldsen, Københavns Universitet
  • ,
  • Matteo Dedola, Københavns Universitet
  • ,
  • Kira S Makarova, National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, USA
  • ,
  • Eugene V Koonin, National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, USA
  • ,
  • Ditlev E Brodersen
  • Xu Peng, Københavns Universitet

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.

TidsskriftNature Microbiology
Sider (fra-til)461-469
Antal sider9
StatusUdgivet - apr. 2018

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