Diversified local CRISPR-Cas immunity to viruses of Sulfolobus islandicus

Matthew D. Pauly, Maria A. Bautista, Jesse A. Black, Rachel J. Whitaker

Research output: Contribution to journalArticlepeer-review


The population diversity and structure of CRISPR-Cas immunity provides key insights into virus - host interactions. Here, we examined two geographically and genetically distinct natural populations of the thermophilic crenarchaeon Sulfolobus islandicus and their interactions with Sulfolobus spindle-shaped viruses (SSVs) and S. islandicus rod-shaped viruses (SIRVs). We found that both virus families can be targeted with high population distributed immunity, whereby most immune strains target a virus using unique unshared CRISPR spacers. In Kamchatka, Russia, we observed high immunity to chronic SSVs that increases over time. In this context, we found that some SSVs had shortened genomes lacking genes that are highly targeted by the S. islandicus population, indicating a potential mechanism of immune evasion. By contrast, in Yellowstone National Park, we found high inter- and intra-strain immune diversity targeting lytic SIRVs and low immunity to chronic SSVs. In this population, we observed evidence of SIRVs evolving immunity through mutations concentrated in the first five bases of protospacers. These results indicate that diversity and structure of antiviral CRISPR-Cas immunity for a single microbial species can differ by both the population and virus type, and suggest that different virus families use different mechanisms to evade CRISPR-Cas immunity. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.

Original languageEnglish (US)
Article number20180093
JournalPhilosophical Transactions of the Royal Society B: Biological Sciences
Issue number1772
StatePublished - May 13 2019


  • CRISPR immunity
  • Joshua Weitz and Sergei Maslov for thoughtful discussion and Ken Ringwald for critical comments on this manuscript
  • Mark Young
  • Microbial evolution
  • Population diversity
  • Russia. We thank David Krause and Rika Anderson for the sequences of S. islandicus genomes
  • Ted Kim for assistance with bioinformatics analysis
  • Virus-host interactions
  • We acknowledge past members of the Whitaker laboratory for sample collection in Yellowstone National Park and Kamchatka

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)


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