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Strong bias in the bacterial CRISPR elements that confer immunity to phage

Author

Listed:
  • David Paez-Espino

    (University of California, Berkeley)

  • Wesley Morovic

    (DuPont - Nutrition and Health)

  • Christine L. Sun

    (University of California, Berkeley
    Plant and Microbial Biology, University of California, Berkeley)

  • Brian C. Thomas

    (University of California, Berkeley)

  • Ken-ichi Ueda

    (University of California, Berkeley)

  • Buffy Stahl

    (DuPont - Nutrition and Health)

  • Rodolphe Barrangou

    (DuPont - Nutrition and Health)

  • Jillian F. Banfield

    (University of California, Berkeley)

Abstract

Clustered regularly interspaced short palindromic repeats (CRISPR)–Cas systems provide adaptive immunity against phage via spacer-encoded CRISPR RNAs that are complementary to invasive nucleic acids. Here, we challenge Streptococcus thermophilus with a bacteriophage, and used PCR-based metagenomics to monitor phage-derived spacers daily for 15 days in two experiments. Spacers that target the host chromosome are infrequent and strongly selected against, suggesting autoimmunity is lethal. In experiments that recover over half a million spacers, we observe early dominance by a few spacer sub-populations and rapid oscillations in sub-population abundances. In two CRISPR systems and in replicate experiments, a few spacers account for the majority of spacer sequences. Nearly all phage locations targeted by the acquired spacers have a proto-spacer adjacent motif (PAM), indicating PAMs are involved in spacer acquisition. We detect a strong and reproducible bias in the phage genome locations from which spacers derive. This may reflect selection for specific spacers based on location and effectiveness.

Suggested Citation

  • David Paez-Espino & Wesley Morovic & Christine L. Sun & Brian C. Thomas & Ken-ichi Ueda & Buffy Stahl & Rodolphe Barrangou & Jillian F. Banfield, 2013. "Strong bias in the bacterial CRISPR elements that confer immunity to phage," Nature Communications, Nature, vol. 4(1), pages 1-7, June.
    • Handle: RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms2440
    DOI: 10.1038/ncomms2440
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    Cited by:

    1. Yekaterina S Pavlova & David Paez-Espino & Andrew Yu Morozov & Ilya S Belalov, 2021. "Searching for fat tails in CRISPR-Cas systems: Data analysis and mathematical modeling," PLOS Computational Biology, Public Library of Science, vol. 17(3), pages 1-21, March.
    2. Serena Bradde & Marija Vucelja & Tiberiu Teşileanu & Vijay Balasubramanian, 2017. "Dynamics of adaptive immunity against phage in bacterial populations," PLOS Computational Biology, Public Library of Science, vol. 13(4), pages 1-16, April.

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