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

David Paez-Espino, Wesley Morovic, Christine L. Sun, Brian C. Thomas, Ken Ichi Ueda, Buffy Stahl, Rodolphe Barrangou, Jillian F. Banfield

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118 Scopus citations

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.

Original languageEnglish (US)
Article number1430
JournalNature communications
Volume4
DOIs
StatePublished - Mar 11 2013

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

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    Paez-Espino, D., Morovic, W., Sun, C. L., Thomas, B. C., Ueda, K. I., Stahl, B., Barrangou, R., & Banfield, J. F. (2013). Strong bias in the bacterial CRISPR elements that confer immunity to phage. Nature communications, 4, [1430]. https://doi.org/10.1038/ncomms2440