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 and Jillian F. Banfield ()
Additional contact information
David Paez-Espino: University of California, Berkeley
Wesley Morovic: DuPont - Nutrition and Health
Christine L. Sun: 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

Nature Communications, 2013, vol. 4, issue 1, 1-7

Abstract: 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.

Date: 2013
References: Add references at CitEc
Citations: View citations in EconPapers (2)

Downloads: (external link)
https://www.nature.com/articles/ncomms2440 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms2440

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/ncomms2440

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().