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
2013 Nature Communications  
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
more » ... iments 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.
doi:10.1038/ncomms2440 pmid:23385575 fatcat:cuzx6l6s4jfwjlx2ug47jf3gn4