Strong bias in the bacterial CRISPR elementsthat confer immunity to phage

摘要

Clustered regularly interspaced short palindromic repeats (CRISPR)–Cas systems provideadaptive immunity against phage via spacer-encoded CRISPR RNAs that are complementaryto 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 twoexperiments. Spacers that target the host chromosome are infrequent and strongly selectedagainst, suggesting autoimmunity is lethal. In experiments that recover over half a millionspacers, we observe early dominance by a few spacer sub-populations and rapid oscillationsin sub-population abundances. In two CRISPR systems and in replicate experiments, a fewspacers account for the majority of spacer sequences. Nearly all phage locations targetedby the acquired spacers have a proto-spacer adjacent motif (PAM), indicating PAMs areinvolved in spacer acquisition.We detect a strong and reproducible bias in the phage genomelocations from which spacers derive. This may reflect selection for specific spacers based onlocation and effectiveness.