Cas9 function and host genome sampling in Type II-A CRISPR–Cas adaptation

To acquire the ability to recognize and destroy virus and plasmid invaders, prokaryotic CRISPR–Cas systems capture fragments of DNA within the host CRISPR locus. Our results indicate that the process of adaptation by a Type II-A CRISPR–Cas system in Streptococcus thermophilus requires Cas1, Cas2, and Csn2. Surprisingly, we found that Cas9, previously identified as the nuclease responsible for ultimate invader destruction, is also essential for adaptation. Cas9 nuclease activity is dispensable for adaptation. In addition, our studies revealed extensive, unbiased acquisition of the self-targeting host genome sequence by the CRISPR–Cas system that is masked in the presence of active target destruction.