Cas9 cleavage of viral genomes generates immunological memories during the type II CRISPR-Cas response.

Type II CRISPR-Cas systems defend prokaryotes from bacteriophage infection through the acquisition of short viral DNA sequences known as spacers, that are transcribed into short RNA guides to specify the targets of the Cas9 nuclease. To counter the potentially devastating propagation of escaper phages with target mutations, the host population acquires many different spacer sequences. Whether and how the presence of pre-existing targeting spacers in type II systems affects the acquisition of new ones is unknown. Here we demonstrate that previously acquired spacers promote additional spacer acquisition from the vicinity of the target site through the cleavage of the target DNA. Therefore CRISPR immune cells can at the same time destroy the infecting virus and acquire additional spacers. This anticipates the rise of escapers or related viruses that could escape targeting by the first spacer acquired. Our results reveal a new role for Cas9 in the generation of immunological memories.