Viral recombination systems limit CRISPR-Cas targeting through the generation of escape mutations. Escherichia coli phage lambda

CRISPR-Cas systems provide immunity to bacteria by programming Cas nucleases with RNA guides that recognize and cleave infecting viral genomes. Bacteria and their viruses each encode recombination systems that could repair the cleaved viral DNA. However, it is unknown whether and how these systems can affect CRISPR immunity. Bacteriophage lambda uses the Red system (gam-exo-bet) to promote recombination between related phages. Here we show that lambda Red also mediates evasion of CRISPR-Cas targeting. Gam inhibits the E. coli RecBCD recombination system, allowing recombination and repair of the cleaved DNA by Exo-Beta, which promotes the generation of mutations within the CRISPR target sequence. Red recombination is strikingly more efficient than the host's RecBCD-RecA in the production of large numbers of phages that escape CRISPR targeting. These results reveal a role for Red-like systems in the protection of bacteriophages against sequence-specific nucleases, which may facilitate their spread across viral genomes.