Viral recombination systems limit CRISPR-Cas targeting through the generation of escape mutations

• Published in: Cell host & microbe 2021-10, Vol.29 (10), p.1482-1495.e12
• Main Authors: Hossain, Amer A., McGinn, Jon, Meeske, Alexander J., Modell, Joshua W., Marraffini, Luciano A.
• Format: Article
• Language: English
• Subjects: Bacteriophage lambda - genetics; Bacteriophage lambda - immunology; Bacteriophage lambda - physiology; Cas9; CRISPR; CRISPR-Cas Systems; Escherichia coli - genetics; Escherichia coli - immunology; Escherichia coli - virology; Escherichia coli Proteins - genetics; Escherichia coli Proteins - immunology; Exodeoxyribonuclease V - genetics; Exodeoxyribonuclease V - immunology; Host-Pathogen Interactions; Lambda; Mutation; recombination; Recombination, Genetic; Red; Viral Proteins - genetics; Viral Proteins - immunology
• ISSN: 1931-3128; 1934-6069
• DOI: 10.1016/j.chom.2021.09.001

CRISPR-Cas systems provide immunity to bacteria by programing 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 λ uses the Red system (gam-exo-bet) to promote recombination between related phages. Here, we show that λ Red also mediates evasion of CRISPR-Cas targeting. Gam inhibits the host E. coli RecBCD recombination system, allowing recombination and repair of the cleaved DNA by phage 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. [Display omitted] •The λ Red recombination system enables phage λ to escape type I and II CRISPR nucleases•Repair of cleaved viral DNA by λ Red leads to the introduction of escaper mutations•Escaper generation is rare when the host’s RecBCD system repairs the viral DNA Bacteriophages harboring mutations at the target site of RNA-guided Cas nucleases can escape CRISPR immunity. Hossain et al. report that the phage λ Red recombination system inhibits the host bacteria RecBCD pathway and introduces mutations that more efficiently mediate escape. These results suggest that phage recombination systems counteract DNA-cleaving bacterial defenses.