Restriction endonuclease cleavage of phage DNA enables resuscitation from Cas13-induced bacterial dormancy

Type VI CRISPR systems protect against phage infection using the RNA-guided nuclease Cas13 to recognize viral messenger RNA. Upon target recognition, Cas13 cleaves phage and host transcripts non-specifically, leading to cell dormancy that is incompatible with phage propagation. However, whether and how infected cells recover from dormancy is unclear. Here we show that type VI CRISPR and DNA-cleaving restriction-modification (RM) systems frequently co-occur and synergize to clear phage infections and resuscitate cells. In the natural type VI CRISPR host Listeria seeligeri, we show that RM cleaves the phage genome, thus removing the source of phage transcripts and enabling cells to recover from Cas13-induced cellular dormancy. We find that phage infections are neutralized more effectively when Cas13 and RM systems operate together. Our work reveals that type VI CRISPR immunity is cell-autonomous and non-abortive when paired with RM, and hints at other synergistic roles for the diverse host-directed immune systems in bacteria. Deployment of some CRISPR-Cas systems stunts host growth by degrading all transcripts, but Listeria seeligeri reverses dormancy using restriction-modification-based phage DNA targeting.

Automated summary

Type VI CRISPR systems use Cas13 to recognize viral mRNA, leading to cell dormancy. This study shows that when combined with DNA-cleaving restriction-modification (RM) systems, type VI CRISPR can help resuscitate cells from dormancy by cleaving the phage genome. The co-occurrence of Cas13 and RM systems enhances the neutralization of phage infections.