Type III CRISPR-Cas provides resistance against nucleus-forming jumbo phages via abortive infection

• Published in: Molecular cell Vol. 82; no. 23; pp. 4471 - 4486.e9
• Main Authors: Mayo-Muñoz, David, Smith, Leah M., Garcia-Doval, Carmela, Malone, Lucia M., Harding, Kate R., Jackson, Simon A., Hampton, Hannah G., Fagerlund, Robert D., Gumy, Laura F., Fineran, Peter C.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.12.2022
• Subjects: abortive infection; accessory DNase; Bacteriophages - genetics; cell death; Cell Nucleus; Chromosomes, Bacterial; CRISPR-Cas Systems; Endonucleases; jumbo phage; NucC; RNA, Messenger; type III CRISPR-Cas; abortive infection; type III CRISPR-Cas; NucC; jumbo phage; cell death; accessory DNase
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2022.10.028

Bacteria have diverse defenses against phages. In response, jumbo phages evade multiple DNA-targeting defenses by protecting their DNA inside a nucleus-like structure. We previously demonstrated that RNA-targeting type III CRISPR-Cas systems provide jumbo phage immunity by recognizing viral mRNA exported from the nucleus for translation. Here, we demonstrate that recognition of phage mRNA by the type III system activates a cyclic triadenylate-dependent accessory nuclease, NucC. Although unable to access phage DNA in the nucleus, NucC degrades the bacterial chromosome, triggers cell death, and disrupts phage replication and maturation. Hence, type-III-mediated jumbo phage immunity occurs via abortive infection, with suppression of the viral epidemic protecting the population. We further show that type III systems targeting jumbo phages have diverse accessory nucleases, including RNases that provide immunity. Our study demonstrates how type III CRISPR-Cas systems overcome the inaccessibility of jumbo phage DNA to provide robust immunity. [Display omitted] •Type III CRISPR-Cas provides immunity against nucleus-forming jumbo phages•Type III recognition of jumbo phage mRNA activates the accessory DNase NucC•NucC degrades the bacterial DNA, triggering cell death to prevent phage replication•Abortive infection protects the clonal population by suppressing the viral epidemic Mayo-Muñoz et al. uncover how RNA-targeting type III CRISPR-Cas systems protect bacteria from jumbo phages that form nucleus-like “shields” during infection to protect their genomes. This study demonstrates how a type III accessory nuclease (NucC) elicits abortive infection and its role in type III phage defense.