Molecular basis for DarT ADP-ribosylation of a DNA base

Schuller, Marion; Butler, Rachel; Ariza, Antonio; Tromans-Coia, Callum; Jankevicius, Gytis; Claridge, Tim; Kendall, Sharon; Goh, Shan; Stewart, Graham; Ahel, Ivan

Abstract

ADP-ribosyltransferases (ARTs) utilise NAD+ to catalyse substrate ADP-ribosylation, thereby regulating cellular pathways or contributing to toxin-mediated pathogenicity of bacteria. Reversible ADP-ribosylation has traditionally been considered a protein-specific modification, but recent in vitro studies have suggested nucleic acids as targets. Here, we present evidence that specific reversible DNA ADP-ribosylation on thymidine bases occurs in cellulo through the DarT/DarG toxin/antitoxin system which is found in a variety of bacteria including global pathogens such as Mycobacterium tuberculosis, EPEC and Pseudomonas aeruginosa. We report the first DarT structure which identifies this protein as a diverged member of the PARP family. Moreover, a set of high-resolution structures in ligand-free, pre-and post-reaction states reveals a specialised mechanism of catalysis that includes a key active-site arginine, extending the canonical ART toolkit. Comparison with the well-established DNA-repair protein ADP-ribosylation complex, PARP/HPF1, offers insights into how the DarT class of ARTs evolved into specific DNA-modifying enzymes. Together, the structural and mechanistic data provide unprecedented detail for a PARP family member and contribute to fundamental understanding of nucleic acid ADP-ribosylation. We furthermore show that thymine-linked ADP-ribose DNA adducts reversed by DarG antitoxin, functioning as non-canonical DNA-repair factor, are utilised not only for targeted DNA damage to induce toxicity but also as a signalling strategy for cellular processes. Using M. tuberculosis as an exemplar we show that DarTG regulates growth by DNA ADP-ribosylation at the origin of chromosome replication

Citation

Schuller, M., Butler, R., Ariza, A., Tromans-Coia, C., Jankevicius, G., Claridge, T., Kendall, S., Goh, S., Stewart, G., & Ahel, I. (2021). Molecular basis for DarT ADP-ribosylation of a DNA base. Nature, https://doi.org/10.1038/s41586-021-03825-4

• Journal Article Type: Article
• Acceptance Date: Jul 15, 2021
• Publication Date: Aug 18, 2021
• Deposit Date: Jul 15, 2021
• Publicly Available Date: Feb 18, 2022
• Journal: Nature
• Print ISSN: 0028-0836
• Electronic ISSN: 1476-4687
• Publisher: Nature Research
• Peer Reviewed: Peer Reviewed
• DOI: https://doi.org/10.1038/s41586-021-03825-4
• Public URL: https://rvc-repository.worktribe.com/output/1550088