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Molecular basis for DarT ADP-ribosylation of a DNA base.
- Source :
-
Nature [Nature] 2021 Aug; Vol. 596 (7873), pp. 597-602. Date of Electronic Publication: 2021 Aug 18. - Publication Year :
- 2021
-
Abstract
- ADP-ribosyltransferases use NAD <superscript>+</superscript> to catalyse substrate ADP-ribosylation <superscript>1</superscript> , and thereby regulate cellular pathways or contribute to toxin-mediated pathogenicity of bacteria <superscript>2-4</superscript> . Reversible ADP-ribosylation has traditionally been considered a protein-specific modification <superscript>5</superscript> , but recent in vitro studies have suggested nucleic acids as targets <superscript>6-9</superscript> . Here we present evidence that specific, reversible ADP-ribosylation of DNA 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, enteropathogenic Escherichia coli and Pseudomonas aeruginosa) <superscript>10</superscript> . We report the structure of DarT, which identifies this protein as a diverged member of the PARP family. We provide a set of high-resolution structures of this enzyme in ligand-free and pre- and post-reaction states, which reveals a specialized mechanism of catalysis that includes a key active-site arginine that extends the canonical ADP-ribosyltransferase toolkit. Comparison with PARP-HPF1, a well-established DNA repair protein ADP-ribosylation complex, offers insights into how the DarT class of ADP-ribosyltransferases evolved into specific DNA-modifying enzymes. Together, our structural and mechanistic data provide details of this PARP family member and contribute to a fundamental understanding of the ADP-ribosylation of nucleic acids. We also show that thymine-linked ADP-ribose DNA adducts reversed by DarG antitoxin (functioning as a noncanonical DNA repair factor) are used 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 DarT-DarG regulates growth by ADP-ribosylation of DNA at the origin of chromosome replication.<br /> (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)
- Subjects :
- Adenosine Diphosphate Ribose metabolism
Antitoxins
Bacterial Proteins chemistry
Bacterial Toxins
Base Sequence
Biocatalysis
DNA genetics
DNA Adducts chemistry
DNA Adducts metabolism
DNA Damage
DNA Repair
DNA Transposable Elements genetics
DNA, Bacterial chemistry
DNA, Bacterial genetics
DNA, Bacterial metabolism
Models, Molecular
Mycobacterium enzymology
Mycobacterium genetics
Nitrogen chemistry
Nitrogen metabolism
Poly(ADP-ribose) Polymerases chemistry
Replication Origin genetics
Substrate Specificity
Thermus enzymology
Thymidine chemistry
Thymidine metabolism
ADP-Ribosylation
Bacterial Proteins metabolism
DNA chemistry
DNA metabolism
Thymine chemistry
Thymine metabolism
Subjects
Details
- Language :
- English
- ISSN :
- 1476-4687
- Volume :
- 596
- Issue :
- 7873
- Database :
- MEDLINE
- Journal :
- Nature
- Publication Type :
- Academic Journal
- Accession number :
- 34408320
- Full Text :
- https://doi.org/10.1038/s41586-021-03825-4