UvrD helicase–RNA polymerase interactions are governed by UvrD’s carboxy-terminal Tudor domain

• Published in: Communications biology 2020-10, Vol.3 (1), p.607, Article 607
• Main Authors: Kawale, Ashish A., Burmann, Björn M.
• Format: Article
• Language: English
• Subjects: 101/6; 631/45/612/1229; 631/535/878/1263; 82/80; 82/83; automated noe assignment; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Biochemistry and Molecular Biology; Biokemi och molekylärbiologi; Biology; Biomedical and Life Sciences; Deoxyribonucleic acid; DNA; DNA damage; DNA Damage - genetics; DNA helicase; DNA Helicases - chemistry; DNA Helicases - genetics; DNA Helicases - metabolism; DNA repair; DNA Repair - genetics; DNA-directed RNA polymerase; DNA-Directed RNA Polymerases - chemistry; DNA-Directed RNA Polymerases - genetics; DNA-Directed RNA Polymerases - metabolism; dynamics; Escherichia coli - genetics; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; escherichia-coli uvrd; Genetics; Genetik; Genomes; helicase; Life Sciences; Life Sciences & Biomedicine - Other Topics; Magnetic resonance spectroscopy; mechanism; mfd protein; Models, Molecular; NMR; Nuclear magnetic resonance; Protein Folding; relaxation; repair; RNA helicase; RNA polymerase; Science & Technology - Other; Spectrum analysis; Staphylococcus aureus - genetics; structural basis; Structure-function relationships; Topics; Transcription; Tudor Domain - genetics; Ultraviolet radiation
• ISSN: 2399-3642; 2399-3642
• DOI: 10.1038/s42003-020-01332-2

All living organisms have to cope with the constant threat of genome damage by UV light and other toxic reagents. To maintain the integrity of their genomes, organisms developed a variety of DNA repair pathways. One of these, the Transcription Coupled DNA-Repair (TCR) pathway, is triggered by stalled RNA Polymerase (RNAP) complexes at DNA damage sites on actively transcribed genes. A recently elucidated bacterial TCR pathway employs the UvrD helicase pulling back stalled RNAP complexes from the damage, stimulating recruitment of the DNA-repair machinery. However, structural and functional aspects of UvrD’s interaction with RNA Polymerase remain elusive. Here we used advanced solution NMR spectroscopy to investigate UvrD’s role within the TCR, identifying that the carboxy-terminal region of the UvrD helicase facilitates RNAP interactions by adopting a Tudor-domain like fold. Subsequently, we functionally analyzed this domain, identifying it as a crucial component for the UvrD–RNAP interaction besides having nucleic-acid affinity. Using advanced solution NMR spectroscopy, Kawale and Burmann show that the carboxy-terminal region of the UvrD helicase adopts a Tudor-domain like fold to facilitate its interaction with RNA polymerase. This study provides molecular insights into the interaction between UvrD and RNA polymerase during DNA repair.