Single-molecule live-cell imaging visualizes parallel pathways of prokaryotic nucleotide excision repair

• Published in: Nature communications Vol. 11; no. 1; p. 1477
• Main Authors: Ghodke, Harshad, Ho, Han Ngoc, van Oijen, Antoine M
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 20.03.2020; Nature Publishing Group UK; Nature Portfolio
• Subjects: Adenosine Triphosphatases - genetics; Adenosine Triphosphatases - metabolism; Biophysics; Damage; Deoxyribonucleic acid; DNA; DNA damage; DNA Damage - physiology; DNA Damage - radiation effects; DNA Helicases - genetics; DNA Helicases - metabolism; DNA Repair - physiology; DNA Repair Enzymes; DNA, Bacterial - metabolism; DNA, Bacterial - radiation effects; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; DNA-directed RNA polymerase; DNA-Directed RNA Polymerases - metabolism; E coli; Escherichia coli; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; Fluorescence; Imaging; Irradiation; Kinetics; Lesions; Nucleotide excision repair; Nucleotides; Optical Imaging - methods; Prokaryotic Cells - metabolism; Recognition; Repair; Ribonucleic acid; RNA; RNA polymerase; Signatures; Transcription; Transcription Factors - metabolism; Transcription-coupled repair; Ultraviolet radiation; Ultraviolet Rays
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-15179-y

In the model organism Escherichia coli, helix distorting lesions are recognized by the UvrAB damage surveillance complex in the global genomic nucleotide excision repair pathway (GGR). Alternately, during transcription-coupled repair (TCR), UvrA is recruited to Mfd at sites of RNA polymerases stalled by lesions. Ultimately, damage recognition is mediated by UvrA, followed by verification by UvrB. Here we characterize the differences in the kinetics of interactions of UvrA with Mfd and UvrB by following functional, fluorescently tagged UvrA molecules in live TCR-deficient or wild-type cells. The lifetimes of UvrA in Mfd-dependent or Mfd-independent interactions in the absence of exogenous DNA damage are comparable in live cells, and are governed by UvrB. Upon UV irradiation, the lifetimes of UvrA strongly depended on, and matched those of Mfd. Overall, we illustrate a non-perturbative, imaging-based approach to quantify the kinetic signatures of damage recognition enzymes participating in multiple pathways in cells.