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

Harshad Ghodke,Antoine M Van Oijen,Han Ngoc Ho

doi:10.1038/s41467-020-15179-y

Abstract

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.

Highlights

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)
Damage detection occurs in two stages during GGR: a dedicated set of damage surveillance factors[1,2,3] constantly survey genomic DNA for lesions
DNA repair triggered at stalled ternary elongation complex (TEC) is termed transcription-coupled repair (TCR)

Summary

Introduction

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). During transcription-coupled repair (TCR), UvrA is recruited to Mfd at sites of RNA polymerases stalled by lesions. At sites of putative DNA damage, these damage recognition factors load specific DNA damage verification factors (UvrB in prokaryotes, TFIIH and homologs in eukaryotes) that unwind the DNA and verify the location of the damage with nucleotide resolution (Fig. 1a) In several studied organisms (barring certain archaea4,5), strand-specific removal of DNA damage occurs following stalling of RNA polymerase (RNAP) at sites of lesions

Methods

Results

Conclusion