Conservation and Divergence in Nucleotide Excision Repair Lesion Recognition

Nicolas Wirth,Jonas Gross,Heide M Roth,Claudia N Buechner,Caroline Kisker,Ingrid Tessmer

doi:10.1074/jbc.m116.739425

Nicolas Wirth, Jonas Gross + Show 4 more

Open Access

https://doi.org/10.1074/jbc.m116.739425

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Abstract

Nucleotide excision repair is an important and highly conserved DNA repair mechanism with an exceptionally large range of chemically and structurally unrelated targets. Lesion verification is believed to be achieved by the helicases UvrB and XPD in the prokaryotic and eukaryotic processes, respectively. Using single molecule atomic force microscopy analyses, we demonstrate that UvrB and XPD are able to load onto DNA and pursue lesion verification in the absence of the initial lesion detection proteins. Interestingly, our studies show different lesion recognition strategies for the two functionally homologous helicases, as apparent from their distinct DNA strand preferences, which can be rationalized from the different structural features and interactions with other nucleotide excision repair protein factors of the two enzymes.

Highlights

Nucleotide excision repair (NER)4 is an important DNA repair mechanism with a large range of chemically and structurally unrelated targets
Using single molecule atomic force microscopy analyses, we demonstrate that UvrB and XPD are able to load onto DNA and pursue lesion verification in the absence of the initial lesion detection proteins
DNA Substrates for Studying UvrB(C) and XPD(/p44) in the Absence of Other Proteins—In the general NER model, DNA interactions by UvrB and XPD are preceded by other proteins (UvrA or XPC and XPB in prokaryotic or eukaryotic NER, respectively) that bend and open dsDNA forming a DNA bubble on which UvrB and XPD can load

Summary

Introduction

Nucleotide excision repair (NER) is an important DNA repair mechanism with a large range of chemically and structurally unrelated targets. Our studies further revealed conformational changes in the specific XPD-lesion complexes [12] Such structural rearrangements may serve to trigger the recruitment of additional proteins, including the two endonucleases (XPG and XPF) in eukaryotic NER, resulting in the excision of a 24 –32-nt stretch containing the lesion, and DNA re-synthesis and ligation by DNA polymerase and ligase, respectively [2]. Many of the mechanistic steps show strong parallels such as the initial ATP-independent sensing of DNA helix distortions by UvrA [14] and XPC [15], or the ATP re-binding induced conformational changes necessary for the formation of a stable lesion-specific complex by UvrB [16, 17] and (archaeal) XPD [12]

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