Dynamics of the polymerase manager protein UmuD: DNA damage tolerance in E. coli

Abstract

In E. coli, the function of specialized Y family DNA polymerases is regulated by UmuD, a small manager protein, and its cleaved form, UmuD′. The different forms of the UmuD proteins play dramatically different roles in the cellular response to DNA damage: UmuD facilitates a primitive DNA damage checkpoint while UmuD′ enables DNA damage‐dependent mutagenesis. The β processivity clamp, which tethers DNA polymerases to the DNA, confers high processivity on normal DNA polymerases. UmuD is known to bind the β clamp and this may modulate the activity of β. The objective of this study is to understand the conformational dynamics of UmuD to determine its effect on DNA damage tolerance. We constructed a library of single cysteine derivatives of UmuD to facilitate labeling for fluorescence resonance energy transfer (FRET) and electron paramagnetic resonance (EPR) studies. All single cysteine derivatives of UmuD were shown to be active in UV‐induced mutagenesis, and will be labeled. Hydrogen‐deuterium exchange mass spectrometry experiments show that UmuD is flexible, while UmuD′ is slightly less so.This work is supported by a Dreyfus Foundation New Faculty Award and the Northeastern University Office of the Provost.