Mechanism of transcription modulation by the transcription-repair coupling factor

Authors

Bishnu P. Paudel, University of Wollongong
Zhi Qiang Xu, University of Wollongong
Slobodan Jergic, University of Wollongong
Aaron J. Oakley, University of Wollongong
Nischal Sharma, University of Wollongong
Simon H.J. Brown, University of Wollongong
James C. Bouwer, University of Wollongong
Peter J. Lewis, University of Wollongong
Nicholas E. Dixon, University of Wollongong
Antoine M. Van Oijen, University of Wollongong
Harshad Ghodke, University of Wollongong

Publication Name

Nucleic Acids Research

Abstract

Elongation by RNA polymerase is dynamically modulated by accessory factors. The transcription-repair coupling factor (TRCF) recognizes paused/stalled RNAPs and either rescues transcription or initiates transcription termination. Precisely how TRCFs choose to execute either outcome remains unclear. With Escherichia coli as a model, we used single-molecule assays to study dynamic modulation of elongation by Mfd, the bacterial TRCF. We found that nucleotide-bound Mfd converts the elongation complex (EC) into a catalytically poised state, presenting the EC with an opportunity to restart transcription. After long-lived residence in this catalytically poised state, ATP hydrolysis by Mfd remodels the EC through an irreversible process leading to loss of the RNA transcript. Further, biophysical studies revealed that the motor domain of Mfd binds and partially melts DNA containing a template strand overhang. The results explain pathway choice determining the fate of the EC and provide a molecular mechanism for transcription modulation by TRCF.

Open Access Status

This publication may be available as open access

Volume

50

Issue

10

First Page

5688

Last Page

5712