Backtracking behavior in viral RNA-dependent RNA polymerase provides the basis for a second initiation site

Journal article (2015)

Authors

D. Dulin BN/Nynke Dekker Lab - AS
Igor D. Vilfan Karius, Inc.
B.A. Berghuis BN/Nynke Dekker Lab - AS
Minna M. Poranen Viikki Biocenter 1
S.M. Depken BN/Martin Depken Lab - AS
N.H. Dekker BN/Nynke Dekker Lab - AS
Research Group
BN/Nynke Dekker Lab (AS) (TU Delft)
More Info
expand_more

Published Date

2015

Language

English

Reuse Rights

Other than for strictly personal use, it is not permitted to download, forward or distribute the text or part of it, without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license such as Creative Commons.

Faculty

Applied Sciences

Department

BN/Bionanoscience

Research Group

BN/Nynke Dekker Lab

Abstract

Transcription in RNA viruses is highly dynamic, with a variety of pauses interrupting nucleotide addition by RNA-dependent RNA polymerase (RdRp). For example, rare but lengthy pauses (>20 s) have been linked to backtracking for viral single-subunit RdRps. However, while such backtracking has been well characterized for multi-subunit RNA polymerases (RNAPs) from bacteria and yeast, little is known about the details of viral RdRp backtracking and its biological roles. Using high-throughput magnetic tweezers, we quantify the backtracking by RdRp from the double-stranded (ds) RNA bacteriophage φ6, a model system for RdRps. We characterize the probability of entering long backtracks as a function of force and propose a model in which the bias toward backtracking is determined by the base paring at the dsRNA fork.We further discover that extensive backtracking provides access to a new 3′-end that allows for the de novo initiation of a second RdRp. This previously unidentified behavior provides a new mechanism for rapid RNA synthesis using coupled RdRps and hints at a possible regulatory pathway for gene expression during viral RNA transcription.