Journal
NUCLEIC ACIDS RESEARCH
Volume 43, Issue 21, Pages 10421-10429Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkv1098
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Funding
- Academy of Finland [272507, 250113, 283192]
- Sigrid Juselius Foundation
- TU Delft startup grant
- EURYI grant from the European Science Foundation
- TOP grant from the Netherlands Organisation for Scientific Research
- ERC-StG at the Consolidator Level [DynGenome]
- Academy of Finland (AKA) [272507, 250113, 283192, 283192, 250113, 272507] Funding Source: Academy of Finland (AKA)
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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 Phi 6, 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.
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