Reciprocating RNA Polymerase batters through roadblocks

Jin Qian, Allison Cartee, Wenxuan Xu, Yan Yan, Bing Wang, Irina Artsimovitch, David Dunlap and Laura Finzi ()
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Jin Qian: Emory University
Allison Cartee: Emory University
Wenxuan Xu: Emory University
Yan Yan: Emory University
Bing Wang: The Ohio State University
Irina Artsimovitch: The Ohio State University
David Dunlap: Emory University
Laura Finzi: Emory University

Nature Communications, 2024, vol. 15, issue 1, 1-11

Abstract: Abstract RNA polymerases must transit through protein roadblocks to produce full-length transcripts. Here we report real-time measurements of Escherichia coli RNA polymerase passing through different barriers. As intuitively expected, assisting forces facilitated, and opposing forces hindered, RNA polymerase passage through lac repressor protein bound to natural binding sites. Force-dependent differences were significant at magnitudes as low as 0.2 pN and were abolished in the presence of the transcript cleavage factor GreA, which rescues backtracked RNA polymerase. In stark contrast, opposing forces promoted passage when the rate of RNA polymerase backtracking was comparable to, or faster than the rate of dissociation of the roadblock, particularly in the presence of GreA. Our experiments and simulations indicate that RNA polymerase may transit after roadblocks dissociate, or undergo cycles of backtracking, recovery, and ramming into roadblocks to pass through. We propose that such reciprocating motion also enables RNA polymerase to break protein-DNA contacts that hold RNA polymerase back during promoter escape and RNA chain elongation. This may facilitate productive transcription in vivo.

Date: 2024
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DOI: 10.1038/s41467-024-47531-x

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