Locking the nontemplate DNA to control transcription

Molecular Microbiology
Yuri NedialkovIrina Artsimovitch

Abstract

Universally conserved NusG/Spt5 factors reduce RNA polymerase pausing and arrest. In a widely accepted model, these proteins bridge the RNA polymerase clamp and lobe domains across the DNA channel, inhibiting the clamp opening to promote pause-free RNA synthesis. However, recent structures of paused transcription elongation complexes show that the clamp does not open and suggest alternative mechanisms of antipausing. Among these mechanisms, direct contacts of NusG/Spt5 proteins with the nontemplate DNA in the transcription bubble have been proposed to prevent unproductive DNA conformations and thus inhibit arrest. We used Escherichia coli RfaH, whose interactions with DNA are best characterized, to test this idea. We report that RfaH stabilizes the upstream edge of the transcription bubble, favoring forward translocation, and protects the upstream duplex DNA from exonuclease cleavage. Modeling suggests that RfaH loops the nontemplate DNA around its surface and restricts the upstream DNA duplex mobility. Strikingly, we show that RfaH-induced DNA protection and antipausing activity can be mimicked by shortening the nontemplate strand in elongation complexes assembled on synthetic scaffolds. We propose that remodeling of the nonte...Continue Reading

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Citations

Feb 12, 2019·Nature Communications·Philipp Konrad ZuberStefan H Knauer
Aug 3, 2018·Molecular Microbiology·Dmitri SvetlovIrina Artsimovitch
May 15, 2018·Molecular Microbiology·Vladimir Svetlov, Evgeny Nudler
Feb 28, 2019·MBio·Irina Artsimovitch, Stefan H Knauer
Jan 26, 2021·Frontiers in Microbiology·Bing Wang, Irina Artsimovitch
Sep 8, 2018·Microbiology Spectrum·Jonathan R Goodson, Wade C Winkler
Aug 5, 2021·Annual Review of Microbiology·Robert Landick

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