Refereed journal article or data article (A1)

Locking the nontemplate DNA to control transcription




List of AuthorsNedialkov Y, Svetlov D, Belogurov GA, Artsimovitch I

PublisherWILEY

Publication year2018

JournalMolecular Microbiology

Journal name in sourceMOLECULAR MICROBIOLOGY

Journal acronymMOL MICROBIOL

Volume number109

Issue number4

Start page445

End page457

Number of pages13

ISSN0950-382X

eISSN1365-2958

DOIhttp://dx.doi.org/10.1111/mmi.13983


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 nontemplate DNA controls recruitment of regulatory factors and R-loop formation during transcription elongation across all life.


Last updated on 2021-24-06 at 11:49