Natural RNA Polymerase Aptamers Regulate Transcription in E. coli.

Natural RNA Polymerase Aptamers Regulate Transcription in E. coli.

Abstract

In search for RNA signals that modulate transcription via direct interaction with RNA polymerase (RNAP), we deep sequenced an E. coli genomic library enriched for RNAP-binding RNAs. Many natural RNAP-binding aptamers, termed RAPs, were mapped to the genome. Over 60% of E. coli genes carry RAPs in their mRNA. Combining in vitro and in vivo approaches, we characterized a subset of inhibitory RAPs (iRAPs) that promote Rho-dependent transcription termination. A representative iRAP within the coding region of the essential gene, nadD, greatly reduces its transcriptional output in stationary phase and under oxidative stress, demonstrating that iRAPs control gene expression in response to changing environment. The mechanism of iRAPs involves active uncoupling of transcription and translation, making nascent RNA accessible to Rho. iRAPs encoded in the antisense strand also promote gene expression by reducing transcriptional interference. In essence, our work uncovers a broad class of cis-acting RNA signals that globally control bacterial transcription.

Grafik Top
Authors
  • Sedlyarova, Nadezda
  • Rescheneder, Philipp
  • Magan, Andres
  • Popitsch, Niko
  • Rziha, Natascha
  • Bilusic, Ivana
  • Epshtein, Vitaly
  • Zimmermann, Bob
  • Lybecker, Meghan
  • Sedlyarov, Vitaly
  • Schroeder, Renée
  • Nudler, Evgeny
Grafik Top
Shortfacts
Category
Journal Paper
Divisions
Bioinformatics and Computational Biology
Journal or Publication Title
Molecular Cell
ISSN
1097-2765
Publisher
Elsevier Inc.
Place of Publication
Amsterdam, Netherlands
Page Range
pp. 30-43
Number
1
Volume
67
Date
6 July 2017
Export
Grafik Top