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Mol Cell. 2017 Jul 6;67(1):30-43.e6. doi: 10.1016/j.molcel.2017.05.025. Epub 2017 Jun 22.

Natural RNA Polymerase Aptamers Regulate Transcription in E. coli.

Author information

1
Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9/5, 1030 Vienna, Austria.
2
Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna & Medical University of Vienna, 1030 Vienna, Austria.
3
Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090 Vienna, Austria.
4
Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
5
Department of Molecular Evolution and Development, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
6
University of Colorado, 1420 Austin Bluffs Parkway, Colorado Springs, CO 80918, USA.
7
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.
8
Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohrgasse 9/5, 1030 Vienna, Austria. Electronic address: renee.schroeder@univie.ac.at.
9
Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA. Electronic address: evgeny.nudler@nyumc.org.

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.

KEYWORDS:

aptamers; regulatory RNA; termination; transcription elongation

PMID:
28648779
PMCID:
PMC5535762
DOI:
10.1016/j.molcel.2017.05.025
[Indexed for MEDLINE]
Free PMC Article

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