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PMID: 27298343 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Temperature-responsive in vitro RNA structurome of Yersinia pseudotuberculosis.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 113 ·No. 26 ·2016-00-28 ·Pages 7237-42

Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH, Stadler PF, Dersch P, Narberhaus F

Abstract

RNA structures are fundamentally important for RNA function. Dynamic, condition-dependent structural changes are able to modulate gene expression as shown for riboswitches and RNA thermometers. By parallel analysis of RNA structures, we mapped the RNA structurome of Yersinia pseudotuberculosis at three different temperatures. This human pathogen is exquisitely responsive to host body temperature (37 °C), which induces a major metabolic transition. Our analysis profiles the structure of more than 1,750 RNAs at 25 °C, 37 °C, and 42 °C. Average mRNAs tend to be unstructured around the ribosome binding site. We searched for 5'-UTRs that are folded at low temperature and identified novel thermoresponsive RNA structures from diverse gene categories. The regulatory potential of 16 candidates was validated. In summary, we present a dynamic bacterial RNA structurome and find that the expression of virulence-relevant functions in Y. pseudotuberculosis and reprogramming of its metabolism in response to temperature is associated with a restructuring of numerous mRNAs.

Keywords
RNA structure RNA thermometer temperature translational control virulence
MeSH Terms
Escherichia coli/genetics Nucleic Acid Conformation RNA, Bacterial/genetics Temperature Transcriptome Yersinia pseudotuberculosis/genetics,growth & development beta-Galactosidase/genetics,metabolism
Chemicals
RNA, Bacterial beta-Galactosidase
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Righetti Francesco
Department of Microbial Biology, Ruhr University Bochum, 44801 Bochum, Germany;
Nuss Aaron M
Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
Twittenhoff Christian
Department of Microbial Biology, Ruhr University Bochum, 44801 Bochum, Germany;
Beele Sascha
Department of Microbial Biology, Ruhr University Bochum, 44801 Bochum, Germany;
Urban Kristina
Department of Microbial Biology, Ruhr University Bochum, 44801 Bochum, Germany;
Will Sebastian
Department of Computer Science, University of Leipzig, 04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany;
Bernhart Stephan H
Department of Computer Science, University of Leipzig, 04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany;
Stadler Peter F ORCID
Department of Computer Science, University of Leipzig, 04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany; Max Planck Institute Mathematics in the Sciences, 04103 Leipzig, Germany; Santa Fe Institute, Santa Fe, NM 87501; Fraunhofer Institute Cell Therapy and Immunology, 04103 Leipzig, Germany.
Dersch Petra
Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
Narberhaus Franz
Department of Microbial Biology, Ruhr University Bochum, 44801 Bochum, Germany; franz.narberhaus@rub.de.
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
1091-6490
DOI
10.1073/pnas.1523004113
Email
franz.narberhaus@rub.de
Published
2016-00-28
Epub
2016-00-13
Pages
7237-42
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC4932938
Subset
IM
External Links
PubMed source DOI: 10.1073/pnas.1523004113 PMC Full Text View journal details
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