Temperature-responsive in vitro RNA structurome of Yersinia pseudotuberculosis.
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.
Department of Microbial Biology, Ruhr University Bochum, 44801 Bochum, Germany;
Francesco
F
Righetti
Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
Aaron M
AM
Nuss
Department of Microbial Biology, Ruhr University Bochum, 44801 Bochum, Germany;
Christian
C
Twittenhoff
Department of Microbial Biology, Ruhr University Bochum, 44801 Bochum, Germany;
Sascha
S
Beele
Department of Microbial Biology, Ruhr University Bochum, 44801 Bochum, Germany;
Kristina
K
Urban
Department of Computer Science, University of Leipzig, 04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany;
Sebastian
S
Will
Department of Computer Science, University of Leipzig, 04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University of Leipzig, 04107 Leipzig, Germany;
Stephan H
SH
Bernhart
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.
Peter F
0000-0002-5016-5191
PF
Stadler
Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
Petra
P
Dersch
Department of Microbial Biology, Ruhr University Bochum, 44801 Bochum, Germany; franz.narberhaus@rub.de.
Franz
F
Narberhaus
D004926:Escherichia coli / Q000235:genetics; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000235:genetics*; D013696:Temperature; D059467:Transcriptome; D015011:Yersinia pseudotuberculosis / Q000235:genetics* / Q000254:growth & development; D001616:beta-Galactosidase / Q000235:genetics / Q000378:metabolism
D012329:RNA, Bacterial; D001616:beta-Galactosidase
RNA structure; RNA thermometer; temperature; translational control; virulence