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Duchardt-Ferner E, Gottstein-Schmidtke SR, Weigand JE, Ohlenschläger O, Wurm JP, Hammann C, Suess B, Wöhnert J. Eine OH-Gruppe ändert alles: konformative Dynamik als Grundlage für die Ligandenspezifität des Neomycin-bindenden RNA-Schalters. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201507365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Elke Duchardt-Ferner
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ); Goethe-Universität Frankfurt; Max-von-Laue-Straße 9 60438 Frankfurt/M Deutschland
| | - Sina R. Gottstein-Schmidtke
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ); Goethe-Universität Frankfurt; Max-von-Laue-Straße 9 60438 Frankfurt/M Deutschland
| | - Julia E. Weigand
- Fachbereich Biologie; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Deutschland
| | - Oliver Ohlenschläger
- Biomolekulare NMR-Spektroskopie; Leibniz-Institut für Altersforschung (Fritz-Lipmann-Institut); Beutenbergstraße 11 07745 Jena Deutschland
| | - Jan-Philip Wurm
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ); Goethe-Universität Frankfurt; Max-von-Laue-Straße 9 60438 Frankfurt/M Deutschland
| | - Christian Hammann
- Ribogenetics Biochemistry Lab; Jacobs Universität Bremen; 28759 Bremen Deutschland
| | - Beatrix Suess
- Fachbereich Biologie; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Deutschland
| | - Jens Wöhnert
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ); Goethe-Universität Frankfurt; Max-von-Laue-Straße 9 60438 Frankfurt/M Deutschland
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Duchardt-Ferner E, Gottstein-Schmidtke SR, Weigand JE, Ohlenschläger O, Wurm JP, Hammann C, Suess B, Wöhnert J. What a Difference an OH Makes: Conformational Dynamics as the Basis for the Ligand Specificity of the Neomycin-Sensing Riboswitch. Angew Chem Int Ed Engl 2015; 55:1527-30. [PMID: 26661511 DOI: 10.1002/anie.201507365] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Indexed: 01/13/2023]
Abstract
To ensure appropriate metabolic regulation, riboswitches must discriminate efficiently between their target ligands and chemically similar molecules that are also present in the cell. A remarkable example of efficient ligand discrimination is a synthetic neomycin-sensing riboswitch. Paromomycin, which differs from neomycin only by the substitution of a single amino group with a hydroxy group, also binds but does not flip the riboswitch. Interestingly, the solution structures of the two riboswitch-ligand complexes are virtually identical. In this work, we demonstrate that the local loss of key intermolecular interactions at the substitution site is translated through a defined network of intramolecular interactions into global changes in RNA conformational dynamics. The remarkable specificity of this riboswitch is thus based on structural dynamics rather than static structural differences. In this respect, the neomycin riboswitch is a model for many of its natural counterparts.
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Affiliation(s)
- Elke Duchardt-Ferner
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M, Deutschland
| | - Sina R Gottstein-Schmidtke
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M, Deutschland
| | - Julia E Weigand
- Fachbereich Biologie, Technische Universität Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Deutschland
| | - Oliver Ohlenschläger
- Biomolekulare NMR-Spektroskopie, Leibniz Institut für Altersforschung (Fritz-Lipmann-Institut), Beutenbergstrasse 11, 07745, Jena, Deutschland
| | - Jan-Philip Wurm
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M, Deutschland
| | - Christian Hammann
- Ribogenetics Biochemistry Lab, Jacobs Universität Bremen, 28759, Bremen, Deutschland
| | - Beatrix Suess
- Fachbereich Biologie, Technische Universität Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Deutschland
| | - Jens Wöhnert
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M, Deutschland.
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Gottstein-Schmidtke SR, Duchardt-Ferner E, Groher F, Weigand JE, Gottstein D, Suess B, Wöhnert J. Building a stable RNA U-turn with a protonated cytidine. RNA 2014; 20:1163-72. [PMID: 24951555 PMCID: PMC4105743 DOI: 10.1261/rna.043083.113] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 05/16/2014] [Indexed: 05/28/2023]
Abstract
The U-turn is a classical three-dimensional RNA folding motif first identified in the anticodon and T-loops of tRNAs. It also occurs frequently as a building block in other functional RNA structures in many different sequence and structural contexts. U-turns induce sharp changes in the direction of the RNA backbone and often conform to the 3-nt consensus sequence 5'-UNR-3' (N = any nucleotide, R = purine). The canonical U-turn motif is stabilized by a hydrogen bond between the N3 imino group of the U residue and the 3' phosphate group of the R residue as well as a hydrogen bond between the 2'-hydroxyl group of the uridine and the N7 nitrogen of the R residue. Here, we demonstrate that a protonated cytidine can functionally and structurally replace the uridine at the first position of the canonical U-turn motif in the apical loop of the neomycin riboswitch. Using NMR spectroscopy, we directly show that the N3 imino group of the protonated cytidine forms a hydrogen bond with the backbone phosphate 3' from the third nucleotide of the U-turn analogously to the imino group of the uridine in the canonical motif. In addition, we compare the stability of the hydrogen bonds in the mutant U-turn motif to the wild type and describe the NMR signature of the C+-phosphate interaction. Our results have implications for the prediction of RNA structural motifs and suggest simple approaches for the experimental identification of hydrogen bonds between protonated C-imino groups and the phosphate backbone.
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Affiliation(s)
- Sina R Gottstein-Schmidtke
- Institute of Molecular Biosciences, Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences, Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany
| | - Florian Groher
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Julia E Weigand
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Daniel Gottstein
- Institute for Biophysical Chemistry, Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences, Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany
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Weigand JE, Gottstein-Schmidtke SR, Demolli S, Groher F, Duchardt-Ferner E, Wöhnert J, Suess B. Sequence elements distal to the ligand binding pocket modulate the efficiency of a synthetic riboswitch. Chembiochem 2014; 15:1627-37. [PMID: 24954073 DOI: 10.1002/cbic.201402067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Indexed: 01/16/2023]
Abstract
Synthetic riboswitches can serve as sophisticated genetic control devices in synthetic biology, regulating gene expression through direct RNA-ligand interactions. We analyzed a synthetic neomycin riboswitch, which folds into a stem loop structure with an internal loop important for ligand binding and regulation. It is closed by a terminal hexaloop containing a U-turn and a looped-out adenine. We investigated the relationship between sequence, structure, and biological activity in the terminal loop by saturating mutagenesis, ITC, and NMR. Mutants corresponding to the canonical U-turn fold retained biological activity. An improvement of stacking interactions in the U-turn led to an RNA element with slightly enhanced regulatory activity. For the first position of the U-turn motif and the looped out base, sequence-activity relationships that could not initially be explained on the basis of the structure of the aptamer-ligand complex were observed. However, NMR studies of these mutants revealed subtle relationships between structure and dynamics of the aptamer in its free or bound state and biological activity.
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Affiliation(s)
- Julia E Weigand
- Department of Biology, Technical University Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt (Germany)
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