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Kraus L, Duchardt-Ferner E, Bräuchle E, Fürbacher S, Kelvin D, Marx H, Boussebayle A, Maurer LM, Bofill-Bosch C, Wöhnert J, Suess B. Development of a novel tobramycin dependent riboswitch. Nucleic Acids Res 2023; 51:11375-11385. [PMID: 37791877 PMCID: PMC10639043 DOI: 10.1093/nar/gkad767] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/30/2023] [Accepted: 09/12/2023] [Indexed: 10/05/2023] Open
Abstract
We herein report the selection and characterization of a new riboswitch dependent on the aminoglycoside tobramycin. Its dynamic range rivals even the tetracycline dependent riboswitch to be the current best performing, synthetic riboswitch that controls translation initiation. The riboswitch was selected with RNA Capture-SELEX, a method that not only selects for binding but also for structural changes in aptamers on binding. This study demonstrates how this method can fundamentally reduce the labour required for the de novo identification of synthetic riboswitches. The initially selected riboswitch candidate harbours two distinct tobramycin binding sites with KDs of 1.1 nM and 2.4 μM, respectively, and can distinguish between tobramycin and the closely related compounds kanamycin A and B. Using detailed genetic and biochemical analyses and 1H NMR spectroscopy, the proposed secondary structure of the riboswitch was verified and the tobramycin binding sites were characterized. The two binding sites were found to be essentially non-overlapping, allowing for a separate investigation of their contribution to the activity of the riboswitch. We thereby found that only the high-affinity binding site was responsible for regulatory activity, which allowed us to engineer a riboswitch from only this site with a minimal sequence size of 33 nt and outstanding performance.
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Affiliation(s)
- Leon Kraus
- Fachbereich Biologie, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, 64287 Darmstadt, Germany
| | - Elke Duchardt-Ferner
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt, Germany
| | - Eric Bräuchle
- Fachbereich Biologie, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Simon Fürbacher
- Fachbereich Biologie, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Daniel Kelvin
- Fachbereich Biologie, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, 64287 Darmstadt, Germany
| | - Hans Marx
- Fachbereich Biologie, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
- Institute of Microbiology and Microbial Biotechnology BOKU University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Adrien Boussebayle
- Fachbereich Biologie, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
- Interdisciplinary Nanoscience Center (iNANO), Gustav Wieds Vej 14, Aarhus University, DK-8000 Aarhus, Denmark
| | - Lisa-Marie Maurer
- Fachbereich Biologie, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, 64287 Darmstadt, Germany
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt, Germany
| | - Cristina Bofill-Bosch
- Fachbereich Biologie, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Jens Wöhnert
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt, Germany
| | - Beatrix Suess
- Fachbereich Biologie, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, 64287 Darmstadt, Germany
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