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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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Sampedro Vallina N, McRae EKS, Hansen BK, Boussebayle A, Andersen ES. RNA origami scaffolds facilitate cryo-EM characterization of a Broccoli-Pepper aptamer FRET pair. Nucleic Acids Res 2023; 51:4613-4624. [PMID: 36999628 DOI: 10.1093/nar/gkad224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/06/2023] [Accepted: 03/28/2023] [Indexed: 04/01/2023] Open
Abstract
Cryogenic electron microscopy (cryo-EM) is a promising method for characterizing the structure of larger RNA structures and complexes. However, the structure of individual aptamers is difficult to solve by cryo-EM due to their low molecular weight and a high signal-to-noise ratio. By placing RNA aptamers on larger RNA scaffolds, the contrast for cryo-EM can be increased to allow the determination of the tertiary structure of the aptamer. Here we use the RNA origami method to scaffold two fluorescent aptamers (Broccoli and Pepper) in close proximity and show that their cognate fluorophores serve as donor and acceptor for FRET. Next, we use cryo-EM to characterize the structure of the RNA origami with the two aptamers to a resolution of 4.4 Å. By characterizing the aptamers with and without ligand, we identify two distinct modes of ligand binding, which are further supported by selective chemical probing. 3D variability analysis of the cryo-EM data show that the relative position between the two bound fluorophores on the origami fluctuate by only 3.5 Å. Our results demonstrate a general approach for using RNA origami scaffolds for characterizing small RNA motifs by cryo-EM and for positioning functional RNA motifs with high spatial precision.
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Affiliation(s)
- Néstor Sampedro Vallina
- Interdisciplinary Nanoscience Center (iNANO), Gustav Wieds Vej 14, Aarhus University, DK-8000 Aarhus, Denmark
| | - Ewan K S McRae
- Interdisciplinary Nanoscience Center (iNANO), Gustav Wieds Vej 14, Aarhus University, DK-8000 Aarhus, Denmark
| | - Bente Kring Hansen
- Interdisciplinary Nanoscience Center (iNANO), Gustav Wieds Vej 14, Aarhus University, DK-8000 Aarhus, Denmark
| | - Adrien Boussebayle
- Interdisciplinary Nanoscience Center (iNANO), Gustav Wieds Vej 14, Aarhus University, DK-8000 Aarhus, Denmark
| | - Ebbe Sloth Andersen
- Interdisciplinary Nanoscience Center (iNANO), Gustav Wieds Vej 14, Aarhus University, DK-8000 Aarhus, Denmark
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, DK-8000 Aarhus, Denmark
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Boussebayle A, Groher F, Suess B. Corrigendum to “RNA-based Capture-SELEX for the selection of small molecule-binding aptamers” [Methods 161 (2019) 10–15]. Methods 2020; 170:90. [DOI: 10.1016/j.ymeth.2019.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Boussebayle A, Torka D, Ollivaud S, Braun J, Bofill-Bosch C, Dombrowski M, Groher F, Hamacher K, Suess B. Next-level riboswitch development-implementation of Capture-SELEX facilitates identification of a new synthetic riboswitch. Nucleic Acids Res 2019; 47:4883-4895. [PMID: 30957848 PMCID: PMC6511860 DOI: 10.1093/nar/gkz216] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/15/2019] [Accepted: 04/04/2019] [Indexed: 02/06/2023] Open
Abstract
The development of synthetic riboswitches has always been a challenge. Although a number of interesting proof-of-concept studies have been published, almost all of these were performed with the theophylline aptamer. There is no shortage of small molecule-binding aptamers; however, only a small fraction of them are suitable for RNA engineering since a classical SELEX protocol selects only for high-affinity binding but not for conformational switching. We now implemented RNA Capture-SELEX in our riboswitch developmental pipeline to integrate the required selection for high-affinity binding with the equally necessary RNA conformational switching. Thus, we successfully developed a new paromomycin-binding synthetic riboswitch. It binds paromomycin with a KD of 20 nM and can discriminate between closely related molecules both in vitro and in vivo. A detailed structure-function analysis confirmed the predicted secondary structure and identified nucleotides involved in ligand binding. The riboswitch was further engineered in combination with the neomycin riboswitch for the assembly of an orthogonal Boolean NOR logic gate. In sum, our work not only broadens the spectrum of existing RNA regulators, but also signifies a breakthrough in riboswitch development, as the effort required for the design of sensor domains for RNA-based devices will in many cases be much reduced.
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Affiliation(s)
- Adrien Boussebayle
- Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Daniel Torka
- Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Sandra Ollivaud
- Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Johannes Braun
- Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Cristina Bofill-Bosch
- Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Max Dombrowski
- Computational Biology and Simulation, Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany
| | - Florian Groher
- Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Kay Hamacher
- Computational Biology and Simulation, Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany
- Department of Physics, Department of Computer Science, TU Darmstadt, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
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Boussebayle A, Groher F, Suess B. RNA-based Capture-SELEX for the selection of small molecule-binding aptamers. Methods 2019; 161:10-15. [PMID: 30953759 DOI: 10.1016/j.ymeth.2019.04.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 11/16/2022] Open
Abstract
Despite their wide applicability, the selection of small molecule-binding RNA aptamers with both high affinity binding and specificity is still challenging. Aptamers that excel at both binding and structure switching are particularly rare and difficult to find. Here, we present the protocol of a Capture-SELEX that specifically allows the in vitro selection of small-molecule binding aptamers, which are essential building blocks for the design process of synthetic riboswitches and biosensors. Moreover, we provide a comparative overview of our proposed methodology versus alternative in vitro selection protocols with a special focus on the design of the pool. Finally, we have included detailed notes to point out useful tips and pitfalls for future application.
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Affiliation(s)
- Adrien Boussebayle
- Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Florian Groher
- Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany.
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