1
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Kramat J, Kraus L, Gunawan VJ, Smyej E, Froehlich P, Weber TE, Spiehl D, Koeppl H, Blaeser A, Suess B. Sensing Levofloxacin with an RNA Aptamer as a Bioreceptor. Biosensors (Basel) 2024; 14:56. [PMID: 38275309 PMCID: PMC10813692 DOI: 10.3390/bios14010056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/27/2024]
Abstract
To combat the growing threat of antibiotic resistance, environmental testing for antibiotic contamination is gaining an increasing role. This study aims to develop an easy-to-use assay for the detection of the fluoroquinolone antibiotic levofloxacin. Levofloxacin is used in human and veterinary medicine and has been detected in wastewater and river water. An RNA aptamer against levofloxacin was selected using RNA Capture-SELEX. The 73 nt long aptamer folds into three stems with a central three-way junction. It binds levofloxacin with a Kd of 6 µM and discriminates the closely related compound ciprofloxacin. Furthermore, the selection process was analyzed using a next-generation sequencing approach to better understand the sequence evolution throughout the selection. The aptamer was used as a bioreceptor for the development of a lateral flow assay. The biosensor exploited the innate characteristic of RNA Capture-SELEX to select aptamers that displace a complementary DNA oligonucleotide upon ligand binding. The lateral flow assay achieved a limit of visual detection of 100 µM. While the sensitivity of this assay constrains its immediate use in environmental testing, the present study can serve as a template for the selection of RNA aptamer-based biosensors.
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Affiliation(s)
- Janice Kramat
- Synthetic RNA Biology, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Leon Kraus
- Synthetic RNA Biology, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Vincent J. Gunawan
- Synthetic RNA Biology, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Elias Smyej
- Synthetic RNA Biology, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Philipp Froehlich
- Self-Organizing Systems, Department of Electrical Engineering and Information Technology, Technical University of Darmstadt, 64283 Darmstadt, Germany
| | - Tim E. Weber
- Institute for BioMedical Printing Technologies, Technical University of Darmstadt, 64289 Darmstadt, Germany
| | - Dieter Spiehl
- Institute for BioMedical Printing Technologies, Technical University of Darmstadt, 64289 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, 64289 Darmstadt, Germany
| | - Heinz Koeppl
- Self-Organizing Systems, Department of Electrical Engineering and Information Technology, Technical University of Darmstadt, 64283 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, 64289 Darmstadt, Germany
| | - Andreas Blaeser
- Institute for BioMedical Printing Technologies, Technical University of Darmstadt, 64289 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, 64289 Darmstadt, Germany
| | - Beatrix Suess
- Synthetic RNA Biology, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, 64289 Darmstadt, Germany
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Vockenhuber MP, Hoetzel J, Maurer LM, Fröhlich P, Weiler S, Muller YA, Koeppl H, Suess B. A Novel RNA Aptamer as Synthetic Inducer of DasR Controlled Transcription. ACS Synth Biol 2024; 13:319-327. [PMID: 38127784 DOI: 10.1021/acssynbio.3c00553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Progress in the synthetic biology field is driven by the development of new tools for synthetic circuit engineering. Traditionally, the focus has relied on protein-based designs. In recent years, the use of RNA-based tools has tremendously increased, due to their versatile functionality and applicability. A promising class of molecules is RNA aptamers, small, single-stranded RNA molecules that bind to a target molecule with high affinity and specificity. When targeting bacterial repressors, RNA aptamers allow one to add a new layer to an established protein-based regulation. In the present study, we selected an RNA aptamer binding the bacterial repressor DasR, preventing its binding to its operator sequence and activating DasR-controlled transcription in vivo. This was made possible only by the combination of an in vitro selection and subsequent in vivo screening. Next-generation sequencing of the selection process proved the importance of the in vivo screening for the discovery of aptamers functioning in the cell. Mutational and biochemical studies led to the identification of the minimal necessary binding motif. Taken together, the resulting combination of bacterial repressor and RNA aptamer enlarges the synthetic biology toolbox by adding a new level of regulation.
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Affiliation(s)
- Michael-Paul Vockenhuber
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Strasse 14, 35043 Marburg, Germany
| | - Janis Hoetzel
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Lisa-Marie Maurer
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Philipp Fröhlich
- Department of Electrical Engineering and Information Technology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Sigrid Weiler
- Lehrstuhl für Biotechnik, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Henkestr. 91, 91052 Erlangen, Germany
| | - Yves A Muller
- Lehrstuhl für Biotechnik, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Henkestr. 91, 91052 Erlangen, Germany
| | - Heinz Koeppl
- Department of Electrical Engineering and Information Technology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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3
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Affiliation(s)
- Beatrix Suess
- Department of Biology, Synthetic RNA Biology, TU Darmstadt, Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, Darmstadt, Germany
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4
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Hetzke T, Vogel M, Halbritter ALJ, Saha S, Suess B, Sigurdsson ST, Prisner TF. Simultaneous Localization of Two High Affinity Divalent Metal Ion Binding Sites in the Tetracycline RNA Aptamer with Mn 2+-Based Pulsed Dipolar EPR Spectroscopy. J Phys Chem Lett 2023; 14:11421-11428. [PMID: 38084602 DOI: 10.1021/acs.jpclett.3c02566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Mg2+ ions play an essential part in stabilizing the tertiary structure of nucleic acids. While the importance of these ions is well documented, their localization and elucidation of their role in the structure and dynamics of nucleic acids are often challenging. In this work, pulsed electron-electron double resonance spectroscopy (PELDOR, also known as DEER) was used to localize two high affinity divalent metal ion binding sites in the tetracycline RNA aptamer with high accuracy. For this purpose, the aptamer was labeled at different positions with a semirigid nitroxide spin label and diamagnetic Mg2+ was replaced with paramagnetic Mn2+, which did not alter the folding process or ligand binding. Out of the several divalent metal ion binding sites that are known from the crystal structure, two binding sites with high affinity were detected: one that is located at the ligand binding center and another at the J1/2 junction of the RNA.
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Affiliation(s)
- Thilo Hetzke
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Marc Vogel
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | | | - Subham Saha
- Department of Chemistry, Science Institute, University of Iceland, 107 Reykjavik, Iceland
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, 107 Reykjavik, Iceland
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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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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Kaiser C, Vogel M, Appel B, Weigand J, Müller S, Suess B, Wachtveitl J. Magnesium Ion-Driven Folding and Conformational Switching Kinetics of Tetracycline Binding Aptamer: Implications for in vivo Riboswitch Engineering. J Mol Biol 2023; 435:168253. [PMID: 37640152 DOI: 10.1016/j.jmb.2023.168253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/22/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023]
Abstract
Engineering in vitro selected RNA aptamers into in vivo functional riboswitches represents a long-standing challenge in molecular biology. The highly specific aptamer domain of the riboswitch undergoes a conformational adjustment in response to ligand sensing, which in turn exerts the regulatory function. Besides essential factors like structural complexity and ligand binding kinetics, the active role of magnesium ions in stabilizing RNA tertiary structures and assisting in ligand binding can be a vital criterion. We present spectroscopic studies on the magnesium ion-driven folding of the Tetracycline binding aptamer. Using fluorescent labels, the aptamer pre-folding and subsequent ligand binding is monitored by magnesium titration experiments and time-resolved stopped-flow measurements. A minimum concentration of 0.5 mM magnesium is required to fold into a magnesium ion-stabilized binding-competent state with a preformed binding pocket. Tetracycline binding causes a pronounced conformational change that results in the establishment of the triple helix core motif, and that further propagates towards the closing stem. By a dynamic acquisition of magnesium ions, a kink motif is formed at the intersection of the triple helix and closing stem regions. This ultimately entails a stabilization of the closing stem which is discussed as a key element in the regulatory function of the Tetracycline aptamer.
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Affiliation(s)
- Christoph Kaiser
- Institute for Physical and Theoretical Chemistry, Goethe University, Frankfurt/Main, Max-von-Laue Str. 9, D-60438, Germany.
| | - Marc Vogel
- Department of Biology, Technical University Darmstadt, Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany
| | - Bettina Appel
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
| | - Julia Weigand
- Department of Biology, Technical University Darmstadt, Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany; Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Marbacher Weg 6, D-35037, Germany. https://twitter.com/WachtveitlLab
| | - Sabine Müller
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany; Centre for Synthetic Biology, Technical University Darmstadt, Darmstadt, Germany.
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry, Goethe University, Frankfurt/Main, Max-von-Laue Str. 9, D-60438, Germany.
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Klein T, Funke F, Rossbach O, Lehmann G, Vockenhuber M, Medenbach J, Suess B, Meister G, Babinger P. Investigating the Prevalence of RNA-Binding Metabolic Enzymes in E. coli. Int J Mol Sci 2023; 24:11536. [PMID: 37511294 PMCID: PMC10380284 DOI: 10.3390/ijms241411536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/19/2023] [Revised: 07/07/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
An open research field in cellular regulation is the assumed crosstalk between RNAs, metabolic enzymes, and metabolites, also known as the REM hypothesis. High-throughput assays have produced extensive interactome data with metabolic enzymes frequently found as hits, but only a few examples have been biochemically validated, with deficits especially in prokaryotes. Therefore, we rationally selected nineteen Escherichia coli enzymes from such datasets and examined their ability to bind RNAs using two complementary methods, iCLIP and SELEX. Found interactions were validated by EMSA and other methods. For most of the candidates, we observed no RNA binding (12/19) or a rather unspecific binding (5/19). Two of the candidates, namely glutamate-5-kinase (ProB) and quinone oxidoreductase (QorA), displayed specific and previously unknown binding to distinct RNAs. We concentrated on the interaction of QorA to the mRNA of yffO, a grounded prophage gene, which could be validated by EMSA and MST. Because the physiological function of both partners is not known, the biological relevance of this interaction remains elusive. Furthermore, we found novel RNA targets for the MS2 phage coat protein that served us as control. Our results indicate that RNA binding of metabolic enzymes in procaryotes is less frequent than suggested by the results of high-throughput studies, but does occur.
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Affiliation(s)
- Thomas Klein
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Franziska Funke
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Oliver Rossbach
- Institute of Biochemistry, Faculty of Biology and Chemistry, University of Giessen, D-35392 Giessen, Germany
| | - Gerhard Lehmann
- Institute of Biochemistry, Genetics and Microbiology, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Michael Vockenhuber
- Centre for Synthetic Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Jan Medenbach
- Institute of Biochemistry, Genetics and Microbiology, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Beatrix Suess
- Centre for Synthetic Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Gunter Meister
- Institute of Biochemistry, Genetics and Microbiology, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Patrick Babinger
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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Abstract
SELEX has enabled the selection of aptamers, nucleic acids that can bind a defined ligand, in some cases with exceptionally high affinity and specificity. The SELEX protocol has been adapted many times to fit a variety of needs. This protocol describes such an adaptation, namely, RNA-Capture SELEX that we have used to successfully develop small molecule-binding RNA aptamers. Our proposed method specifically selects not only for excellent binding but also for conformational switching. In consequence, we found this SELEX method to be particularly suitable for identifying aptamers for further application in synthetic riboswitch engineering.
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Affiliation(s)
- Leon Kraus
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany.
- Center for Synthetic Biology, Technical University of Darmstadt, Darmstadt, Germany.
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Kelvin D, Suess B. Tapping the potential of synthetic riboswitches: reviewing the versatility of the tetracycline aptamer. RNA Biol 2023; 20:457-468. [PMID: 37459466 DOI: 10.1080/15476286.2023.2234732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/20/2023] Open
Abstract
Synthetic riboswitches are a versatile class of regulatory elements that are becoming increasingly established in synthetic biology applications. They are characterized by their compact size and independence from auxiliary protein factors. While naturally occurring riboswitches were mostly discovered in bacteria, synthetic riboswitches have been designed for all domains of life. Published design strategies far exceed the number of riboswitches found in nature. A core element of any riboswitch is a binding domain, called an aptamer, which is characterized by high specificity and affinity for its ligand. Aptamers can be selected de novo, allowing the design of synthetic riboswitches against a broad spectrum of targets. The tetracycline aptamer has proven to be well suited for riboswitch engineering. Since its selection, it has been used in a variety of applications and is considered to be well established and characterized. Using the tetracycline aptamer as an example, we aim to discuss a large variety of design approaches for synthetic riboswitch engineering and their application. We aim to demonstrate the versatility of riboswitches in general and the high potential of synthetic RNA devices for creating new solutions in both the scientific and medical fields.
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Affiliation(s)
- Daniel Kelvin
- Fachbereich Biologie, TU Darmstadt, Darmstadt, Germany
| | - Beatrix Suess
- Fachbereich Biologie, TU Darmstadt, Darmstadt, Germany
- Centre for Synthetic Biology, TU Darmstadt, Darmstadt, Germany
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Hoetzel J, Suess B. Structural changes in aptamers are essential for synthetic riboswitch engineering. J Mol Biol 2022; 434:167631. [PMID: 35595164 DOI: 10.1016/j.jmb.2022.167631] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 11/19/2022]
Abstract
Synthetic riboswitches are powerful tools in synthetic biology in which sensing and execution are consolidated in a single RNA molecule. By using SELEX to select aptamers in vitro, synthetic riboswitches can in theory be engineered against any ligand of choice. Surprisingly, very few in vitro selected aptamers have been used for the engineering of synthetic riboswitches. In-depth studies of these aptamers suggest that the key characteristics of such regulatory active RNAs are their structural switching abilities and their binding dynamics. Conventional SELEX approaches seem to be inadequate to select for these characteristics, which may explain the lack of in vitro selected aptamers suited for engineering of synthetic riboswitches. In this review, we explore the functional principles of synthetic riboswitches, identify key characteristics of regulatory active in vitro selected aptamers and integrate these findings in context with available in vitro selection methods. Based on these insights, we propose to use a combination of capture-SELEX and subsequent functional screening for a more successful in vitro selection of aptamers that can be applied for the engineering of synthetic riboswitches.
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Affiliation(s)
- Janis Hoetzel
- Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany. https://www.twitter.com/J_Hoetzel
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany; Center for Synthetic Biology, Technical University of Darmstadt, Germany.
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11
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Kramat J, Suess B. Efficient Method to Identify Synthetic Riboswitches Using RNA-Based Capture-SELEX Combined with In Vivo Screening. Methods Mol Biol 2022; 2518:157-177. [PMID: 35666445 DOI: 10.1007/978-1-0716-2421-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Synthetic riboswitches are a promising tool for conditional gene expression. In vitro selected aptamers used as binding domains for the design of RNA-based switches have to exhibit excellent binding affinity as well as ligand binding-induced structural changes. Selection via Capture-SELEX favors the enrichment of aptamers which exhibit both characteristics. For the Capture-SELEX, an RNA pool is used that gets immobilized onto a capture oligonucleotide by hybridization. Addition of the ligand frees the aptamers by their binding to the ligand, resulting in the release from the capture oligonucleotide through structural changes. These sequences get reverse transcribed, PCR amplified, and used for the following selection rounds. In this publication, we present a detailed protocol for Capture-SELEX, followed by screening in yeast to identify aptamers suitable for the design of synthetic riboswitches.
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Affiliation(s)
- Janice Kramat
- Department of Biology, Technical University Darmstadt, Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Darmstadt, Germany.
- Centre of Synthetic Biology, Technical University Darmstadt, Darmstadt, Germany.
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12
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Abstract
In recent years, synthetic riboswitches have become increasingly important to construct genetic circuits in all three domains of life. In bacteria, synthetic translational riboswitches are often employed that modulate gene expression by masking the Shine-Dalgarno (SD) sequence in the absence or presence of a cognate ligand. For (halo-)archaeal translation, a SD sequence is not strictly required. The application of synthetic riboswitches in haloarchaea is therefore limited so far, also because of the molar intracellular salt concentrations found in these microbes. In this study, we applied synthetic theophylline-dependent translational riboswitches in the archaeon Haloferax volcanii. The riboswitch variants A through E and E∗ were chosen since they not only mask the SD sequence but also the AUG start codon by forming a secondary structure in the absence of the ligand theophylline. Upon addition of the ligand, the ribosomal binding site and start codon become accessible for translation initiation. Riboswitch E mediated a dose-dependent, up to threefold activation of the bgaH reporter gene expression. Raising the salt concentration of the culture media from 3 to 4 M NaCl resulted in a 12-fold increase in the switching capacity of riboswitch E, and switching activity increased up to 26-fold when the cultivating temperature was reduced from 45 to 30°C. To construct a genetic circuit, riboswitch E was applied to regulate the synthesis of the transcriptional activator GvpE allowing a dose-dependent activation of the mgfp6 reporter gene under P pA promoter control.
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Affiliation(s)
| | | | - Beatrix Suess
- Synthetic RNA Biology, Department of Biology, Technical University Darmstadt, Darmstadt, Germany.,Centre of Synthetic Biology, Technical University Darmstadt, Darmstadt, Germany
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13
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Kaiser C, Schneider J, Groher F, Suess B, Wachtveitl J. What defines a synthetic riboswitch? - Conformational dynamics of ciprofloxacin aptamers with similar binding affinities but varying regulatory potentials. Nucleic Acids Res 2021; 49:3661-3671. [PMID: 33772594 PMCID: PMC8053125 DOI: 10.1093/nar/gkab166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 02/25/2021] [Accepted: 03/23/2021] [Indexed: 11/16/2022] Open
Abstract
Among the many in vitro-selected aptamers derived from SELEX protocols, only a small fraction has the potential to be applied for synthetic riboswitch engineering. Here, we present a comparative study of the binding properties of three different aptamers that bind to ciprofloxacin with similar KD values, yet only two of them can be applied as riboswitches. We used the inherent ligand fluorescence that is quenched upon binding as the reporter signal in fluorescence titration and in time-resolved stopped-flow experiments. Thus, we were able to demonstrate differences in the binding kinetics of regulating and non-regulating aptamers. All aptamers studied underwent a two-step binding mechanism that suggests an initial association step followed by a reorganization of the aptamer to accommodate the ligand. We show that increasing regulatory potential is correlated with a decreasing back-reaction rate of the second binding step, thus resulting in a virtually irreversible last binding step of regulating aptamers. We suggest that a highly favoured structural adaption of the RNA to the ligand during the final binding step is essential for turning an aptamer into a riboswitch. In addition, our results provide an explanation for the fact that so few aptamers with regulating capacity have been found to date. Based on our data, we propose an adjustment of the selection protocol for efficient riboswitch detection.
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Affiliation(s)
- Christoph Kaiser
- Institute for Physical and Theoretical Chemistry, Goethe-Universität Frankfurt, Max-von-Laue-Straße 8, D-60438 Frankfurt am Main, Germany
| | - Jeannine Schneider
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany
| | - Florian Groher
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany.,Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry, Goethe-Universität Frankfurt, Max-von-Laue-Straße 8, D-60438 Frankfurt am Main, Germany
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14
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Schwich OD, Blümel N, Keller M, Wegener M, Setty ST, Brunstein ME, Poser I, Mozos IRDL, Suess B, Münch C, McNicoll F, Zarnack K, Müller-McNicoll M. SRSF3 and SRSF7 modulate 3'UTR length through suppression or activation of proximal polyadenylation sites and regulation of CFIm levels. Genome Biol 2021; 22:82. [PMID: 33706811 PMCID: PMC7948361 DOI: 10.1186/s13059-021-02298-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 02/11/2021] [Indexed: 12/23/2022] Open
Abstract
Background Alternative polyadenylation (APA) refers to the regulated selection of polyadenylation sites (PASs) in transcripts, which determines the length of their 3′ untranslated regions (3′UTRs). We have recently shown that SRSF3 and SRSF7, two closely related SR proteins, connect APA with mRNA export. The mechanism underlying APA regulation by SRSF3 and SRSF7 remained unknown. Results Here we combine iCLIP and 3′-end sequencing and find that SRSF3 and SRSF7 bind upstream of proximal PASs (pPASs), but they exert opposite effects on 3′UTR length. SRSF7 enhances pPAS usage in a concentration-dependent but splicing-independent manner by recruiting the cleavage factor FIP1, generating short 3′UTRs. Protein domains unique to SRSF7, which are absent from SRSF3, contribute to FIP1 recruitment. In contrast, SRSF3 promotes distal PAS (dPAS) usage and hence long 3′UTRs directly by counteracting SRSF7, but also indirectly by maintaining high levels of cleavage factor Im (CFIm) via alternative splicing. Upon SRSF3 depletion, CFIm levels decrease and 3′UTRs are shortened. The indirect SRSF3 targets are particularly sensitive to low CFIm levels, because here CFIm serves a dual function; it enhances dPAS and inhibits pPAS usage by binding immediately downstream and assembling unproductive cleavage complexes, which together promotes long 3′UTRs. Conclusions We demonstrate that SRSF3 and SRSF7 are direct modulators of pPAS usage and show how small differences in the domain architecture of SR proteins can confer opposite effects on pPAS regulation. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02298-y.
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Affiliation(s)
- Oliver Daniel Schwich
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Nicole Blümel
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany
| | - Mario Keller
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany.,Faculty of Biological Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Marius Wegener
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Samarth Thonta Setty
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Melinda Elaine Brunstein
- Institute of Biochemistry II, Medical School, Goethe University Frankfurt, Sandhofstr. 2-4, 60528, Frankfurt am Main, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany
| | | | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - Christian Münch
- Institute of Biochemistry II, Medical School, Goethe University Frankfurt, Sandhofstr. 2-4, 60528, Frankfurt am Main, Germany
| | - François McNicoll
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany. .,Faculty of Biological Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
| | - Michaela Müller-McNicoll
- Institute for Molecular Bio Science, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt, Germany.
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15
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Abstract
Correct cellular localization is essential for the function of many eukaryotic proteins and hence cell physiology. Here, we present a synthetic genetic device that allows the control of nuclear and cytosolic localization based on controlled alternative splicing in human cells. The device is based on the fact that an alternative 3' splice site is located within a TetR aptamer that in turn is positioned between the branch point and the canonical splice site. The novel splice site is only recognized when the TetR repressor is bound. Addition of doxycycline prevents TetR aptamer binding and leads to recognition of the canonical 3' splice site. It is thus possible to produce two independent splice isoforms. Since the terminal loop of the aptamer may be replaced with any sequence of choice, one of the two isoforms may be extended by the respective sequence of choice depending on the presence of doxycycline. In a proof-of-concept study, we fused a nuclear localization sequence to a cytosolic target protein, thus directing the protein into the nucleus. However, the system is not limited to the control of nuclear localization. In principle, any target sequence can be integrated into the aptamer, allowing not only the production of a variety of different isoforms on demand, but also to study the function of mislocalized proteins. Moreover, it also provides a valuable tool for investigating the mechanism of alternative splicing in human cells.
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Affiliation(s)
- Adam A Mol
- Department of Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Marc Vogel
- Department of Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
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16
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Uebbing S, Kreiß M, Scholl F, Häfner AK, Sürün D, Garscha U, Werz O, Basavarajappa D, Samuelsson B, Rådmark O, Suess B, Steinhilber D. Modulation of microRNA processing by 5-lipoxygenase. FASEB J 2020; 35:e21193. [PMID: 33205517 DOI: 10.1096/fj.202002108r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 09/11/2020] [Revised: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 12/20/2022]
Abstract
The miRNA biogenesis is tightly regulated to avoid dysfunction and consequent disease development. Here, we describe modulation of miRNA processing as a novel noncanonical function of the 5-lipoxygenase (5-LO) enzyme in monocytic cells. In differentiated Mono Mac 6 (MM6) cells, we found an in situ interaction of 5-LO with Dicer, a key enzyme in miRNA biogenesis. RNA sequencing of small noncoding RNAs revealed a functional impact, knockout of 5-LO altered the expression profile of several miRNAs. Effects of 5-LO could be observed at two levels. qPCR analyses thus indicated that (a) 5-LO promotes the transcription of the evolutionarily conserved miR-99b/let-7e/miR-125a cluster and (b) the 5-LO-Dicer interaction downregulates the processing of pre-let-7e, resulting in an increase in miR-125a and miR-99b levels by 5-LO without concomitant changes in let-7e levels in differentiated MM6 cells. Our observations suggest that 5-LO regulates the miRNA profile by modulating the Dicer-mediated processing of distinct pre-miRNAs. 5-LO inhibits the formation of let-7e which is a well-known inducer of cell differentiation, but promotes the generation of miR-99b and miR-125a known to induce cell proliferation and the maintenance of leukemic stem cell functions.
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Affiliation(s)
- Stella Uebbing
- Department of Biology, Technical University, Darmstadt, Germany.,Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt/Main, Germany.,Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Marius Kreiß
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt/Main, Germany
| | - Friederike Scholl
- Department of Biology, Technical University, Darmstadt, Germany.,Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt/Main, Germany.,Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Ann-Kathrin Häfner
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt/Main, Germany
| | - Duran Sürün
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Ulrike Garscha
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
| | - Devaraj Basavarajappa
- Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Bengt Samuelsson
- Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Olof Rådmark
- Division of Physiological Chemistry II, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Beatrix Suess
- Department of Biology, Technical University, Darmstadt, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt/Main, Germany
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17
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Schmidt M, Hamacher K, Reinhardt F, Lotz TS, Groher F, Suess B, Jager S. SICOR: Subgraph Isomorphism Comparison of RNA Secondary Structures. IEEE/ACM Trans Comput Biol Bioinform 2020; 17:2189-2195. [PMID: 31295116 DOI: 10.1109/tcbb.2019.2926711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
RNA aptamer selection during SELEX experiments builds on secondary structural diversity. Advanced structural comparison methods can focus this diversity. We develop SICOR, which uses probabilistic subgraph isomorphisms for graph distances between RNA secondary structure graphs. SICOR outperforms other comparison methods and is applicable to many structural comparisons in experimental design.
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18
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Grau FC, Jaeger J, Groher F, Suess B, Muller YA. The complex formed between a synthetic RNA aptamer and the transcription repressor TetR is a structural and functional twin of the operator DNA-TetR regulator complex. Nucleic Acids Res 2020; 48:3366-3378. [PMID: 32052019 PMCID: PMC7102968 DOI: 10.1093/nar/gkaa083] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/22/2020] [Accepted: 02/11/2020] [Indexed: 02/06/2023] Open
Abstract
RNAs play major roles in the regulation of gene expression. Hence, designer RNA molecules are increasingly explored as regulatory switches in synthetic biology. Among these, the TetR-binding RNA aptamer was selected by its ability to compete with operator DNA for binding to the bacterial repressor TetR. A fortuitous finding was that induction of TetR by tetracycline abolishes both RNA aptamer and operator DNA binding in TetR. This enabled numerous applications exploiting both the specificity of the RNA aptamer and the efficient gene repressor properties of TetR. Here, we present the crystal structure of the TetR-RNA aptamer complex at 2.7 Å resolution together with a comprehensive characterization of the TetR–RNA aptamer versus TetR–operator DNA interaction using site-directed mutagenesis, size exclusion chromatography, electrophoretic mobility shift assays and isothermal titration calorimetry. The fold of the RNA aptamer bears no resemblance to regular B-DNA, and neither does the thermodynamic characterization of the complex formation reaction. Nevertheless, the functional aptamer-binding epitope of TetR is fully contained within its DNA-binding epitope. In the RNA aptamer complex, TetR adopts the well-characterized DNA-binding-competent conformation of TetR, thus revealing how the synthetic TetR-binding aptamer strikes the chords of the bimodal allosteric behaviour of TetR to function as a synthetic regulator.
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Affiliation(s)
- Florian C Grau
- Lehrstuhl für Biotechnik, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Henkestr. 91, D-91052 Erlangen, Germany
| | - Jeannine Jaeger
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287 Darmstadt, Germany
| | - Florian Groher
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, D-64287 Darmstadt, Germany.,Centre for Synthetic Biology, Technische Universität Darmstadt
| | - Yves A Muller
- Lehrstuhl für Biotechnik, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Henkestr. 91, D-91052 Erlangen, Germany
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19
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Mol AA, Groher F, Schreiber B, Rühmkorff C, Suess B. Robust gene expression control in human cells with a novel universal TetR aptamer splicing module. Nucleic Acids Res 2020; 47:e132. [PMID: 31504742 PMCID: PMC6846422 DOI: 10.1093/nar/gkz753] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 01/12/2023] Open
Abstract
Fine-tuning of gene expression is desirable for a wide range of applications in synthetic biology. In this context, RNA regulatory devices provide a powerful and highly functional tool. We developed a versatile, robust and reversible device to control gene expression by splicing regulation in human cells using an aptamer that is recognized by the Tet repressor TetR. Upon insertion in proximity to the 5′ splice site, intron retention can be controlled via the binding of TetR to the aptamer. Although we were able to demonstrate regulation for different introns, the genomic context had a major impact on regulation. In consequence, we advanced the aptamer to develop a splice device. Our novel device contains the aptamer integrated into a context of exonic and intronic sequences that create and maintain an environment allowing a reliable and robust splicing event. The exon-born, additional amino acids will then be cleaved off by a self-cleaving peptide. This design allows portability of the splicing device, which we confirmed by demonstrating its functionality in different gene contexts. Intriguingly, our splicing device shows a high dynamic range and low basal activity, i.e. desirable features that often prove a major challenge when implementing synthetic biology in mammalian cell lines.
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Affiliation(s)
- Adam A Mol
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Florian Groher
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Britta Schreiber
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Ciaran Rühmkorff
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
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20
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Engel F, Ossipova E, Jakobsson PJ, Vockenhuber MP, Suess B. sRNA scr5239 Involved in Feedback Loop Regulation of Streptomyces coelicolor Central Metabolism. Front Microbiol 2020; 10:3121. [PMID: 32117084 PMCID: PMC7025569 DOI: 10.3389/fmicb.2019.03121] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/24/2019] [Indexed: 12/26/2022] Open
Abstract
In contrast to transcriptional regulation, post-transcriptional regulation and the role of small non-coding RNAs (sRNAs) in streptomycetes are not well studied. Here, we focus on the highly conserved sRNA scr5239 in Streptomyces coelicolor. A proteomics approach revealed that the sRNA regulates several metabolic enzymes, among them phosphoenolpyruvate carboxykinase (PEPCK), a key enzyme of the central carbon metabolism. The sRNA scr5239 represses pepck at the post-transcriptional level and thus modulates the intracellular level of phosphoenolpyruvate (PEP). The expression of scr5239 in turn is dependent on the global transcriptional regulator DasR, thus creating a feedback loop regulation of the central carbon metabolism. By post-transcriptional regulation of PEPCK and in all likelihood other targets, scr5239 adds an additional layer to the DasR regulatory network and provides a tool to control the metabolism dependent on the available carbon source.
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Affiliation(s)
- Franziska Engel
- Synthetic Genetic Circuits, Department of Biology, Darmstadt University Technology, Darmstadt, Germany
| | - Elena Ossipova
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Solna, Sweden
| | - Per-Johan Jakobsson
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Solna, Sweden
| | - Michael-Paul Vockenhuber
- Synthetic Genetic Circuits, Department of Biology, Darmstadt University Technology, Darmstadt, Germany
- *Correspondence: Michael-Paul Vockenhuber,
| | - Beatrix Suess
- Synthetic Genetic Circuits, Department of Biology, Darmstadt University Technology, Darmstadt, Germany
- Beatrix Suess,
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21
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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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22
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Lehr FX, Hanst M, Vogel M, Kremer J, Göringer HU, Suess B, Koeppl H. Cell-Free Prototyping of AND-Logic Gates Based on Heterogeneous RNA Activators. ACS Synth Biol 2019; 8:2163-2173. [PMID: 31393707 DOI: 10.1021/acssynbio.9b00238] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
RNA-based devices controlling gene expression bear great promise for synthetic biology, as they offer many advantages such as short response times and light metabolic burden compared to protein-circuits. However, little work has been done regarding their integration to multilevel regulated circuits. In this work, we combined a variety of small transcriptional activator RNAs (STARs) and toehold switches to build highly effective AND-gates. To characterize the components and their dynamic range, we used an Escherichia coli (E. coli) cell-free transcription-translation (TX-TL) system dispensed via nanoliter droplets. We analyzed a prototype gate in vitro as well as in silico, employing parametrized ordinary differential equations (ODEs), for which parameters were inferred via parallel tempering, a Markov chain Monte Carlo (MCMC) method. On the basis of this analysis, we created nine additional AND-gates and tested them in vitro. The functionality of the gates was found to be highly dependent on the concentration of the activating RNA for either the STAR or the toehold switch. All gates were successfully implemented in vivo, offering a dynamic range comparable to the level of protein circuits. This study shows the potential of a rapid prototyping approach for RNA circuit design, using cell-free systems in combination with a model prediction.
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Affiliation(s)
- François-Xavier Lehr
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Maleen Hanst
- Department of Electrical Engineering, Technische Universität Darmstadt, 64283 Darmstadt, Germany
| | - Marc Vogel
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Jennifer Kremer
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - H. Ulrich Göringer
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Heinz Koeppl
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
- Department of Electrical Engineering, Technische Universität Darmstadt, 64283 Darmstadt, Germany
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23
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Daube D, Vogel M, Suess B, Corzilius B. Dynamic nuclear polarization on a hybridized hammerhead ribozyme: An explorative study of RNA folding and direct DNP with a paramagnetic metal ion cofactor. Solid State Nucl Magn Reson 2019; 101:21-30. [PMID: 31078101 DOI: 10.1016/j.ssnmr.2019.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 06/09/2023]
Abstract
While uniform isotope labeling of ribonucleic acids (RNA) can simply and efficiently be achieved by in-vitro transcription, the specific introduction of nucleotides in larger constructs is non-trivial and often ineffective. Here, we demonstrate how a medium-sized (67-mer), biocatalytically relevant RNA (hammerhead ribozyme, HHRz) can be formed by spontaneous hybridization of two differently isotope-labeled strands, each individually synthesized by in-vitro transcription. This allows on the one hand for a significant reduction in the number of isotope-labeled nucleotides and thus spectral overlap particularly under magic-angle spinning (MAS) dynamic nuclear polarization (DNP) NMR conditions, on the other hand for orthogonal 13C/15N-labeling of complementary strands and thus for specific investigation of structurally or functionally relevant inter-strand and/or inter-stem contacts. By this method, we are able to confirm a non-canonical interaction due to single-site resolution and unique spectral assignments by two-dimensional 13C-13C (PDSD) as well as 15N-13C (TEDOR) correlation spectroscopy under "conventional" DNP enhancement. This contact is indicative of the ribozyme's functional conformation, and is present in frozen solution irrespective of the presence or absence of a Mg2+ co-factor. Finally, we use different isotope-labeling schemes in order to investigate the distance dependence of paramagnetic interactions and direct metal-ion DNP if the diamagnetic Mg2+ is substituted by paramagnetic Mn2+.
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Affiliation(s)
- Diane Daube
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt am Main, Germany
| | - Marc Vogel
- Fachbereich Biologie, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Fachbereich Biologie, Technische Universität Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | - Björn Corzilius
- Institute of Physical and Theoretical Chemistry, Institute of Biophysical Chemistry, and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt am Main, Germany; Institut für Chemie, Universität Rostock, Albert-Einstein-Str. 3a, 18059 Rostock, Germany; Department LL&M, Universität Rostock, Albert-Einstein-Str. 25, 18059 Rostock, Germany.
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24
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Lotz TS, Halbritter T, Kaiser C, Rudolph MM, Kraus L, Groher F, Steinwand S, Wachtveitl J, Heckel A, Suess B. A light-responsive RNA aptamer for an azobenzene derivative. Nucleic Acids Res 2019; 47:2029-2040. [PMID: 30517682 PMCID: PMC6393235 DOI: 10.1093/nar/gky1225] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 12/20/2022] Open
Abstract
Regulation of complex biological networks has proven to be a key bottleneck in synthetic biology. Interactions between the structurally flexible RNA and various other molecules in the form of riboswitches have shown a high-regulation specificity and efficiency and synthetic riboswitches have filled the toolbox of devices in many synthetic biology applications. Here we report the development of a novel, small molecule binding RNA aptamer, whose binding is dependent on light-induced change of conformation of its small molecule ligand. As ligand we chose an azobenzene because of its reliable photoswitchability and modified it with chloramphenicol for a better interaction with RNA. The synthesis of the ligand 'azoCm' was followed by extensive biophysical analysis regarding its stability and photoswitchability. RNA aptamers were identified after several cycles of in vitro selection and then studied regarding their binding specificity and affinity toward the ligand. We show the successful development of an RNA aptamer that selectively binds to only the trans photoisomer of azoCm with a KD of 545 nM. As the aptamer cannot bind to the irradiated ligand (λ = 365 nm), a light-selective RNA binding system is provided. Further studies may now result in the engineering of a reliable, light-responsible riboswitch.
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Affiliation(s)
- Thea S Lotz
- Technische Universität Darmstadt, Department of Biology, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Thomas Halbritter
- Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 9, 60438 Frankfurt (M), Germany
| | - Christoph Kaiser
- Goethe-University Frankfurt, Institute for Physical and Theoretical Chemistry, Max-von-Laue-Strasse 7, 60438 Frankfurt (M), Germany
| | - Martin M Rudolph
- Technische Universität Darmstadt, Department of Biology, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Leon Kraus
- Technische Universität Darmstadt, Department of Biology, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Florian Groher
- Technische Universität Darmstadt, Department of Biology, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Sabrina Steinwand
- Goethe-University Frankfurt, Institute for Physical and Theoretical Chemistry, Max-von-Laue-Strasse 7, 60438 Frankfurt (M), Germany
| | - Josef Wachtveitl
- Goethe-University Frankfurt, Institute for Physical and Theoretical Chemistry, Max-von-Laue-Strasse 7, 60438 Frankfurt (M), Germany
| | - Alexander Heckel
- Goethe-University Frankfurt, Institute for Organic Chemistry and Chemical Biology, Max-von-Laue-Strasse 9, 60438 Frankfurt (M), Germany
| | - Beatrix Suess
- Technische Universität Darmstadt, Department of Biology, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
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25
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Vogel M, Weigand JE, Kluge B, Grez M, Suess B. A small, portable RNA device for the control of exon skipping in mammalian cells. Nucleic Acids Res 2019; 46:e48. [PMID: 29420816 PMCID: PMC5934650 DOI: 10.1093/nar/gky062] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 01/29/2018] [Indexed: 12/17/2022] Open
Abstract
Splicing is an essential and highly regulated process in mammalian cells. We developed a synthetic riboswitch that efficiently controls alternative splicing of a cassette exon in response to the small molecule ligand tetracycline. The riboswitch was designed to control the accessibility of the 3' splice site by placing the latter inside the closing stem of a conformationally controlled tetracycline aptamer. In the presence of tetracycline, the cassette exon is skipped, whereas it is included in the ligand's absence. The design allows for an easy, context-independent integration of the regulatory device into any gene of interest. Portability of the device was shown through its functionality in four different systems: a synthetic minigene, a reporter gene and two endogenous genes. Furthermore, riboswitch functionality to control cellular signaling cascades was demonstrated by using it to specifically induce cell death through the conditionally controlled expression of CD20, which is a target in cancer therapy.
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Affiliation(s)
- Marc Vogel
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Julia E Weigand
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Britta Kluge
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Manuel Grez
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt/M, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
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26
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Abstract
Over the last years, many microRNAs (miRNAs) have been identified that regulate the formation of bioactive lipid mediators such as prostanoids and leukotrienes. Many of these miRNAs are involved in complex regulatory circuits necessary for the fine-tuning of biological functions including inflammatory processes or cell growth. A better understanding of these networks will contribute to the development of novel therapeutic strategies for the treatment of inflammatory diseases and cancer. In this review, we provide an overview of the current knowledge of miRNA regulation in eicosanoid pathways with special focus on novel miRNA functions and regulatory circuits of leukotriene and prostaglandin biosynthesis.
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Affiliation(s)
- Meike J Saul
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Anne C Emmerich
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany.,Institute of Pharmaceutical Chemistry, Goethe Universität Frankfurt, Frankfurt, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry, Goethe Universität Frankfurt, Frankfurt, Germany
| | - Beatrix Suess
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
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27
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Hetzke T, Bowen AM, Vogel M, Gauger M, Suess B, Prisner TF. Binding of tetracycline to its aptamer determined by 2D-correlated Mn 2+ hyperfine spectroscopy. J Magn Reson 2019; 303:105-114. [PMID: 31039520 DOI: 10.1016/j.jmr.2019.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 03/13/2019] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 06/09/2023]
Abstract
The tetracycline-binding RNA aptamer (TC-aptamer) binds its cognate ligand the antibiotic tetracycline (TC) via a Mg2+ or Mn2+ ion with high affinity at high divalent metal ion concentrations (KD=800pM, ⩾10 mM). These concentrations lie above the physiological divalent metal ion concentration of ca. 1 mM and it is known from literature, that the binding affinity decreases upon decreasing the divalent metal ion concentration. This work uses a Mn2+ concentration of 1 mM and 1D-hyperfine experiments reveal two pronounced 31P couplings from the RNA besides the 13C signal of 13C-labeled TC. From these 1D-hyperfine data alone, however, no conclusions can be drawn on the binding of TC. Either TC may bind via Mn2+ to the aptamer or TC may form a free Mn-TC complex and some Mn2+ also binds to the aptamer. In this work, we show using 2D-correlated hyperfine spectroscopy at Q-band frequencies (34 GHz), that the 13C and 31P signals can be correlated; thus arising from a single species. We use THYCOS (triple hyperfine correlation spectroscopy) and 2D ELDOR-detected NMR (2D electron electron double resonance detected NMR) for this purpose showing that they are suitable techniques to correlate two different nuclear spin species (13C and 31P) on two different molecules (RNA and TC) to the same electron spin (Mn2+). Out of the two observed 31P-hyperfine couplings, only one shows a clear correlation to 13C. Although THYCOS and 2D EDNMR yield identical results, 2D EDNMR is far more sensitive. THYCOS spectra needed a time factor of ×20 in comparison to 2D EDNMR to achieve a comparable signal-to-noise.
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Affiliation(s)
- Thilo Hetzke
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Alice M Bowen
- Center for Advanced Electron Spin Resonance (CAESR), Inorganic Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Marc Vogel
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Maximilian Gauger
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany.
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28
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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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29
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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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30
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Aladin V, Vogel M, Binder R, Burghardt I, Suess B, Corzilius B. Complex Formation of the Tetracycline‐Binding Aptamer Investigated by Specific Cross‐Relaxation under DNP. Angew Chem Int Ed Engl 2019; 58:4863-4868. [DOI: 10.1002/anie.201811941] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/18/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Victoria Aladin
- Institute of Physical and Theoretical ChemistryInstitute of Biophysical ChemistryCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University Frankfurt Max-von-Laue-Str. 7–9 60438 Frankfurt am Main Germany
| | - Marc Vogel
- Fachbereich BiologieTechnische Universität Darmstadt Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Robert Binder
- Institute of Physical and Theoretical ChemistryGoethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Irene Burghardt
- Institute of Physical and Theoretical ChemistryGoethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Beatrix Suess
- Fachbereich BiologieTechnische Universität Darmstadt Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Björn Corzilius
- Institute of Physical and Theoretical ChemistryInstitute of Biophysical ChemistryCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University Frankfurt Max-von-Laue-Str. 7–9 60438 Frankfurt am Main Germany
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31
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Aladin V, Vogel M, Binder R, Burghardt I, Suess B, Corzilius B. Complex Formation of the Tetracycline‐Binding Aptamer Investigated by Specific Cross‐Relaxation under DNP. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201811941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Victoria Aladin
- Institute of Physical and Theoretical ChemistryInstitute of Biophysical ChemistryCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University Frankfurt Max-von-Laue-Str. 7–9 60438 Frankfurt am Main Germany
| | - Marc Vogel
- Fachbereich BiologieTechnische Universität Darmstadt Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Robert Binder
- Institute of Physical and Theoretical ChemistryGoethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Irene Burghardt
- Institute of Physical and Theoretical ChemistryGoethe University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt am Main Germany
| | - Beatrix Suess
- Fachbereich BiologieTechnische Universität Darmstadt Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Björn Corzilius
- Institute of Physical and Theoretical ChemistryInstitute of Biophysical ChemistryCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University Frankfurt Max-von-Laue-Str. 7–9 60438 Frankfurt am Main Germany
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32
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Saul MJ, Baumann I, Bruno A, Emmerich AC, Wellstein J, Ottinger SM, Contursi A, Dovizio M, Donnini S, Tacconelli S, Raouf J, Idborg H, Stein S, Korotkova M, Savai R, Terzuoli E, Sala G, Seeger W, Jakobsson PJ, Patrignani P, Suess B, Steinhilber D. miR-574-5p as RNA decoy for CUGBP1 stimulates human lung tumor growth by mPGES-1 induction. FASEB J 2019; 33:6933-6947. [PMID: 30922080 DOI: 10.1096/fj.201802547r] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
MicroRNAs (miRs) are important posttranscriptional regulators of gene expression. Besides their well-characterized inhibitory effects on mRNA stability and translation, miRs can also activate gene expression. In this study, we identified a novel noncanonical function of miR-574-5p. We found that miR-574-5p acts as an RNA decoy to CUG RNA-binding protein 1 (CUGBP1) and antagonizes its function. MiR-574-5p induces microsomal prostaglandin E synthase-1 (mPGES-1) expression by preventing CUGBP1 binding to its 3'UTR, leading to an enhanced alternative splicing and generation of an mPGES-1 3'UTR isoform, increased mPGES-1 protein expression, PGE2 formation, and tumor growth in vivo. miR-574-5p-induced tumor growth in mice could be completely inhibited with the mPGES-1 inhibitor CIII. Moreover, miR-574-5p is induced by IL-1β and is strongly overexpressed in human nonsmall cell lung cancer where high mPGES-1 expression correlates with a low survival rate. The discovered function of miR-574-5p as a CUGBP1 decoy opens up new therapeutic opportunities. It might serve as a stratification marker to select lung tumor patients who respond to the pharmacological inhibition of PGE2 formation.-Saul, M. J., Baumann, I., Bruno, A., Emmerich, A. C., Wellstein, J., Ottinger, S. M., Contursi, A., Dovizio, M., Donnini, S., Tacconelli, S., Raouf, J., Idborg, H., Stein, S., Korotkova, M., Savai, R., Terzuoli, E., Sala, G., Seeger, W., Jakobsson, P.-J., Patrignani, P., Suess, B., Steinhilber, D. miR-574-5p as RNA decoy for CUGBP1 stimulates human lung tumor growth by mPGES-1 induction.
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Affiliation(s)
- Meike J Saul
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany.,Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Isabell Baumann
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany.,Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Annalisa Bruno
- Department of Neuroscience, Imaging, and Clinical Science, Section of Cardiovascular and Pharmacological Sciences, School of Medicine, G. d'Annunzio University, Chieti, Italy.,Centro Scienze dell' Invecchiamento e Medicina Traslazionale (CeSI-MeT), G. d'Annunzio University, Chieti, Italy
| | - Anne C Emmerich
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany.,Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Julia Wellstein
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany.,Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Sarah M Ottinger
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Annalisa Contursi
- Department of Neuroscience, Imaging, and Clinical Science, Section of Cardiovascular and Pharmacological Sciences, School of Medicine, G. d'Annunzio University, Chieti, Italy.,Centro Scienze dell' Invecchiamento e Medicina Traslazionale (CeSI-MeT), G. d'Annunzio University, Chieti, Italy
| | - Melania Dovizio
- Department of Neuroscience, Imaging, and Clinical Science, Section of Cardiovascular and Pharmacological Sciences, School of Medicine, G. d'Annunzio University, Chieti, Italy.,Centro Scienze dell' Invecchiamento e Medicina Traslazionale (CeSI-MeT), G. d'Annunzio University, Chieti, Italy
| | - Sandra Donnini
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Stefania Tacconelli
- Department of Neuroscience, Imaging, and Clinical Science, Section of Cardiovascular and Pharmacological Sciences, School of Medicine, G. d'Annunzio University, Chieti, Italy.,Centro Scienze dell' Invecchiamento e Medicina Traslazionale (CeSI-MeT), G. d'Annunzio University, Chieti, Italy
| | - Joan Raouf
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Helena Idborg
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | - Marina Korotkova
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Rajkumar Savai
- Department of Lung Development and Remodeling, German Center for Lung Research (DZL), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Erika Terzuoli
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Gianluca Sala
- Centro Scienze dell' Invecchiamento e Medicina Traslazionale (CeSI-MeT), G. d'Annunzio University, Chieti, Italy.,Department of Medical and Oral Sciences and Biotechnologies, G. d'Annunzio University, Chieti, Italy; and
| | - Werner Seeger
- Department of Lung Development and Remodeling, German Center for Lung Research (DZL), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,Department of Internal Medicine II, Marburg Lung Center (UGMLC), University of Giessen, Giessen, Germany
| | - Per-Johan Jakobsson
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Paola Patrignani
- Department of Neuroscience, Imaging, and Clinical Science, Section of Cardiovascular and Pharmacological Sciences, School of Medicine, G. d'Annunzio University, Chieti, Italy.,Centro Scienze dell' Invecchiamento e Medicina Traslazionale (CeSI-MeT), G. d'Annunzio University, Chieti, Italy
| | - Beatrix Suess
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
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33
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Groher AC, Jager S, Schneider C, Groher F, Hamacher K, Suess B. Tuning the Performance of Synthetic Riboswitches using Machine Learning. ACS Synth Biol 2019; 8:34-44. [PMID: 30513199 DOI: 10.1021/acssynbio.8b00207] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Riboswitch development for clinical, technological, and synthetic biology applications constantly seeks to optimize regulatory behavior. Here, we present a machine learning approach to improve the regulation of a tetracycline (tc)-dependent riboswitch device composed of two individual tc aptamers. We developed a bioinformatics model that combines random forest analysis with a convolutional neural network to predict the switching behavior of such tandem riboswitches. We found that both biophysical parameters and the hydrogen bond pattern influence regulation. Our new design pipeline led to significant improvement of the tc riboswitch device with a dynamic range extension from 8.5 to 40-fold. We are confident that our novel method not only results in an excellent tc-dependent riboswitch device but further holds great promise and potential for the optimization of other riboswitches.
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34
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Jaeger J, Groher F, Stamm J, Spiehl D, Braun J, Dörsam E, Suess B. Characterization and Inkjet Printing of an RNA Aptamer for Paper-Based Biosensing of Ciprofloxacin. Biosensors (Basel) 2019; 9:E7. [PMID: 30609709 PMCID: PMC6468496 DOI: 10.3390/bios9010007] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 12/24/2018] [Accepted: 12/26/2018] [Indexed: 12/25/2022]
Abstract
The excessive use of antibiotics in food-producing animals causes a steady rise of multiple antibiotic resistance in foodborne bacteria. Next to sulfonamides, the most common antibiotics groups are fluoroquinolones, aminoglycosides, and ß-lactams. Therefore, there is a need for a quick, efficient, and low-cost detection procedure for antibiotics. In this study, we propose an inkjet-printed aptamer-based biosensor developed for the detection of the fluoroquinolone ciprofloxacin. Due to their extraordinary high affinity and specificity, aptamers are already widely used in various applications. Here we present a ciprofloxacin-binding RNA aptamer developed by systematic evolution of ligands by exponential enrichment (SELEX). We characterized the secondary structure of the aptamer and determined the KD to 36 nM that allow detection of antibiotic contamination in a relevant range. We demonstrate that RNA aptamers can be inkjet-printed, dried, and resolved while keeping their functionality consistently intact. With this proof of concept, we are paving the way for a potential range of additional aptamer-based, printable biosensors.
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Affiliation(s)
- Jeannine Jaeger
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany.
| | - Florian Groher
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany.
| | - Jacqueline Stamm
- Institute for Printing Science and Technology, Technische Universität Darmstadt, 64289 Darmstadt, Germany.
| | - Dieter Spiehl
- Institute for Printing Science and Technology, Technische Universität Darmstadt, 64289 Darmstadt, Germany.
| | - Johannes Braun
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany.
| | - Edgar Dörsam
- Institute for Printing Science and Technology, Technische Universität Darmstadt, 64289 Darmstadt, Germany.
| | - Beatrix Suess
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany.
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35
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Hetzke T, Vogel M, Gophane DB, Weigand JE, Suess B, Sigurdsson ST, Prisner TF. Influence of Mg 2+ on the conformational flexibility of a tetracycline aptamer. RNA 2019; 25:158-167. [PMID: 30337459 PMCID: PMC6298572 DOI: 10.1261/rna.068684.118] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 09/06/2018] [Accepted: 10/16/2018] [Indexed: 05/06/2023]
Abstract
The tetracycline-binding RNA aptamer (TC-aptamer) is a synthetic riboswitch that binds the antibiotic tetracycline (TC) with exceptionally high affinity. Although a crystal structure exists of the TC-bound state, little is known about the conformational dynamics and changes upon ligand binding. In this study, pulsed electron paramagnetic resonance techniques for measuring distances (PELDOR) in combination with rigid nitroxide spin labels (Çm spin label) were used to investigate the conformational flexibility of the TC-aptamer in the presence and absence of TC at different Mg2+ concentrations. TC was found to be the essential factor for stabilizing the tertiary structure at intermediate Mg2+ concentrations. At higher Mg2+ concentrations, Mg2+ alone is sufficient to stabilize the tertiary structure. In addition, the orientation of the two spin-labeled RNA helices with respect to each other was analyzed with orientation-selective PELDOR and compared to the crystal structure. These results demonstrate for the first time the unique value of the Çm spin label in combination with PELDOR to provide information about conformational flexibilities and orientations of secondary structure elements of biologically relevant RNAs.
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Affiliation(s)
- Thilo Hetzke
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Marc Vogel
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Dnyaneshwar B Gophane
- Department of Chemistry, Science Institute, University of Iceland, 101 Reykjavik, Iceland
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, 101 Reykjavik, Iceland
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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36
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Abstract
Inhibitory aptamers against a protein are promising as antagonistic reagents and repressive genetic components. Typically, improvement of such aptamers is achieved by acquiring higher binding affinity. Here, we report an alternative mechanism for the improvement of aptamer activity. Recently, we reported a transcriptional activator based on an inhibitory RNA aptamer against lambda cI repressor. We improved the aptamer through in vitro selection (SELEX) from a randomly mutagenized aptamer pool, followed by in vivo screening and truncation. Biochemical analyses indicated that the activity improvement was achieved by alteration of the complex formation stoichiometry, rather than by higher affinity or expression. Our results suggest an alternative strategy for improving aptamer activity.
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Affiliation(s)
- Shoji Ohuchi
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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Suess B, Kemmerer K, Weigand JE. Splicing and Alternative Splicing Impact on Gene Design. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Beatrix Suess
- Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Katrin Kemmerer
- Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Julia E. Weigand
- Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
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Groher F, Bofill-Bosch C, Schneider C, Braun J, Jager S, Geißler K, Hamacher K, Suess B. Riboswitching with ciprofloxacin-development and characterization of a novel RNA regulator. Nucleic Acids Res 2018; 46:2121-2132. [PMID: 29346617 PMCID: PMC5829644 DOI: 10.1093/nar/gkx1319] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [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: 11/03/2017] [Revised: 12/22/2017] [Accepted: 12/28/2017] [Indexed: 11/24/2022] Open
Abstract
RNA molecules play important and diverse regulatory roles in the cell. Inspired by this natural versatility, RNA devices are increasingly important for many synthetic biology applications, e.g. optimizing engineered metabolic pathways, gene therapeutics or building up complex logical units. A major advantage of RNA is the possibility of de novo design of RNA-based sensing domains via an in vitro selection process (SELEX). Here, we describe development of a novel ciprofloxacin-responsive riboswitch by in vitro selection and next-generation sequencing-guided cellular screening. The riboswitch recognizes the small molecule drug ciprofloxacin with a KD in the low nanomolar range and adopts a pseudoknot fold stabilized by ligand binding. It efficiently interferes with gene expression both in lower and higher eukaryotes. By controlling an auxotrophy marker and a resistance gene, respectively, we demonstrate efficient, scalable and programmable control of cellular survival in yeast. The applied strategy for the development of the ciprofloxacin riboswitch is easily transferrable to any small molecule target of choice and will thus broaden the spectrum of RNA regulators considerably.
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Affiliation(s)
- Florian Groher
- Synthetic Genetic Circuits, Dept. of Biology, TU Darmstadt, Darmstadt, Germany
| | | | | | - Johannes Braun
- Synthetic Genetic Circuits, Dept. of Biology, TU Darmstadt, Darmstadt, Germany
| | - Sven Jager
- Computational Biology and Simulation, Dept. of Biology, TU Darmstadt, Darmstadt, Germany
| | - Katharina Geißler
- Synthetic Genetic Circuits, Dept. of Biology, TU Darmstadt, Darmstadt, Germany
| | - Kay Hamacher
- Computational Biology and Simulation, Dept. of Biology, TU Darmstadt, Darmstadt, Germany
- Dept. of Physics, Dept. of Computer Science, TU Darmstadt, Darmstadt, Germany
| | - Beatrix Suess
- Synthetic Genetic Circuits, Dept. of Biology, TU Darmstadt, Darmstadt, Germany
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Atanasov J, Groher F, Weigand JE, Suess B. Design and implementation of a synthetic pre-miR switch for controlling miRNA biogenesis in mammals. Nucleic Acids Res 2018; 45:e181. [PMID: 29036355 PMCID: PMC5727447 DOI: 10.1093/nar/gkx858] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 09/20/2017] [Indexed: 01/07/2023] Open
Abstract
Synthetic RNA-based systems have increasingly been used for the regulation of eukaryotic gene expression. Due to their structural properties, riboregulators provide a convenient basis for the development of ligand-dependent controllable systems. Here, we demonstrate reversible conditional control of miRNA biogenesis with an aptamer domain as a sensing unit connected to a natural miRNA precursor for the first time. For the design of the pre-miR switch, we replaced the natural terminal loop with the TetR aptamer. Thus, the TetR aptamer was positioned close to the Dicer cleavage sites, which allowed sterical control over pre-miR processing by Dicer. Our design proved to be highly versatile, allowing us to regulate the biogenesis of three structurally different miRNAs: miR-126, -34a and -199a. Dicer cleavage was inhibited up to 143-fold via co-expression of the TetR protein, yet could be completely restored upon addition of doxycycline. Moreover, we showed the functionality of the pre-miR switches for gene regulation through the interaction of the respective miRNA with its specific target sequence. Our designed device is capable of robust and reversible control of miRNA abundance. Thus, we offer a novel investigational tool for functional miRNA analysis.
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Affiliation(s)
- Janina Atanasov
- Department of Biology, Technical University Darmstadt, Darmstadt 64287, Germany
| | - Florian Groher
- Department of Biology, Technical University Darmstadt, Darmstadt 64287, Germany
| | - Julia E Weigand
- Department of Biology, Technical University Darmstadt, Darmstadt 64287, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Darmstadt 64287, Germany
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Saul MJ, Groher F, Hegewald AB, Müller-McNicoll M, Marschalek R, Suess B, Steinhilber D. TGFβ/SMAD signalling modulates MLL and MLL-AF4 mediated 5-lipoxygenase promoter activation. Prostaglandins Other Lipid Mediat 2017; 133:60-67. [DOI: 10.1016/j.prostaglandins.2017.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 06/28/2017] [Accepted: 07/31/2017] [Indexed: 01/11/2023]
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Kim YB, Wacker A, Laer KV, Rogov VV, Suess B, Schwalbe H. Ligand binding to 2΄-deoxyguanosine sensing riboswitch in metabolic context. Nucleic Acids Res 2017; 45:5375-5386. [PMID: 28115631 PMCID: PMC5435998 DOI: 10.1093/nar/gkx016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/04/2017] [Indexed: 12/30/2022] Open
Abstract
The mfl-riboswitch is a transcriptional off-switch, which down-regulates expression of subunit β of ribonucleotide reductase in Mesoplasma florum upon 2΄-deoxyguanosine binding. We characterized binding of 2΄-deoxyguanosine to the mfl-aptamer domain (WT aptamer) and a sequence-stabilized aptamer (MT aptamer) under in vitro and ‘in-cell-like’ conditions by isothermal titration calorimetry (ITC) and nuclear magnetic resonance (NMR) spectroscopy. ‘In-cell-like’ environment was simulated by Bacillus subtilis cell extract, in which both aptamers remained sufficiently stable to detect the resonances of structural elements and ligand binding in 2D NMR experiments. Under ‘in-cell-like’-environment, (i) the WT aptamer bound the endogenous metabolite guanosine and (ii) 2΄-deoxyguanosine efficiently displaced guanosine from the WT aptamer. In contrast, MT aptamer exhibited moderate binding to 2΄-deoxyguanosine and weak binding to guanosine. NMR experiments indicated that binding of guanosine was not limited to the aptamer domain of the riboswitch but also the full-length mfl-riboswitch bound guanosine, impacting on the regulation efficiency of the riboswitch and hinting that, in addition to 2΄-deoxyguanosine, guanosine plays a role in riboswitch function in vivo. Reporter gene assays in B. subtilis demonstrated the regulation capacity of the WT aptamer, whereas the MT aptamer with lower affinity to 2΄-deoxyguanosine was not able to regulate gene expression.
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Affiliation(s)
- Yong-Boum Kim
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, D-60438 Frankfurt/Main, Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, D-60438 Frankfurt/Main, Germany
| | - Karl von Laer
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Vladimir V Rogov
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 7, D-60438 Frankfurt/Main, Germany
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Schneider C, Bronstein L, Diemer J, Koeppl H, Suess B. ROC'n'Ribo: Characterizing a Riboswitching Expression System by Modeling Single-Cell Data. ACS Synth Biol 2017; 6:1211-1224. [PMID: 28591515 DOI: 10.1021/acssynbio.6b00322] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
RNA-engineered systems offer simple and versatile control over gene expression in many organisms. In particular, the design and implementation of riboswitches presents a unique opportunity to manipulate any reporter device in cis, executing tight temporal and spatial control at low metabolic costs. Assembled to higher order genetic circuits, such riboswitch-regulated devices may efficiently process logical operations. Here, we propose a hierarchical stochastic modeling approach to characterize an in silico repressor gate based on neomycin- and tetracycline-sensitive riboswitches. The model was calibrated on rich, transient in vivo single-cell data to account for cell-to-cell variability. To capture the effect of this variability on gate performance we employed the well-known ROC-analysis and derived a novel performance indicator for logic gates. Introduction of such a performance measure is necessary, since we aimed to assess the correct functionality of the gate at the single-cell level-a prerequisite for its further adaption to a genetic circuitry. Our results may be applied to other genetic devices to analyze their efficiency and ensure their correct performance in the light of cell-to-cell variability.
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Affiliation(s)
- Christopher Schneider
- Department
of Biology, Synthetic Genetic Circuits, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Leo Bronstein
- Department
of Electrical Engineering and Information Technology, Bioinspired
Communications, TU Darmstadt, Rundeturmstrasse 12, 64283 Darmstadt, Germany
| | - Jascha Diemer
- Department
of Electrical Engineering and Information Technology, Bioinspired
Communications, TU Darmstadt, Rundeturmstrasse 12, 64283 Darmstadt, Germany
| | - Heinz Koeppl
- Department
of Electrical Engineering and Information Technology, Bioinspired
Communications, TU Darmstadt, Rundeturmstrasse 12, 64283 Darmstadt, Germany
| | - Beatrix Suess
- Department
of Biology, Synthetic Genetic Circuits, TU Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
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Steinert H, Sochor F, Wacker A, Buck J, Helmling C, Hiller F, Keyhani S, Noeske J, Grimm S, Rudolph MM, Keller H, Mooney RA, Landick R, Suess B, Fürtig B, Wöhnert J, Schwalbe H. Pausing guides RNA folding to populate transiently stable RNA structures for riboswitch-based transcription regulation. eLife 2017; 6. [PMID: 28541183 PMCID: PMC5459577 DOI: 10.7554/elife.21297] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 05/24/2017] [Indexed: 01/18/2023] Open
Abstract
In bacteria, the regulation of gene expression by cis-acting transcriptional riboswitches located in the 5'-untranslated regions of messenger RNA requires the temporal synchronization of RNA synthesis and ligand binding-dependent conformational refolding. Ligand binding to the aptamer domain of the riboswitch induces premature termination of the mRNA synthesis of ligand-associated genes due to the coupled formation of 3'-structural elements acting as terminators. To date, there has been no high resolution structural description of the concerted process of synthesis and ligand-induced restructuring of the regulatory RNA element. Here, we show that for the guanine-sensing xpt-pbuX riboswitch from Bacillus subtilis, the conformation of the full-length transcripts is static: it exclusively populates the functional off-state but cannot switch to the on-state, regardless of the presence or absence of ligand. We show that only the combined matching of transcription rates and ligand binding enables transcription intermediates to undergo ligand-dependent conformational refolding. DOI:http://dx.doi.org/10.7554/eLife.21297.001
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Affiliation(s)
- Hannah Steinert
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Florian Sochor
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Anna Wacker
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Janina Buck
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Christina Helmling
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Fabian Hiller
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Sara Keyhani
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Jonas Noeske
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Steffen Grimm
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Martin M Rudolph
- Department of Biology, Technical University Darmstadt, Darmstadt, Germany
| | - Heiko Keller
- Center for Biomolecular Magnetic Resonance, Institute of Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Rachel Anne Mooney
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Darmstadt, Germany
| | - Boris Fürtig
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Jens Wöhnert
- Center for Biomolecular Magnetic Resonance, Institute of Molecular Biosciences, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
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44
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Ohuchi S, Suess B. An inhibitory RNA aptamer against the lambda cI repressor shows transcriptional activator activity in vivo. FEBS Lett 2017; 591:1429-1436. [PMID: 28407231 DOI: 10.1002/1873-3468.12653] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/14/2017] [Accepted: 04/08/2017] [Indexed: 01/03/2023]
Abstract
RNA aptamers are one of the promising components for constructing artificial genetic circuits. In this study, we developed a transcriptional activator based on an RNA aptamer against one of the most frequently applied repressor proteins, lambda phage cI. In vitro selection (Systematic Evolution of Ligands by EXponential enrichment) and following in vivo screening identified an RNA aptamer with the intended transcriptional activator activity from an RNA pool containing a 40-nucleotide long random region. Quantitative analysis showed a 35-fold elevation of reporter expression upon aptamer expression. These results suggest that the diversity of artificial transcriptional activators can be extended by employing RNA aptamers against repressor proteins to broaden the parts for constructing genetic circuits.
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Affiliation(s)
- Shoji Ohuchi
- Department of Biology, Technische Universität Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technische Universität Darmstadt, Germany
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Groher F, Suess B. In vitro selection of antibiotic-binding aptamers. Methods 2016; 106:42-50. [PMID: 27223401 DOI: 10.1016/j.ymeth.2016.05.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/10/2016] [Accepted: 05/15/2016] [Indexed: 01/06/2023] Open
Abstract
Despite its wide applicability the selection of small molecule-binding RNA aptamers with high affinity binding and specificity is still challenging. We will present here a protocol which allows the in vitro selection of antibiotic-binding aptamers which turned out to be important building blocks for the design process of synthetic riboswitches. The presented methods will be compared with alternative in vitro selection protocols. A detailed note section will point out useful tips and pitfalls.
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Affiliation(s)
- Florian Groher
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany.
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Affiliation(s)
- Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark.
| | - Beatrix Suess
- Technische Universität Darmstadt, 64287 Darmstadt, Germany
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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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49
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Schneider C, Suess B. Identification of RNA aptamers with riboswitching properties. Methods 2015; 97:44-50. [PMID: 26672481 DOI: 10.1016/j.ymeth.2015.12.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/07/2015] [Accepted: 12/01/2015] [Indexed: 12/21/2022] Open
Abstract
During the past years customized gene network design has become of tremendous interest among various disciplines in life science. The identification of artificial genetic elements sensitive to internal or external stimuli constitutes the foundation for the design and realization of conditional gene expression systems. Typically, strategies involving selection or screening steps are employed alongside approaches focusing on rational design to select for the desired functionality of a given element. Here we present a fluorescence-based in vivo screening approach that combines an initial in vitro selection with subsequent extensive screening steps and a final rational design to identify RNA based regulators in baker's yeast. These artificial RNA regulators, termed synthetic riboswitches, are derived from RNA aptamers. Our method allows for the separation of aptamers featuring the potential to be transformed into a riboswitch from those inherently unable to confer control over gene expression. The system may be applied to virtually all existing aptamer-ligand pairs and as such presents a powerful means to enhance the setup of switchable genetic circuits.
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Affiliation(s)
- Christopher Schneider
- Department of Biology, Technical University Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany.
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50
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Berens C, Groher F, Suess B. RNA aptamers as genetic control devices: the potential of riboswitches as synthetic elements for regulating gene expression. Biotechnol J 2015; 10:246-57. [PMID: 25676052 DOI: 10.1002/biot.201300498] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/23/2014] [Accepted: 01/15/2015] [Indexed: 12/16/2022]
Abstract
RNA utilizes many different mechanisms to control gene expression. Among the regulatory elements that respond to external stimuli, riboswitches are a prominent and elegant example. They consist solely of RNA and couple binding of a small molecule ligand to the so-called "aptamer domain" with a conformational change in the downstream "expression platform" which then determines system output. The modular organization of riboswitches and the relative ease with which ligand-binding RNA aptamers can be selected in vitro against almost any molecule have led to the rapid and widespread adoption of engineered riboswitches as artificial genetic control devices in biotechnology and synthetic biology over the past decade. This review highlights proof-of-principle applications to demonstrate the versatility and robustness of engineered riboswitches in regulating gene expression in pro- and eukaryotes. It then focuses on strategies and parameters to identify aptamers that can be integrated into synthetic riboswitches that are functional in vivo, before finishing with a reflection on how to improve the regulatory properties of engineered riboswitches, so that we can not only further expand riboswitch applicability, but also finally fully exploit their potential as control elements in regulating gene expression.
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Affiliation(s)
- Christian Berens
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Jena, Germany
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