1
|
Eladl O, Yamaoki Y, Kondo K, Nagata T, Katahira M. Detection of interaction between an RNA aptamer and its target compound in living human cells using 2D in-cell NMR. Chem Commun (Camb) 2022; 59:102-105. [PMID: 36475447 DOI: 10.1039/d2cc05576g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We introduced an isotopically labeled RNA aptamer for HIV-1 Tat prepared by E. coli transcription into HeLa cells. We successfully recorded the first heteronuclear 2D in-cell NMR spectra, which makes it possible to study the interaction of the RNA aptamer with argininamide in living human cells with higher resolution.
Collapse
Affiliation(s)
- Omar Eladl
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan. .,Graduate School of Energy Science, Kyoto University, Yoshida-hommachi, Sakyo-ku, Kyoto 606-8501, Japan.,Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Yudai Yamaoki
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan. .,Graduate School of Energy Science, Kyoto University, Yoshida-hommachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Keiko Kondo
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
| | - Takashi Nagata
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan. .,Graduate School of Energy Science, Kyoto University, Yoshida-hommachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan. .,Graduate School of Energy Science, Kyoto University, Yoshida-hommachi, Sakyo-ku, Kyoto 606-8501, Japan
| |
Collapse
|
2
|
Ali GK, Omer KM. Nanozyme and Stimulated Fluorescent Cu-Based Metal-Organic Frameworks (Cu-MOFs) Functionalized with Engineered Aptamers as a Molecular Recognition Element for Thrombin Detection in the Plasma of COVID-19 Patients. ACS OMEGA 2022; 7:36804-36810. [PMID: 36278053 PMCID: PMC9583328 DOI: 10.1021/acsomega.2c05232] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/23/2022] [Indexed: 05/19/2023]
Abstract
An essential tool in the management and control of the COVID-19 pandemic is the development of a fast, selective, sensitive, and inexpensive COVID-19 biomarkers detection method. Herein, an ultrasensitive and label-free biosensing strategy was described for the colorimetric and fluorimetric detection of thrombin. A dual-mode aptasensing method based on integrating engineered ssDNA with a stimulated fluorescent enzyme-mimetic copper-based metal-organic framework (Cu-MOF) as a molecular recognition element for thrombin was investigated. Cu-MOFs displayed stimulated fluorescence and enzyme-mimetic peroxidase activities that oxidize the chromogenic colorless substance TMB to blue-colored oxTMB. The thrombin-based aptamer (ssDNA) can be immobilized on the Cu-MOF surface to form a functionalized composite, ssDNA/MOF, and quench the stimulated fluorescence emission and the enzymatic activity of the Cu-MOF. Later, addition of thrombin recovers the fluorescence and enzymatic activity of the MOF. Thus, a turn-on colorimetry/fluorimetry aptasensing probe was designed for the detection of thrombin. Based on colorimetric assay, 350 pM was recorded as the lower limit of detection (LOD), while based on the fluorescence mode, 110 fM was recorded as the LOD (when S/N = 3). The label-free aptasensing probe was used successfully for the detection of thrombin in COVID-19 patients with satisfactory recoveries, 95-98%. Since the detection time of our aptasensor is relatively rapid (45 min) and due to the low-cost precursors and easy-to-operate characteristics, we believe that it has great potential to be used in point-of-care testing (POCT).
Collapse
Affiliation(s)
- Gona K. Ali
- Department
of Chemistry, College of Science, University
of Sulaimani, Slemani
City 46002, Kurdistan
Region, Iraq
| | - Khalid M. Omer
- Department
of Chemistry, College of Science, University
of Sulaimani, Slemani
City 46002, Kurdistan
Region, Iraq
- Center
for Biomedical Analysis, Department of Chemistry, College of Science, University of Sulaimani, Slemani City 46002, Kurdistan Region, Iraq
| |
Collapse
|
3
|
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] [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.
Collapse
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.
| |
Collapse
|
4
|
Verbič A, Praznik A, Jerala R. A guide to the design of synthetic gene networks in mammalian cells. FEBS J 2020; 288:5265-5288. [PMID: 33289352 DOI: 10.1111/febs.15652] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/06/2020] [Accepted: 11/01/2020] [Indexed: 12/22/2022]
Abstract
Synthetic biology aims to harness natural and synthetic biological parts and engineering them in new combinations and systems, producing novel therapies, diagnostics, bioproduction systems, and providing information on the mechanism of function of biological systems. Engineering cell function requires the rewiring or de novo construction of cell information processing networks. Using natural and synthetic signal processing elements, researchers have demonstrated a wide array of signal sensing, processing and propagation modules, using transcription, translation, or post-translational modification to program new function. The toolbox for synthetic network design is ever-advancing and has still ample room to grow. Here, we review the diversity of synthetic gene networks, types of building modules, techniques of regulation, and their applications.
Collapse
Affiliation(s)
- Anže Verbič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Arne Praznik
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| |
Collapse
|
5
|
Mc Cafferty S, De Temmerman J, Kitada T, Becraft JR, Weiss R, Irvine DJ, Devreese M, De Baere S, Combes F, Sanders NN. In Vivo Validation of a Reversible Small Molecule-Based Switch for Synthetic Self-Amplifying mRNA Regulation. Mol Ther 2020; 29:1164-1173. [PMID: 33186690 DOI: 10.1016/j.ymthe.2020.11.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/03/2020] [Accepted: 11/05/2020] [Indexed: 12/01/2022] Open
Abstract
Synthetic mRNA therapeutics have the potential to revolutionize healthcare, as they enable patients to produce therapeutic proteins inside their own bodies. However, convenient methods that allow external control over the timing and magnitude of protein production after in vivo delivery of synthetic mRNA are lacking. In this study, we validate the in vivo utility of a synthetic self-amplifying mRNA (RNA replicon) whose expression can be turned off using a genetic switch that responds to oral administration of trimethoprim (TMP), a US Food and Drug Administration (FDA)-approved small-molecule drug. After intramuscular electroporation, the engineered RNA replicon exhibited dose-dependent and reversible expression of its encoded protein upon TMP administration. The TMP serum level needed for maximal downregulation of protein translation was approximately 45-fold below that used in humans for therapeutic purposes. To demonstrate the therapeutic potential of the technology, we injected mice with a TMP-responsive RNA replicon encoding erythropoietin (EPO) and successfully controlled the timing and magnitude of EPO production as well as changes in hematocrit. This work demonstrates the feasibility of controlling mRNA kinetics in vivo, thereby broadly expanding the clinical versatility of mRNA therapeutics.
Collapse
Affiliation(s)
- Sean Mc Cafferty
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium
| | - Joyca De Temmerman
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium; Department of Pathology, Bacteriology and Poultry diseases, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | | | | | - Ron Weiss
- Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Darrell J Irvine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA; Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Mathias Devreese
- Laboratory of Pharmacology and Toxicology, Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Siegrid De Baere
- Laboratory of Pharmacology and Toxicology, Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Francis Combes
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium
| | - Niek N Sanders
- Laboratory of Gene Therapy, Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, 9000 Ghent, Belgium.
| |
Collapse
|
6
|
Chinnappan R, Al Faraj A, Abdel Rahman AM, Abu-Salah KM, Mouffouk F, Zourob M. Anti-VCAM-1 and Anti-IL4Rα Aptamer-Conjugated Super Paramagnetic Iron Oxide Nanoparticles for Enhanced Breast Cancer Diagnosis and Therapy. Molecules 2020; 25:E3437. [PMID: 32751068 PMCID: PMC7435411 DOI: 10.3390/molecules25153437] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 12/03/2022] Open
Abstract
The surface protein overexpressed on cancer cells can be used as biomarkers for early detection of specific diseases. Anti-VCAM-1 and anti-IL4Rα DNA aptamers specific to VCAM-1 and IL4Rα receptors that are overexpressed in 4T1 tumor-bearing mice could be used as potential biomarker for both diagnostic and therapeutic applications in cancer biology. Cell Viability and luciferase assay of 4T1-Luc2 cancer cells in the presence of anti-VCAM-1 ssDNA or anti-IL4Rα RNA aptamers was assessed by monitoring the changes in the absorbance and the fluorescence of Alamar blue dye. The aptamer-conjugated SPIO magnetic beads, used for the selective targeting to tumor sites, were monitored using noninvasive MRI and Bioluminescence imaging (BLI). Cell viability and luciferase assays showed that both anti-VCAM-1 and anti-IL4Rα aptamers favor the depletion of cancer cells and limit tumor progression. Microscopic analyses confirmed that the target specific aptamers significantly trigger tumor cell apoptosis and limit cancer cell growth in vitro. The intravenous injection of SPIO nanoparticle-conjugated aptamers were further confirmed using noninvasive MRI and Bioluminescence imaging. Anti-VCAM1 and anti-IL4Rα aptamers, specific to VCAM-1 and IL4Rα receptors overexpressed in 4T1-Luc2 tumor-bearing mice, were used as diagnostic and therapeutic tools.
Collapse
Affiliation(s)
- Raja Chinnappan
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Rd, Riyadh 11533, Saudi Arabia;
| | - Achraf Al Faraj
- Department of Radiologic Sciences, Faculty of Health Sciences, American University of Science and Technology, Ashrafieh, Alfred Naccash Avenue, Beirut 1100, Lebanon
| | - Anas M. Abdel Rahman
- Department of Genentics, King Faisal Specialist Hospital and Research Center, Zahrawi Street, Al Maather, Riyadh 12713, Saudi Arabia;
- Department of Biochemistry and Molecular Medicine, College of Medicine, Al Faisal University, Riyadh 11533, Saudi Arabia
- Department of Chemistry, Memorial University of Newfoundland, St. John’s, NL A1B 3X7, Canada
| | - Khalid M. Abu-Salah
- Department of Nanomedicine, King Abdullah International Medical Research Center/King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh 11481, Saudi Arabia;
| | - Fouzi Mouffouk
- Department of Chemistry, Kuwait University, P.O. Box 5969, Safat 13060, Kuwait;
| | - Mohammed Zourob
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Rd, Riyadh 11533, Saudi Arabia;
- Department of Genentics, King Faisal Specialist Hospital and Research Center, Zahrawi Street, Al Maather, Riyadh 12713, Saudi Arabia;
| |
Collapse
|
7
|
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: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [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.
Collapse
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
| |
Collapse
|
8
|
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: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [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.
Collapse
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
| |
Collapse
|
9
|
Buerger J, Gronenberg LS, Genee HJ, Sommer MOA. Wiring cell growth to product formation. Curr Opin Biotechnol 2019; 59:85-92. [PMID: 30928842 DOI: 10.1016/j.copbio.2019.02.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 01/24/2019] [Accepted: 02/19/2019] [Indexed: 01/07/2023]
Abstract
Microbial cell factories offer new and sustainable production routes for high-value chemicals. However, identification of high producers within a library of clones remains a challenge. When product formation is coupled to growth, millions of metabolic variants can be effectively interrogated by growth selection, dramatically increasing the throughput of strain evaluation. While growth-coupled selections for cell factories have a long history of success based on metabolite auxotrophies and toxic antimetabolites, such methods are generally restricted to molecules native to their host metabolism. New synthetic biology tools offer the opportunity to rewire cellular metabolism to depend on specific and non-native products for growth.
Collapse
Affiliation(s)
- Josi Buerger
- Biosyntia ApS, DK-2100 Copenhagen OE, Denmark; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | | | | | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| |
Collapse
|
10
|
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: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [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.
Collapse
|
11
|
Findeiß S, Hammer S, Wolfinger MT, Kühnl F, Flamm C, Hofacker IL. In silico design of ligand triggered RNA switches. Methods 2018; 143:90-101. [PMID: 29660485 DOI: 10.1016/j.ymeth.2018.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/06/2018] [Accepted: 04/06/2018] [Indexed: 02/06/2023] Open
Abstract
This contribution sketches a work flow to design an RNA switch that is able to adapt two structural conformations in a ligand-dependent way. A well characterized RNA aptamer, i.e., knowing its Kd and adaptive structural features, is an essential ingredient of the described design process. We exemplify the principles using the well-known theophylline aptamer throughout this work. The aptamer in its ligand-binding competent structure represents one structural conformation of the switch while an alternative fold that disrupts the binding-competent structure forms the other conformation. To keep it simple we do not incorporate any regulatory mechanism to control transcription or translation. We elucidate a commonly used design process by explicitly dissecting and explaining the necessary steps in detail. We developed a novel objective function which specifies the mechanistics of this simple, ligand-triggered riboswitch and describe an extensive in silico analysis pipeline to evaluate important kinetic properties of the designed sequences. This protocol and the developed software can be easily extended or adapted to fit novel design scenarios and thus can serve as a template for future needs.
Collapse
Affiliation(s)
- Sven Findeiß
- Bioinformatics, Institute of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany; University of Vienna, Faculty of Computer Science, Research Group Bioinformatics and Computational Biology, Währingerstraße 29, 1090 Vienna, Austria; University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstraße 17, 1090 Vienna, Austria.
| | - Stefan Hammer
- Bioinformatics, Institute of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany; University of Vienna, Faculty of Computer Science, Research Group Bioinformatics and Computational Biology, Währingerstraße 29, 1090 Vienna, Austria; University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstraße 17, 1090 Vienna, Austria
| | - Michael T Wolfinger
- University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstraße 17, 1090 Vienna, Austria; Medical University of Vienna, Center for Anatomy and Cell Biology, Währingerstraße 13, 1090 Vienna, Austria
| | - Felix Kühnl
- Bioinformatics, Institute of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Christoph Flamm
- University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstraße 17, 1090 Vienna, Austria
| | - Ivo L Hofacker
- University of Vienna, Faculty of Computer Science, Research Group Bioinformatics and Computational Biology, Währingerstraße 29, 1090 Vienna, Austria; University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstraße 17, 1090 Vienna, Austria
| |
Collapse
|
12
|
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: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [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.
Collapse
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
| |
Collapse
|
13
|
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 2017; 45:e181. [PMID: 29036355 PMCID: PMC5727447 DOI: 10.1093/nar/gkx858] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/22/2017] [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.
Collapse
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
| |
Collapse
|
14
|
Specific Light-Up System for Protein and Metabolite Targets Triggered by Initiation Complex Formation. Sci Rep 2017; 7:15191. [PMID: 29123195 PMCID: PMC5680199 DOI: 10.1038/s41598-017-15697-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/01/2017] [Indexed: 12/11/2022] Open
Abstract
Gene regulation systems are mimicked by simple quantitative detection of non-nucleic acid molecular targets such as protein and metabolite. Here, we describe a one-tube, one-step real-time quantitative detection methodology for isothermal signal amplification of those targets. Using this system, real-time quantitative detection of thrombin and streptomycin, which were used as examples for protein and metabolite targets, was successfully demonstrated with detection limits of at most 50 pM and 75 nM, respectively. Notably, the dynamic range of target concentrations could be obtained for over four orders of magnitude. Thus, our method is expected to serve as a point-of-care or on-site test for medical diagnosis and food and environmental hygiene.
Collapse
|
15
|
McKeague M. Aptamers for DNA Damage and Repair. Int J Mol Sci 2017; 18:ijms18102212. [PMID: 29065503 PMCID: PMC5666892 DOI: 10.3390/ijms18102212] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/17/2017] [Accepted: 10/20/2017] [Indexed: 12/14/2022] Open
Abstract
DNA is damaged on a daily basis, which can lead to heritable mutations and the activation of proto-oncogenes. Therefore, DNA damage and repair are critical risk factors in cancer, aging and disease, and are the underlying bases of most frontline cancer therapies. Much of our current understanding of the mechanisms that maintain DNA integrity has been obtained using antibody-based assays. The oligonucleotide equivalents of antibodies, known as aptamers, have emerged as potential molecular recognition rivals. Aptamers possess several ideal properties including chemical stability, in vitro selection and lack of batch-to-batch variability. These properties have motivated the incorporation of aptamers into a wide variety of analytical, diagnostic, research and therapeutic applications. However, their use in DNA repair studies and DNA damage therapies is surprisingly un-tapped. This review presents an overview of the progress in selecting and applying aptamers for DNA damage and repair research.
Collapse
Affiliation(s)
- Maureen McKeague
- Department of Health Sciences and Technology, ETH Zürich, Schmelzbergstrasse 9, 8092 Zurich, Switzerland.
| |
Collapse
|
16
|
Domin G, Findeiß S, Wachsmuth M, Will S, Stadler PF, Mörl M. Applicability of a computational design approach for synthetic riboswitches. Nucleic Acids Res 2017; 45:4108-4119. [PMID: 27994029 PMCID: PMC5397205 DOI: 10.1093/nar/gkw1267] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/06/2016] [Indexed: 02/07/2023] Open
Abstract
Riboswitches have gained attention as tools for synthetic biology, since they enable researchers to reprogram cells to sense and respond to exogenous molecules. In vitro evolutionary approaches produced numerous RNA aptamers that bind such small ligands, but their conversion into functional riboswitches remains difficult. We previously developed a computational approach for the design of synthetic theophylline riboswitches based on secondary structure prediction. These riboswitches have been constructed to regulate ligand-dependent transcription termination in Escherichia coli. Here, we test the usability of this design strategy by applying the approach to tetracycline and streptomycin aptamers. The resulting tetracycline riboswitches exhibit robust regulatory properties in vivo. Tandem fusions of these riboswitches with theophylline riboswitches represent logic gates responding to two different input signals. In contrast, the conversion of the streptomycin aptamer into functional riboswitches appears to be difficult. Investigations of the underlying aptamer secondary structure revealed differences between in silico prediction and structure probing. We conclude that only aptamers adopting the minimal free energy (MFE) structure are suitable targets for construction of synthetic riboswitches with design approaches based on equilibrium thermodynamics of RNA structures. Further improvements in the design strategy are required to implement aptamer structures not corresponding to the calculated MFE state.
Collapse
Affiliation(s)
- Gesine Domin
- Leipzig University, Institute for Biochemistry, 04103 Leipzig, Germany
| | - Sven Findeiß
- University of Vienna, Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, A-1090 Vienna, Austria.,University of Vienna, Institute for Theoretical Chemistry, A-1090 Vienna, Austria
| | - Manja Wachsmuth
- Leipzig University, Institute for Biochemistry, 04103 Leipzig, Germany
| | - Sebastian Will
- Leipzig University, Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, 04107 Leipzig, Germany
| | - Peter F Stadler
- University of Vienna, Institute for Theoretical Chemistry, A-1090 Vienna, Austria.,Leipzig University, Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, 04107 Leipzig, Germany.,Max Planck Institute for Mathematics in the Science, 04103 Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, 04103 Leipzig, Germany.,Santa Fe Institute, Santa Fe NM 87501, USA
| | - Mario Mörl
- Leipzig University, Institute for Biochemistry, 04103 Leipzig, Germany
| |
Collapse
|
17
|
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] [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.
Collapse
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
| |
Collapse
|
18
|
|
19
|
Pfeiffer F, Mayer G. Selection and Biosensor Application of Aptamers for Small Molecules. Front Chem 2016; 4:25. [PMID: 27379229 PMCID: PMC4908669 DOI: 10.3389/fchem.2016.00025] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 05/30/2016] [Indexed: 12/12/2022] Open
Abstract
Small molecules play a major role in the human body and as drugs, toxins, and chemicals. Tools to detect and quantify them are therefore in high demand. This review will give an overview about aptamers interacting with small molecules and their selection. We discuss the current state of the field, including advantages as well as problems associated with their use and possible solutions to tackle these. We then discuss different kinds of small molecule aptamer-based sensors described in literature and their applications, ranging from detecting drinking water contaminations to RNA imaging.
Collapse
Affiliation(s)
- Franziska Pfeiffer
- Department of Chemical Biology, Life and Medical Sciences Institute, University of Bonn Bonn, Germany
| | - Günter Mayer
- Department of Chemical Biology, Life and Medical Sciences Institute, University of Bonn Bonn, Germany
| |
Collapse
|
20
|
Wang Z, Cirino PC. New and improved tools and methods for enhanced biosynthesis of natural products in microorganisms. Curr Opin Biotechnol 2016; 42:159-168. [PMID: 27284635 DOI: 10.1016/j.copbio.2016.05.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 12/28/2022]
Abstract
Engineering efficient biosynthesis of natural products in microorganisms requires optimizing gene expression levels to balance metabolite flux distributions and to minimize accumulation of toxic intermediates. Such metabolic optimization is challenged with identifying the right gene targets, and then determining and achieving appropriate gene expression levels. After decades of having a relatively limited set of gene regulation tools available, metabolic engineers are recently enjoying an ever-growing repertoire of more precise and tunable gene expression platforms. Here we review recent applications of natural and designed transcriptional and translational regulatory machinery for engineering biosynthesis of natural products in microorganisms. Customized trans-acting RNAs (sgRNA, asRNA and sRNA), along with appropriate accessory proteins, are allowing for unparalleled tuning of gene expression. Meanwhile metabolite-responsive transcription factors and riboswitches have been implemented in strain screening and evolution, and in dynamic gene regulation. Further refinements and expansions on these platform technologies will circumvent many long-term obstacles in natural products biosynthesis.
Collapse
Affiliation(s)
- Zhiqing Wang
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Patrick C Cirino
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA.
| |
Collapse
|