1
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Liu Y, Zhou Z, Wu Y, Wang L, Cheng J, Zhu L, Dong Y, Zheng J, Xu W. Engineered transcription factor-binding diversed functional nucleic acid-based synthetic biosensor. Biotechnol Adv 2024:108463. [PMID: 39374798 DOI: 10.1016/j.biotechadv.2024.108463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 08/30/2024] [Accepted: 10/04/2024] [Indexed: 10/09/2024]
Abstract
Engineered transcription factors (eTFs) binding diversed functional nucleic acids (dFNAs), as innovative biorecognition systems, have gradually become indispensable core elements for building synthetic biosensors. They not only circumvent the limitations of the original TF-based biosensing technologies, but also inject new vitality into the field of synthetic biosensing. This review aims to provide the first comprehensive and systematic dissection of the eTF-dFNA synthetic biosensor concept. Firstly, the core principles and interaction mechanisms of eTF-dFNA biosensors are clarified. Next, we elaborate on the construction strategies of eTF-dFNA synthetic biosensors, detailing methods for the personalized customization of eTFs (irrational design, rational design, and semi-rational design) and dFNAs (SELEX, modifying and predicting), along with the exploration of strategies for the flexible selection of signal amplification and output modes. Furthermore, we discuss the exceptional performance and substantial advantages of eTF-dFNA synthetic biosensors, analyzing them from four perspectives: recognition domain, detection speed, sensitivity, and construction methodology. Building upon this analysis, we present their outstanding applications in point-of-care diagnostics, food-safety detection, environmental monitoring, and production control. Finally, we address the current limitations of eTF-dFNA synthetic biosensors candidly and envision the future direction of this technology, aiming to provide valuable insights for further research and applications in this burgeoning field.
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Affiliation(s)
- Yanger Liu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, Ministry of Education, China Agricultural University, Beijing 100193, China; Key Laboratory of Veterinary Anatomy, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Ziying Zhou
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Yifan Wu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Lei Wang
- Key Laboratory of Veterinary Anatomy, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jiageng Cheng
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, Ministry of Education, China Agricultural University, Beijing 100193, China.
| | - Yulan Dong
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, Ministry of Education, China Agricultural University, Beijing 100193, China; Key Laboratory of Veterinary Anatomy, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Jie Zheng
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, China.
| | - Wentao Xu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, Ministry of Education, China Agricultural University, Beijing 100193, China.
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2
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Helenek C, Krzysztoń R, Petreczky J, Wan Y, Cabral M, Coraci D, Balázsi G. Synthetic gene circuit evolution: Insights and opportunities at the mid-scale. Cell Chem Biol 2024; 31:1447-1459. [PMID: 38925113 PMCID: PMC11330362 DOI: 10.1016/j.chembiol.2024.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/07/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024]
Abstract
Directed evolution focuses on optimizing single genetic components for predefined engineering goals by artificial mutagenesis and selection. In contrast, experimental evolution studies the adaptation of entire genomes in serially propagated cell populations, to provide an experimental basis for evolutionary theory. There is a relatively unexplored gap at the middle ground between these two techniques, to evolve in vivo entire synthetic gene circuits with nontrivial dynamic function instead of single parts or whole genomes. We discuss the requirements for such mid-scale evolution, with hypothetical examples for evolving synthetic gene circuits by appropriate selection and targeted shuffling of a seed set of genetic components in vivo. Implementing similar methods should aid the rapid generation, functionalization, and optimization of synthetic gene circuits in various organisms and environments, accelerating both the development of biomedical and technological applications and the understanding of principles guiding regulatory network evolution.
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Affiliation(s)
- Christopher Helenek
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA
| | - Rafał Krzysztoń
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Julia Petreczky
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yiming Wan
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Mariana Cabral
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA
| | - Damiano Coraci
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Gábor Balázsi
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA.
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3
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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] [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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4
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Ono H, Saito H. Sensing intracellular signatures with synthetic mRNAs. RNA Biol 2023; 20:588-602. [PMID: 37582192 PMCID: PMC10431736 DOI: 10.1080/15476286.2023.2244791] [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] [Revised: 06/30/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023] Open
Abstract
The bottom-up assembly of biological components in synthetic biology has contributed to a better understanding of natural phenomena and the development of new technologies for practical applications. Over the past few decades, basic RNA research has unveiled the regulatory roles of RNAs underlying gene regulatory networks; while advances in RNA biology, in turn, have highlighted the potential of a wide variety of RNA elements as building blocks to construct artificial systems. In particular, synthetic mRNA-based translational regulators, which respond to signals in cells and regulate the production of encoded output proteins, are gaining attention with the recent rise of mRNA therapeutics. In this Review, we discuss recent progress in RNA synthetic biology, mainly focusing on emerging technologies for sensing intracellular protein and RNA molecules and controlling translation.
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Affiliation(s)
- Hiroki Ono
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Sakyo-Ku, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Sakyo-Ku, Japan
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5
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Bertram R, Neumann B, Schuster CF. Status quo of tet regulation in bacteria. Microb Biotechnol 2022; 15:1101-1119. [PMID: 34713957 PMCID: PMC8966031 DOI: 10.1111/1751-7915.13926] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/02/2021] [Accepted: 09/04/2021] [Indexed: 11/27/2022] Open
Abstract
The tetracycline repressor (TetR) belongs to the most popular, versatile and efficient transcriptional regulators used in bacterial genetics. In the tetracycline (Tc) resistance determinant tet(B) of transposon Tn10, tetR regulates the expression of a divergently oriented tetA gene that encodes a Tc antiporter. These components of Tn10 and of other natural or synthetic origins have been used for tetracycline-dependent gene regulation (tet regulation) in at least 40 bacterial genera. Tet regulation serves several purposes such as conditional complementation, depletion of essential genes, modulation of artificial genetic networks, protein overexpression or the control of gene expression within cell culture or animal infection models. Adaptations of the promoters employed have increased tet regulation efficiency and have made this system accessible to taxonomically distant bacteria. Variations of TetR, different effector molecules and mutated DNA binding sites have enabled new modes of gene expression control. This article provides a current overview of tet regulation in bacteria.
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Affiliation(s)
- Ralph Bertram
- Institute of Clinical Hygiene, Medical Microbiology and InfectiologyParacelsus Medical UniversityProf.‐Ernst‐Nathan‐Straße 1Nuremberg90419Germany
| | - Bernd Neumann
- Institute of Clinical Hygiene, Medical Microbiology and InfectiologyParacelsus Medical UniversityProf.‐Ernst‐Nathan‐Straße 1Nuremberg90419Germany
| | - Christopher F. Schuster
- Department of Infectious DiseasesDivision of Nosocomial Pathogens and Antibiotic ResistancesRobert Koch InstituteBurgstraße 37Wernigerode38855Germany
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6
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Dietler J, Schubert R, Krafft TGA, Meiler S, Kainrath S, Richter F, Schweimer K, Weyand M, Janovjak H, Möglich A. A Light-Oxygen-Voltage Receptor Integrates Light and Temperature. J Mol Biol 2021; 433:167107. [PMID: 34146595 DOI: 10.1016/j.jmb.2021.167107] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/31/2021] [Accepted: 06/09/2021] [Indexed: 10/21/2022]
Abstract
Sensory photoreceptors enable organisms to adjust their physiology, behavior, and development in response to light, generally with spatiotemporal acuity and reversibility. These traits underlie the use of photoreceptors as genetically encoded actuators to alter by light the state and properties of heterologous organisms. Subsumed as optogenetics, pertinent approaches enable regulating diverse cellular processes, not least gene expression. Here, we controlled the widely used Tet repressor by coupling to light-oxygen-voltage (LOV) modules that either homodimerize or dissociate under blue light. Repression could thus be elevated or relieved, and consequently protein expression was modulated by light. Strikingly, the homodimeric RsLOV module from Rhodobacter sphaeroides not only dissociated under light but intrinsically reacted to temperature. The limited light responses of wild-type RsLOV at 37 °C were enhanced in two variants that exhibited closely similar photochemistry and structure. One variant improved the weak homodimerization affinity of 40 µM by two-fold and thus also bestowed light sensitivity on a receptor tyrosine kinase. Certain photoreceptors, exemplified by RsLOV, can evidently moonlight as temperature sensors which immediately bears on their application in optogenetics and biotechnology. Properly accounted for, the temperature sensitivity can be leveraged for the construction of signal-responsive cellular circuits.
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Affiliation(s)
- Julia Dietler
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Roman Schubert
- Biophysical Chemistry, Humboldt-University Berlin, 10115 Berlin, Germany
| | - Tobias G A Krafft
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Simone Meiler
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Stephanie Kainrath
- Australian Regenerative Medicine Institute (ARMI), Monash University, Clayton, Victoria 3800, Australia
| | - Florian Richter
- Biophysical Chemistry, Humboldt-University Berlin, 10115 Berlin, Germany
| | - Kristian Schweimer
- Biopolymers, University of Bayreuth, 95447 Bayreuth, Germany; North-Bavarian NMR Center, University of Bayreuth, 95447 Bayreuth, Germany
| | - Michael Weyand
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Harald Janovjak
- Australian Regenerative Medicine Institute (ARMI), Monash University, Clayton, Victoria 3800, Australia
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany; Biophysical Chemistry, Humboldt-University Berlin, 10115 Berlin, Germany; Bayreuth Center for Biochemistry & Molecular Biology, University of Bayreuth, 95447 Bayreuth, Germany; North-Bavarian NMR Center, University of Bayreuth, 95447 Bayreuth, Germany.
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7
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Kim J, Quijano JF, Kim J, Yeung E, Murray RM. Synthetic logic circuits using RNA aptamer against T7 RNA polymerase. Biotechnol J 2021; 17:e2000449. [PMID: 33813787 DOI: 10.1002/biot.202000449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/05/2021] [Accepted: 03/30/2021] [Indexed: 12/23/2022]
Abstract
Recent advances in nucleic acids engineering introduced several RNA-based regulatory components for synthetic gene circuits, expanding the toolsets to engineer organisms. In this work, we designed genetic circuits implementing an RNA aptamer previously described to have the capability of binding to the T7 RNA polymerase and inhibiting its activity in vitro. We first demonstrated the utility of the RNA aptamer in combination with programmable synthetic transcription networks in vitro. As a step to quickly assess the feasibility of aptamer functions in vivo, we tested the aptamer and its sequence variants in the cell-free expression system, verifying the aptamer functionality in the cell-free testbed. The expression of aptamer in E. coli demonstrated control over GFP expression driven by T7 RNA polymerase, indicating its ability to serve as building blocks for logic circuits and transcriptional cascades. This work elucidates the potential of T7 RNA polymerase aptamer as regulators for synthetic biological circuits and metabolic engineering.
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Affiliation(s)
- Jongmin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea.,Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Juan F Quijano
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Jeongwon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Enoch Yeung
- Department of Control and Dynamical Systems, California Institute of Technology, Pasadena, California, USA.,Department of Mechanical Engineering, University of California, Santa Barbara, California, USA
| | - Richard M Murray
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA.,Department of Control and Dynamical Systems, California Institute of Technology, Pasadena, California, USA
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8
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Mol AA, Vogel M, Suess B. Inducible nuclear import by TetR aptamer-controlled 3' splice site selection. RNA (NEW YORK, N.Y.) 2021; 27:234-241. [PMID: 33148600 PMCID: PMC7812871 DOI: 10.1261/rna.077453.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
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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9
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Kawasaki S, Ono H, Hirosawa M, Saito H. RNA and protein-based nanodevices for mammalian post-transcriptional circuits. Curr Opin Biotechnol 2020; 63:99-110. [DOI: 10.1016/j.copbio.2019.11.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/16/2019] [Accepted: 11/22/2019] [Indexed: 12/26/2022]
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10
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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: 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.
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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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11
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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] [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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12
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Yokobayashi Y. Aptamer-based and aptazyme-based riboswitches in mammalian cells. Curr Opin Chem Biol 2019; 52:72-78. [PMID: 31238268 PMCID: PMC7108311 DOI: 10.1016/j.cbpa.2019.05.018] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 05/17/2019] [Accepted: 05/21/2019] [Indexed: 11/22/2022]
Abstract
Molecular recognition by RNA aptamers has been exploited to control gene expression in response to small molecules in mammalian cells. These mammalian synthetic riboswitches offer attractive features such as small genetic size and lower risk of immunological complications compared to protein-based transcriptional gene switches. The diversity of gene regulatory mechanisms that involve RNA has also inspired the development of mammalian riboswitches that harness various regulatory mechanisms. In this report, recent advances in synthetic riboswitches that function in mammalian cells are reviewed focusing on the regulatory mechanisms they exploit such as mRNA degradation, microRNA processing, and programmed ribosomal frameshifting.
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Affiliation(s)
- Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan.
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13
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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: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [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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14
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Yoon S, Rossi JJ. Aptamers: Uptake mechanisms and intracellular applications. Adv Drug Deliv Rev 2018; 134:22-35. [PMID: 29981799 PMCID: PMC7126894 DOI: 10.1016/j.addr.2018.07.003] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 06/06/2018] [Accepted: 07/04/2018] [Indexed: 01/10/2023]
Abstract
The structural flexibility and small size of aptamers enable precise recognition of cellular elements for imaging and therapeutic applications. The process by which aptamers are taken into cells depends on their targets but is typically clathrin-mediated endocytosis or macropinocytosis. After internalization, most aptamers are transported to endosomes, lysosomes, endoplasmic reticulum, Golgi apparatus, and occasionally mitochondria and autophagosomes. Intracellular aptamers, or “intramers,” have versatile functions ranging from intracellular RNA imaging, gene regulation, and therapeutics to allosteric modulation, which we discuss in this review. Immune responses to therapeutic aptamers and the effects of G-quadruplex structure on aptamer function are also discussed.
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15
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Ohuchi S, Suess B. Altered stoichiometry of an evolved RNA aptamer. RNA (NEW YORK, N.Y.) 2018; 24:480-485. [PMID: 29284756 PMCID: PMC5855949 DOI: 10.1261/rna.063610.117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 12/21/2017] [Indexed: 06/07/2023]
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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16
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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: 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.
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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 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.
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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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18
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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] [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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19
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Ausländer S, Ausländer D, Fussenegger M. Synthetische Biologie - die Synthese der Biologie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
| | - David Ausländer
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering; ETH Zürich; Mattenstrasse 26 4058 Basel Schweiz
- Faculty of Science; Universität Basel; Mattenstrasse 26 4058 Basel Schweiz
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20
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Ausländer S, Ausländer D, Fussenegger M. Synthetic Biology-The Synthesis of Biology. Angew Chem Int Ed Engl 2017; 56:6396-6419. [PMID: 27943572 DOI: 10.1002/anie.201609229] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/17/2016] [Indexed: 01/01/2023]
Abstract
Synthetic biology concerns the engineering of man-made living biomachines from standardized components that can perform predefined functions in a (self-)controlled manner. Different research strategies and interdisciplinary efforts are pursued to implement engineering principles to biology. The "top-down" strategy exploits nature's incredible diversity of existing, natural parts to construct synthetic compositions of genetic, metabolic, or signaling networks with predictable and controllable properties. This mainly application-driven approach results in living factories that produce drugs, biofuels, biomaterials, and fine chemicals, and results in living pills that are based on engineered cells with the capacity to autonomously detect and treat disease states in vivo. In contrast, the "bottom-up" strategy seeks to be independent of existing living systems by designing biological systems from scratch and synthesizing artificial biological entities not found in nature. This more knowledge-driven approach investigates the reconstruction of minimal biological systems that are capable of performing basic biological phenomena, such as self-organization, self-replication, and self-sustainability. Moreover, the syntheses of artificial biological units, such as synthetic nucleotides or amino acids, and their implementation into polymers inside living cells currently set the boundaries between natural and artificial biological systems. In particular, the in vitro design, synthesis, and transfer of complete genomes into host cells point to the future of synthetic biology: the creation of designer cells with tailored desirable properties for biomedicine and biotechnology.
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Affiliation(s)
- Simon Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - David Ausländer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.,Faculty of Science, University of Basel, Mattenstrasse 26, 4058, Basel, Switzerland
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21
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Higo A, Isu A, Fukaya Y, Hisabori T. Designing Synthetic Flexible Gene Regulation Networks Using RNA Devices in Cyanobacteria. ACS Synth Biol 2017; 6:55-61. [PMID: 27636301 DOI: 10.1021/acssynbio.6b00201] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In recent years, studies on the development of gene regulation tools in cyanobacteria have been extensively conducted toward efficient production of valuable chemicals. However, there is considerable scope for improving the economic feasibility of production. To improve a recently reported gene induction system using anhydrotetracycline (aTc)-TetR and an endogenous gene repression system using small antisense RNA in the filamentous nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120 (Anabaena), we constructed a positive feedback loop, in which gfp and a small antisense RNA for tetR are controlled by an aTc-inducible promoter. GFP expression in this improved system was higher and longer than the system lacking tetR repression. In addition, by using TetR aptamer and a riboswitch, we succeeded in achieving a superior and longer induction of GFP expression even under high-light conditions. Hence, efficient gene induction systems were established in Anabaena by designing a gene regulation network using RNA-based tools.
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Affiliation(s)
- Akiyoshi Higo
- Laboratory
for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-ku, Yokohama 226-8503, Japan
- Core
Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo 102-0075, Japan
| | - Atsuko Isu
- Laboratory
for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-ku, Yokohama 226-8503, Japan
- Core
Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo 102-0075, Japan
| | - Yuki Fukaya
- Laboratory
for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-ku, Yokohama 226-8503, Japan
- Core
Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo 102-0075, Japan
| | - Toru Hisabori
- Laboratory
for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta 4259-R1-8, Midori-ku, Yokohama 226-8503, Japan
- Core
Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo 102-0075, Japan
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22
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Kellermann SJ, Rentmeister A. A FACS-based screening strategy to assess sequence-specific RNA-binding of Pumilio protein variants in E. coli. Biol Chem 2017; 398:69-75. [DOI: 10.1515/hsz-2016-0214] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/15/2016] [Indexed: 12/22/2022]
Abstract
Abstract
Sequence-specific and programmable binding of proteins to RNA bears the potential to detect and manipulate target RNAs. Applications include analysis of subcellular RNA localization or post-transcriptional regulation but require sequence-specificity to be readily adjustable to any target RNA. The Pumilio homology domain binds an eight nucleotide target sequence in a predictable manner allowing for rational design of variants with new specificities. We describe a high-throughput system for screening Pumilio variants based on fluorescence-activated cell sorting of E. coli. Our approach should help optimizing variants obtained from rational design regarding folding and stability or identifying new variants with alternative binding modes.
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23
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Andries O, Kitada T, Bodner K, Sanders NN, Weiss R. Synthetic biology devices and circuits for RNA-based ‘smart vaccines’: a propositional review. Expert Rev Vaccines 2015; 14:313-31. [DOI: 10.1586/14760584.2015.997714] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Webster WAJ, McFadden GI. From the genome to the phenome: tools to understand the basic biology of Plasmodium falciparum. J Eukaryot Microbiol 2014; 61:655-71. [PMID: 25227912 DOI: 10.1111/jeu.12176] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/01/2014] [Accepted: 09/02/2014] [Indexed: 11/30/2022]
Abstract
Malaria plagues one out of every 30 humans and contributes to almost a million deaths, and the problem could worsen. Our current therapeutic options are compromised by emerging resistance by the parasite to our front line drugs. It is thus imperative to better understand the basic biology of the parasite and develop novel drugs to stem this disease. The most facile approach to analyse a gene's function is to remove it from the genome or inhibit its activity. Although genetic manipulation of the human malaria parasite Plasmodium falciparum is a relatively standard procedure, there is no optimal method to perturb genes essential to the intraerythrocytic development cycle--the part of the life cycle that produces the clinical manifestation of malaria. This is a severe impediment to progress because the phenotype we wish to study is exactly the one that is so elusive. In the absence of any utilitarian way to conditionally delete essential genes, we are prevented from investigating the parasite's most vulnerable points. This review aims to focus on the development of tools identifying essential genes of P. falciparum and our ability to elicit phenotypic mutation.
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Affiliation(s)
- Wesley A J Webster
- Centre for Regional and Rural Futures, School of Life and Environmental Sciences, Deakin University, Burwood, 3125, Victoria, Australia; Plant Cell Biology Research Centre, School of Botany, University of Melbourne, Melbourne, 3010, Victoria, Australia
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25
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Weigand JE, Gottstein-Schmidtke SR, Demolli S, Groher F, Duchardt-Ferner E, Wöhnert J, Suess B. Sequence elements distal to the ligand binding pocket modulate the efficiency of a synthetic riboswitch. Chembiochem 2014; 15:1627-37. [PMID: 24954073 DOI: 10.1002/cbic.201402067] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Indexed: 01/16/2023]
Abstract
Synthetic riboswitches can serve as sophisticated genetic control devices in synthetic biology, regulating gene expression through direct RNA-ligand interactions. We analyzed a synthetic neomycin riboswitch, which folds into a stem loop structure with an internal loop important for ligand binding and regulation. It is closed by a terminal hexaloop containing a U-turn and a looped-out adenine. We investigated the relationship between sequence, structure, and biological activity in the terminal loop by saturating mutagenesis, ITC, and NMR. Mutants corresponding to the canonical U-turn fold retained biological activity. An improvement of stacking interactions in the U-turn led to an RNA element with slightly enhanced regulatory activity. For the first position of the U-turn motif and the looped out base, sequence-activity relationships that could not initially be explained on the basis of the structure of the aptamer-ligand complex were observed. However, NMR studies of these mutants revealed subtle relationships between structure and dynamics of the aptamer in its free or bound state and biological activity.
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Affiliation(s)
- Julia E Weigand
- Department of Biology, Technical University Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt (Germany)
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26
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Groher F, Suess B. Synthetic riboswitches - A tool comes of age. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:964-973. [PMID: 24844178 DOI: 10.1016/j.bbagrm.2014.05.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 04/29/2014] [Accepted: 05/08/2014] [Indexed: 12/14/2022]
Abstract
Within the last decade, it has become obvious that RNA plays an important role in regulating gene expression. This has led to a plethora of approaches aiming at exploiting the outstanding chemical properties of RNA to develop synthetic RNA regulators for conditional gene expression systems. Consequently, many different regulators have been developed to act on various stages of gene expression. They can be engineered to respond to almost any ligand of choice and are, therefore, of great interest for applications in synthetic biology. This review presents an overview of such engineered riboswitches, discusses their applicability and points out recent trends in their development. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Florian Groher
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany.
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27
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Vazquez-Anderson J, Contreras LM. Regulatory RNAs: charming gene management styles for synthetic biology applications. RNA Biol 2013; 10:1778-97. [PMID: 24356572 DOI: 10.4161/rna.27102] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
RNAs have many important functional properties, including that they are independently controllable and highly tunable. As a result of these advantageous properties, their use in a myriad of sophisticated devices has been widely explored. Yet, the exploitation of RNAs for synthetic applications is highly dependent on the ability to characterize the many new molecules that continue to be discovered by large-scale sequencing and high-throughput screening techniques. In this review, we present an exhaustive survey of the most recent synthetic bacterial riboswitches and small RNAs while emphasizing their virtues in gene expression management. We also explore the use of these RNA components as building blocks in the RNA synthetic biology toolbox and discuss examples of synthetic RNA components used to rewire bacterial regulatory circuitry. We anticipate that this field will expand its catalog of smart devices by mimicking and manipulating natural RNA mechanisms and functions.
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Affiliation(s)
- Jorge Vazquez-Anderson
- McKetta Department of Chemical Engineering; University of Texas at Austin; Austin, TX USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering; University of Texas at Austin; Austin, TX USA
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28
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29
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Meitert J, Aram R, Wiesemann K, Weigand JE, Suess B. Monitoring the expression level of coding and non-coding RNAs using a TetR inducing aptamer tag. Bioorg Med Chem 2013; 21:6233-8. [PMID: 23993971 DOI: 10.1016/j.bmc.2013.07.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/21/2013] [Accepted: 07/17/2013] [Indexed: 01/31/2023]
Abstract
RNA aptamers have been widely used as regulators for conditional gene expression. The TetR binding aptamer can activate tetracycline repressor TetR controlled gene expression with high efficiency. Here we demonstrate that the aptamer can also activate TetR controlled gene expression when expressed in the context of a natural transcripts. The aptamer was inserted into the untranslated regions of mRNAs as well as into small non-coding RNAs and was expressed both from a plasmid and from an endogenous locus. Our data suggest that the aptamer is a valuable tool to easily monitor the expression level of different RNAs, and it therefore represents a powerful tool for the construction of complex synthetic gene networks.
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Affiliation(s)
- Johannes Meitert
- Institut für Molekulare Biowissenschaften, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt/M., Germany
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30
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Ketzer P, Haas SF, Engelhardt S, Hartig JS, Nettelbeck DM. Synthetic riboswitches for external regulation of genes transferred by replication-deficient and oncolytic adenoviruses. Nucleic Acids Res 2012; 40:e167. [PMID: 22885302 PMCID: PMC3505972 DOI: 10.1093/nar/gks734] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Therapeutic gene transfer by replication-defective viral vectors or, for cancer treatment, by replication-competent oncolytic viruses shows high promise for treatment of major diseases. To ensure safety, timing or dosing in patients, external control of therapeutic gene expression is desirable or even required. In this study, we explored the potential of artificial aptazymes, ligand-dependent self-cleaving ribozymes, as an innovative tool for regulation of therapeutic gene expression. Importantly, aptazymes act on RNA intrinsically, independent of regulatory protein–nucleic acid interactions and stoichiometry, are non-immunogenic and of small size. These are key advantages compared with the widely used inducible promoters, which were also reported to lose regulation at high copy numbers, e.g. after replication of oncolytic viruses. We characterized aptazymes in therapeutic gene transfer utilizing adenovectors (AdVs), adeno-associated vectors (AAVs) and oncolytic adenoviruses (OAds), which are all in advanced clinical testing. Our results show similar aptazyme-mediated regulation of gene expression by plasmids, AdVs, AAVs and OAds. Insertion into the 5′-, 3′- or both untranslated regions of several transgenes resulted in ligand-responsive gene expression. Notably, aptazyme regulation was retained during OAd replication and spread. In conclusion, our study demonstrates the fidelity of aptazymes in viral vectors and oncolytic viruses and highlights the potency of riboswitches for medical applications.
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Affiliation(s)
- Patrick Ketzer
- Helmholtz-University Group Oncolytic Adenoviruses, Deutsches Krebsforschungszentrum (DKFZ, German Cancer Research Center) and Department of Dermatology, Heidelberg University Hospital, Im Neuenheimer Feld 242, 69120 Heidelberg, Germany
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31
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Goodson MS, Lynch JA, Lamkin T, Kramer R. Elucidation of small RNAs that activate transcription in bacteria. ACS Synth Biol 2012; 1:181-9. [PMID: 23651156 DOI: 10.1021/sb2000275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small non-coding RNA (sRNA) control of gene expression has been shown to play a prominent role in genetic regulation. While the majority of identified bacterial sRNAs exert their control at the translational level, a few examples of bacterial sRNAs that inhibit transcription have also been identified. Using an engineered combinatorial RNA library, we have elucidated bacterial sRNAs that activate transcription of a target gene in E. coli to varying degrees. Mutation of the strongest activator modified its activation potential. Our results suggest that transcriptional activation of our target gene results from recruitment of the bacterial RNA polymerase complex to the promoter region. These data, coupled with the malleability of RNA, provide a context to define synthetic control of genes in bacteria at the transcriptional level.
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Affiliation(s)
- Michael S. Goodson
- 711th Human Performance Wing, Air
Force Research Laboratory, 2510 Fifth Street, Building 840, Wright-Patterson
Air Force Base, Ohio 45433, United States
| | - John A. Lynch
- Department of Chemistry, University of Cincinnati,
Cincinnati, Ohio 45267, United States
| | - Thomas Lamkin
- 711th Human Performance Wing, Air Force Research Laboratory, University
of Cincinnati, 231 Albert Sabin Way, Medical Sciences Building, Cincinnati,
Ohio 45221, United States
| | - Ryan Kramer
- 711th Human Performance Wing, Air Force Research Laboratory, University
of Cincinnati, 231 Albert Sabin Way, Medical Sciences Building, Cincinnati,
Ohio 45221, United States
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32
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Foundations for the design and implementation of synthetic genetic circuits. Nat Rev Genet 2012; 13:406-20. [DOI: 10.1038/nrg3227] [Citation(s) in RCA: 190] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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33
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Wittmann A, Suess B. Engineered riboswitches: Expanding researchers' toolbox with synthetic RNA regulators. FEBS Lett 2012; 586:2076-83. [PMID: 22710175 DOI: 10.1016/j.febslet.2012.02.038] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 02/20/2012] [Accepted: 02/20/2012] [Indexed: 12/22/2022]
Abstract
Riboswitches are natural RNA-based genetic switches that sense small-molecule metabolites and regulate in response the expression of the corresponding metabolic genes. Within the last years, several engineered riboswitches have been developed that act on various stages of gene expression. These switches can be engineered to respond to any ligand of choice and are therefore of great interest for synthetic biology. In this review, we present an overview of engineered riboswitches and discuss their application in conditional gene expression systems. We will provide structural and mechanistic insights and point out problems and recent trends in the development of engineered riboswitches.
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Affiliation(s)
- Alexander Wittmann
- Institute of Molecular Biosciences, Goethe University Frankfurt am Main, Max-von-Laue Straße 9, 60438 Frankfurt am Main, Germany
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34
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Chang AL, Wolf JJ, Smolke CD. Synthetic RNA switches as a tool for temporal and spatial control over gene expression. Curr Opin Biotechnol 2012; 23:679-88. [PMID: 22305712 DOI: 10.1016/j.copbio.2012.01.005] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 01/10/2012] [Accepted: 01/12/2012] [Indexed: 11/17/2022]
Abstract
The engineering of biological systems offers significant promise for advances in areas including health and medicine, chemical synthesis, energy production, and environmental sustainability. Realizing this potential requires tools that enable design of sophisticated genetic systems. The functional diversity of RNA makes it an attractive and versatile substrate for programming sensing, information processing, computation, and control functions. Recent advances in the design of synthetic RNA switches capable of detecting and responding to molecular and environmental signals enable dynamic modulation of gene expression through diverse mechanisms, including transcription, splicing, stability, RNA interference, and translation. Furthermore, implementation of these switches in genetic circuits highlights the potential for building synthetic cell systems targeted to applications in environmental remediation and next-generation therapeutics and diagnostics.
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Affiliation(s)
- Andrew L Chang
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
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35
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Wieland M, Ausländer D, Fussenegger M. Engineering of ribozyme-based riboswitches for mammalian cells. Methods 2012; 56:351-7. [PMID: 22305857 DOI: 10.1016/j.ymeth.2012.01.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 01/13/2012] [Accepted: 01/17/2012] [Indexed: 12/15/2022] Open
Abstract
Artificial RNA riboswitches--apart from protein-based gene regulation systems, which have been known about for a long time--have become increasingly important in biotechnology and synthetic biology. Aptamer-controlled hammerhead ribozymes (so-called aptazymes) have been shown to be a versatile platform for the engineering of novel gene regulators. Since aptazymes are cis-acting elements that are located in the untranslated regions of a gene of interest, their application does not need any further protein co-factor. This presents the opportunity to simplify complex gene networks while simultaneously expanding the repertoire of available parts. Nevertheless, the generation of novel aptazymes requires a functional aptamer-ribozyme connection, which can be difficult to engineer. This article describes a novel approach for using fluorescence activated cell sorting (FACS) in order to identify functional aptazymes in bacteria and their subsequent transfer into mammalian cells.
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Affiliation(s)
- Markus Wieland
- ETH Zurich, Department of Biosystems Science and Bioengineering (D-BSSE), Mattenstrasse 26, CH-4058 Basel, Switzerland
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36
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Abstract
A brief historical introduction describes early attempts to silence specific genes using the antisense oligonucleotides that flourished in the 1980s. Early aspirations for therapeutic applications were almost extinguished by the unexpected complexity of oligonucleotide pharmacology. Once the biochemistry and molecular biology behind some of the pharmacology was worked out, new approaches became apparent for using oligonucleotides to treat disease. The biochemistry of small nucleic acids is outlined in Section 2. Various approaches employing oligonucleotides to control cellular functions are reviewed in Section 3. These include antisense oligonucleotides and siRNA that bind to RNA, antigene oligonucleotides that bind to DNA, and aptamers, decoys, and CpG oligonucleotides that bind to proteins.
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MESH Headings
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/pharmacology
- Aptamers, Nucleotide/therapeutic use
- Communicable Diseases/drug therapy
- Communicable Diseases/pathology
- CpG Islands
- DNA/chemistry
- DNA/metabolism
- DNA, Catalytic/chemistry
- DNA, Catalytic/pharmacology
- DNA, Catalytic/therapeutic use
- Diabetes Mellitus/drug therapy
- Diabetes Mellitus/pathology
- Humans
- MicroRNAs/chemistry
- MicroRNAs/pharmacology
- MicroRNAs/therapeutic use
- Molecular Targeted Therapy/methods
- Neoplasms/drug therapy
- Neoplasms/pathology
- Neurodegenerative Diseases/drug therapy
- Neurodegenerative Diseases/pathology
- Nucleic Acid Hybridization
- Oligonucleotides/chemistry
- Oligonucleotides/pharmacology
- Oligonucleotides/therapeutic use
- Oligonucleotides, Antisense/chemistry
- Oligonucleotides, Antisense/pharmacology
- Oligonucleotides, Antisense/therapeutic use
- RNA, Catalytic/chemistry
- RNA, Catalytic/pharmacology
- RNA, Catalytic/therapeutic use
- RNA, Small Interfering/chemistry
- RNA, Small Interfering/pharmacology
- RNA, Small Interfering/therapeutic use
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Affiliation(s)
- John Goodchild
- Department of Chemistry, Worcester State University, Worcester, MA 01602-2597, USA.
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37
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Steber M, Arora A, Hofmann J, Brutschy B, Suess B. Mechanistic basis for RNA aptamer-based induction of TetR. Chembiochem 2011; 12:2608-14. [PMID: 22021209 DOI: 10.1002/cbic.201100503] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Indexed: 12/16/2022]
Abstract
The TetR aptamer induces TetR controlled gene expression, and represents an interesting tool for application in synthetic biology. We have analysed the mechanistic basis for RNA aptamer-based induction of TetR. The aptamer binds TetR with a high affinity in the order of 10(7) M(-1), which is similar to operator DNA binding under the used ionic conditions. We identified the binding epitope of the aptamer on TetR, which consists of amino acids T27, N47 and K48 of both monomers, using loss-of-function analysis and electrophoretic mobility shift assays. Tetracycline-induced conformational changes of TetR led to reorientation of the DNA reading head. This movement destroys the composite binding epitope for the aptamer and leads to reduced RNA binding by one order of magnitude. The aptamer can actively displace TetR from the operator DNA; this could be the key factor for its activity in vivo.
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Affiliation(s)
- Markus Steber
- Institut für Molekulare Biowissenschaften, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt/Main, Germany
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38
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Ausländer D, Wieland M, Ausländer S, Tigges M, Fussenegger M. Rational design of a small molecule-responsive intramer controlling transgene expression in mammalian cells. Nucleic Acids Res 2011; 39:e155. [PMID: 21984476 PMCID: PMC3239198 DOI: 10.1093/nar/gkr829] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aptamers binding proteins or small molecules have been shown to be versatile and powerful building blocks for the construction of artificial genetic switches. In this study, we present a novel aptamer-based construct regulating the Tet Off system in a tetracycline-independent manner thus achieving control of transgene expression. For this purpose, a TetR protein-inhibiting aptamer was engineered for use in mammalian cells, enabling the RNA-responsive control of the tetracycline-dependent transactivator (tTA). By rationally attaching the theophylline aptamer as a sensor, the inhibitory TetR aptamer and thus tTA activity became dependent on the ligand of the sensor aptamer. Addition of the small molecule theophylline resulted in enhanced binding to the corresponding protein in vitro and in inhibition of reporter gene expression in mammalian cell lines. By using aptamers as adaptors in order to control protein activity by a predetermined small molecule, we present a simple and straightforward approach for future applications in the field of Chemical Biology. Moreover, aptamer-based control of the widely used Tet system introduces a new layer of regulation thereby facilitating the construction of more complex gene networks.
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Affiliation(s)
- David Ausländer
- ETH Zurich, Department of Biosystems Science and Bioengineering (D-BSSE), Mattenstrasse 26, CH-4058 Basel, Switzerland
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39
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Wittmann A, Suess B. Selection of tetracycline inducible self-cleaving ribozymes as synthetic devices for gene regulation in yeast. MOLECULAR BIOSYSTEMS 2011; 7:2419-27. [PMID: 21603688 DOI: 10.1039/c1mb05070b] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Synthetic regulatory devices are key components for the development of complex biological systems and the reprogramming of cellular functions and networks. Here we describe the selection of tetracycline inducible hammerhead ribozymes. A tetracycline aptamer was fused to the full-length hammerhead ribozyme via a variable linker region. 11 rounds of in vitro selection were applied to isolate linker sequences that mediate tetracycline dependent hammerhead cleavage. We identified allosteric ribozymes that cleave in the presence of 1 μM tetracycline as fast as the full-length ribozyme whereas cleavage is inhibited up to 333-fold in the absence of tetracycline. Reporter gene assays indicate that the allosteric ribozymes can be employed to control gene expression in yeast.
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Affiliation(s)
- Alexander Wittmann
- Institute for Molecular Biosciences, Goethe Universität Frankfurt am Main, Frankfurt am Main, Germany
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40
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Belmont BJ, Niles JC. Engineering a direct and inducible protein-RNA interaction to regulate RNA biology. ACS Chem Biol 2010; 5:851-61. [PMID: 20545348 DOI: 10.1021/cb100070j] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The importance and pervasiveness of naturally occurring regulation of RNA function in biology is increasingly being recognized. A common mechanism uses inducible protein-RNA interactions to shape diverse aspects of cellular RNA fate. Recapitulating this regulatory mode in cells using a novel set of protein-RNA interactions is appealing given the potential to subsequently modulate RNA biology in a manner decoupled from endogenous cellular physiology. Achieving this outcome, however, has previously proven challenging. Here, we describe a ligand-responsive protein-RNA interaction module, which can be used to target a specific RNA for subsequent regulation. Using the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) method, RNA aptamers binding to the bacterial Tet Repressor protein (TetR) with low- to subnanomolar affinities were obtained. This interaction is reversibly controlled by tetracycline in a manner analogous to the interaction of TetR with its cognate DNA operator. Aptamer minimization and mutational analyses support a functional role for two conserved sequence motifs in TetR binding. As an initial illustration of using this system to achieve protein-based regulation of RNA function in living cells, insertion of a TetR aptamer into the 5'-UTR of a reporter mRNA confers post-transcriptionally regulated, ligand-inducible protein synthesis in E. coli. Altogether, these results define and validate an inducible protein-RNA interaction module that incorporates desirable aspects of a ubiquitous mechanism for regulating RNA function in Nature and can be used as a foundational interaction for functionally and reversibly controlling the multiple fates of RNA in cells.
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Affiliation(s)
- Brian J. Belmont
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Jacquin C. Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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41
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Sinha J, Reyes SJ, Gallivan JP. Reprogramming bacteria to seek and destroy an herbicide. Nat Chem Biol 2010; 6:464-70. [PMID: 20453864 PMCID: PMC2873063 DOI: 10.1038/nchembio.369] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Accepted: 04/06/2010] [Indexed: 12/26/2022]
Abstract
A major goal of synthetic biology is to reprogram cells to perform complex tasks. Here we show how a combination of in vitro and in vivo selection rapidly identifies a synthetic riboswitch that activates protein translation in response to the herbicide atrazine. We further demonstrate that this riboswitch can reprogram bacteria to migrate in the presence of atrazine. Finally, we show that incorporating a gene from an atrazine catabolic pathway allows these cells to seek and destroy atrazine.
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Affiliation(s)
- Joy Sinha
- Department of Chemistry and Center for Fundamental and Applied Molecular Evolution, Emory University, Atlanta, Georgia, USA
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42
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Chang TW, Blank M, Janardhanan P, Singh BR, Mello C, Blind M, Cai S. In vitro selection of RNA aptamers that inhibit the activity of type A botulinum neurotoxin. Biochem Biophys Res Commun 2010; 396:854-60. [PMID: 20452328 DOI: 10.1016/j.bbrc.2010.05.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 05/03/2010] [Indexed: 10/19/2022]
Abstract
The category A agent, botulinum neurotoxin (BoNT), is the most toxic molecule known to mankind. The endopeptidase activity of light chain domain of BoNT is the cause for the inhibition of the neurotransmitter release and the flaccid paralysis that leads to lethality in botulism. Currently, antidotes are not available to reverse the flaccid paralysis caused by BoNT. In the present study, we have identified three RNA aptamers through SELEX-process, which bind strongly to the light chain of type A BoNT (BoNT/A) and inhibit the endopeptidase activity, with IC(50) in low nM range. Inhibition kinetic studies reveal low nM K(I) and non-competitive nature of their inhibition. Aptamers are unique group of molecules as therapeutics, and this is first report of their development as an antidote against botulism. These data on K(I) and IC(50) strongly suggest that the aptamers have strong potential as antidotes that can reverse the symptom caused by BoNT/A.
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Affiliation(s)
- Tzuu-Wang Chang
- Department of Chemistry and Biochemistry, and Botulinum Research Center, University of Massachusetts Dartmouth, North Dartmouth, MA 02747, USA
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43
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Toroney R, Nallagatla SR, Boyer JA, Cameron CE, Bevilacqua PC. Regulation of PKR by HCV IRES RNA: importance of domain II and NS5A. J Mol Biol 2010; 400:393-412. [PMID: 20447405 DOI: 10.1016/j.jmb.2010.04.059] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 04/27/2010] [Accepted: 04/28/2010] [Indexed: 02/05/2023]
Abstract
Protein kinase R (PKR) is an essential component of the innate immune response. In the presence of double-stranded RNA (dsRNA), PKR is autophosphorylated, which enables it to phosphorylate its substrate, eukaryotic initiation factor 2alpha, leading to translation cessation. Typical activators of PKR are long dsRNAs produced during viral infection, although certain other RNAs can also activate. A recent study indicated that full-length internal ribosome entry site (IRES), present in the 5'-untranslated region of hepatitis C virus (HCV) RNA, inhibits PKR, while another showed that it activates. We show here that both activation and inhibition by full-length IRES are possible. The HCV IRES has a complex secondary structure comprising four domains. While it has been demonstrated that domains III-IV activate PKR, we report here that domain II of the IRES also potently activates. Structure mapping and mutational analysis of domain II indicate that while the double-stranded regions of the RNA are important for activation, loop regions contribute as well. Structural comparison reveals that domain II has multiple, non-Watson-Crick features that mimic A-form dsRNA. The canonical and noncanonical features of domain II cumulate to a total of approximately 33 unbranched base pairs, the minimum length of dsRNA required for PKR activation. These results provide further insight into the structural basis of PKR activation by a diverse array of RNA structural motifs that deviate from the long helical stretches found in traditional PKR activators. Activation of PKR by domain II of the HCV IRES has implications for the innate immune response when the other domains of the IRES may be inaccessible. We also study the ability of the HCV nonstructural protein 5A (NS5A) to bind various domains of the IRES and alter activation. A model is presented for how domain II of the IRES and NS5A operate to control host and viral translation during HCV infection.
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Affiliation(s)
- Rebecca Toroney
- Department of Chemistry, Pennsylvania State University, 104 Chemistry Building, University Park, PA 16802, USA
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44
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Pastuszka MK, Mackay JA. Biomolecular engineering of intracellular switches in eukaryotes. J Drug Deliv Sci Technol 2010; 20:163-169. [PMID: 21209849 DOI: 10.1016/s1773-2247(10)50025-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Tools to selectively and reversibly control gene expression are useful to study and model cellular functions. When optimized, these cellular switches can turn a protein's function "on" and "off" based on cues designated by the researcher. These cues include small molecules, drugs, hormones, and even temperature variations. Here we review three distinct areas in gene expression that are commonly targeted when designing cellular switches. Transcriptional switches target gene expression at the level of mRNA polymerization, with examples including the tetracycline gene induction system as well as nuclear receptors. Translational switches target the process of turning the mRNA signal into protein, with examples including riboswitches and RNA interference. Post-translational switches control how proteins interact with one another to attenuate or relay signals. Examples of post-translational modification include dimerization and intein splicing. In general, the delay times between switch and effect decreases from transcription to translation to post-translation; furthermore, the fastest switches may offer the most elegant opportunities to influence and study cell behavior. We discuss the pros and cons of these strategies, which directly influence their usefulness to study and implement drug targeting at the tissue and cellular level.
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Affiliation(s)
- M K Pastuszka
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033-9121, United States
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45
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Carothers JM, Goler JA, Keasling JD. Chemical synthesis using synthetic biology. Curr Opin Biotechnol 2009; 20:498-503. [PMID: 19720519 DOI: 10.1016/j.copbio.2009.08.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 08/04/2009] [Accepted: 08/04/2009] [Indexed: 12/22/2022]
Abstract
An immense array of naturally occurring biological systems have evolved that convert simple substrates into the products that cells need for growth and persistence. Through the careful application of metabolic engineering and synthetic biology, this biotransformation potential can be harnessed to produce chemicals that address unmet clinical and industrial needs. Developing the capacity to utilize biology to perform chemistry is a matter of increasing control over both the function of synthetic biological systems and the engineering of those systems. Recent efforts have improved general techniques and yielded successes in the use of synthetic biology for the production of drugs, bulk chemicals, and fuels in microbial platform hosts. Synthetic promoter systems and novel RNA-based, or riboregulator, mechanisms give more control over gene expression. Improved methods for isolating, engineering, and evolving enzymes give more control over substrate and product specificity and better catalysis inside the cell. New computational tools and methods for high-throughput system assembly and analysis may lead to more rapid forward engineering. We highlight research that reduces reliance upon natural biological components and point to future work that may enable more rational design and assembly of synthetic biological systems for synthetic chemistry.
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Affiliation(s)
- James M Carothers
- California Institute for Quantitative Biosciences and Berkeley Center for Synthetic Biology, University of California, Berkeley, CA 94720, USA.
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