1
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Chyży P, Kulik M, Shinobu A, Re S, Sugita Y, Trylska J. Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch. Proc Natl Acad Sci U S A 2024; 121:e2317197121. [PMID: 38579011 PMCID: PMC11009640 DOI: 10.1073/pnas.2317197121] [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: 10/08/2023] [Accepted: 02/15/2024] [Indexed: 04/07/2024] Open
Abstract
Riboswitches are messenger RNA (mRNA) fragments binding specific small molecules to regulate gene expression. A synthetic N1 riboswitch, inserted into yeast mRNA controls the translation of a reporter gene in response to neomycin. However, its regulatory activity is sensitive to single-point RNA mutations, even those distant from the neomycin binding site. While the association paths of neomycin to N1 and its variants remain unknown, recent fluorescence kinetic experiments indicate a two-step process driven by conformational selection. This raises the question of which step is affected by mutations. To address this, we performed all-atom two-dimensional replica-exchange molecular dynamics simulations for N1 and U14C, U14C[Formula: see text], U15A, and A17G mutants, ensuring extensive conformational sampling of both RNA and neomycin. The obtained neomycin association and binding paths, along with multidimensional free-energy profiles, revealed a two-step binding mechanism, consisting of conformational selection and induced fit. Neomycin binds to a preformed N1 conformation upon identifying a stable upper stem and U-turn motif in the riboswitch hairpin. However, the positioning of neomycin in the binding site occurs at different RNA-neomycin distances for each mutant, which may explain their different regulatory activities. The subsequent induced fit arises from the interactions of the neomycin's N3 amino group with RNA, causing the G9 backbone to rearrange. In the A17G mutant, the critical C6-A17/G17 stacking forms at a closer RNA-neomycin distance compared to N1. These findings together with estimated binding free energies coincide with experiments and elucidate why the A17G mutation decreases and U15A enhances N1 activity in response to neomycin.
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Affiliation(s)
- Piotr Chyży
- Centre of New Technologies, University of Warsaw, 02-097Warsaw, Poland
| | - Marta Kulik
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-093Warsaw, Poland
| | - Ai Shinobu
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 650-0047Kobe, Japan
| | - Suyong Re
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 650-0047Kobe, Japan
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health, and Nutrition, 567-0085Ibaraki, Japan
| | - Yuji Sugita
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 650-0047Kobe, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 351-0198Wako, Japan
- RIKEN Center for Computational Science, 650-0047Kobe, Japan
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, 02-097Warsaw, Poland
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2
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Aptamers, Riboswitches, and Ribozymes in S. cerevisiae Synthetic Biology. Life (Basel) 2021; 11:life11030248. [PMID: 33802772 PMCID: PMC8002509 DOI: 10.3390/life11030248] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 01/09/2023] Open
Abstract
Among noncoding RNA sequences, riboswitches and ribozymes have attracted the attention of the synthetic biology community as circuit components for translation regulation. When fused to aptamer sequences, ribozymes and riboswitches are enabled to interact with chemicals. Therefore, protein synthesis can be controlled at the mRNA level without the need for transcription factors. Potentially, the use of chemical-responsive ribozymes/riboswitches would drastically simplify the design of genetic circuits. In this review, we describe synthetic RNA structures that have been used so far in the yeast Saccharomyces cerevisiae. We present their interaction mode with different chemicals (e.g., theophylline and antibiotics) or proteins (such as the RNase III) and their recent employment into clustered regularly interspaced short palindromic repeats–CRISPR-associated protein 9 (CRISPR-Cas) systems. Particular attention is paid, throughout the whole paper, to their usage and performance into synthetic gene circuits.
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3
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Kulik M, Mori T, Sugita Y, Trylska J. Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides. Nucleic Acids Res 2019; 46:9960-9970. [PMID: 30239867 PMCID: PMC6212780 DOI: 10.1093/nar/gky833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 09/07/2018] [Indexed: 01/14/2023] Open
Abstract
A synthetic riboswitch N1, inserted into the 5'-untranslated mRNA region of yeast, regulates gene expression upon binding ribostamycin and neomycin. Interestingly, a similar aminoglycoside, paromomycin, differing from neomycin by only one substituent (amino versus hydroxyl), also binds to the N1 riboswitch, but without affecting gene expression, despite NMR evidence that the N1 riboswitch binds all aminoglycosides in a similar way. Here, to explore the details of structural dynamics of the aminoglycoside-N1 riboswitch complexes, we applied all-atom molecular dynamics (MD) and temperature replica-exchange MD simulations in explicit solvent. Indeed, we found that ribostamycin and neomycin affect riboswitch dynamics similarly but paromomycin allows for more flexibility because its complex lacks the contact between the distinctive 6' hydroxyl group and the G9 phosphate. Instead, a transient hydrogen bond of 6'-OH with A17 is formed, which partially diminishes interactions between the bulge and apical loop of the riboswitch, likely contributing to riboswitch inactivity. In many ways, the paromomycin complex mimics the conformations, interactions, and Na+ distribution of the free riboswitch. The MD-derived interaction network helps understand why riboswitch activity depends on aminoglycoside type, whereas for another aminoglycoside-binding site, aminoacyl-tRNA site in 16S rRNA, activity is not discriminatory.
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Affiliation(s)
- Marta Kulik
- RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan.,Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | | | - Yuji Sugita
- RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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4
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Duchardt-Ferner E, Gottstein-Schmidtke SR, Weigand JE, Ohlenschläger O, Wurm JP, Hammann C, Suess B, Wöhnert J. Eine OH-Gruppe ändert alles: konformative Dynamik als Grundlage für die Ligandenspezifität des Neomycin-bindenden RNA-Schalters. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201507365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Elke Duchardt-Ferner
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ); Goethe-Universität Frankfurt; Max-von-Laue-Straße 9 60438 Frankfurt/M Deutschland
| | - Sina R. Gottstein-Schmidtke
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ); Goethe-Universität Frankfurt; Max-von-Laue-Straße 9 60438 Frankfurt/M Deutschland
| | - Julia E. Weigand
- Fachbereich Biologie; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Deutschland
| | - Oliver Ohlenschläger
- Biomolekulare NMR-Spektroskopie; Leibniz-Institut für Altersforschung (Fritz-Lipmann-Institut); Beutenbergstraße 11 07745 Jena Deutschland
| | - Jan-Philip Wurm
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ); Goethe-Universität Frankfurt; Max-von-Laue-Straße 9 60438 Frankfurt/M Deutschland
| | - Christian Hammann
- Ribogenetics Biochemistry Lab; Jacobs Universität Bremen; 28759 Bremen Deutschland
| | - Beatrix Suess
- Fachbereich Biologie; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Deutschland
| | - Jens Wöhnert
- Institut für Molekulare Biowissenschaften und Zentrum für Biomolekulare Magnetische Resonanz (BMRZ); Goethe-Universität Frankfurt; Max-von-Laue-Straße 9 60438 Frankfurt/M Deutschland
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5
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Duchardt-Ferner E, Gottstein-Schmidtke SR, Weigand JE, Ohlenschläger O, Wurm JP, Hammann C, Suess B, Wöhnert J. What a Difference an OH Makes: Conformational Dynamics as the Basis for the Ligand Specificity of the Neomycin-Sensing Riboswitch. Angew Chem Int Ed Engl 2015; 55:1527-30. [PMID: 26661511 DOI: 10.1002/anie.201507365] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Indexed: 01/13/2023]
Abstract
To ensure appropriate metabolic regulation, riboswitches must discriminate efficiently between their target ligands and chemically similar molecules that are also present in the cell. A remarkable example of efficient ligand discrimination is a synthetic neomycin-sensing riboswitch. Paromomycin, which differs from neomycin only by the substitution of a single amino group with a hydroxy group, also binds but does not flip the riboswitch. Interestingly, the solution structures of the two riboswitch-ligand complexes are virtually identical. In this work, we demonstrate that the local loss of key intermolecular interactions at the substitution site is translated through a defined network of intramolecular interactions into global changes in RNA conformational dynamics. The remarkable specificity of this riboswitch is thus based on structural dynamics rather than static structural differences. In this respect, the neomycin riboswitch is a model for many of its natural counterparts.
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Affiliation(s)
- Elke Duchardt-Ferner
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M, Deutschland
| | - Sina R Gottstein-Schmidtke
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M, Deutschland
| | - Julia E Weigand
- Fachbereich Biologie, Technische Universität Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Deutschland
| | - Oliver Ohlenschläger
- Biomolekulare NMR-Spektroskopie, Leibniz Institut für Altersforschung (Fritz-Lipmann-Institut), Beutenbergstrasse 11, 07745, Jena, Deutschland
| | - Jan-Philip Wurm
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M, Deutschland
| | - Christian Hammann
- Ribogenetics Biochemistry Lab, Jacobs Universität Bremen, 28759, Bremen, Deutschland
| | - Beatrix Suess
- Fachbereich Biologie, Technische Universität Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Deutschland
| | - Jens Wöhnert
- Institut für Molekulare Biowissenschaften and Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Goethe-Universität Frankfurt, Max-von-Laue Str. 9, 60438, Frankfurt/M, Deutschland.
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6
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Duchardt-Ferner E, Weigand JE, Ohlenschläger O, Schmidtke SR, Suess B, Wöhnert J. Highly modular structure and ligand binding by conformational capture in a minimalistic riboswitch. Angew Chem Int Ed Engl 2015; 49:6216-9. [PMID: 20632338 DOI: 10.1002/anie.201001339] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Elke Duchardt-Ferner
- Institute for Molecular Biosciences, Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
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7
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Klauser B, Atanasov J, Siewert LK, Hartig JS. Ribozyme-based aminoglycoside switches of gene expression engineered by genetic selection in S. cerevisiae. ACS Synth Biol 2015; 4:516-25. [PMID: 24871672 DOI: 10.1021/sb500062p] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Systems for conditional gene expression are powerful tools in basic research as well as in biotechnology. For future applications, it is of great importance to engineer orthogonal genetic switches that function reliably in diverse contexts. RNA-based switches have the advantage that effector molecules interact immediately with regulatory modules inserted into the target RNAs, getting rid of the need of transcription factors usually mediating genetic control. Artificial riboswitches are characterized by their simplicity and small size accompanied by a high degree of modularity. We have recently reported a series of hammerhead ribozyme-based artificial riboswitches that allow for post-transcriptional regulation of gene expression via switching mRNA, tRNA, or rRNA functions. A more widespread application was so far hampered by moderate switching performances and a limited set of effector molecules available. Here, we report the re-engineering of hammerhead ribozymes in order to respond efficiently to aminoglycoside antibiotics. We first established an in vivo selection protocol in Saccharomyces cerevisiae that enabled us to search large sequence spaces for optimized switches. We then envisioned and characterized a novel strategy of attaching the aptamer to the ribozyme catalytic core, increasing the design options for rendering the ribozyme ligand-dependent. These innovations enabled the development of neomycin-dependent RNA modules that switch gene expression up to 25-fold. The presented aminoglycoside-responsive riboswitches belong to the best-performing RNA-based genetic regulators reported so far. The developed in vivo selection protocol should allow for sampling of large sequence spaces for engineering of further optimized riboswitches.
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Affiliation(s)
- Benedikt Klauser
- Department of Chemistry, Konstanz Research School Chemical
Biology (KoRSCB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Janina Atanasov
- Department of Chemistry, Konstanz Research School Chemical
Biology (KoRSCB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Lena K. Siewert
- Department of Chemistry, Konstanz Research School Chemical
Biology (KoRSCB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Jörg S. Hartig
- Department of Chemistry, Konstanz Research School Chemical
Biology (KoRSCB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
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8
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Gottstein-Schmidtke SR, Duchardt-Ferner E, Groher F, Weigand JE, Gottstein D, Suess B, Wöhnert J. Building a stable RNA U-turn with a protonated cytidine. RNA (NEW YORK, N.Y.) 2014; 20:1163-72. [PMID: 24951555 PMCID: PMC4105743 DOI: 10.1261/rna.043083.113] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 05/16/2014] [Indexed: 05/28/2023]
Abstract
The U-turn is a classical three-dimensional RNA folding motif first identified in the anticodon and T-loops of tRNAs. It also occurs frequently as a building block in other functional RNA structures in many different sequence and structural contexts. U-turns induce sharp changes in the direction of the RNA backbone and often conform to the 3-nt consensus sequence 5'-UNR-3' (N = any nucleotide, R = purine). The canonical U-turn motif is stabilized by a hydrogen bond between the N3 imino group of the U residue and the 3' phosphate group of the R residue as well as a hydrogen bond between the 2'-hydroxyl group of the uridine and the N7 nitrogen of the R residue. Here, we demonstrate that a protonated cytidine can functionally and structurally replace the uridine at the first position of the canonical U-turn motif in the apical loop of the neomycin riboswitch. Using NMR spectroscopy, we directly show that the N3 imino group of the protonated cytidine forms a hydrogen bond with the backbone phosphate 3' from the third nucleotide of the U-turn analogously to the imino group of the uridine in the canonical motif. In addition, we compare the stability of the hydrogen bonds in the mutant U-turn motif to the wild type and describe the NMR signature of the C+-phosphate interaction. Our results have implications for the prediction of RNA structural motifs and suggest simple approaches for the experimental identification of hydrogen bonds between protonated C-imino groups and the phosphate backbone.
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Affiliation(s)
- Sina R Gottstein-Schmidtke
- Institute of Molecular Biosciences, Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany
| | - Elke Duchardt-Ferner
- Institute of Molecular Biosciences, Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany
| | - Florian Groher
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Julia E Weigand
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Daniel Gottstein
- Institute for Biophysical Chemistry, Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, 64287 Darmstadt, Germany
| | - Jens Wöhnert
- Institute of Molecular Biosciences, Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt/M., 60438 Frankfurt, Germany
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9
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Fosso MY, Li Y, Garneau-Tsodikova S. New trends in aminoglycosides use. MEDCHEMCOMM 2014; 5:1075-1091. [PMID: 25071928 PMCID: PMC4111210 DOI: 10.1039/c4md00163j] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Despite their inherent toxicity and the acquired bacterial resistance that continuously threaten their long-term clinical use, aminoglycosides (AGs) still remain valuable components of the antibiotic armamentarium. Recent literature shows that the AGs' role has been further expanded as multi-tasking players in different areas of study. This review aims at presenting some of the new trends observed in the use of AGs in the past decade, along with the current understanding of their mechanisms of action in various bacterial and eukaryotic cellular processes.
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Affiliation(s)
- Marina Y. Fosso
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy, BioPharm Complex, Room 423, 789 South Limestone Street, Lexington, KY, 40536-0596, U.S.A
| | - Yijia Li
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy, BioPharm Complex, Room 423, 789 South Limestone Street, Lexington, KY, 40536-0596, U.S.A
| | - Sylvie Garneau-Tsodikova
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy, BioPharm Complex, Room 423, 789 South Limestone Street, Lexington, KY, 40536-0596, U.S.A
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10
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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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11
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Abstract
RNA molecules are highly modular components that can be used in a variety of contexts for building new metabolic, regulatory and genetic circuits in cells. The majority of synthetic RNA systems to date predominately rely on two-dimensional modularity. However, a better understanding and integration of three-dimensional RNA modularity at structural and functional levels is critical to the development of more complex, functional bio-systems and molecular machines for synthetic biology applications.
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Affiliation(s)
- Wade Grabow
- Department of Chemistry and Biochemistry, Seattle Pacific University3307 Third Avenue West, Seattle, WA 98119USA
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Bio-Molecular Science and Engineering Program, University of CaliforniaSanta Barbara, CA 93106-9510USA
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12
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Quarta G, Sin K, Schlick T. Dynamic energy landscapes of riboswitches help interpret conformational rearrangements and function. PLoS Comput Biol 2012; 8:e1002368. [PMID: 22359488 PMCID: PMC3280964 DOI: 10.1371/journal.pcbi.1002368] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 12/19/2011] [Indexed: 11/23/2022] Open
Abstract
Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes. However, the way in which sequence dictates alternative folding pathways of gene regulation remains unclear. In this study, we compute energy landscapes, which describe the accessible secondary structures for a range of sequence lengths, to analyze the transcriptional process as a given sequence elongates to full length. In line with experimental evidence, we find that most riboswitch landscapes can be characterized by three broad classes as a function of sequence length in terms of the distribution and barrier type of the conformational clusters: low-barrier landscape with an ensemble of different conformations in equilibrium before encountering a substrate; barrier-free landscape in which a direct, dominant “downhill” pathway to the minimum free energy structure is apparent; and a barrier-dominated landscape with two isolated conformational states, each associated with a different biological function. Sharing concepts with the “new view” of protein folding energy landscapes, we term the three sequence ranges above as the sensing, downhill folding, and functional windows, respectively. We find that these energy landscape patterns are conserved in various riboswitch classes, though the order of the windows may vary. In fact, the order of the three windows suggests either kinetic or thermodynamic control of ligand binding. These findings help understand riboswitch structure/function relationships and open new avenues to riboswitch design. Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes. However, the way that sequence dictates alternative folding pathways of gene regulation remains unclear. In this study, we mimic transcription by computing energy landscapes which describe accessible secondary structures for a range of sequence lengths. Consistent with experimental evidence, we find that most riboswitch landscapes can be characterized by three broad classes as a function of sequence length in terms of the distribution and barrier type of the conformational clusters: Low-barrier landscape with an ensemble of conformations in equilibrium before encountering a substrate; barrier-free landscape with a dominant “downhill” pathway to the minimum free energy structure; and barrier-dominated landscape with two isolated conformational states with different functions. Sharing concepts with the “new view” of protein folding energy landscapes, we term the three sequence ranges above as the sensing, downhill folding, and functional windows, respectively. We find that these energy landscape patterns are conserved between riboswitch classes, though the order of the windows may vary. In fact, the order of the three windows suggests either kinetic or thermodynamic control of ligand binding. These findings help understand riboswitch structure/function relationships and open new avenues to riboswitch design.
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Affiliation(s)
- Giulio Quarta
- Department of Chemistry, New York University, New York, New York, United States of America
- Howard Hughes Medical Institute - Medical Research Fellows Program, Chevy Chase, Maryland, United States of America
| | - Ken Sin
- Department of Chemistry, New York University, New York, New York, United States of America
| | - Tamar Schlick
- Department of Chemistry, New York University, New York, New York, United States of America
- Courant Institute of Mathematical Sciences, New York University, New York, New York, United States of America
- * E-mail:
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13
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Duchardt-Ferner E, Ferner J, Wöhnert J. Direkte Identifizierung von nichtkanonischen RNA-Strukturelementen durch den Nachweis von OH⋅⋅⋅OP-, NH⋅⋅⋅OP- und NH2⋅⋅⋅OP-Wasserstoffbrücken mit NMR-Spektroskopie in Lösung. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101743] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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14
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Duchardt-Ferner E, Ferner J, Wöhnert J. Rapid identification of noncanonical RNA structure elements by direct detection of OH···O=P, NH···O=P, and NH2···O=P hydrogen bonds in solution NMR spectroscopy. Angew Chem Int Ed Engl 2011; 50:7927-30. [PMID: 21837618 DOI: 10.1002/anie.201101743] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 05/31/2011] [Indexed: 12/24/2022]
Affiliation(s)
- Elke Duchardt-Ferner
- Institute of Molecular Biosciences, Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-Universität Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
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15
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Weigand JE, Schmidtke SR, Will TJ, Duchardt-Ferner E, Hammann C, Wöhnert J, Suess B. Mechanistic insights into an engineered riboswitch: a switching element which confers riboswitch activity. Nucleic Acids Res 2010; 39:3363-72. [PMID: 21149263 PMCID: PMC3082870 DOI: 10.1093/nar/gkq946] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
While many different RNA aptamers have been identified that bind to a plethora of small molecules only very few are capable of acting as engineered riboswitches. Even for aptamers binding the same ligand large differences in their regulatory potential were observed. We address here the molecular basis for these differences by using a set of unrelated neomycin-binding aptamers. UV melting analyses showed that regulating aptamers are thermally stabilized to a significantly higher degree upon ligand binding than inactive ones. Regulating aptamers show high ligand-binding affinity in the low nanomolar range which is necessary but not sufficient for regulation. NMR data showed that a destabilized, open ground state accompanied by extensive structural changes upon ligand binding is important for regulation. In contrast, inactive aptamers are already pre-formed in the absence of the ligand. By a combination of genetic, biochemical and structural analyses, we identified a switching element responsible for destabilizing the ligand free state without compromising the bound form. Our results explain for the first time the molecular mechanism of an engineered riboswitch.
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Affiliation(s)
- Julia E Weigand
- RNA Biochemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt/M, Germany
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Nozinovic S, Richter C, Rinnenthal J, Fürtig B, Duchardt-Ferner E, Weigand JE, Schwalbe H. Quantitative 2D and 3D Gamma-HCP experiments for the determination of the angles alpha and zeta in the phosphodiester backbone of oligonucleotides. J Am Chem Soc 2010; 132:10318-29. [PMID: 20614918 DOI: 10.1021/ja910015n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The quantitative Gamma-(HCP) experiment, a novel heteronuclear NMR pulse sequence for the determination of the RNA backbone angles alpha(O3'(i-1)-P(i)-O5'(i)-C5'(i)) and zeta(C3'(i)-O3'(i)-P(i+1)-O5'(i+1)) in (13)C-labeled RNA, is introduced. The experiment relies on the interaction between the CH bond vector dipole and the (31)P chemical shift anisotropy (CSA), which affects the relaxation of the (13)C,(31)P double- and zero-quantum coherence and thus the intensity of the detectable magnetization. With the new pulse sequence, five different cross-correlated relaxation rates along the phosphodiester backbone can be measured in a quantitative manner, allowing projection-angle and torsion-angle restraints for the two backbone angles alpha and zeta to be extracted. Two versions of the pulse sequence optimized for the CH and CH(2) groups are introduced and demonstrated for a 14-mer cUUCGg tetraloop RNA model system and for a 27-mer RNA with a previously unknown structure. The restraints were incorporated into the calculation of a very high resolution structure of the RNA model system (Nozinovic, S.; et al. Nucleic Acids Res. 2010, 38, 683). Comparison with the X-ray structure of the cUUCGg tetraloop confirmed the high quality of the data, suggesting that the method can significantly improve the quality of RNA structure determination.
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Affiliation(s)
- Senada Nozinovic
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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Duchardt-Ferner E, Weigand J, Ohlenschläger O, Schmidtke S, Suess B, Wöhnert J. Hochmodulare Struktur und Ligandenbindung durch “Conformational Capture” in einem minimalistischen RNA-Schalter. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001339] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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