1
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Kallert E, Behrendt M, Frey A, Kersten C, Barthels F. Non-covalent dyes in microscale thermophoresis for studying RNA ligand interactions and modifications. Chem Sci 2023; 14:9827-9837. [PMID: 37736627 PMCID: PMC10510756 DOI: 10.1039/d3sc02993j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/27/2023] [Indexed: 09/23/2023] Open
Abstract
Microscale Thermophoresis (MST) is a powerful biophysical technique that measures the mobility of biomolecules in response to a temperature gradient, making it useful for investigating the interactions between biological molecules. This study presents a novel methodology for studying RNA-containing samples using non-covalent nucleic acid-sensitive dyes in MST. This "mix-and-measure" protocol uses non-covalent dyes, such as those from the Syto or Sybr series, which lead to the statistical binding of one fluorophore per RNA oligo showing key advantages over traditional covalent labelling approaches. This new approach has been successfully used to study the binding of ligands to RNA molecules (e.g., SAM- and PreQ1 riboswitches) and the identification of modifications (e.g., m6A) in short RNA oligos which can be written by the RNA methyltransferase METTL3/14.
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Affiliation(s)
- Elisabeth Kallert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz Staudingerweg 5 55128 Mainz Germany
| | - Malte Behrendt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz Staudingerweg 5 55128 Mainz Germany
| | - Ariane Frey
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz Staudingerweg 5 55128 Mainz Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz Staudingerweg 5 55128 Mainz Germany
| | - Fabian Barthels
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University of Mainz Staudingerweg 5 55128 Mainz Germany
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2
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Marton Menendez A, Nesbitt DJ. Ionic Cooperativity between Lysine and Potassium in the Lysine Riboswitch: Single-Molecule Kinetic and Thermodynamic Studies. J Phys Chem B 2023; 127:2430-2440. [PMID: 36916791 DOI: 10.1021/acs.jpcb.3c00245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Functionality in many biological systems, including proteins and nucleic acid structures, including protein and nucleic acid riboswitch structures, can depend on cooperative kinetic behavior between multiple small molecule ligands. In this work, single-molecule FRET data on the Bacillus subtilis lysine riboswitch reveals that affinity for the cognate lysine ligand increases significantly with K+, providing evidence for synergism between lysine/K+ binding to the aptamer and successful folding of the riboswitch. To describe/interpret this more complex kinetic scenario, we explore the conventional 4-state ("square") model for aptamer binding as a function of K+. Extension into this additional dimension generates a novel "cube" model for riboswitch folding dynamics with respect to lysine/K+ binding, revealing that riboswitch folding (kfold) and unfolding (kunfold) rate constants increase and decrease dramatically with K+, respectively. Furthermore, temperature-dependent single-molecule kinetic studies indicate that the presence of K+ entropically enhances the transition state barrier to folding but partially compensates for this by increasing the overall exothermicity for lysine binding. We rationalize this behavior as evidence that K+ facilitates hydrogen bonding between the negatively charged carboxyl group of lysine and the RNA, increasing structural rigidity and lowering entropy in the binding pocket. Finally, we explore the effects of cation size with Na+ and Cs+ studies to demonstrate that K+ is optimally suited for bridging interactions between lysine and the riboswitch aptamer domain. Regulation of lysine production and transport, dictated by the riboswitch's ability to recognize and bind lysine, is therefore intimately tied to the presence of K+ in the binding pocket and is strongly modulated by local cation conditions. The results suggest an increase in lysine riboswitch functionality by sensitivity to additional species in the cellular riboswitch environment.
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Affiliation(s)
- Andrea Marton Menendez
- JILA, University of Colorado Boulder and National Institute of Standards and Technology, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - David J Nesbitt
- JILA, University of Colorado Boulder and National Institute of Standards and Technology, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Department of Physics, University of Colorado Boulder, Boulder, Colorado 80309, United States
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3
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Zheng L, Song Q, Xu X, Shen X, Li C, Li H, Chen H, Ren A. Structure-based insights into recognition and regulation of SAM-sensing riboswitches. SCIENCE CHINA. LIFE SCIENCES 2023; 66:31-50. [PMID: 36459353 DOI: 10.1007/s11427-022-2188-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/17/2022] [Indexed: 12/03/2022]
Abstract
Riboswitches are highly conserved RNA elements that located in the 5'-UTR of mRNAs, which undergo real-time structure conformational change to achieve the regulation of downstream gene expression by sensing their cognate ligands. S-adenosylmethionine (SAM) is a ubiquitous methyl donor for transmethylation reactions in all living organisms. SAM riboswitch is one of the most abundant riboswitches that bind to SAM with high affinity and selectivity, serving as regulatory modules in multiple metabolic pathways. To date, seven SAM-specific riboswitch classes that belong to four families, one SAM/SAH riboswitch and one SAH riboswitch have been identified. Each SAM riboswitch family has a well-organized tertiary core scaffold to support their unique ligand-specific binding pocket. In this review, we summarize the current research progress on the distribution, structure, ligand recognition and gene regulation mechanism of these SAM-related riboswitch families, and further discuss their evolutionary prospects and potential applications.
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Affiliation(s)
- Luqian Zheng
- Department of Gastroenterology, Department of Cardiology of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China.,Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.,The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Qianqian Song
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Xiaochen Xu
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Xin Shen
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Chunyan Li
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Hongcheng Li
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Hao Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Aiming Ren
- Department of Gastroenterology, Department of Cardiology of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China. .,Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.
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4
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Kallert E, Fischer TR, Schneider S, Grimm M, Helm M, Kersten C. Protein-Based Virtual Screening Tools Applied for RNA-Ligand Docking Identify New Binders of the preQ 1-Riboswitch. J Chem Inf Model 2022; 62:4134-4148. [PMID: 35994617 DOI: 10.1021/acs.jcim.2c00751] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Targeting RNA with small molecules is an emerging field. While several ligands for different RNA targets are reported, structure-based virtual screenings (VSs) against RNAs are still rare. Here, we elucidated the general capabilities of protein-based docking programs to reproduce native binding modes of small-molecule RNA ligands and to discriminate known binders from decoys by the scoring function. The programs were found to perform similar compared to the RNA-based docking tool rDOCK, and the challenges faced during docking, namely, protomer and tautomer selection, target dynamics, and explicit solvent, do not largely differ from challenges in conventional protein-ligand docking. A prospective VS with the Bacillus subtilis preQ1-riboswitch aptamer domain performed with FRED, HYBRID, and FlexX followed by microscale thermophoresis assays identified six active compounds out of 23 tested VS hits with potencies between 29.5 nM and 11.0 μM. The hits were selected not solely based on their docking score but for resembling key interactions of the native ligand. Therefore, this study demonstrates the general feasibility to perform structure-based VSs against RNA targets, while at the same time it highlights pitfalls and their potential solutions when executing RNA-ligand docking.
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Affiliation(s)
- Elisabeth Kallert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Simon Schneider
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Maike Grimm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
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5
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Marton Menendez A, Nesbitt DJ. Lysine-Dependent Entropy Effects in the B. subtilis Lysine Riboswitch: Insights from Single-Molecule Thermodynamic Studies. J Phys Chem B 2021; 126:69-79. [PMID: 34958583 DOI: 10.1021/acs.jpcb.1c07833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Riboswitches play an important role in RNA-based sensing/gene regulation control for many bacteria. In particular, the accessibility of multiple conformational states at physiological temperatures allows riboswitches to selectively bind a cognate ligand in the aptamer domain, which triggers secondary structural changes in the expression platform, and thereby "switching" between on or off transcriptional or translational states for the downstream RNA. The present work exploits temperature-controlled, single-molecule total internal reflection fluorescence (TIRF) microscopy to study the thermodynamic landscape of such ligand binding/folding processes, specifically for the Bacillus subtilis lysine riboswitch. The results confirm that the riboswitch folds via an induced-fit (IF) mechanism, in which cognate lysine ligand first binds to the riboswitch before structural rearrangement takes place. The transition state to folding is found to be enthalpically favored (ΔHfold‡ < 0), yet with a free-energy barrier that is predominantly entropic (-TΔSfold‡ > 0), which results in folding (unfolding) rate constants strongly dependent (independent) of lysine concentration. Analysis of the single-molecule kinetic "trajectories" reveals this rate constant dependence of kfold on lysine to be predominantly entropic in nature, with the additional lysine conferring preferential advantage to the folding process by the presence of ligands correctly oriented with respect to the riboswitch platform. By way of contrast, van't Hoff analysis reveals enthalpic contributions to the overall folding thermodynamics (ΔH0) to be surprisingly constant and robustly independent of lysine concentration. The results demonstrate the crucial role of hydrogen bonding between the ligand and riboswitch platform but with only a relatively modest fraction (45%) of the overall enthalpy change needed to access the transition state and initiate transcriptional switching.
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Affiliation(s)
- Andrea Marton Menendez
- JILA, University of Colorado Boulder and National Institute of Standards and Technology, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - David J Nesbitt
- JILA, University of Colorado Boulder and National Institute of Standards and Technology, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States.,Department of Physics, University of Colorado Boulder, Boulder, Colorado 80309, United States
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6
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Manz C, Kobitski AY, Samanta A, Nienhaus K, Jäschke A, Nienhaus GU. Exploring the energy landscape of a SAM-I riboswitch. J Biol Phys 2021; 47:371-386. [PMID: 34698957 PMCID: PMC8603990 DOI: 10.1007/s10867-021-09584-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/25/2021] [Indexed: 11/30/2022] Open
Abstract
SAM-I riboswitches regulate gene expression through transcription termination upon binding a S-adenosyl-L-methionine (SAM) ligand. In previous work, we characterized the conformational energy landscape of the full-length Bacillus subtilis yitJ SAM-I riboswitch as a function of Mg2+ and SAM ligand concentrations. Here, we have extended this work with measurements on a structurally similar ligand, S-adenosyl-l-homocysteine (SAH), which has, however, a much lower binding affinity. Using single-molecule Förster resonance energy transfer (smFRET) microscopy and hidden Markov modeling (HMM) analysis, we identified major conformations and determined their fractional populations and dynamics. At high Mg2+ concentration, FRET analysis yielded four distinct conformations, which we assigned to two terminator and two antiterminator states. In the same solvent, but with SAM added at saturating concentrations, four states persisted, although their populations, lifetimes and interconversion dynamics changed. In the presence of SAH instead of SAM, HMM revealed again four well-populated states and, in addition, a weakly populated ‘hub’ state that appears to mediate conformational transitions between three of the other states. Our data show pronounced and specific effects of the SAM and SAH ligands on the RNA conformational energy landscape. Interestingly, both SAM and SAH shifted the fractional populations toward terminator folds, but only gradually, so the effect cannot explain the switching action. Instead, we propose that the noticeably accelerated dynamics of interconversion between terminator and antiterminator states upon SAM binding may be essential for control of transcription.
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Affiliation(s)
- Christoph Manz
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131, Karlsruhe, Germany
| | - Andrei Yu Kobitski
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131, Karlsruhe, Germany
| | - Ayan Samanta
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany.,Department of Chemistry, Uppsala University, Box 538, 751 21, Uppsala, Sweden
| | - Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131, Karlsruhe, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Gerd Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131, Karlsruhe, Germany. .,Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany. .,Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany. .,Department of Physics, University of Illinois at Urbana-Champaign, 1110 W. Green St, Urbana, IL, 61801, USA.
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7
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Sarkar R, Jaiswar A, Hennelly SP, Onuchic JN, Sanbonmatsu KY, Roy S. Chelated Magnesium Logic Gate Regulates Riboswitch Pseudoknot Formation. J Phys Chem B 2021; 125:6479-6490. [PMID: 34106719 DOI: 10.1021/acs.jpcb.1c02467] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Magnesium plays a critical role in the structure, dynamics, and function of RNA. The precise microscopic effect of chelated magnesium on RNA structure is yet to be explored. Magnesium is known to act through its diffuse cloud around RNA, through the outer sphere (water-mediated), inner sphere, and often chelated ion-mediated interactions. A mechanism is proposed for the role of experimentally discovered site-specific chelated magnesium ions on the conformational dynamics of SAM-I riboswitch aptamers in bacteria. This mechanism is observed with atomistic simulations performed in a physiological mixed salt environment at a high temperature. The simulations were validated with phosphorothioate interference mapping experiments that help to identify crucial inner-sphere Mg2+ sites prescribing an appropriate initial distribution of inner- and outer-sphere magnesium ions to maintain a physiological ion concentration of monovalent and divalent salts. A concerted role of two chelated magnesium ions is newly discovered since the presence of both supports the formation of the pseudoknot. This constitutes a logical AND gate. The absence of any of these magnesium ions instigates the dissociation of long-range pseudoknot interaction exposing the inner core of the RNA. A base triple is the epicenter of the magnesium chelation effect. It allosterically controls RNA pseudoknot by bolstering the direct effect of magnesium chelation in protecting the functional fold of RNA to control ON and OFF transcription switching.
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Affiliation(s)
- Raju Sarkar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Kolkata, West Bengal 741246, India
| | - Akhilesh Jaiswar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Kolkata, West Bengal 741246, India
| | - Scott P Hennelly
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.,New Mexico Consortium, Los Alamos, New Mexico 87544, United States
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States.,Departments of Physics and Astronomy, Chemistry, and Biosciences, Rice University, Houston, Texas 77005, United States
| | - Karissa Y Sanbonmatsu
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.,New Mexico Consortium, Los Alamos, New Mexico 87544, United States
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Kolkata, West Bengal 741246, India
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8
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Roy S, Hennelly SP, Lammert H, Onuchic JN, Sanbonmatsu KY. Magnesium controls aptamer-expression platform switching in the SAM-I riboswitch. Nucleic Acids Res 2019; 47:3158-3170. [PMID: 30605518 PMCID: PMC6451092 DOI: 10.1093/nar/gky1311] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/19/2018] [Accepted: 12/28/2018] [Indexed: 12/23/2022] Open
Abstract
Investigations of most riboswitches remain confined to the ligand-binding aptamer domain. However, during the riboswitch mediated transcription regulation process, the aptamer domain and the expression platform compete for a shared strand. If the expression platform dominates, an anti-terminator helix is formed, and the transcription process is active (ON state). When the aptamer dominates, transcription is terminated (OFF state). Here, we use an expression platform switching experimental assay and structure-based electrostatic simulations to investigate this ON-OFF transition of the full length SAM-I riboswitch and its magnesium concentration dependence. Interestingly, we find the ratio of the OFF population to the ON population to vary non-monotonically as magnesium concentration increases. Upon addition of magnesium, the aptamer domain pre-organizes, populating the OFF state, but only up to an intermediate magnesium concentration level. Higher magnesium concentration preferentially stabilizes the anti-terminator helix, populating the ON state, relatively destabilizing the OFF state. Magnesium mediated aptamer-expression platform domain closure explains this relative destabilization of the OFF state at higher magnesium concentration. Our study reveals the functional potential of magnesium in controlling transcription of its downstream genes and underscores the importance of a narrow concentration regime near the physiological magnesium concentration ranges, striking a balance between the OFF and ON states in bacterial gene regulation.
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Affiliation(s)
- Susmita Roy
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Scott P Hennelly
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Heiko Lammert
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.,Departments of Physics and Astronomy, Chemistry, and Biosciences, Rice University, Houston, TX 77005, USA
| | - Karissa Y Sanbonmatsu
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,New Mexico Consortium, Los Alamos, NM 87544, USA
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9
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Seelam PP, Mitra A, Sharma P. Pairing interactions between nucleobases and ligands in aptamer:ligand complexes of riboswitches: crystal structure analysis, classification, optimal structures, and accurate interaction energies. RNA (NEW YORK, N.Y.) 2019; 25:1274-1290. [PMID: 31315914 PMCID: PMC6800475 DOI: 10.1261/rna.071530.119] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
In the present work, 67 crystal structures of the aptamer domains of RNA riboswitches are chosen for analysis of the structure and strength of hydrogen bonding (pairing) interactions between nucleobases constituting the aptamer binding pockets and the bound ligands. A total of 80 unique base:ligand hydrogen-bonded pairs containing at least two hydrogen bonds were identified through visual inspection. Classification of these contacts in terms of the interacting edge of the aptamer nucleobase revealed that interactions involving the Watson-Crick edge are the most common, followed by the sugar edge of purines and the Hoogsteen edge of uracil. Alternatively, classification in terms of the chemical constitution of the ligand yields five unique classes of base:ligand pairs: base:base, base:amino acid, base:sugar, base:phosphate, and base:other. Further, quantum mechanical (QM) geometry optimizations revealed that 67 out of 80 pairs exhibit stable geometries and optimal deviations from their macromolecular crystal occurrences. This indicates that these contacts are well-defined RNA aptamer:ligand interaction motifs. QM calculated interaction energies of base:ligand pairs reveal a rich hydrogen bonding landscape, ranging from weak interactions (base:other, -3 kcal/mol) to strong (base:phosphate, -48 kcal/mol) contacts. The analysis was further extended to study the biological importance of base:ligand interactions in the binding pocket of the tetrahydrofolate riboswitch and thiamine pyrophosphate riboswitch. Overall, our study helps in understanding the structural and energetic features of base:ligand pairs in riboswitches, which could aid in developing meaningful hypotheses in the context of RNA:ligand recognition. This can, in turn, contribute toward current efforts to develop antimicrobials that target RNAs.
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Affiliation(s)
- Preethi P Seelam
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad, Telangana 500032, India
| | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad, Telangana 500032, India
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
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10
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Vicens Q, Mondragón E, Reyes FE, Coish P, Aristoff P, Berman J, Kaur H, Kells KW, Wickens P, Wilson J, Gadwood RC, Schostarez HJ, Suto RK, Blount KF, Batey RT. Structure-Activity Relationship of Flavin Analogues That Target the Flavin Mononucleotide Riboswitch. ACS Chem Biol 2018; 13:2908-2919. [PMID: 30107111 DOI: 10.1021/acschembio.8b00533] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The flavin mononucleotide (FMN) riboswitch is an emerging target for the development of novel RNA-targeting antibiotics. We previously discovered an FMN derivative, 5FDQD, that protects mice against diarrhea-causing Clostridium difficile bacteria. Here, we present the structure-based drug design strategy that led to the discovery of this fluoro-phenyl derivative with antibacterial properties. This approach involved the following stages: (1) structural analysis of all available free and bound FMN riboswitch structures; (2) design, synthesis, and purification of derivatives; (3) in vitro testing for productive binding using two chemical probing methods; (4) in vitro transcription termination assays; and (5) resolution of the crystal structures of the FMN riboswitch in complex with the most mature candidates. In the process, we delineated principles for productive binding to this riboswitch, thereby demonstrating the effectiveness of a coordinated structure-guided approach to designing drugs against RNA.
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Affiliation(s)
- Quentin Vicens
- Department of Chemistry and Biochemistry, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
| | - Estefanía Mondragón
- Department of Chemistry and Biochemistry, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
| | - Francis E. Reyes
- Department of Chemistry and Biochemistry, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
| | - Philip Coish
- BioRelix Inc., 124 Washington Street, Foxborough, Massachusetts 02035, United States
| | - Paul Aristoff
- Aristoff Consulting LLC, 3726 Green Spring Drive, Fort Collins, Colorado 80528, United States
| | - Judd Berman
- Dalton Pharma Services, 349 Wildcat Road, Toronto, ON M3J 2S3, Canada
| | - Harpreet Kaur
- Dalton Pharma Services, 349 Wildcat Road, Toronto, ON M3J 2S3, Canada
| | - Kevin W. Kells
- Dalton Pharma Services, 349 Wildcat Road, Toronto, ON M3J 2S3, Canada
| | - Phil Wickens
- Dalton Pharma Services, 349 Wildcat Road, Toronto, ON M3J 2S3, Canada
| | - Jeffery Wilson
- Dalton Pharma Services, 349 Wildcat Road, Toronto, ON M3J 2S3, Canada
| | - Robert C. Gadwood
- Kalexsyn, Inc., 4502 Campus Drive, Kalamazoo, Michigan 49008, United States
| | | | - Robert K. Suto
- Xtal BioStructures, Inc., 12 Michigan Drive, Natick, Massachusetts 01760, United States
| | - Kenneth F. Blount
- BioRelix Inc., 124 Washington Street, Foxborough, Massachusetts 02035, United States
| | - Robert T. Batey
- Department of Chemistry and Biochemistry, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
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11
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Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018; 118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 336] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
Abstract
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory, Department of Biology , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Richard A Cunha
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Giovanni Pinamonti
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Simón Poblete
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
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12
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Manz C, Kobitski AY, Samanta A, Jäschke A, Nienhaus GU. The multi-state energy landscape of the SAM-I riboswitch: A single-molecule Förster resonance energy transfer spectroscopy study. J Chem Phys 2018; 148:123324. [DOI: 10.1063/1.5003783] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Christoph Manz
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- HEiKA–Heidelberg Karlsruhe Research Partnership, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Andrei Yu. Kobitski
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Ayan Samanta
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Andres Jäschke
- HEiKA–Heidelberg Karlsruhe Research Partnership, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - G. Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
- HEiKA–Heidelberg Karlsruhe Research Partnership, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Institute of Nanotechnology and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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13
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Designing fluorescent biosensors using circular permutations of riboswitches. Methods 2018; 143:102-109. [PMID: 29458090 DOI: 10.1016/j.ymeth.2018.02.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/31/2018] [Accepted: 02/14/2018] [Indexed: 02/06/2023] Open
Abstract
RNA-based fluorescent (RBF) biosensors have been applied to detect a variety of metabolites in vitro and in live cells. They are designed by combining the ligand sensing domain of natural riboswitches with in vitro selected fluorogenic aptamers. Different biosensor topologies have been developed to accommodate the diversity of riboswitch structures. Here we show that circular permutation of the riboswitch ligand sensing domain also gives functional biosensors, using the SAM-I riboswitch as our model. We reveal that this design can enhance fluorescence turn-on and ligand binding affinity compared to the non-permuted topology.
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14
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Gong S, Wang Y, Wang Z, Sun Y, Zhang W. Folding behaviors of purine riboswitch aptamers. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/s11859-018-1292-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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15
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Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, Verma V, Keedy DA, Hintze BJ, Chen VB, Jain S, Lewis SM, Arendall WB, Snoeyink J, Adams PD, Lovell SC, Richardson JS, Richardson DC. MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci 2018; 27:293-315. [PMID: 29067766 PMCID: PMC5734394 DOI: 10.1002/pro.3330] [Citation(s) in RCA: 2341] [Impact Index Per Article: 390.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 10/19/2017] [Accepted: 10/23/2017] [Indexed: 12/27/2022]
Abstract
This paper describes the current update on macromolecular model validation services that are provided at the MolProbity website, emphasizing changes and additions since the previous review in 2010. There have been many infrastructure improvements, including rewrite of previous Java utilities to now use existing or newly written Python utilities in the open-source CCTBX portion of the Phenix software system. This improves long-term maintainability and enhances the thorough integration of MolProbity-style validation within Phenix. There is now a complete MolProbity mirror site at http://molprobity.manchester.ac.uk. GitHub serves our open-source code, reference datasets, and the resulting multi-dimensional distributions that define most validation criteria. Coordinate output after Asn/Gln/His "flip" correction is now more idealized, since the post-refinement step has apparently often been skipped in the past. Two distinct sets of heavy-atom-to-hydrogen distances and accompanying van der Waals radii have been researched and improved in accuracy, one for the electron-cloud-center positions suitable for X-ray crystallography and one for nuclear positions. New validations include messages at input about problem-causing format irregularities, updates of Ramachandran and rotamer criteria from the million quality-filtered residues in a new reference dataset, the CaBLAM Cα-CO virtual-angle analysis of backbone and secondary structure for cryoEM or low-resolution X-ray, and flagging of the very rare cis-nonProline and twisted peptides which have recently been greatly overused. Due to wide application of MolProbity validation and corrections by the research community, in Phenix, and at the worldwide Protein Data Bank, newly deposited structures have continued to improve greatly as measured by MolProbity's unique all-atom clashscore.
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Affiliation(s)
| | - Jeffrey J. Headd
- Department of BiochemistryDuke UniversityDurhamNC27710USA
- Present address:
Janssen Research and DevelopmentSpring HousePA19477USA
| | - Nigel W. Moriarty
- Molecular Biosciences and Integrated BioimagingLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | | | | | - Lindsay N. Deis
- Department of BiochemistryDuke UniversityDurhamNC27710USA
- Present address:
Department of BiochemistryStanford University, StanfordCA95126USA
| | - Vishal Verma
- Department of Computer ScienceUniversity of North CarolinaChapel HillNC27599USA
| | - Daniel A. Keedy
- Department of BiochemistryDuke UniversityDurhamNC27710USA
- Present address:
Structural Biology Initiative and Department of Chemistry & BiochemistryCUNY Advanced Science Research Center, City University of New YorkNew YorkNY10031USA
| | | | | | - Swati Jain
- Department of BiochemistryDuke UniversityDurhamNC27710USA
- Present address:
Department of ChemistryNew York UniversityNew YorkNYUSA
| | - Steven M. Lewis
- Department of BiochemistryDuke UniversityDurhamNC27710USA
- Present address:
Cyrus Biotechnology, 500 Union Street, Suite 320SeattleWA98101USA
| | | | - Jack Snoeyink
- Department of Computer ScienceUniversity of North CarolinaChapel HillNC27599USA
| | - Paul D. Adams
- Molecular Biosciences and Integrated BioimagingLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Simon C. Lovell
- School of Biological SciencesUniversity of ManchesterManchesterM13 9PTUK
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16
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Dussault AM, Dubé A, Jacques F, Grondin JP, Lafontaine DA. Ligand recognition and helical stacking formation are intimately linked in the SAM-I riboswitch regulatory mechanism. RNA (NEW YORK, N.Y.) 2017; 23:1539-1551. [PMID: 28701520 PMCID: PMC5602112 DOI: 10.1261/rna.061796.117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/10/2017] [Indexed: 06/07/2023]
Abstract
Riboswitches are noncoding mRNA elements that control gene expression by altering their structure upon metabolite binding. Although riboswitch crystal structures provide detailed information about RNA-ligand interactions, little knowledge has been gathered to understand how riboswitches modulate gene expression. Here, we study the molecular recognition mechanism of the S-adenosylmethionine SAM-I riboswitch by characterizing the formation of a helical stacking interaction involving the ligand-binding process. We show that ligand binding is intimately linked to the formation of the helical stacking, which is dependent on the presence of three conserved purine residues that are flanked by stacked helices. We also find that these residues are important for the formation of a crucial long-range base pair formed upon SAM binding. Together, our results lend strong support to a critical role for helical stacking in the folding pathway and suggest a particularly important function in the formation of the long-range base pair.
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Affiliation(s)
- Anne-Marie Dussault
- Department of Biology, Faculty of Sciences, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Audrey Dubé
- Department of Biology, Faculty of Sciences, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Frédéric Jacques
- Department of Biology, Faculty of Sciences, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Jonathan P Grondin
- Department of Biology, Faculty of Sciences, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
| | - Daniel A Lafontaine
- Department of Biology, Faculty of Sciences, RNA Group, Université de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
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17
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Manz C, Kobitski AY, Samanta A, Keller BG, Jäschke A, Nienhaus GU. Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch. Nat Chem Biol 2017; 13:1172-1178. [DOI: 10.1038/nchembio.2476] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 08/03/2017] [Indexed: 11/09/2022]
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18
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Roy S, Onuchic JN, Sanbonmatsu KY. Cooperation between Magnesium and Metabolite Controls Collapse of the SAM-I Riboswitch. Biophys J 2017; 113:348-359. [PMID: 28746845 DOI: 10.1016/j.bpj.2017.06.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/25/2017] [Accepted: 06/22/2017] [Indexed: 12/23/2022] Open
Abstract
The S-adenosylmethionine (SAM)-I riboswitch is a noncoding RNA that regulates the transcription termination process in response to metabolite (SAM) binding. The aptamer portion of the riboswitch may adopt an open or closed state depending on the presence of metabolite. Although the transition between the open and closed states is critical for the switching process, its atomistic details are not well understood. Using atomistic simulations, we calculate the effect of SAM and magnesium ions on the folding free energy landscape of the SAM-I riboswitch. These molecular simulation results are consistent with our previous wetlab experiments and aid in interpreting the SHAPE probing measurements. Here, molecular dynamics simulations explicitly identify target RNA motifs sensitive to magnesium ions and SAM. In the simulations, we observe that, whereas the metabolite mostly stabilizes the P1 and P3 helices, magnesium serves an important role in stabilizing a pseudoknot interaction between the P2 and P4 helices, even at high metabolite concentrations. The pseudoknot stabilization by magnesium, in combination with P1 stabilization by SAM, explains the requirement of both SAM and magnesium to form the fully collapsed metabolite-bound closed state of the SAM-I riboswitch. In the absence of SAM, frequent open-to-closed conformational transitions of the pseudoknot occur, akin to breathing. These pseudoknot fluctuations disrupt the binding site by facilitating fluctuations in the 5'-end of helix P1. Magnesium biases the landscape toward a collapsed state (preorganization) by coordinating pseudoknot and 5'-P1 fluctuations. The cooperation between SAM and magnesium in stabilizing important tertiary interactions elucidates their functional significance in transcription regulation.
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Affiliation(s)
- Susmita Roy
- Center for Theoretical Biological Physics, Chemistry, and Biosciences, Rice University, Houston, Texas
| | - José N Onuchic
- Center for Theoretical Biological Physics, Chemistry, and Biosciences, Rice University, Houston, Texas; Departments of Physics and Astronomy, Chemistry, and Biosciences, Rice University, Houston, Texas.
| | - Karissa Y Sanbonmatsu
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico; New Mexico Consortium, Los Alamos, New Mexico.
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19
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Gong S, Wang Y, Wang Z, Zhang W. Co-Transcriptional Folding and Regulation Mechanisms of Riboswitches. Molecules 2017; 22:molecules22071169. [PMID: 28703767 PMCID: PMC6152003 DOI: 10.3390/molecules22071169] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 07/07/2017] [Accepted: 07/09/2017] [Indexed: 11/16/2022] Open
Abstract
Riboswitches are genetic control elements within non-coding regions of mRNA. These self-regulatory elements have been found to sense a range of small metabolites, ions, and other physical signals to exert regulatory control of transcription, translation, and splicing. To date, more than a dozen riboswitch classes have been characterized that vary widely in size and secondary structure. Extensive experiments and theoretical studies have made great strides in understanding the general structures, genetic mechanisms, and regulatory activities of individual riboswitches. As the ligand-dependent co-transcriptional folding and unfolding dynamics of riboswitches are the key determinant of gene expression, it is important to investigate the thermodynamics and kinetics of riboswitches both in the presence and absence of metabolites under the transcription. This review will provide a brief summary of the studies about the regulation mechanisms of the pbuE, SMK, yitJ, and metF riboswitches based on the ligand-dependent co-transcriptional folding of the riboswitches.
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Affiliation(s)
- Sha Gong
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal University, Huanggang 438000, Hubei, China.
| | - Yanli Wang
- Department of Physics, Wuhan University, Wuhan 430072, Hubei, China.
| | - Zhen Wang
- Department of Physics, Wuhan University, Wuhan 430072, Hubei, China.
| | - Wenbing Zhang
- Department of Physics, Wuhan University, Wuhan 430072, Hubei, China.
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20
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Polaski JT, Webster SM, Johnson JE, Batey RT. Cobalamin riboswitches exhibit a broad range of ability to discriminate between methylcobalamin and adenosylcobalamin. J Biol Chem 2017; 292:11650-11658. [PMID: 28483920 DOI: 10.1074/jbc.m117.787176] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/04/2017] [Indexed: 12/15/2022] Open
Abstract
Riboswitches are a widely distributed class of regulatory RNAs in bacteria that modulate gene expression via small-molecule-induced conformational changes. Generally, these RNA elements are grouped into classes based upon conserved primary and secondary structure and their cognate effector molecule. Although this approach has been very successful in identifying new riboswitch families and defining their distributions, small sequence differences between structurally related RNAs can alter their ligand selectivity and regulatory behavior. Herein, we use a structure-based mutagenic approach to demonstrate that cobalamin riboswitches have a broad spectrum of preference for the two biological forms of cobalamin in vitro using isothermal titration calorimetry. This selectivity is primarily mediated by the interaction between a peripheral element of the RNA that forms a T-loop module and a subset of nucleotides in the cobalamin-binding pocket. Cell-based fluorescence reporter assays in Escherichia coli revealed that mutations that switch effector preference in vitro lead to differential regulatory responses in a biological context. These data demonstrate that a more comprehensive analysis of representative sequences of both previously and newly discovered classes of riboswitches might reveal subgroups of RNAs that respond to different effectors. Furthermore, this study demonstrates a second distinct means by which tertiary structural interactions in cobalamin riboswitches dictate ligand selectivity.
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Affiliation(s)
- Jacob T Polaski
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309
| | - Samantha M Webster
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309
| | - James E Johnson
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309
| | - Robert T Batey
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309.
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21
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Jones CP, Ferré-D'Amaré AR. Long-Range Interactions in Riboswitch Control of Gene Expression. Annu Rev Biophys 2017; 46:455-481. [PMID: 28375729 DOI: 10.1146/annurev-biophys-070816-034042] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Riboswitches are widespread RNA motifs that regulate gene expression in response to fluctuating metabolite concentrations. Known primarily from bacteria, riboswitches couple specific ligand binding and changes in RNA structure to mRNA expression in cis. Crystal structures of the ligand binding domains of most of the phylogenetically widespread classes of riboswitches, each specific to a particular metabolite or ion, are now available. Thus, the bound states-one end point-have been thoroughly characterized, but the unbound states have been more elusive. Consequently, it is less clear how the unbound, sensing riboswitch refolds into the ligand binding-induced output state. The ligand recognition mechanisms of riboswitches are diverse, but we find that they share a common structural strategy in positioning their binding sites at the point of the RNA three-dimensional fold where the residues farthest from one another in sequence meet. We review how riboswitch folds adhere to this fundamental strategy and propose future research directions for understanding and harnessing their ability to specifically control gene expression.
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Affiliation(s)
- Christopher P Jones
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824;
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824;
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22
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Wang R, Luo Z, He K, Delaney MO, Chen D, Sheng J. Base pairing and structural insights into the 5-formylcytosine in RNA duplex. Nucleic Acids Res 2016; 44:4968-77. [PMID: 27079978 PMCID: PMC4889945 DOI: 10.1093/nar/gkw235] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 03/24/2016] [Indexed: 12/20/2022] Open
Abstract
5-Formylcytidine (f5C), a previously discovered natural nucleotide in the mitochondrial tRNA of many species including human, has been recently detected as the oxidative product of 5-methylcytidine (m5C) through 5-hydroxymethylcytidine (hm5C) in total RNA of mammalian cells. The discovery indicated that these cytosine derivatives in RNA might also play important epigenetic roles similar as in DNA, which has been intensively investigated in the past few years. In this paper, we studied the base pairing specificity of f5C in different RNA duplex contexts. We found that the 5-formyl group could increase duplex thermal stability and enhance base pairing specificity. We present three high-resolution crystal structures of an octamer RNA duplex [5′-GUA(f5C)GUAC-3′]2 that have been solved under three crystallization conditions with different buffers and pH values. Our results showed that the 5-formyl group is located in the same plane as the cytosine base and forms an intra-residue hydrogen bond with the amino group in the N4 position. In addition, this modification increases the base stacking between the f5C and the neighboring bases while not causing significant global and local structure perturbations. This work provides insights into the effects of 5-formylcytosine on RNA duplex.
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Affiliation(s)
- Rui Wang
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Zhipu Luo
- Synchrotron Radiation Research Section, MCL National Cancer Institute, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Kaizhang He
- Dharmacon, GE Healthcare, Lafayette, CO 80026, USA
| | | | - Doris Chen
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Jia Sheng
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
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23
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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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24
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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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25
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Aboul-ela F, Huang W, Abd Elrahman M, Boyapati V, Li P. Linking aptamer-ligand binding and expression platform folding in riboswitches: prospects for mechanistic modeling and design. WILEY INTERDISCIPLINARY REVIEWS. RNA 2015; 6:631-50. [PMID: 26361734 PMCID: PMC5049679 DOI: 10.1002/wrna.1300] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 07/27/2015] [Accepted: 07/28/2015] [Indexed: 11/23/2022]
Abstract
The power of riboswitches in regulation of bacterial metabolism derives from coupling of two characteristics: recognition and folding. Riboswitches contain aptamers, which function as biosensors. Upon detection of the signaling molecule, the riboswitch transduces the signal into a genetic decision. The genetic decision is coupled to refolding of the expression platform, which is distinct from, although overlapping with, the aptamer. Early biophysical studies of riboswitches focused on recognition of the ligand by the aptamer-an important consideration for drug design. A mechanistic understanding of ligand-induced riboswitch RNA folding can further enhance riboswitch ligand design, and inform efforts to tune and engineer riboswitches with novel properties. X-ray structures of aptamer/ligand complexes point to mechanisms through which the ligand brings together distal strand segments to form a P1 helix. Transcriptional riboswitches must detect the ligand and form this P1 helix within the timescale of transcription. Depending on the cell's metabolic state and cellular environmental conditions, the folding and genetic outcome may therefore be affected by kinetics of ligand binding, RNA folding, and transcriptional pausing, among other factors. Although some studies of isolated riboswitch aptamers found homogeneous, prefolded conformations, experimental, and theoretical studies point to functional and structural heterogeneity for nascent transcripts. Recently it has been shown that some riboswitch segments, containing the aptamer and partial expression platforms, can form binding-competent conformers that incorporate an incomplete aptamer secondary structure. Consideration of the free energy landscape for riboswitch RNA folding suggests models for how these conformers may act as transition states-facilitating rapid, ligand-mediated aptamer folding.
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Affiliation(s)
- Fareed Aboul-ela
- Center for X-Ray Determination of the Structure of Matter, University of Science and Technology at Zewail City, Giza, Egypt
| | - Wei Huang
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH, USA
| | - Maaly Abd Elrahman
- Center for X-Ray Determination of the Structure of Matter, University of Science and Technology at Zewail City, Giza, Egypt
- Therapeutical Chemistry Department, National Research Center, El Buhouth St., Dokki, Cairo, Egypt
| | - Vamsi Boyapati
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Pan Li
- Department of Biological Sciences, University at Albany-SUNY, Albany, NY, USA
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26
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Wostenberg C, Ceres P, Polaski JT, Batey RT. A Highly Coupled Network of Tertiary Interactions in the SAM-I Riboswitch and Their Role in Regulatory Tuning. J Mol Biol 2015; 427:3473-3490. [PMID: 26343759 DOI: 10.1016/j.jmb.2015.07.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 07/27/2015] [Accepted: 07/30/2015] [Indexed: 01/24/2023]
Abstract
RNA folding in vivo is significantly influenced by transcription, which is not necessarily recapitulated by Mg(2+)-induced folding of the corresponding full-length RNA in vitro. Riboswitches that regulate gene expression at the transcriptional level are an ideal system for investigating this aspect of RNA folding as ligand-dependent termination is obligatorily co-transcriptional, providing a clear readout of the folding outcome. The folding of representative members of the SAM-I family of riboswitches has been extensively analyzed using approaches focusing almost exclusively upon Mg(2+) and/or S-adenosylmethionine (SAM)-induced folding of full-length transcripts of the ligand binding domain. To relate these findings to co-transcriptional regulatory activity, we have investigated a set of structure-guided mutations of conserved tertiary architectural elements of the ligand binding domain using an in vitro single-turnover transcriptional termination assay, complemented with phylogenetic analysis and isothermal titration calorimetry data. This analysis revealed a conserved internal loop adjacent to the SAM binding site that significantly affects ligand binding and regulatory activity. Conversely, most single point mutations throughout key conserved features in peripheral tertiary architecture supporting the SAM binding pocket have relatively little impact on riboswitch activity. Instead, a secondary structural element in the peripheral subdomain appears to be the key determinant in observed differences in regulatory properties across the SAM-I family. These data reveal a highly coupled network of tertiary interactions that promote high-fidelity co-transcriptional folding of the riboswitch but are only indirectly linked to regulatory tuning.
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Affiliation(s)
- Christopher Wostenberg
- Department of Chemistry and Biochemistry, University of Colorado Boulder, 596 UCB, Boulder, CO 80309-0596, USA
| | - Pablo Ceres
- Department of Chemistry and Biochemistry, University of Colorado Boulder, 596 UCB, Boulder, CO 80309-0596, USA
| | - Jacob T Polaski
- Department of Chemistry and Biochemistry, University of Colorado Boulder, 596 UCB, Boulder, CO 80309-0596, USA
| | - Robert T Batey
- Department of Chemistry and Biochemistry, University of Colorado Boulder, 596 UCB, Boulder, CO 80309-0596, USA.
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27
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Dutta D, Wedekind JE. Gene Regulation Gets in Tune: How Riboswitch Tertiary-Structure Networks Adapt to Meet the Needs of Their Transcription Units. J Mol Biol 2015; 427:3469-3472. [PMID: 26255959 DOI: 10.1016/j.jmb.2015.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Debapratim Dutta
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester NY 14642, USA
| | - Joseph E Wedekind
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester NY 14642, USA.
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28
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Gong S, Wang Y, Zhang W. The regulation mechanism ofyitJandmetFriboswitches. J Chem Phys 2015; 143:045103. [DOI: 10.1063/1.4927390] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Sha Gong
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
| | - Yujie Wang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
| | - Wenbing Zhang
- Department of Physics, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
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29
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Sheng J, Larsen A, Heuberger BD, Blain JC, Szostak JW. Crystal structure studies of RNA duplexes containing s(2)U:A and s(2)U:U base pairs. J Am Chem Soc 2014; 136:13916-24. [PMID: 25188906 PMCID: PMC4183603 DOI: 10.1021/ja508015a] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
Structural studies of modified nucleobases
in RNA duplexes are
critical for developing a full understanding of the stability and
specificity of RNA base pairing. 2-Thio-uridine (s2U) is
a modified nucleobase found in certain tRNAs. Thermodynamic studies
have evaluated the effects of s2U on base pairing in RNA,
where it has been shown to stabilize U:A pairs and destabilize U:G
wobble pairs. Surprisingly, no high-resolution crystal structures
of s2U-containing RNA duplexes have yet been reported.
We present here two high-resolution crystal structures of heptamer
RNA duplexes (5′-uagcs2Ucc-3′ paired with 3′-aucgAgg-5′ and with 3′-aucgUgg-5′) containing s2U:A and s2U:U pairs, respectively. For comparison, we also present the structures
of their native counterparts solved under identical conditions. We
found that replacing O2 with S2 stabilizes the U:A base pair without
any detectable structural perturbation. In contrast, an s2U:U base pair is strongly stabilized in one specific U:U pairing
conformation out of four observed for the native U:U base pair. This
s2U:U stabilization appears to be due at least in part
to an unexpected sulfur-mediated hydrogen bond. This work provides
additional insights into the effects of 2-thio-uridine on RNA base
pairing.
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Affiliation(s)
- Jia Sheng
- Howard Hughes Medical Institute, Center for Computational and Integrative Biology, and Department of Molecular Biology, Simches Research Center, Massachusetts General Hospital , Boston, Massachusetts 02114, United States
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30
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Chen X, Wang X, Feng J, Chen Y, Fang Y, Zhao S, Zhao A, Zhang M, Liu L. Structural insights into the catalytic mechanism of Synechocystis magnesium protoporphyrin IX O-methyltransferase (ChlM). J Biol Chem 2014; 289:25690-8. [PMID: 25077963 DOI: 10.1074/jbc.m114.584920] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Magnesium protoporphyrin IX O-methyltransferase (ChlM) catalyzes transfer of the methyl group from S-adenosylmethionine to the carboxyl group of the C13 propionate side chain of magnesium protoporphyrin IX. This reaction is the second committed step in chlorophyll biosynthesis from protoporphyrin IX. Here we report the crystal structures of ChlM from the cyanobacterium Synechocystis sp. PCC 6803 in complex with S-adenosylmethionine and S-adenosylhomocysteine at resolutions of 1.6 and 1.7 Å, respectively. The structures illustrate the molecular basis for cofactor and substrate binding and suggest that conformational changes of the two "arm" regions may modulate binding and release of substrates/products to and from the active site. Tyr-28 and His-139 were identified to play essential roles for methyl transfer reaction but are not indispensable for cofactor/substrate binding. Based on these structural and functional findings, a catalytic model is proposed.
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Affiliation(s)
- Xuemin Chen
- From the Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China, the University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Wang
- From the Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China, the University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Feng
- From the Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China, the University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuhong Chen
- From the Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ying Fang
- From the Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China, the University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shun Zhao
- From the Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China, the University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Aiguo Zhao
- From the Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China, the University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Zhang
- the Engineering Research Center for Biomedical Materials, School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China, and
| | - Lin Liu
- From the Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China,
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31
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Price IR, Grigg JC, Ke A. Common themes and differences in SAM recognition among SAM riboswitches. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:931-938. [PMID: 24863160 DOI: 10.1016/j.bbagrm.2014.05.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 05/13/2014] [Accepted: 05/15/2014] [Indexed: 12/19/2022]
Abstract
The recent discovery of short cis-acting RNA elements termed riboswitches has caused a paradigm shift in our understanding of genetic regulatory mechanisms. The three distinct superfamilies of S-adenosyl-l-methionine (SAM) riboswitches are the most commonly found riboswitch classes in nature. These RNAs represent three independent evolutionary solutions to achieve specific SAM recognition. This review summarizes research on 1) modes of gene regulatory mechanisms, 2) common themes and differences in ligand recognition, and 3) ligand-induced conformational dynamics among SAM riboswitch families. The body of work on the SAM riboswitch families constitutes a useful primer to the topic of gene regulatory RNAs as a whole. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Ian R Price
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jason C Grigg
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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32
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Structural basis for diversity in the SAM clan of riboswitches. Proc Natl Acad Sci U S A 2014; 111:6624-9. [PMID: 24753586 DOI: 10.1073/pnas.1312918111] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In bacteria, sulfur metabolism is regulated in part by seven known families of riboswitches that bind S-adenosyl-l-methionine (SAM). Direct binding of SAM to these mRNA regulatory elements governs a downstream secondary structural switch that communicates with the transcriptional and/or translational expression machinery. The most widely distributed SAM-binding riboswitches belong to the SAM clan, comprising three families that share a common SAM-binding core but differ radically in their peripheral architecture. Although the structure of the SAM-I member of this clan has been extensively studied, how the alternative peripheral architecture of the other families supports the common SAM-binding core remains unknown. We have therefore solved the X-ray structure of a member of the SAM-I/IV family containing the alternative "PK-2" subdomain shared with the SAM-IV family. This structure reveals that this subdomain forms extensive interactions with the helix housing the SAM-binding pocket, including a highly unusual mode of helix packing in which two helices pack in a perpendicular fashion. Biochemical and genetic analysis of this RNA reveals that SAM binding induces many of these interactions, including stabilization of a pseudoknot that is part of the regulatory switch. Despite strong structural similarity between the cores of SAM-I and SAM-I/IV members, a phylogenetic analysis of sequences does not indicate that they derive from a common ancestor.
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33
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Baird NJ, Ferré-D'Amaré AR. Analysis of riboswitch structure and ligand binding using small-angle X-ray scattering (SAXS). Methods Mol Biol 2014; 1103:211-25. [PMID: 24318897 PMCID: PMC4049135 DOI: 10.1007/978-1-62703-730-3_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Small-angle X-ray scattering (SAXS) is a powerful tool for examining the global conformation of riboswitches in solution, and how this is modulated by binding of divalent cations and small molecule ligands. SAXS experiments, which typically require only minutes per sample, directly yield two quantities describing the size and shape of the RNA: the radius of gyration (Rg) and the maximum linear dimension (Dmax). Examination of these quantities can reveal if a riboswitch undergoes cation-induced compaction. Comparison of the Rg and Dmax values between samples containing different concentrations of ligand reveals the overall structural response of the riboswitch to ligand. The Kratky plot (a graphical representation that emphasizes the higher-resolution SAXS data) and the P(r) plot or pair-probability distribution (an indirect Fourier transform, or power spectrum of the data) can provide additional evidence of riboswitch conformational changes. Simulation methods have been developed for generating three-dimensional reconstructions consistent with the one-dimensional SAXS data. These low-resolution molecular envelopes can aid in deciphering the relative helical arrangement within the RNA.
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Affiliation(s)
- Nathan J. Baird
- Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA
| | - Adrian R. Ferré-D'Amaré
- Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA
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34
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Moll I, Fabbretti A, Brandi L, Gualerzi CO. Inhibitors Targeting Riboswitches and Ribozymes. Antibiotics (Basel) 2013. [DOI: 10.1002/9783527659685.ch13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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35
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Huang W, Kim J, Jha S, Aboul-ela F. The impact of a ligand binding on strand migration in the SAM-I riboswitch. PLoS Comput Biol 2013; 9:e1003069. [PMID: 23704854 PMCID: PMC3656099 DOI: 10.1371/journal.pcbi.1003069] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 04/09/2013] [Indexed: 11/29/2022] Open
Abstract
Riboswitches sense cellular concentrations of small molecules and use this information to adjust synthesis rates of related metabolites. Riboswitches include an aptamer domain to detect the ligand and an expression platform to control gene expression. Previous structural studies of riboswitches largely focused on aptamers, truncating the expression domain to suppress conformational switching. To link ligand/aptamer binding to conformational switching, we constructed models of an S-adenosyl methionine (SAM)-I riboswitch RNA segment incorporating elements of the expression platform, allowing formation of an antiterminator (AT) helix. Using Anton, a computer specially developed for long timescale Molecular Dynamics (MD), we simulated an extended (three microseconds) MD trajectory with SAM bound to a modeled riboswitch RNA segment. Remarkably, we observed a strand migration, converting three base pairs from an antiterminator (AT) helix, characteristic of the transcription ON state, to a P1 helix, characteristic of the OFF state. This conformational switching towards the OFF state is observed only in the presence of SAM. Among seven extended trajectories with three starting structures, the presence of SAM enhances the trend towards the OFF state for two out of three starting structures tested. Our simulation provides a visual demonstration of how a small molecule (<500 MW) binding to a limited surface can trigger a large scale conformational rearrangement in a 40 kDa RNA by perturbing the Free Energy Landscape. Such a mechanism can explain minimal requirements for SAM binding and transcription termination for SAM-I riboswitches previously reported experimentally.
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Affiliation(s)
- Wei Huang
- Department of Biological Science, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Center for Computation & Technology, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Joohyun Kim
- Center for Computation & Technology, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Shantenu Jha
- Center for Computation & Technology, Louisiana State University, Baton Rouge, Louisiana, United States of America
- Department of Electrical and Computer Engineering, Rutgers University, Piscataway, New Jersey, United States of America
| | - Fareed Aboul-ela
- Department of Biological Science, Louisiana State University, Baton Rouge, Louisiana, United States of America
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36
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Daldrop P, Lilley DM. The plasticity of a structural motif in RNA: structural polymorphism of a kink turn as a function of its environment. RNA (NEW YORK, N.Y.) 2013; 19:357-64. [PMID: 23325110 PMCID: PMC3677246 DOI: 10.1261/rna.036657.112] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The k-turn is a widespread structural motif that introduces a tight kink into the helical axis of double-stranded RNA. The adenine bases of consecutive G•A pairs are directed toward the minor groove of the opposing helix, hydrogen bonding in a typical A-minor interaction. We show here that the available structures of k-turns divide into two classes, depending on whether N3 or N1 of the adenine at the 2b position accepts a hydrogen bond from the O2' at the -1n position. There is a coordinated structural change involving a number of hydrogen bonds between the two classes. We show here that Kt-7 can adopt either the N3 or N1 structures depending on environment. While it has the N1 structure in the ribosome, on engineering it into the SAM-I riboswitch, it changes to the N3 structure, resulting in a significant alteration in the trajectory of the helical arms.
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37
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Watson PY, Fedor MJ. The ydaO motif is an ATP-sensing riboswitch in Bacillus subtilis. Nat Chem Biol 2012; 8:963-5. [PMID: 23086297 DOI: 10.1038/nchembio.1095] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 09/21/2012] [Indexed: 01/01/2023]
Abstract
We report what is to our knowledge the first natural RNA that regulates gene expression in response to intracellular ATP. Using a biochemical screen, we found that several putative riboswitches bind ATP in vitro. The ydaO motif specifically bound ATP and regulated expression of endogenous and reporter genes in response to ATP concentrations in Bacillus subtilis. This discovery demonstrates a role for RNAs in regulating gene expression in response to energy balance in bacteria.
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Affiliation(s)
- Peter Y Watson
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA
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38
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Garst AD, Porter EB, Batey RT. Insights into the regulatory landscape of the lysine riboswitch. J Mol Biol 2012; 423:17-33. [PMID: 22771573 DOI: 10.1016/j.jmb.2012.06.038] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 06/21/2012] [Accepted: 06/26/2012] [Indexed: 12/11/2022]
Abstract
A prevalent means of regulating gene expression in bacteria is by riboswitches found within mRNA leader sequences. Like protein repressors, these RNA elements must bind an effector molecule with high specificity against a background of other cellular metabolites of similar chemical structure to elicit the appropriate regulatory response. Current crystal structures of the lysine riboswitch do not provide a complete understanding of selectivity as recognition is substantially mediated through main-chain atoms of the amino acid. Using a directed set of lysine analogs and other amino acids, we have determined the relative contributions of the polar functional groups to binding affinity and the regulatory response. Our results reveal that the lysine riboswitch has >1000-fold specificity for lysine over other amino acids. The aptamer is highly sensitive to the precise placement of the ε-amino group and relatively tolerant of alterations to the main-chain functional groups in order to achieve this specificity. At low nucleotide triphosphate (NTP) concentrations, we observe good agreement between the half-maximal regulatory activity (T(50)) and the affinity of the receptor for lysine (K(d)), as well as many of its analogs. However, above 400 μM [NTP], the concentration of lysine required to elicit transcription termination rises, moving into the riboswitch into a kinetic control regime. These data demonstrate that, under physiologically relevant conditions, riboswitches can integrate both effector and NTP concentrations to generate a regulatory response appropriate for global metabolic state of the cell.
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Affiliation(s)
- Andrew D Garst
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, 596 UCB, Boulder, CO 80309-0596, USA
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39
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Schroeder KT, Daldrop P, McPhee SA, Lilley DM. Structure and folding of a rare, natural kink turn in RNA with an A*A pair at the 2b*2n position. RNA (NEW YORK, N.Y.) 2012; 18:1257-66. [PMID: 22539525 PMCID: PMC3358647 DOI: 10.1261/rna.032409.112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 03/28/2012] [Indexed: 05/20/2023]
Abstract
The kink turn (k-turn) is a frequently occurring motif, comprising a bulge followed by G•A and A•G pairs that introduces a sharp axial bend in duplex RNA. Natural k-turn sequences exhibit significant departures from the consensus, including the A•G pairs that form critical interactions stabilizing the core of the structure. Kt-23 found in the small ribosomal subunit differs from the consensus in many organisms, particularly in the second A•G pair distal to the bulge (2b•2n). Analysis of many Kt-23 sequences shows that the frequency of occurrence at the 2n position (i.e., on the nonbulged strand, normally G in standard k-turns) is U>C>G>A. Less than 1% of sequences have A at the 2n position, but one such example occurs in Thelohania solenopsae Kt-23. This sequence folds only weakly in the presence of Mg²⁺ ions but is induced to fold normally by the binding of L7Ae protein. Introduction of this sequence into the SAM-I riboswitch resulted in normal binding of SAM ligand, indicating that tertiary RNA contacts have resulted in k-turn folding. X-ray crystallography shows that the T. solenopsae Kt-23 adopts a standard k-turn geometry, making the key, conserved hydrogen bonds in the core and orienting the 1n (of the bulge-proximal A•G pair) and 2b adenine nucleobases in position facing the opposing minor groove. The 2b and 2n adenine nucleobases are not directly hydrogen bonded, but each makes hydrogen bonds to their opposing strands.
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Affiliation(s)
- Kersten T. Schroeder
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Peter Daldrop
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Scott A. McPhee
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
| | - David M.J. Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, United Kingdom
- Corresponding author.E-mail .
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40
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Boyapati VK, Huang W, Spedale J, Aboul-ela F. Basis for ligand discrimination between ON and OFF state riboswitch conformations: the case of the SAM-I riboswitch. RNA (NEW YORK, N.Y.) 2012; 18:1230-1243. [PMID: 22543867 PMCID: PMC3358645 DOI: 10.1261/rna.032177.111] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Accepted: 03/17/2012] [Indexed: 05/31/2023]
Abstract
Riboswitches are RNA elements that bind to effector ligands and control gene expression. Most consist of two domains. S-Adenosyl Methionine (SAM) binds the aptamer domain of the SAM-I riboswitch and induces conformational changes in the expression domain to form an intrinsic terminator (transcription OFF state). Without SAM the riboswitch forms the transcription ON state, allowing read-through transcription. The mechanistic link between the SAM/aptamer recognition event and subsequent secondary structure rearrangement by the riboswitch is unclear. We probed for those structural features of the Bacillus subtilis yitJ SAM-I riboswitch responsible for discrimination between the ON and OFF states by SAM. We designed SAM-I riboswitch RNA segments forming "hybrid" structures of the ON and OFF states. The choice of segment constrains the formation of a partial P1 helix, characteristic of the OFF state, together with a partial antiterminator (AT) helix, characteristic of the ON state. For most choices of P1 vs. AT helix lengths, SAM binds with micromolar affinity according to equilibrium dialysis. Mutational analysis and in-line probing confirm that the mode of SAM binding by hybrid structures is similar to that of the aptamer. Altogether, binding measurements and in-line probing are consistent with the hypothesis that when SAM is present, stacking interactions with the AT helix stabilize a partially formed P1 helix in the hybrids. Molecular modeling indicates that continuous stacking between the P1 and the AT helices is plausible with SAM bound. Our findings raise the possibility that conformational intermediates may play a role in ligand-induced aptamer folding.
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Affiliation(s)
- Vamsi Krishna Boyapati
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70802, USA
| | - Wei Huang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70802, USA
| | - Jessica Spedale
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70802, USA
| | - Fareed Aboul-ela
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70802, USA
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41
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Ghai R, Falconer RJ, Collins BM. Applications of isothermal titration calorimetry in pure and applied research--survey of the literature from 2010. J Mol Recognit 2012; 25:32-52. [PMID: 22213449 DOI: 10.1002/jmr.1167] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Isothermal titration calorimetry (ITC) is a biophysical technique for measuring the formation and dissociation of molecular complexes and has become an invaluable tool in many branches of science from cell biology to food chemistry. By measuring the heat absorbed or released during bond formation, ITC provides accurate, rapid, and label-free measurement of the thermodynamics of molecular interactions. In this review, we survey the recent literature reporting the use of ITC and have highlighted a number of interesting studies that provide a flavour of the diverse systems to which ITC can be applied. These include measurements of protein-protein and protein-membrane interactions required for macromolecular assembly, analysis of enzyme kinetics, experimental validation of molecular dynamics simulations, and even in manufacturing applications such as food science. Some highlights include studies of the biological complex formed by Staphylococcus aureus enterotoxin C3 and the murine T-cell receptor, the mechanism of membrane association of the Parkinson's disease-associated protein α-synuclein, and the role of non-specific tannin-protein interactions in the quality of different beverages. Recent developments in automation are overcoming limitations on throughput imposed by previous manual procedures and promise to greatly extend usefulness of ITC in the future. We also attempt to impart some practical advice for getting the most out of ITC data for those researchers less familiar with the method.
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Affiliation(s)
- Rajesh Ghai
- Institute for Molecular Bioscience (IMB), University of Queensland, St. Lucia, Queensland, 4072, Australia
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Baird NJ, Zhang J, Hamma T, Ferré-D'Amaré AR. YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops. RNA (NEW YORK, N.Y.) 2012; 18:759-70. [PMID: 22355167 PMCID: PMC3312563 DOI: 10.1261/rna.031518.111] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 12/24/2011] [Indexed: 05/20/2023]
Abstract
The archaeal protein L7Ae and eukaryotic homologs such as L30e and 15.5kD comprise the best characterized family of K-turn-binding proteins. K-turns are an RNA motif comprised of a bulge flanked by canonical and noncanonical helices. They are widespread in cellular RNAs, including bacterial gene-regulatory RNAs such as the c-di-GMP-II, lysine, and SAM-I riboswitches, and the T-box. The existence in bacteria of K-turn-binding proteins of the L7Ae family has not been proven, although two hypothetical proteins, YbxF and YlxQ, have been proposed to be L7Ae homologs based on sequence conservation. Using purified, recombinant proteins, we show that Bacillus subtilis YbxF and YlxQ bind K-turns (K(d) ~270 nM and ~2300 nM, respectively). Crystallographic structure determination demonstrates that both YbxF and YlxQ adopt the same overall fold as L7Ae. Unlike the latter, neither bacterial protein recognizes K-loops, a structural motif that lacks the canonical helix of the K-turn. This property is shared between the bacterial and eukaryal family members. Comparison of our structure of YbxF in complex with the K-turn of the SAM-I riboswitch and previously determined structures of archaeal and eukaryal homologs bound to RNA indicates that L7Ae approaches the K-turn at a unique angle, which results in a considerably larger RNA-protein interface dominated by interactions with the noncanonical helix of the K-turn. Thus, the inability of the bacterial and eukaryal L7Ae homologs to bind K-loops probably results from their reliance on interactions with the canonical helix. The biological functions of YbxF and YlxQ remain to be determined.
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Affiliation(s)
- Nathan J. Baird
- Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892-8012, USA
| | - Jinwei Zhang
- Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892-8012, USA
| | - Tomoko Hamma
- Pacific Northwest University of Health Sciences, Yakima, Washington 98901, USA
| | - Adrian R. Ferré-D'Amaré
- Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892-8012, USA
- Corresponding author.E-mail .
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43
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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44
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Huang W, Kim J, Jha S, Aboul-Ela F. Conformational heterogeneity of the SAM-I riboswitch transcriptional ON state: a chaperone-like role for S-adenosyl methionine. J Mol Biol 2012; 418:331-49. [PMID: 22425639 DOI: 10.1016/j.jmb.2012.02.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 02/09/2012] [Accepted: 02/15/2012] [Indexed: 10/28/2022]
Abstract
Riboswitches are promising targets for the design of novel antibiotics and engineering of portable genetic regulatory elements. There is evidence that variability in riboswitch properties allows tuning of expression for genes involved in different stages of biosynthetic pathways by mechanisms that are not currently understood. Here, we explore the mechanism for tuning of S-adenosyl methionine (SAM)-I riboswitch folding. Most SAM-I riboswitches function at the transcriptional level by sensing the cognate ligand SAM. SAM-I riboswitches orchestrate the biosynthetic pathways of cysteine, methionine, SAM, and so forth. We use base-pair probability predictions to examine the secondary-structure folding landscape of several SAM-I riboswitch sequences. We predict different folding behaviors for different SAM-I riboswitch sequences. We identify several "decoy" base-pairing interactions involving 5' riboswitch residues that can compete with the formation of a P1 helix, a component of the ligand-bound "transcription OFF" state, in the absence of SAM. We hypothesize that blockage of these interactions through SAM contacts contributes to stabilization of the OFF state in the presence of ligand. We also probe folding patterns for a SAM-I riboswitch RNA using constructs with different 3' truncation points experimentally. Folding was monitored through fluorescence, susceptibility to base-catalyzed cleavage, nuclear magnetic resonance, and indirectly through SAM binding. We identify key decision windows at which SAM can affect the folding pathway towards the OFF state. The presence of decoy conformations and differential sensitivities to SAM at different transcript lengths is crucial for SAM-I riboswitches to modulate gene expression in the context of global cellular metabolism.
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Affiliation(s)
- Wei Huang
- Department of Biological Science, Louisiana State University, Baton Rouge, LA 70803, USA
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45
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Eschbach SH, St-Pierre P, Penedo JC, Lafontaine DA. Folding of the SAM-I riboswitch: a tale with a twist. RNA Biol 2012; 9:535-41. [PMID: 22336759 DOI: 10.4161/rna.19648] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Riboswitches are ligand-dependent RNA genetic regulators that control gene expression by altering their structures. The elucidation of riboswitch conformational changes before and after ligand recognition is crucial to understand how riboswitches can achieve high ligand binding affinity and discrimination against cellular analogs. The detailed characterization of riboswitch folding pathways suggest that they may use their intrinsic conformational dynamics to sample a large array of structures, some of which being nearly identical to ligand-bound molecules. Some of these structural conformers can be "captured" upon ligand binding, which is crucial for the outcome of gene regulation. Recent studies about the SAM-I riboswitch have revealed unexpected and previously unknown RNA folding mechanisms. For instance, the observed helical twist of the P1 stem upon ligand binding to the SAM-I aptamer adds a new element in the repertoire of RNA strategies for recognition of small metabolites. From an RNA folding perspective, these findings also strongly indicate that the SAM-I riboswitch could achieve ligand recognition by using an optimized combination of conformational capture and induced-fit approaches, a feature that may be shared by other RNA regulatory sequences.
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Affiliation(s)
- Sébastien H Eschbach
- Groupe ARN/RNA Group, Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
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46
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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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47
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Doshi U, Kelley JM, Hamelberg D. Atomic-level insights into metabolite recognition and specificity of the SAM-II riboswitch. RNA (NEW YORK, N.Y.) 2012; 18:300-7. [PMID: 22194311 PMCID: PMC3264916 DOI: 10.1261/rna.028779.111] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 11/18/2011] [Indexed: 05/23/2023]
Abstract
Although S-adenosylhomocysteine (SAH), a metabolic by-product of S-adenosylmethionine (SAM), differs from SAM only by a single methyl group and an overall positive charge, SAH binds the SAM-II riboswitch with more than 1000-fold less affinity than SAM. Using atomistic molecular dynamics simulations, we investigated the molecular basis of such high selectivity in ligand recognition by SAM-II riboswitch. The biosynthesis of SAM exclusively generates the (S,S) stereoisomer, and (S,S)-SAM can spontaneously convert to the (R,S) form. We, therefore, also examined the effects of (R,S)-SAM binding to SAM-II and its potential biological function. We find that the unfavorable loss in entropy in SAM-II binding is greater for (S,S)- and (R,S)-SAM than SAH, which is compensated by stabilizing electrostatic interactions with the riboswitch. The positively charged sulfonium moiety on SAM acts as the crucial anchor point responsible for the formation of key ionic interactions as it fits favorably in the negatively charged binding pocket. In contrast, SAH, with its lone pair of electrons on the sulfur, experiences repulsion in the binding pocket of SAM-II and is enthalpically destabilized. In the presence of SAH, similar to the unbound riboswitch, the pseudoknot structure of SAM-II is not completely formed, thus exposing the Shine-Dalgarno sequence. Unlike SAM, this may further facilitate ribosomal assembly and translation initiation. Our analysis of the conformational ensemble sampled by SAM-II in the absence of ligands and when bound to SAM or SAH reveals that ligand binding follows a combination of conformational selection and induced-fit mechanisms.
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Affiliation(s)
- Urmi Doshi
- Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, USA
| | - Jennifer M. Kelley
- Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, USA
| | - Donald Hamelberg
- Department of Chemistry and the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, USA
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48
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Wrońska M, Wrzesinski J, Jeżowska-Bojczuk M, Szczepanik W, Starosta R, Barys M, Ciunik Z, Ciesiołka J. The impact of isomers of hemiaminal-1,2,4-triazole conjugates differently substituted in the phenyl ring and their Cu2+ complexes on the catalytic activity of the antigenomic delta ribozyme. J Inorg Biochem 2012; 108:62-8. [PMID: 22266462 DOI: 10.1016/j.jinorgbio.2011.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 11/30/2011] [Accepted: 12/16/2011] [Indexed: 02/05/2023]
Abstract
The ability of four stable hemiaminals differently substituted in the phenyl ring and their complexes with Cu(2+) ions to inhibit catalytic cleavage of the antigenomic delta ribozyme was compared. The hemiaminals were novel chiral derivatives of 1,2,4-triazole [i.e. (2,4-dinitrophenyl)(4H-1,2,4-triazol-4-ylamino) methanol (2,4-dnbald), (2-nitrophenyl)(4H-1,2,4-triazol-4-ylamino) methanol (2-nbald), (3-nitrophenyl)(4H-1,2,4-triazol-4-ylamino) methanol (3-nbald) and (4-nitrophenyl)(4H-1,2,4-triazol-4-ylamino) methanol (4-nbald)]. The complexes of nbalds with Cu(2+) were characterized using UV and EPR methods and additionally, the formation of 2,4-dnbald-Cu(2+) complex with CuL(2) stoichiometry was confirmed by mass spectrometry. The data suggest that there are two ways in which nbalds and their Cu(2+) complexes can influence catalytic cleavage of antigenomic delta ribozyme. The coordinated Cu(2+) ions may play the role of new cationic ligands increasing the affinity of the complexes to the ribozyme. Such situation occurs in the case of 2- and 2,4-nbald. Their Cu(2+) complexes decrease ribozyme cleavage rates twice more efficiently than uncomplexed compounds. Moreover, the Cu(2+) complexes displace the catalytic divalent metal ions from their strong binding sites located in the ribozyme J4/2 region as shown by the Pb(2+)-induced cleavage approach. On the other hand, 3- and 4-nbald inhibit catalysis more strongly as compared to 2-nbald and 2,4-dnbald but the ribozyme cleavage rates are changed only slightly upon Cu(2+) complexation. The mechanism of ribozyme inhibition by interfering with the formation of a correct ribozyme tertiary structure seems to operate in this case.
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49
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Schroeder KT, Daldrop P, Lilley DMJ. RNA tertiary interactions in a riboswitch stabilize the structure of a kink turn. Structure 2011; 19:1233-40. [PMID: 21893284 PMCID: PMC3651934 DOI: 10.1016/j.str.2011.07.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 06/26/2011] [Accepted: 07/02/2011] [Indexed: 01/31/2023]
Abstract
The kink turn is a widespread RNA motif that introduces an acute kink into the axis of duplex RNA, typically comprising a bulge followed by a G⋅A and A⋅G pairs. The kinked conformation is stabilized by metal ions, or the binding of proteins including L7Ae. We now demonstrate a third mechanism for the stabilization of k-turn structure, involving tertiary interactions within a larger RNA structure. The SAM-I riboswitch contains an essential standard k-turn sequence that kinks a helix so that its terminal loop can make a long-range interaction. We find that some sequence variations in the k-turn within the riboswitch do not prevent SAM binding, despite preventing the folding of the k-turn in isolation. Furthermore, two crystal structures show that the sequence-variant k-turns are conventionally folded within the riboswitch. This study shows that the folded structure of the k-turn can be stabilized by tertiary interactions within a larger RNA structure.
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Affiliation(s)
- Kersten T Schroeder
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, UK
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50
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Lee SG, Haakenson W, McCarter JP, Williams DJ, Hresko MC, Jez JM. Thermodynamic evaluation of ligand binding in the plant-like phosphoethanolamine methyltransferases of the parasitic nematode Haemonchus contortus. J Biol Chem 2011; 286:38060-38068. [PMID: 21914812 PMCID: PMC3207426 DOI: 10.1074/jbc.m111.290619] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 09/02/2011] [Indexed: 01/29/2023] Open
Abstract
Nematodes are a major cause of disease and the discovery of new pathways not found in hosts is critical for development of therapeutic targets. Previous studies suggest that Caenorhabditis elegans synthesizes phosphocholine via two S-adenosylmethionine (AdoMet)-dependent phosphoethanolamine methyltransferases (PMT). Here we examine two PMT from the parasitic nematode Haemonchus contortus. Sequence analysis suggests that HcPMT1 contains a methyltransferase domain in the N-terminal half of the protein and that HcPMT2 encodes a C-terminal methyltransferase domain, as in the C. elegans proteins. Kinetic analysis demonstrates that HcPMT1 catalyzes the conversion of phosphoethanolamine to phosphomonomethylethanolamine (pMME) and that HcPMT2 methylates pMME to phosphodimethylethanolamine (pDME) and pDME to phosphocholine. The IC(50) values for miltefosine, sinefungin, amodiaquine, diphenhydramine, and tacrine suggest differences in the active sites of these two enzymes. To examine the interaction of AdoMet and S-adenosylhomocysteine (AdoCys), isothermal titration calorimetry confirmed the presence of a single binding site in each enzyme. Binding of AdoMet and AdoCys is tight (K(d) ∼2-25 μm) over a range of temperatures (5-25 °C) and NaCl concentrations (0.05-0.5 m). Heat capacity changes for AdoMet and AdoCys binding suggests that each HcPMT differs in interaction surface area. Nonlinear van't Hoff plots also indicate a possible conformational change upon AdoMet/AdoCys binding. Functional analysis of the PMT from a parasitic nematode provides new insights on inhibitor and AdoMet/AdoCys binding to these enzymes.
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Affiliation(s)
- Soon Goo Lee
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | | | | | | | | | - Joseph M Jez
- Department of Biology, Washington University, St. Louis, Missouri 63130.
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