1
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Zhang J, Fakharzadeh A, Roland C, Sagui C. RNA as a Major-Groove Ligand: RNA-RNA and RNA-DNA Triplexes Formed by GAA and UUC or TTC Sequences. ACS OMEGA 2022; 7:38728-38743. [PMID: 36340174 PMCID: PMC9631886 DOI: 10.1021/acsomega.2c04358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Friedreich's ataxia is associated with noncanonical nucleic acid structures that emerge when GAA:TTC repeats in the first intron of the FXN gene expand beyond a critical number of repeats. Specifically, the noncanonical repeats are associated with both triplexes and R-loops. Here, we present an in silico investigation of all possible triplexes that form by attaching a third RNA strand to an RNA:RNA or DNA:DNA duplex, complementing previous DNA-based triplex studies. For both new triplexes results are similar. For a pyridimine UUC+ third strand, the parallel orientation is stable while its antiparallel counterpart is unstable. For a neutral GAA third strand, the parallel conformation is stable. A protonated GA+A third strand is stable in both parallel and antiparallel orientations. We have also investigated Na+ and Mg2+ ion distributions around the triplexes. The presence of Mg2+ ions helps stabilize neutral, antiparallel GAA triplexes. These results (along with previous DNA-based studies) allow for the emergence of a complete picture of the stability and structural characteristics of triplexes based on the GAA and TTC/UUC sequences, thereby contributing to the field of trinucleotide repeats and the associated unusual structures that trigger expansion.
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2
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Zhao S, Li X, Wen Z, Zou M, Yu G, Liu X, Mao J, Zhang L, Xue Y, Fu R, Wang S. Dynamics of base pairs with low stability in RNA by solid-state nuclear magnetic resonance exchange spectroscopy. iScience 2022; 25:105322. [DOI: 10.1016/j.isci.2022.105322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/07/2022] [Accepted: 10/07/2022] [Indexed: 11/28/2022] Open
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3
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Vikram, Mishra V, Rana A, Ahire JJ. Riboswitch-mediated regulation of riboflavin biosynthesis genes in prokaryotes. 3 Biotech 2022; 12:278. [PMID: 36275359 PMCID: PMC9474784 DOI: 10.1007/s13205-022-03348-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 09/02/2022] [Indexed: 11/01/2022] Open
Abstract
Prokaryotic organisms frequently use riboswitches to quantify intracellular metabolite concentration via high-affinity metabolite receptors. Riboswitches possess a metabolite-sensing system that controls gene regulation in a cis-acting fashion at the initiation of transcriptional/translational level by binding with a specific metabolite and controlling various biochemical pathways. Riboswitch binds with flavin mononucleotide (FMN), a phosphorylated form of riboflavin and controls gene expression involved in riboflavin biosynthesis and transport pathway. The first step of the riboflavin biosynthesis pathway is initiated by the conversion of guanine nucleotide triphosphate (GTP), which is an intermediate of the purine biosynthesis pathway. An alternative pentose phosphate pathway of riboflavin biosynthesis includes the enzymatic conversion of ribulose-5-phosphate into 3, 4 dihydroxy-2-butanone-4-phosphates by DHBP synthase. The product of ribAB interferes with both GTP cyclohydrolase II as well as DHBP synthase activities, which catalyze the cleavage of GTP and converts DHBP Ribu5P in the initial steps of both riboflavin biosynthesis branches. Riboswitches are located in the 5' untranslated region (5' UTR) of messenger RNAs and contain an aptamer domain (highly conserved in sequence) where metabolite binding leads to a conformational change in an aptamer domain, which modulate the regulation of gene expression located on bacterial mRNA. In this review, we focus on how riboswitch regulates the riboflavin biosynthesis pathway in Bacillus subtilis and Lactobacillus plantarum.
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Affiliation(s)
- Vikram
- Department of Basic and Applied Sciences, National Institute of Food Technology, Entrepreneurship and Management (NIFTEM), Sonipat, Haryana India
| | - Vijendra Mishra
- Department of Basic and Applied Sciences, National Institute of Food Technology, Entrepreneurship and Management (NIFTEM), Sonipat, Haryana India
| | - Ananya Rana
- Department of Basic and Applied Sciences, National Institute of Food Technology, Entrepreneurship and Management (NIFTEM), Sonipat, Haryana India
| | - Jayesh J. Ahire
- Centre for Research and Development, Unique Biotech Ltd., Plot No. 2, Phase II, MN Park, Hyderabad, Telangana India
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4
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Janzen E, Shen Y, Vázquez-Salazar A, Liu Z, Blanco C, Kenchel J, Chen IA. Emergent properties as by-products of prebiotic evolution of aminoacylation ribozymes. Nat Commun 2022; 13:3631. [PMID: 35752631 PMCID: PMC9233669 DOI: 10.1038/s41467-022-31387-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 06/16/2022] [Indexed: 11/24/2022] Open
Abstract
Systems of catalytic RNAs presumably gave rise to important evolutionary innovations, such as the genetic code. Such systems may exhibit particular tolerance to errors (error minimization) as well as coding specificity. While often assumed to result from natural selection, error minimization may instead be an emergent by-product. In an RNA world, a system of self-aminoacylating ribozymes could enforce the mapping of amino acids to anticodons. We measured the activity of thousands of ribozyme mutants on alternative substrates (activated analogs for tryptophan, phenylalanine, leucine, isoleucine, valine, and methionine). Related ribozymes exhibited shared preferences for substrates, indicating that adoption of additional amino acids by existing ribozymes would itself lead to error minimization. Furthermore, ribozyme activity was positively correlated with specificity, indicating that selection for increased activity would also lead to increased specificity. These results demonstrate that by-products of ribozyme evolution could lead to adaptive value in specificity and error tolerance.
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Affiliation(s)
- Evan Janzen
- Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA, 93106, USA.,Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA
| | - Yuning Shen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA.,Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Alberto Vázquez-Salazar
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Ziwei Liu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Celia Blanco
- Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Josh Kenchel
- Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA, 93106, USA.,Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA.,Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Irene A Chen
- Program in Biomolecular Science and Engineering, University of California, Santa Barbara, CA, 93106, USA. .,Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, 93106, USA. .,Department of Chemical and Biomolecular Engineering, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA.
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5
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Cheng L, White EN, Brandt NL, Yu AM, Chen AA, Lucks J. Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch. Nucleic Acids Res 2022; 50:12001-12018. [PMID: 35348734 PMCID: PMC9756952 DOI: 10.1093/nar/gkac102] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/17/2022] [Accepted: 02/02/2022] [Indexed: 12/24/2022] Open
Abstract
RNA folds cotranscriptionally to traverse out-of-equilibrium intermediate structures that are important for RNA function in the context of gene regulation. To investigate this process, here we study the structure and function of the Bacillus subtilis yxjA purine riboswitch, a transcriptional riboswitch that downregulates a nucleoside transporter in response to binding guanine. Although the aptamer and expression platform domain sequences of the yxjA riboswitch do not completely overlap, we hypothesized that a strand exchange process triggers its structural switching in response to ligand binding. In vivo fluorescence assays, structural chemical probing data and experimentally informed secondary structure modeling suggest the presence of a nascent intermediate central helix. The formation of this central helix in the absence of ligand appears to compete with both the aptamer's P1 helix and the expression platform's transcriptional terminator. All-atom molecular dynamics simulations support the hypothesis that ligand binding stabilizes the aptamer P1 helix against central helix strand invasion, thus allowing the terminator to form. These results present a potential model mechanism to explain how ligand binding can induce downstream conformational changes by influencing local strand displacement processes of intermediate folds that could be at play in multiple riboswitch classes.
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Affiliation(s)
- Luyi Cheng
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
| | - Elise N White
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Naomi L Brandt
- Department of Chemistry and the RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Angela M Yu
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA 98195, USA
| | - Alan A Chen
- Correspondence may also be addressed to Alan A. Chen. Tel: +1 518 437 4420;
| | - Julius B Lucks
- To whom correspondence should be addressed. Tel: +1 847 467 2943;
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6
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Zou W, Huang H, Wu H, Cao Y, Lu W, He Y. Preparation, Antibacterial Potential, and Antibacterial Components of Fermented Compound Chinese Medicine Feed Additives. Front Vet Sci 2022; 9:808846. [PMID: 35400112 PMCID: PMC8987234 DOI: 10.3389/fvets.2022.808846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/10/2022] [Indexed: 11/13/2022] Open
Abstract
This experiment was conducted to compare the antibacterial ability and to identify the antibacterial components of different fermented compound Chinese medicine feed additives in order to develop one fermented compound Chinese medicine feed additive product that can effectively alleviate metritis, vaginitis, and mastitis of sows. The Oxford cup method and double dilution method were used to compare the antibacterial ability of three fermented compound Chinese medicine feed additives (A, B, and C). UHPLC-QE-MS-based untargeted metabolomics was used to identify the antibacterial components of fermented compound Chinese medicine feed additives. Results showed that among fermented compound Chinese medicine feed additives A, B, and C, additive A had the strongest ability to inhibit the growth of Staphylococcus aureus, Salmonella cholerae suis, Escherichia coli, and Streptococcus agalactiae. The MIC and MBC of additive A were the lowest for Staphylococcus aureus compared to that for the other three pathogens. The concentrations of 23 Chinese medicine ingredients (ellagic acid, guanine, camphor, L-valine, sinapine, dipropylphthalate, 3-hydroxy-5-isopropylidene-3,8-dimethyl-2,3,3a,4,5,8a-hexahydro-6(1H)-azulenone, 7-dihydroxy-2-(4-hydroxyphenyl)-8-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-6-(3,4,5-trihydroxyoxan-2-yl)chromen-4-one, acetylcholine, farrerol, pyrogallol, ethyl gallate, demethylwedelolactone, methyl gallate, kaempferide, gallic acid, eriodictyol, threonic acid, inositol, 3′,4′,7-trihydroxyflavanone, taxifolin, asiatic acid, and isorhamnetin) in additive A were significantly (p < 0.05 or p < 0.01) higher than those in additive B, respectively. It is concluded that the mixture composed of 23 active components in fermented compound Chinese medicine feed additive A plays an important role in inhibiting the growth of Staphylococcus aureus, Salmonella cholerae suis, Escherichia coli, and Streptococcus agalactiae.
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Affiliation(s)
- Wanjie Zou
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang, China
| | - Honglan Huang
- Forest Institution, Jiangxi Environmental Engineering Vocational College, Ganzhou, China
| | - Huadong Wu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yuandong Cao
- Department of Technology, Jiangxi Jiabo Bioengineering Co. Ltd., Jiujiang, China
| | - Wei Lu
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang, China
- *Correspondence: Wei Lu
| | - Yuyong He
- Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development, Jiangxi Agricultural University, Nanchang, China
- Yuyong He
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7
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Jezuita A, Wieczorkiewicz PA, Szatylowicz H, Krygowski TM. Effect of the Solvent and Substituent on Tautomeric Preferences of Amine-Adenine Tautomers. ACS OMEGA 2021; 6:18890-18903. [PMID: 34337229 PMCID: PMC8320138 DOI: 10.1021/acsomega.1c02118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Adenine is one of the basic molecules of life; it is also an important building block in the synthesis of new pharmaceuticals, electrochemical (bio)sensors, or self-assembling molecular materials. Therefore, it is important to know the effects of the solvent and substituent on the electronic structure of adenine tautomers and their stability. The four most stable adenine amino tautomers (9H, 7H, 3H, and 1H), modified by substitution (C2- or C8-) of electron-withdrawing NO2 and electron-donating NH2 groups, are studied theoretically in the gas phase and in solvents of different polarities (1 ≤ ε < 109). Solvents have been modeled using the polarizable continuum model. Comparison of the stability of substituted adenine tautomers in various solvents shows that substitution can change tautomeric preferences with respect to the unsubstituted adenine. Moreover, C8 substitution results in slight energy differences between tautomers in polar solvents (<1 kcal/mol), which suggests that in aqueous solution, C8-X-substituted adenine systems may consist of a considerable amount of two tautomers-9H and 7H for X = NH2 and 3H and 9H for X = NO2. Furthermore, solvation enhances the effect of the nitro group; however, the enhancement strongly depends on the proximity effects. This enhancement for the NO2 group with two repulsive N···ON contacts can be threefold higher than that for the NO2 with one attractive NH···ON contact. The proximity effects are even more significant for the NH2 group, as the solvation may increase or decrease its electron-donating ability, depending on the type of proximity.
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Affiliation(s)
- Anna Jezuita
- Faculty of Science and Technology, Jan Dlugosz University in Czestochowa, Al. Armii Krajowej 113/15, 42-200 Czestochowa, Poland
| | | | - Halina Szatylowicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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8
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Wu L, Liu Z, Liu Y. Thermal adaptation of structural dynamics and regulatory function of adenine riboswitch. RNA Biol 2021; 18:2007-2015. [PMID: 33573442 DOI: 10.1080/15476286.2021.1886755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Ligand binding and temperature play important roles in riboswitch RNAs' structures and functions. However, most studies focused on studying structural dynamics or gene-regulation function of riboswitches from the aspect of ligand, instead of temperature. Here we combined NMR, ITC, stopped-flow and in vivo assays to investigate the ligand-triggered switch of adenine riboswitch from 10 to 45°C. Our results demonstrated that at single-nucleotide resolution, structural regions sensed ligand and temperature diversely. Temperature had opposite effects on ligand-binding and gene-regulation of adenine riboswitch. Compared with higher temperature, the RNA bound with its cognate ligand obviously stronger, while its regulatory capacity was weakened at lower temperature. In addition, application of specific-labelled RNAs to the stopped-flow experiments identified the real-time folding of the specific positions upon ligand addition at different temperatures. The kissing loop and internal loop at the riboswitch responded to ligand and temperature differently. The distinct thermo-dynamics of adenine riboswitch exposed here may contribute to the fields of RNA sensors and drug design.
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Affiliation(s)
- Lin Wu
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhijun Liu
- National Facility for Protein Science (Shanghai), Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai, China
| | - Yu Liu
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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9
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Abdelsattar AS, Mansour Y, Aboul-Ela F. The Perturbed Free-Energy Landscape: Linking Ligand Binding to Biomolecular Folding. Chembiochem 2021; 22:1499-1516. [PMID: 33351206 DOI: 10.1002/cbic.202000695] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/19/2020] [Indexed: 12/24/2022]
Abstract
The effects of ligand binding on biomolecular conformation are crucial in drug design, enzyme mechanisms, the regulation of gene expression, and other biological processes. Descriptive models such as "lock and key", "induced fit", and "conformation selection" are common ways to interpret such interactions. Another historical model, linked equilibria, proposes that the free-energy landscape (FEL) is perturbed by the addition of ligand binding energy for the bound population of biomolecules. This principle leads to a unified, quantitative theory of ligand-induced conformation change, building upon the FEL concept. We call the map of binding free energy over biomolecular conformational space the "binding affinity landscape" (BAL). The perturbed FEL predicts/explains ligand-induced conformational changes conforming to all common descriptive models. We review recent experimental and computational studies that exemplify the perturbed FEL, with emphasis on RNA. This way of understanding ligand-induced conformation dynamics motivates new experimental and theoretical approaches to ligand design, structural biology and systems biology.
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Affiliation(s)
- Abdallah S Abdelsattar
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
| | - Youssef Mansour
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
| | - Fareed Aboul-Ela
- Center for X-Ray Determination of the Structure of Matter, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, 12578, Giza, Egypt
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10
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Baulin E, Metelev V, Bogdanov A. Base-intercalated and base-wedged stacking elements in 3D-structure of RNA and RNA-protein complexes. Nucleic Acids Res 2020; 48:8675-8685. [PMID: 32687167 PMCID: PMC7470943 DOI: 10.1093/nar/gkaa610] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/05/2020] [Accepted: 07/15/2020] [Indexed: 12/25/2022] Open
Abstract
Along with nucleobase pairing, base-base stacking interactions are one of the two main types of strong non-covalent interactions that define the unique secondary and tertiary structure of RNA. In this paper we studied two subfamilies of nucleobase-inserted stacking structures: (i) with any base intercalated between neighboring nucleotide residues (base-intercalated element, BIE, i + 1); (ii) with any base wedged into a hydrophobic cavity formed by heterocyclic bases of two nucleotides which are one nucleotide apart in sequence (base-wedged element, BWE, i + 2). We have exploited the growing database of natively folded RNA structures in Protein Data Bank to analyze the distribution and structural role of these motifs in RNA. We found that these structural elements initially found in yeast tRNAPhe are quite widespread among the tertiary structures of various RNAs. These motifs perform diverse roles in RNA 3D structure formation and its maintenance. They contribute to the folding of RNA bulges and loops and participate in long-range interactions of single-stranded stretches within RNA macromolecules. Furthermore, both base-intercalated and base-wedged motifs participate directly or indirectly in the formation of RNA functional centers, which interact with various ligands, antibiotics and proteins.
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Affiliation(s)
- Eugene Baulin
- Laboratory of Applied Mathematics, Institute of Mathematical Problems of Biology RAS - the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Valeriy Metelev
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexey Bogdanov
- To whom correspondence should be addressed. Tel: +7 495 9393143; Fax: +7 495 9393181;
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11
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Wilt HM, Yu P, Tan K, Wang YX, Stagno JR. FMN riboswitch aptamer symmetry facilitates conformational switching through mutually exclusive coaxial stacking configurations. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100035. [PMID: 33103111 PMCID: PMC7573352 DOI: 10.1016/j.yjsbx.2020.100035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/29/2020] [Accepted: 08/02/2020] [Indexed: 11/16/2022]
Abstract
Knowledge of both apo and holo states of riboswitches aid in elucidating the various mechanisms of ligand-induced conformational “switching” that underpin their gene-regulating capabilities. Previous structural studies on the flavin mononucleotide (FMN)-binding aptamer of the FMN riboswitch, however, have revealed minimal conformational changes associated with ligand binding that do not adequately explain the basis for the switching behavior. We have determined a 2.7-Å resolution crystal structure of the ligand-free FMN riboswitch aptamer that is distinct from previously reported structures, particularly in the conformation and orientation of the P1 and P4 helices. The nearly symmetrical tertiary structure provides a mechanism by which one of two pairs of adjacent helices (P3/P4 or P1/P6) undergo collinear stacking in a mutually exclusive manner, in the absence or presence of ligand, respectively. Comparison of these structures suggests the stem-loop that includes P4 and L4 is important for maintaining a global conformational state that, in the absence of ligand, disfavors formation of the P1 regulatory helix. Together, these results provide further insight to the structural basis for conformational switching of the FMN riboswitch.
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Affiliation(s)
- Haley M Wilt
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.,Washington College, Chestertown, Maryland 21620, USA
| | - Ping Yu
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Kemin Tan
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Ave., Lemont, IL 60439, USA
| | - Yun-Xing Wang
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Jason R Stagno
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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12
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Abstract
Riboswitches alter gene expression in response to ligand binding, coupling sensing and regulatory functions to help bacteria respond to their environment. The structural determinants of ligand binding in the prequeuosine (7-aminomethyl-7-deazaguanine, preQ1) bacterial riboswitches have been studied, but the functional consequences of structural perturbations are less known. A new article combining biophysical and cell-based readouts of 15 mutants of the preQ1-II riboswitch from Lactobacillus rhamnosus demonstrates that ligand binding does not ensure successful gene regulation, providing new insights into these shapeshifting sequences.
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Affiliation(s)
- Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
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13
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Abstract
RNA molecules fold into complex three-dimensional structures that sample alternate conformations ranging from minor differences in tertiary structure dynamics to major differences in secondary structure. This allows them to form entirely different substructures with each population potentially giving rise to a distinct biological outcome. The substructures can be partitioned along an existing energy landscape given a particular static cellular cue or can be shifted in response to dynamic cues such as ligand binding. We review a few key examples of RNA molecules that sample alternate conformations and how these are capitalized on for control of critical regulatory functions.
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Affiliation(s)
- Marie Teng-Pei Wu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Victoria D'Souza
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
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14
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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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15
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Ding J, Swain M, Yu P, Stagno JR, Wang YX. Conformational flexibility of adenine riboswitch aptamer in apo and bound states using NMR and an X-ray free electron laser. JOURNAL OF BIOMOLECULAR NMR 2019; 73:509-518. [PMID: 31606878 PMCID: PMC6817744 DOI: 10.1007/s10858-019-00278-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/12/2019] [Indexed: 06/10/2023]
Abstract
Riboswitches are structured cis-regulators mainly found in the untranslated regions of messenger RNA. The aptamer domain of a riboswitch serves as a sensor for its ligand, the binding of which triggers conformational changes that regulate the behavior of its expression platform. As a model system for understanding riboswitch structures and functions, the add adenine riboswitch has been studied extensively. However, there is a need for further investigation of the conformational dynamics of the aptamer in light of the recent real-time crystallographic study at room temperature (RT) using an X-ray free electron laser (XFEL) and femtosecond X-ray crystallography (SFX). Herein, we investigate the conformational motions of the add adenine riboswitch aptamer domain, in the presence or absence of adenine, using nuclear magnetic resonance relaxation measurements and analysis of RT atomic displacement factors (B-factors). In the absence of ligand, the P1 duplex undergoes a fast exchange where the overall molecule exhibits a motion at kex ~ 319 s-1, based on imino signals. In the presence of ligand, the P1 duplex adopts a highly ordered conformation, with kex~ 83 s-1, similar to the global motion of the molecule, excluding the loops and binding pocket, at 84 s-1. The µs-ms motions in both the apo and bound states are consistent with RT B-factors. Reduced spatial atomic fluctuation, ~ 50%, in P1 upon ligand binding coincides with significantly attenuated temporal dynamic exchanges. The binding pocket is structured in the absence or presence of ligand, as evidenced by relatively low and similar RT B-factors. Therefore, despite the dramatic rearrangement of the binding pocket, those residues exhibit similar spatial thermal fluctuation before and after binding.
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Affiliation(s)
- Jienv Ding
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD, 21702, USA.
| | - Monalisa Swain
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD, 21702, USA
| | - Ping Yu
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD, 21702, USA
| | - Jason R Stagno
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD, 21702, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institute of Health, Frederick, MD, 21702, USA.
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16
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Jones C, Tran B, Conrad C, Stagno J, Trachman R, Fischer P, Meents A, Ferré-D'Amaré A. Co-crystal structure of the Fusobacterium ulcerans ZTP riboswitch using an X-ray free-electron laser. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2019; 75:496-500. [PMID: 31282869 DOI: 10.1107/s2053230x19008549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/15/2019] [Indexed: 11/10/2022]
Abstract
Riboswitches are conformationally dynamic RNAs that regulate gene expression by binding specific small molecules. ZTP riboswitches bind the purine-biosynthetic intermediate 5-aminoimidazole-4-carboxamide riboside 5'-monophosphate (ZMP) and its triphosphorylated form (ZTP). Ligand binding to this riboswitch ultimately upregulates genes involved in folate and purine metabolism. Using an X-ray free-electron laser (XFEL), the room-temperature structure of the Fusobacterium ulcerans ZTP riboswitch bound to ZMP has now been determined at 4.1 Å resolution. This model, which was refined against a data set from ∼750 diffraction images (each from a single crystal), was found to be consistent with that previously obtained from data collected at 100 K using conventional synchrotron X-radiation. These experiments demonstrate the feasibility of time-resolved XFEL experiments to understand how the ZTP riboswitch accommodates cognate ligand binding.
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Affiliation(s)
- Christopher Jones
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892, USA
| | - Brandon Tran
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892, USA
| | - Chelsie Conrad
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Jason Stagno
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Robert Trachman
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892, USA
| | - Pontus Fischer
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Alke Meents
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Adrian Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892, USA
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17
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Jones CP, Piszczek G, Ferré-D'Amaré AR. Isothermal Titration Calorimetry Measurements of Riboswitch-Ligand Interactions. Methods Mol Biol 2019; 1964:75-87. [PMID: 30929236 DOI: 10.1007/978-1-4939-9179-2_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
One of the many ways by which bacteria control gene expression is through cis-acting regulatory mRNA elements called riboswitches. By specifically binding to small molecules or metabolites and pairing the binding event to an RNA structure change, riboswitches link a metabolic input to a transcriptional or translational output. For over a decade, isothermal titration calorimetry (ITC) has been used to investigate how riboswitches interact with small molecules. We present methods for assaying RNA-ligand interactions using ITC and analyzing resulting data to estimate thermodynamic parameters associated with binding.
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Affiliation(s)
- Christopher P Jones
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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18
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Battaglia RA, Ke A. Guanidine-sensing riboswitches: How do they work and what do they regulate? WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1482. [DOI: 10.1002/wrna.1482] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/14/2018] [Accepted: 03/19/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Robert A. Battaglia
- Department of Molecular Biology and Genetics; Cornell University; Ithaca New York
| | - Ailong Ke
- Department of Molecular Biology and Genetics; Cornell University; Ithaca New York
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19
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Khani A, Popp N, Kreikemeyer B, Patenge N. A Glycine Riboswitch in Streptococcus pyogenes Controls Expression of a Sodium:Alanine Symporter Family Protein Gene. Front Microbiol 2018. [PMID: 29527194 PMCID: PMC5829553 DOI: 10.3389/fmicb.2018.00200] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Regulatory RNAs play important roles in the control of bacterial gene expression. In this study, we investigated gene expression regulation by a putative glycine riboswitch located in the 5'-untranslated region of a sodium:alanine symporter family (SAF) protein gene in the group A Streptococcus pyogenes serotype M49 strain 591. Glycine-dependent gene expression mediated by riboswitch activity was studied using a luciferase reporter gene system. Maximal reporter gene expression was observed in the absence of glycine and in the presence of low glycine concentrations. Differences in glycine-dependent gene expression were not based on differential promoter activity. Expression of the SAF protein gene and the downstream putative cation efflux protein gene was investigated in wild-type bacteria by RT-qPCR transcript analyses. During growth in the presence of glycine (≥1 mM), expression of the genes were downregulated. Northern blot analyses revealed premature transcription termination in the presence of high glycine concentrations. Growth in the presence of 0.1 mM glycine led to the production of a full-length transcript. Furthermore, stability of the SAF protein gene transcript was drastically reduced in the presence of glycine. We conclude that the putative glycine riboswitch in S. pyogenes serotype M49 strain 591 represses expression of the SAF protein gene and the downstream putative cation efflux protein gene in the presence of high glycine concentrations. Sequence and secondary structure comparisons indicated that the streptococcal riboswitch belongs to the class of tandem aptamer glycine riboswitches.
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Affiliation(s)
- Afsaneh Khani
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Nicole Popp
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Nadja Patenge
- Institute of Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
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20
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Tian S, Kladwang W, Das R. Allosteric mechanism of the V. vulnificus adenine riboswitch resolved by four-dimensional chemical mapping. eLife 2018; 7:29602. [PMID: 29446752 PMCID: PMC5847336 DOI: 10.7554/elife.29602] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 02/13/2018] [Indexed: 12/23/2022] Open
Abstract
The structural interconversions that mediate the gene regulatory functions of RNA molecules may be different from classic models of allostery, but the relevant structural correlations have remained elusive in even intensively studied systems. Here, we present a four-dimensional expansion of chemical mapping called lock-mutate-map-rescue (LM2R), which integrates multiple layers of mutation with nucleotide-resolution chemical mapping. This technique resolves the core mechanism of the adenine-responsive V. vulnificus add riboswitch, a paradigmatic system for which both Monod-Wyman-Changeux (MWC) conformational selection models and non-MWC alternatives have been proposed. To discriminate amongst these models, we locked each functionally important helix through designed mutations and assessed formation or depletion of other helices via compensatory rescue evaluated by chemical mapping. These LM2R measurements give strong support to the pre-existing correlations predicted by MWC models, disfavor alternative models, and suggest additional structural heterogeneities that may be general across ligand-free riboswitches.
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Affiliation(s)
- Siqi Tian
- Department of Biochemistry, Stanford University, Stanford, United States
| | - Wipapat Kladwang
- Department of Biochemistry, Stanford University, Stanford, United States
| | - Rhiju Das
- Department of Physics, Stanford University, Stanford, United States
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21
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Yan LH, Le Roux A, Boyapelly K, Lamontagne AM, Archambault MA, Picard-Jean F, Lalonde-Seguin D, St-Pierre E, Najmanovich RJ, Fortier LC, Lafontaine D, Marsault É. Purine analogs targeting the guanine riboswitch as potential antibiotics against Clostridioides difficile. Eur J Med Chem 2017; 143:755-768. [PMID: 29220796 DOI: 10.1016/j.ejmech.2017.11.079] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 11/22/2017] [Accepted: 11/27/2017] [Indexed: 12/14/2022]
Abstract
Riboswitches recently emerged as possible targets for the development of alternative antimicrobial approaches. Guanine-sensing riboswitches in the bacterial pathogen Clostridioides difficile (formerly known as Clostridium difficile) constitute potential targets based on their involvement in the regulation of basal metabolic control of purine compounds. In this study, we deciphered the structure-activity relationship of several guanine derivatives on the guanine riboswitch and determined their antimicrobial activity. We describe the synthesis of purine analogs modified in ring B as well as positions 2 and 6. Their biological activity was determined by measuring their affinity for the C. difficile guanine riboswitch and their inhibitory effect on bacterial growth, including a counter-screen to discriminate against riboswitch-independent antibacterial effects. Altogether, our results suggest that improvements in riboswitch binding affinity in vitro do not necessarily translate into improved antibacterial activity in bacteria, despite the fact that some structure-activity relationship was observed at least with respect to binding affinity.
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Affiliation(s)
- Lok-Hang Yan
- Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada; Department of Pharmacology-Physiology, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada
| | - Antoine Le Roux
- Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada; Department of Pharmacology-Physiology, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada
| | - Kumaraswamy Boyapelly
- Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada; Department of Pharmacology-Physiology, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada
| | - Anne-Marie Lamontagne
- Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada; Department of Biology, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada
| | - Marie-Ann Archambault
- Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada; Department of Biology, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada
| | - Frédéric Picard-Jean
- Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada; Department of Biology, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada
| | - David Lalonde-Seguin
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada
| | - Emilie St-Pierre
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada
| | - Rafael J Najmanovich
- Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada; Department of Biochemistry, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada
| | - Louis-Charles Fortier
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada.
| | - Daniel Lafontaine
- Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada; Department of Biology, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada.
| | - Éric Marsault
- Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada; Department of Pharmacology-Physiology, Université de Sherbrooke, 3001, 12e av nord, Sherbrooke, Québec, J1H 5N4, Canada.
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22
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Hanke CA, Gohlke H. Tertiary Interactions in the Unbound Guanine-Sensing Riboswitch Focus Functional Conformational Variability on the Binding Site. J Chem Inf Model 2017; 57:2822-2832. [DOI: 10.1021/acs.jcim.7b00567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Christian A. Hanke
- Mathematisch-Naturwissenschaftliche
Fakultät, Institut für Pharmazeutische und Medizinische
Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche
Fakultät, Institut für Pharmazeutische und Medizinische
Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) & Institute for Complex Systems - Structural Biochemistry (ICS 6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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23
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Stagno JR, Bhandari YR, Conrad CE, Liu Y, Wang YX. Real-time crystallographic studies of the adenine riboswitch using an X-ray free-electron laser. FEBS J 2017; 284:3374-3380. [PMID: 28504865 DOI: 10.1111/febs.14110] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/27/2017] [Accepted: 05/12/2017] [Indexed: 11/26/2022]
Abstract
Structures of the four reaction states of the adenine riboswitch aptamer domain, including a transient intermediate state were solved by serial femtosecond crystallography. The structures not only demonstrate the use of X-ray free-electron lasers for RNA crystallography but have also proven that transient states can be determined in real time by mix-and-inject crystallography. These results illustrate the structural basis for the ligand-induced conformational changes associated with the molecular 'switch'.
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Affiliation(s)
- Jason R Stagno
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Yuba R Bhandari
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Chelsie E Conrad
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Yu Liu
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Yun-Xing Wang
- Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA
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24
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An excited state underlies gene regulation of a transcriptional riboswitch. Nat Chem Biol 2017; 13:968-974. [PMID: 28719589 PMCID: PMC5562522 DOI: 10.1038/nchembio.2427] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/22/2017] [Indexed: 11/08/2022]
Abstract
Riboswitches control gene expression through ligand-dependent structural rearrangements of the sensing aptamer domain. However, we found that the Bacillus cereus fluoride riboswitch aptamer adopts identical tertiary structures in solution with and without ligand. Using chemical-exchange saturation transfer (CEST) NMR spectroscopy, we revealed that the structured ligand-free aptamer transiently accesses a low-populated (∼1%) and short-lived (∼3 ms) excited conformational state that unravels a conserved 'linchpin' base pair to signal transcription termination. Upon fluoride binding, this highly localized, fleeting process is allosterically suppressed, which activates transcription. We demonstrated that this mechanism confers effective fluoride-dependent gene activation over a wide range of transcription rates, which is essential for robust toxicity responses across diverse cellular conditions. These results unveil a novel switching mechanism that employs ligand-dependent suppression of an aptamer excited state to coordinate regulatory conformational transitions rather than adopting distinct aptamer ground-state tertiary architectures, exemplifying a new mode of ligand-dependent RNA regulation.
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25
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Hanke CA, Gohlke H. Ligand-mediated and tertiary interactions cooperatively stabilize the P1 region in the guanine-sensing riboswitch. PLoS One 2017; 12:e0179271. [PMID: 28640851 PMCID: PMC5480868 DOI: 10.1371/journal.pone.0179271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 05/27/2017] [Indexed: 12/18/2022] Open
Abstract
Riboswitches are genetic regulatory elements that control gene expression depending on ligand binding. The guanine-sensing riboswitch (Gsw) binds ligands at a three-way junction formed by paired regions P1, P2, and P3. Loops L2 and L3 cap the P2 and P3 helices and form tertiary interactions. Part of P1 belongs to the switching sequence dictating the fate of the mRNA. Previous studies revealed an intricate relationship between ligand binding and presence of the tertiary interactions, and between ligand binding and influence on the P1 region. However, no information is available on the interplay among these three main regions in Gsw. Here we show that stabilization of the L2-L3 region by tertiary interactions, and the ligand binding site by ligand binding, cooperatively influences the structural stability of terminal base pairs in the P1 region in the presence of Mg2+ ions. The results are based on molecular dynamics simulations with an aggregate simulation time of ~10 μs across multiple systems of the unbound state of the Gsw aptamer and a G37A/C61U mutant, and rigidity analyses. The results could explain why the three-way junction is a central structural element also in other riboswitches and how the cooperative effect could become contextual with respect to intracellular Mg2+ concentration. The results suggest that the transmission of allosteric information to P1 can be entropy-dominated.
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Affiliation(s)
- Christian A. Hanke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
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26
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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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27
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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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28
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Chandra V, Hannan Z, Xu H, Mandal M. Single-molecule analysis reveals multi-state folding of a guanine riboswitch. Nat Chem Biol 2016; 13:194-201. [PMID: 27941758 DOI: 10.1038/nchembio.2252] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 10/03/2016] [Indexed: 12/29/2022]
Abstract
Guanine-responsive riboswitches undergo ligand-dependent structural rearrangements to control gene expression by transcription termination. While the molecular basis for ligand recognition is well established, the associated structural rearrangements and the kinetics involved in the formation of the aptamer domain are less well understood. Using high-resolution optical tweezers, we followed the folding trajectories of a single molecule of the xpt-pbuX guanine aptamer from Bacillus subtilis. We report a rapid six-state conformational rearrangement, in which three of the states are guanine dependent, during the transition from the linear to the native receptor conformation. The folding completes in <1 s. The force-dependent equilibrium kinetics and the mutational data indicated that the flexible J2-J3 junction undergoes a ligand-dependent conformational switching, which triggers the formation of the long-range tertiary interactions and the P1 helix. In the absence of the right ligand, the junction failed to initiate the series of conformational rearrangements required for the riboswitch activities.
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Affiliation(s)
- Vishnu Chandra
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Zain Hannan
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Huizhong Xu
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Maumita Mandal
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.,Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.,Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography. Nature 2016; 541:242-246. [PMID: 27841871 DOI: 10.1038/nature20599] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/04/2016] [Indexed: 12/27/2022]
Abstract
Riboswitches are structural RNA elements that are generally located in the 5' untranslated region of messenger RNA. During regulation of gene expression, ligand binding to the aptamer domain of a riboswitch triggers a signal to the downstream expression platform. A complete understanding of the structural basis of this mechanism requires the ability to study structural changes over time. Here we use femtosecond X-ray free electron laser (XFEL) pulses to obtain structural measurements from crystals so small that diffusion of a ligand can be timed to initiate a reaction before diffraction. We demonstrate this approach by determining four structures of the adenine riboswitch aptamer domain during the course of a reaction, involving two unbound apo structures, one ligand-bound intermediate, and the final ligand-bound conformation. These structures support a reaction mechanism model with at least four states and illustrate the structural basis of signal transmission. The three-way junction and the P1 switch helix of the two apo conformers are notably different from those in the ligand-bound conformation. Our time-resolved crystallographic measurements with a 10-second delay captured the structure of an intermediate with changes in the binding pocket that accommodate the ligand. With at least a 10-minute delay, the RNA molecules were fully converted to the ligand-bound state, in which the substantial conformational changes resulted in conversion of the space group. Such notable changes in crystallo highlight the important opportunities that micro- and nanocrystals may offer in these and similar time-resolved diffraction studies. Together, these results demonstrate the potential of 'mix-and-inject' time-resolved serial crystallography to study biochemically important interactions between biomacromolecules and ligands, including those that involve large conformational changes.
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Molecular prejudice: RNA discrimination against purines allows response to a cellular alarm. Nat Struct Mol Biol 2016; 22:754-6. [PMID: 26439636 DOI: 10.1038/nsmb.3095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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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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Lussier A, Bastet L, Chauvier A, Lafontaine DA. A kissing loop is important for btuB riboswitch ligand sensing and regulatory control. J Biol Chem 2015; 290:26739-51. [PMID: 26370077 DOI: 10.1074/jbc.m115.684134] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Indexed: 12/18/2022] Open
Abstract
RNA-based genetic regulation is exemplified by metabolite-binding riboswitches that modulate gene expression through conformational changes. Crystal structures show that the Escherichia coli btuB riboswitch contains a kissing loop interaction that is in close proximity to the bound ligand. To analyze the role of the kissing loop interaction in the riboswitch regulatory mechanism, we used RNase H cleavage assays to probe the structure of nascent riboswitch transcripts produced by the E. coli RNA polymerase. By monitoring the folding of the aptamer, kissing loop, and riboswitch expression platform, we established the conformation of each structural component in the absence or presence of bound adenosylcobalamin. We found that the kissing loop interaction is not essential for ligand binding. However, we showed that kissing loop formation improves ligand binding efficiency and is required to couple ligand binding to the riboswitch conformational changes involved in regulating gene expression. These results support a mechanism by which the btuB riboswitch modulates the formation of a tertiary structure to perform metabolite sensing and regulate gene expression.
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Affiliation(s)
- Antony Lussier
- From the Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - Laurène Bastet
- From the Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - Adrien Chauvier
- From the Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - Daniel A Lafontaine
- From the Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
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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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Jones CP, Ferré-D'Amaré AR. Recognition of the bacterial alarmone ZMP through long-distance association of two RNA subdomains. Nat Struct Mol Biol 2015; 22:679-85. [PMID: 26280533 PMCID: PMC4824399 DOI: 10.1038/nsmb.3073] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/22/2015] [Indexed: 12/22/2022]
Abstract
The bacterial alarmone 5-aminoimidazole-4-carboxamide riboside 5'-triphosphate (ZTP), derived from the monophosphorylated purine precursor ZMP, accumulates during folate starvation. ZTP regulates genes involved in purine and folate metabolism through a cognate riboswitch. The linker connecting this riboswitch’s two sub-domains varies in length by over 100 nucleotides. We report the co-crystal structure of the Fusobacterium ulcerans riboswitch bound to ZMP, which spans the two sub-domains whose interface also comprises a pseudoknot and ribose zipper. The riboswitch recognizes the carboxamide oxygen of ZMP through an unprecedented inner-sphere coordination with a Mg2+ ion. We demonstrate that the affinity of the riboswitch for ZMP is modulated by the linker length. Notably, ZMP can bind to the two sub-domains together even when synthesized as separate RNAs. The ZTP riboswitch demonstrates how specific small-molecule binding can drive association of distant non-coding RNA domains to regulate 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, USA
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
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Trausch JJ, Marcano-Velázquez JG, Matyjasik MM, Batey RT. Metal Ion-Mediated Nucleobase Recognition by the ZTP Riboswitch. ACTA ACUST UNITED AC 2015; 22:829-37. [PMID: 26144884 DOI: 10.1016/j.chembiol.2015.06.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 05/30/2015] [Accepted: 06/02/2015] [Indexed: 01/14/2023]
Abstract
The ZTP riboswitch is a widespread family of regulatory RNAs that upregulate de novo purine synthesis in response to increased intracellular levels of ZTP or ZMP. As an important intermediate in purine biosynthesis, ZMP also serves as a proxy for the concentration of N10-formyl-tetrahydrofolate, a key component of one-carbon metabolism. Here, we report the structure of the ZTP riboswitch bound to ZMP at a resolution of 1.80 Å. The RNA contains two subdomains brought together through a long-range pseudoknot further stabilized through helix-helix packing. ZMP is bound at the subdomain interface of the RNA through a set of interactions with the base, ribose sugar, and phosphate moieties of the ligand. Unique to nucleobase recognition by RNAs, the Z base is inner-sphere coordinated to a magnesium cation bound by two backbone phosphates. This interaction, along with steric hindrance by the backbone, imparts specificity over chemically similar compounds such as ATP/AMP.
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Affiliation(s)
- Jeremiah J Trausch
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA
| | - Joan G Marcano-Velázquez
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA
| | - Michal M Matyjasik
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA
| | - Robert T Batey
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA.
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Abstract
Riboswitches are noncoding regulatory elements that control gene expression in response to the presence of metabolites, which bind to the aptamer domain. Metabolite binding appears to occur through a combination of conformational selection and induced fit mechanism. This demands to characterize the structural dynamics of the apo state of aptamer domains. In principle, molecular dynamics (MD) simulations can give insights at the atomistic level into the dynamics of the aptamer domain. However, it is unclear to what extent contemporary force fields can bias such insights. Here, we show that the Amber force field ff99 yields the best agreement with detailed experimental observations on differences in the structural dynamics of wild type and mutant aptamer domains of the guanine-sensing riboswitch (Gsw), including a pronounced influence of Mg2+. In contrast, applying ff99 with parmbsc0 and parmχOL modifications (denoted ff10) results in strongly damped motions and overly stable tertiary loop-loop interactions. These results are based on 58 MD simulations with an aggregate simulation time>11 μs, careful modeling of Mg2+ ions, and thorough statistical testing. Our results suggest that the moderate stabilization of the χ-anti region in ff10 can have an unwanted damping effect on functionally relevant structural dynamics of marginally stable RNA systems. This suggestion is supported by crystal structure analyses of Gsw aptamer domains that reveal χ torsions with high-anti values in the most mobile regions. We expect that future RNA force field development will benefit from considering marginally stable RNA systems and optimization toward good representations of dynamics in addition to structural characteristics.
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Affiliation(s)
- Christian A Hanke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.
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37
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Zhao C, Devany M, Greenbaum NL. Measurement of chemical exchange between RNA conformers by 19F NMR. Biochem Biophys Res Commun 2014; 453:692-5. [PMID: 25301553 DOI: 10.1016/j.bbrc.2014.09.075] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 09/18/2014] [Indexed: 01/03/2023]
Abstract
Many noncoding RNA molecules adopt alternative secondary and tertiary conformations that are critical for their roles in gene expression. Although many of these rearrangements are mediated by other biomolecular components, it is important to evaluate the equilibrium relationship of the conformers. To measure the spontaneous interconversion in a bi-stable RNA stem loop sequence into which a single (19)F-uridine label was incorporated, a (19)F-(19)F EXSY experiment was employed. The kinetic exchange rate measured from EXSY experiments for this system was 37.3±2.8s(-1). The advantage of this approach is that exchange kinetics can be monitored in any RNA sequence into which a single (19)F nucleotide is incorporated by commercial synthesis. This method is therefore suitable for application to biologically significant systems in which dynamic conformational rearrangement is important for function and may therefore facilitate studies of RNA structure-function relationships.
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Affiliation(s)
- Caijie Zhao
- Department of Chemistry and Biochemistry, Hunter College of The City University of New York, New York, NY, United States
| | - Matthew Devany
- Department of Chemistry and Biochemistry, Hunter College of The City University of New York, New York, NY, United States
| | - Nancy L Greenbaum
- Department of Chemistry and Biochemistry, Hunter College of The City University of New York, New York, NY, United States.
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38
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Porter EB, Marcano-Velázquez JG, Batey RT. The purine riboswitch as a model system for exploring RNA biology and chemistry. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1839:919-930. [PMID: 24590258 PMCID: PMC4148472 DOI: 10.1016/j.bbagrm.2014.02.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 02/17/2014] [Accepted: 02/20/2014] [Indexed: 12/11/2022]
Abstract
Over the past decade the purine riboswitch, and in particular its nucleobase-binding aptamer domain, has emerged as an important model system for exploring various aspects of RNA structure and function. Its relatively small size, structural simplicity and readily observable activity enable application of a wide variety of experimental approaches towards the study of this RNA. These analyses have yielded important insights into small molecule recognition, co-transcriptional folding and secondary structural switching, and conformational dynamics that serve as a paradigm for other RNAs. In this article, the current state of understanding of the purine riboswitch family and how this growing knowledge base is starting to be exploited in the creation of novel RNA devices are examined. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Ely B Porter
- Department of Chemistry and Biochemistry, 596 UCB, University of Colorado, Boulder, CO 80309-0596, USA
| | - Joan G Marcano-Velázquez
- Department of Chemistry and Biochemistry, 596 UCB, University of Colorado, Boulder, CO 80309-0596, USA
| | - Robert T Batey
- Department of Chemistry and Biochemistry, 596 UCB, University of Colorado, Boulder, CO 80309-0596, USA.
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39
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Devi G, Zhou Y, Zhong Z, Toh DFK, Chen G. RNA triplexes: from structural principles to biological and biotech applications. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:111-28. [DOI: 10.1002/wrna.1261] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 06/30/2014] [Accepted: 07/14/2014] [Indexed: 12/29/2022]
Affiliation(s)
- Gitali Devi
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
| | - Yuan Zhou
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
| | - Zhensheng Zhong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
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40
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Havill JT, Bhatiya C, Johnson SM, Sheets JD, Thompson JS. A new approach for detecting riboswitches in DNA sequences. ACTA ACUST UNITED AC 2014; 30:3012-9. [PMID: 25015992 DOI: 10.1093/bioinformatics/btu479] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
MOTIVATION Riboswitches are short sequences of messenger RNA that can change their structural conformation to regulate the expression of adjacent genes. Computational prediction of putative riboswitches can provide direction to molecular biologists studying riboswitch-mediated gene expression. RESULTS The Denison Riboswitch Detector (DRD) is a new computational tool with a Web interface that can quickly identify putative riboswitches in DNA sequences on the scale of bacterial genomes. Riboswitch descriptions are easily modifiable and new ones are easily created. The underlying algorithm converts the problem to a 'heaviest path' problem on a multipartite graph, which is then solved using efficient dynamic programming. We show that DRD can achieve ∼ 88-99% sensitivity and >99.99% specificity on 13 riboswitch families. AVAILABILITY AND IMPLEMENTATION DRD is available at http://drd.denison.edu.
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Affiliation(s)
- Jessen T Havill
- Department of Mathematics and Computer Science, Department of Biology, Denison University, Granville, OH 43023, Capco, New York, NY, 10005, Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Chinmoy Bhatiya
- Department of Mathematics and Computer Science, Department of Biology, Denison University, Granville, OH 43023, Capco, New York, NY, 10005, Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Steven M Johnson
- Department of Mathematics and Computer Science, Department of Biology, Denison University, Granville, OH 43023, Capco, New York, NY, 10005, Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Joseph D Sheets
- Department of Mathematics and Computer Science, Department of Biology, Denison University, Granville, OH 43023, Capco, New York, NY, 10005, Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jeffrey S Thompson
- Department of Mathematics and Computer Science, Department of Biology, Denison University, Granville, OH 43023, Capco, New York, NY, 10005, Department of Computer Science, Wake Forest University, Winston-Salem, NC 27109 and College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
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Šponer J, Banáš P, Jurečka P, Zgarbová M, Kührová P, Havrila M, Krepl M, Stadlbauer P, Otyepka M. Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome. J Phys Chem Lett 2014; 5:1771-82. [PMID: 26270382 DOI: 10.1021/jz500557y] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the simulations, namely, the molecular mechanics (MM) force field (FF) approximation and limited time scale. Further, we discuss relations and differences between simulations and experiments, compare standard and enhanced sampling simulations, discuss the role of starting structures, comment on different versions of nucleic acid FFs, and relate MM computations with contemporary quantum chemistry. Despite its limitations, we show that MD is a powerful technique for studying the structural dynamics of nucleic acids with a fast growing potential that substantially complements experimental results and aids their interpretation.
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Affiliation(s)
- Jiří Šponer
- †Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- ‡CEITEC - Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavel Banáš
- §Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petr Jurečka
- §Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Marie Zgarbová
- §Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petra Kührová
- §Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Marek Havrila
- †Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- ‡CEITEC - Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Miroslav Krepl
- †Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petr Stadlbauer
- †Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- §Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
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42
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Eichhorn CD, Kang M, Feigon J. Structure and function of preQ 1 riboswitches. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:939-950. [PMID: 24798077 DOI: 10.1016/j.bbagrm.2014.04.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 04/22/2014] [Accepted: 04/25/2014] [Indexed: 12/17/2022]
Abstract
PreQ1 riboswitches help regulate the biosynthesis and transport of preQ1 (7-aminomethyl-7-deazaguanine), a precursor of the hypermodified guanine nucleotide queuosine (Q), in a number of Firmicutes, Proteobacteria, and Fusobacteria. Queuosine is almost universally found at the wobble position of the anticodon in asparaginyl, tyrosyl, histidyl and aspartyl tRNAs, where it contributes to translational fidelity. Two classes of preQ1 riboswitches have been identified (preQ1-I and preQ1-II), and structures of examples from both classes have been determined. Both classes form H-type pseudoknots upon preQ1 binding, each of which has distinct unusual features and modes of preQ1 recognition. These features include an unusually long loop 2 in preQ1-I pseudoknots and an embedded hairpin in loop 3 in preQ1-II pseudoknots. PreQ1-I riboswitches are also notable for their unusually small aptamer domain, which has been extensively investigated by NMR, X-ray crystallography, FRET, and other biophysical methods. Here we review the discovery, structural biology, ligand specificity, cation interactions, folding, dynamics, and applications to biotechnology of preQ1 riboswitches. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Catherine D Eichhorn
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Mijeong Kang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA; UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
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43
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Global analysis of riboswitches by small-angle X-ray scattering and calorimetry. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1020-1029. [PMID: 24769285 DOI: 10.1016/j.bbagrm.2014.04.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 04/10/2014] [Accepted: 04/13/2014] [Indexed: 11/22/2022]
Abstract
Riboswitches are phylogenetically widespread non-coding mRNA domains that directly bind cellular metabolites and regulate transcription, translation, RNA stability or splicing via alternative RNA structures modulated by ligand binding. The details of ligand recognition by many riboswitches have been elucidated using X-ray crystallography and NMR. However, the global dynamics of riboswitch-ligand interactions and their thermodynamic driving forces are less understood. By compiling the work of many laboratories investigating riboswitches using small-angle X-ray scattering (SAXS) and isothermal titration calorimetry (ITC), we uncover general trends and common themes. There is a pressing need for community-wide consensus experimental conditions to allow results of riboswitch studies to be compared rigorously. Nonetheless, our meta-analysis reveals considerable diversity in the extent to which ligand binding reorganizes global riboswitch structures. It also demonstrates a wide spectrum of enthalpy-entropy compensation regimes across riboswitches that bind a diverse set of ligands, giving rise to a relatively narrow range of physiologically relevant free energies and ligand affinities. From the strongly entropy-driven binding of glycine to the predominantly enthalpy-driven binding of c-di-GMP to their respective riboswitches, these distinct thermodynamic signatures reflect the versatile strategies employed by RNA to adapt to the chemical natures of diverse ligands. Riboswitches have evolved to use a combination of long-range tertiary interactions, conformational selection, and induced fit to work with distinct ligand structure, charge, and solvation properties. This article is part of a Special Issue entitled: Riboswitches.
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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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Savinov A, Perez CF, Block SM. Single-molecule studies of riboswitch folding. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1030-1045. [PMID: 24727093 DOI: 10.1016/j.bbagrm.2014.04.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/27/2014] [Accepted: 04/03/2014] [Indexed: 10/25/2022]
Abstract
The folding dynamics of riboswitches are central to their ability to modulate gene expression in response to environmental cues. In most cases, a structural competition between the formation of a ligand-binding aptamer and an expression platform (or some other competing off-state) determines the regulatory outcome. Here, we review single-molecule studies of riboswitch folding and function, predominantly carried out using single-molecule FRET or optical trapping approaches. Recent results have supplied new insights into riboswitch folding energy landscapes, the mechanisms of ligand binding, the roles played by divalent ions, the applicability of hierarchical folding models, and kinetic vs. thermodynamic control schemes. We anticipate that future work, based on improved data sets and potentially combining multiple experimental techniques, will enable the development of more complete models for complex RNA folding processes. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Andrew Savinov
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | | | - Steven M Block
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA.
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Peselis A, Serganov A. Themes and variations in riboswitch structure and function. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:908-918. [PMID: 24583553 DOI: 10.1016/j.bbagrm.2014.02.012] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/14/2014] [Accepted: 02/20/2014] [Indexed: 11/19/2022]
Abstract
The complexity of gene expression control by non-coding RNA has been highlighted by the recent progress in the field of riboswitches. Discovered a decade ago, riboswitches represent a diverse group of non-coding mRNA regions that possess a unique ability to directly sense cellular metabolites and modulate gene expression through formation of alternative metabolite-free and metabolite-bound conformations. Such protein-free metabolite sensing domains utilize sophisticated three-dimensional folding of RNA molecules to discriminate between a cognate ligand from related compounds so that only the right ligand would trigger a genetic response. Given the variety of riboswitch ligands ranging from small cations to large coenzymes, riboswitches adopt a great diversity of structures. Although many riboswitches share structural principles to build metabolite-competent folds, form precise ligand-binding pockets, and communicate a ligand-binding event to downstream regulatory regions, virtually all riboswitch classes possess unique features for ligand recognition, even those tuned to recognize the same metabolites. Here we present an overview of the biochemical and structural research on riboswitches with a major focus on common principles and individual characteristics adopted by these regulatory RNA elements during evolution to specifically target small molecules and exert genetic responses. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Alla Peselis
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Alexander Serganov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA.
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Di Palma F, Colizzi F, Bussi G. Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch. RNA (NEW YORK, N.Y.) 2013; 19:1517-1524. [PMID: 24051105 PMCID: PMC3851719 DOI: 10.1261/rna.040493.113] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/02/2013] [Indexed: 05/28/2023]
Abstract
Riboswitches are structured mRNA elements that modulate gene expression. They undergo conformational changes triggered by highly specific interactions with sensed metabolites. Among the structural rearrangements engaged by riboswitches, the forming and melting of the aptamer terminal helix, the so-called P1 stem, is essential for genetic control. The structural mechanisms by which this conformational change is modulated upon ligand binding mostly remain to be elucidated. Here, we used pulling molecular dynamics simulations to study the thermodynamics of the P1 stem in the add adenine riboswitch. The P1 ligand-dependent stabilization was quantified in terms of free energy and compared with thermodynamic data. This comparison suggests a model for the aptamer folding in which direct P1-ligand interactions play a minor role on the conformational switch when compared with those related to the ligand-induced aptamer preorganization.
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Ceres P, Garst AD, Marcano-Velázquez JG, Batey RT. Modularity of select riboswitch expression platforms enables facile engineering of novel genetic regulatory devices. ACS Synth Biol 2013; 2:463-72. [PMID: 23654267 DOI: 10.1021/sb4000096] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RNA-based biosensors and regulatory devices have received significant attention for their potential in a broad array of synthetic biology applications. One of the primary difficulties in engineering these molecules is the lack of facile methods to link sensory modules, or aptamers, to readout domains. Such efforts typically require extensive screening or selection of sequences that facilitate interdomain communication. Bacteria have evolved a widespread form of gene regulation known as riboswitches that perform this task with sufficient fidelity to control expression of biosynthetic and transport proteins essential for normal cellular homeostasis. In this work, we demonstrate that select riboswitch readout domains, called expression platforms, are modular in that they can host a variety of natural and synthetic aptamers to create novel chimeric RNAs that regulate transcription both in vitro and in vivo. Importantly, this technique does not require selection of device-specific "communication modules" required to transmit ligand binding to the regulatory domain, enabling rapid engineering of novel functional RNAs.
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Affiliation(s)
- Pablo Ceres
- Department
of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 596,
Boulder, Colorado 80309-0596, United States
| | - Andrew D. Garst
- Department
of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 596,
Boulder, Colorado 80309-0596, United States
| | - Joan G. Marcano-Velázquez
- Department
of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 596,
Boulder, Colorado 80309-0596, United States
| | - Robert T. Batey
- Department
of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 596,
Boulder, Colorado 80309-0596, United States
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Allnér O, Nilsson L, Villa A. Loop-loop interaction in an adenine-sensing riboswitch: a molecular dynamics study. RNA (NEW YORK, N.Y.) 2013; 19:916-926. [PMID: 23716711 PMCID: PMC3683926 DOI: 10.1261/rna.037549.112] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 03/28/2013] [Indexed: 06/01/2023]
Abstract
Riboswitches are mRNA-based molecules capable of controlling the expression of genes. They undergo conformational changes upon ligand binding, and as a result, they inhibit or promote the expression of the associated gene. The close connection between structural rearrangement and function makes a detailed knowledge of the molecular interactions an important step to understand the riboswitch mechanism and efficiency. We have performed all-atom molecular dynamics simulations of the adenine-sensing add A-riboswitch to study the breaking of the kissing loop, one key tertiary element in the aptamer structure. We investigated the aptamer domain of the add A-riboswitch in complex with its cognate ligand and in the absence of the ligand. The opening of the hairpins was simulated using umbrella sampling using the distance between two loops as the reaction coordinate. A two-step process was observed in all the simulated systems. First, a general loss of stacking and hydrogen bond interactions is seen. The last interactions that break are the two base pairs G37-C61 and G38-C60, but the break does not affect the energy profile, indicating their pivotal role in the tertiary structure formation but not in the structure stabilization. The junction area is partially organized before the kissing loop formation and residue A24 anchors together the loop helices. Moreover, when the distance between the loops is increased, one of the hairpins showed more flexibility by changing its orientation in the structure, while the other conserved its coaxial arrangement with the rest of the structure.
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Affiliation(s)
- Olof Allnér
- Department of Biosciences and Nutrition, Karolinska Institutet, Center for Biosciences, SE-14183 Huddinge, Sweden.
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Structure of a class II preQ1 riboswitch reveals ligand recognition by a new fold. Nat Chem Biol 2013; 9:353-5. [PMID: 23584677 PMCID: PMC3661761 DOI: 10.1038/nchembio.1231] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 03/14/2013] [Indexed: 11/26/2022]
Abstract
PreQ1 riboswitches regulate genes by binding the pyrrolopyrimidine intermediate preQ1 during biosynthesis of the essential tRNA base queuosine. We report the first preQ1-II riboswitch structure at 2.3 Å resolution, which uses a novel fold to achieve effector recognition at the confluence of a three-way-helical junction flanking a pseudoknotted ribosome-binding site (RBS). The results account for preQ1-II-riboswitch-mediated translational control, and expand the known repertoire of ligand binding modes utilized by regulatory RNAs.
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