Riboswitches: Methods and Protocols

ISBN-13: 9781934115886 / Angielski / Twarda / 2009 / 366 str.

Alexander Serganov

Opis

The transfer of hereditary information from genes to proteins is one of the essential pr- esses in all living organisms on our planet. Some genes are expressed without modu- tion throughout the life of a cell, while many others require various degrees of control to precisely balance cellular metabolism with environmental conditions. For many years, researchers attributed this regulatory function to protein molecules, which can direct gene expression at multiple levels, in response to various input signals, and with different degrees of selectivity. Even when the control of gene expression was achieved via direct interactions between proteins and mRNAs, the active role was routinely assigned to p- teins, while RNAs were considered merely as recipient molecules. The discovery of RNA interference and multiple bacterial regulatory RNAs caused a shift from the perception of proteins as the predominant regulators of gene expression to the acknowledgement of the importance of RNAs in many regulatory circuits. Such a viewpoint received strong support several years ago after the discovery of riboswitches and related RNA sensors - mRNA regions capable of alternating their conformations in response to the presence of cellular metabolites and other physical or chemical cues. These classes of RNA pass on cellular and environmental information directly to transcription or translation machinery without the assistance of proteins. The riboswitches are commonly defined as evolutionarily conserved mRNA regions capable of specific binding to metabolite molecules, and, as a result, adopting a particular RNA conformation that modulates gene expression.

Recenzje

From the reviews:

"Riboswitches are among the latest additions to the growing field of RNA-based gene expression control systems found in both prokaryotic and eukaryotic cells. ... useful in various aspects of work on riboswitches and other regulatory RNAs. ... It also refers to pertinent and up-to-date literature. ... The reviewed book can be strongly recommended to RNA researchers with different levels of expertise, as well as to those who learn or teach in this field." (Joanna Ciesla, Acta Biochimica Polonica, Vol. 56 (3), 2009)

"This book is a good collection of 'Methods and Protocols' for studying ... riboswitches as well as some other RNAs involved in gene expression. ... Readers are introduced to a broad range of RNA methodologies from basic to applied in this book. I ... recommend the book for researchers who work in the area of riboswitches, but also for other scientists who are involved in RNA-relevant studies." (Atsushi Ogawa, ChemBioChem, Vol. 10, 2009)

Spis treści

1. Predicting Riboswitch Regulation on a Genomic Scale Jeffrey E. Barrick 2. Enzymatic Ligation Strategies for the Preparation of Purine Riboswitches with Site-Specific Chemical Modifications Renate Rieder, Claudia Höbartner, and Ronald Micura 3. Application of Fluorescent Measurements for Characterization of Riboswitch-Ligand Interactions Benoit Heppell, Jérôme Mulhbacher, J. Carlos Penedo, and Daniel A. Lafontaine 4. Transcriptional Approaches to Riboswitch Studies Alexander Mironov, Vitaly Epshtein, and Evgeny Nudler 5. Kinetics of Riboswitch Regulation Studied By In Vitro Transcription J. Kenneth Wickiser 6. Molecular Basis of RNA-Mediated Gene Regulation on the Adenine Riboswitch by Single-Molecule Approaches Jean-François Lemay, J. Carlos Penedo, Jérôme Mulhbacher, and Daniel A. Lafontaine 7. Methods for Analysis of Ligand-Induced RNA Conformational Changes Chad A. Brautigam, Catherine A. Wakeman, and Wade C. Winkler 8. Monitoring RNA-Ligand Interactions Using Isothermal Titration Calorimetry Sunny D. Gilbert and Robert T. Batey 9. Preparation and Crystallization of Riboswitch-Ligand Complexes Olga Pikovskaya, Artem A. Serganov, Anna Polonskaia, Alexander Serganov, and Dinshaw J. Patel 10. Crystallization of the glmS Ribozyme-Riboswitch Daniel J. Klein and Adrian R. Ferré-D’Amaré 11. Riboswitch Conformations Revealed by Small-Angle X-Ray Scattering Jan Lipfert, Daniel Herschlag, and Sebastian Doniach 12. Time-Resolved NMR Spectroscopy: Ligand-Induced Refolding of Riboswitches Janina Buck, Boris Fürtig, Jonas Noeske, Jens Wöhnert, and Harald Schwalbe 13. Analysis of the RNA Backbone: Structural Analysis of Riboswitches by In-Line Probing and Selective 2'-Hydroxyl Acylation and PrimerExtension (SHAPE) Catherine A. Wakeman and Wade C. Winkler 14. Identification of Metabolite-Riboswitch Interactions Using Nucleotide Analog Interference Mapping and Suppression Juliane K. Soukup and Garrett A. Soukup 15. RNA-Dependent RNA Switches in Bacteria Tina M. Henkin 16. Probing mRNA Structure and sRNA-mRNA Interactions in Bacteria Using Enzymes and Lead(II) Clément Chevalier, Thomas Geissmann, Anne-Catherine Helfer, and Pascale Romby 17. Structural Probing of RNA Thermosensors Claude Chiaruttini, Frédéric Allemand, and Mathias Springer 18. Ribosomal Initiation Complexes Probed by Toeprinting and Effect of trans-Acting Translational Regulators in Bacteria Pierre Fechter, Clément Chevalier, Gulnara Yusupova, Marat Yusupov, Pascale Romby, and Stefano Marzi 19. Isolation and Characterization of the Heat Shock RNA 1 (HSR1) Ilya Shamovsky and Evgeny Nudler 20. Analysis of tRNA-Directed Transcription Antitermination in the T Box System in vivo Tina M. Henkin 21. In vitro Selection of Conformational Probes for Riboswitches Günter Mayer and Michael Famulok 22. A Green Fluorescent Protein (GFP) Based Plasmid System to Study Post-Transcriptional Control of Gene Expression in vivo Johannes H. Urban and Jörg Vogel 23. High-Throughput Screens to Discover Synthetic Riboswitches Sean A. Lynch, Shana Topp, and Justin P. Gallivan 24. A Mammalian Cell-Based Assay for Screening Inhibitors of RNA Cleavage Laising Yen, Brent R. Stockwell, and Richard C. Mulligan 25. In vitro Selection of glmS Ribozymes Kristian H. Link and Ronald R. Breaker

Blurb

The revolutionary discoveries of RNA interference and bacterial regulatory RNAs led to further breakthroughs such as the identification of riboswitches and related RNA sensors, mRNA regions capable of alternating their conformations in response to the presence of cellular metabolites and other physical or chemical cues.  In Riboswitches: Methods and Protocols, expert researchers provide comprehensive and up-to-date coverage of various methods used to study riboswitches and other RNAs involved in gene expression control.  Examining biochemical and modern biophysical techniques, the volume focuses on mRNAs responding to small organic molecules but expands the definition of a riboswitch to incorporate classes of RNA that undergo conformational transitions in response to other stimuli in order to control the expression of genes.  Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls.

Cutting-edge and authoritative, Riboswitches: Methods and Protocols promises to inspire both novices and experts working in a wide range of contemporary biological areas who wish to further develop their RNA methodology.