c-di-GMP signaling : methods and protocols

Description

This volume provides a collection of protocols for the common experimental approaches used in the in the burgeoning field of c-di-GMP-dependent signaling. The chapters, divided into eight major parts, guide readers through methods on synthesis, detection, quantitation, modulation of the levels of c-di-GMP present in cells, procedures to detect and evaluate the interaction of c-di-GMP, and up and coming approaches focusing on the inhibition of c-di-GMP signaling.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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, c-di-GMP Signaling: Methods and Protocols aims to inspire researchers to try new approaches. Front Matter ....Pages i-xiv Discovery of the Second Messenger Cyclic di-GMP (Ute Römling, Michael Y. Galperin)....Pages 1-8 Front Matter ....Pages 9-9 Enzymatic Production of c-di-GMP Using a Thermophilic Diguanylate Cyclase (Prabhadevi Venkataramani, Zhao-Xun Liang)....Pages 11-22 Synthesis of [32P]-c-di-GMP for Diguanylate Cyclase and Phosphodiesterase Activity Determinations (Barbara I. Kazmierczak)....Pages 23-29 Front Matter ....Pages 31-31 High-Performance Liquid Chromatography (HPLC)-Based Detection and Quantitation of Cellular c-di-GMP (Olga E. Petrova, Karin Sauer)....Pages 33-43 Identification and Quantification of Cyclic Di-Guanosine Monophosphate and Its Linear Metabolites by Reversed-Phase LC-MS/MS (Heike Bähre, Volkhard Kaever)....Pages 45-58 Detection of Cyclic Dinucleotides by STING (Xiao-Xia Du, Xiao-Dong Su)....Pages 59-69 Spectrophotometric and Mass Spectroscopic Methods for the Quantification and Kinetic Evaluation of In Vitro c-di-GMP Synthesis (Geoffrey B. Severin, Christopher M. Waters)....Pages 71-84 Front Matter ....Pages 85-85 Gauging and Visualizing c-di-GMP Levels in Pseudomonas aeruginosa Using Fluorescence-Based Biosensors (Morten Rybtke, Song Lin Chua, Joey Kuok Hoong Yam, Michael Givskov, Liang Yang, Tim Tolker-Nielsen)....Pages 87-98 Cyclic di-GMP-Responsive Transcriptional Reporter Bioassays in Pseudomonas aeruginosa (Bradley R. Borlee, Grace I. Borlee, Kevin H. Martin, Yasuhiko Irie)....Pages 99-110 Live Flow Cytometry Analysis of c-di-GMP Levels in Single Cell Populations (Jongchan Yeo, Xin C. Wang, Ming C. Hammond)....Pages 111-130 Front Matter ....Pages 131-131 Experimental Detection and Visualization of the Extracellular Matrix in Macrocolony Biofilms (Diego O. Serra, Regine Hengge)....Pages 133-145 Congo Red Stain Identifies Matrix Overproduction and Is an Indirect Measurement for c-di-GMP in Many Species of Bacteria (Christopher J. Jones, Daniel J. Wozniak)....Pages 147-156 Type IV Pili-Dependent Motility as a Tool to Determine the Activity of c-di-GMP Modulating Enzymes in Myxococcus xanthus (Dorota Skotnicka, Lotte Søgaard-Andersen)....Pages 157-165 Front Matter ....Pages 167-167 Using Light-Activated Enzymes for Modulating Intracellular c-di-GMP Levels in Bacteria (Min-Hyung Ryu, Anastasia Fomicheva, Lindsey O’Neal, Gladys Alexandre, Mark Gomelsky)....Pages 169-186 Analysis of c-di-GMP Levels Synthesized by a Photoreceptor Protein in Response to Different Light Qualities Using an In Vitro Enzymatic Assay (Veronika Angerer, Lars-Oliver Essen, Annegret Wilde)....Pages 187-204 Probing the Role of Cyclic di-GMP Signaling Systems in Disease Using Chinese Radish (Shi-Qi An, Ji-Liang Tang, J. Maxwell Dow)....Pages 205-212 Contribution of Cyclic di-GMP in the Control of Type III and Type VI Secretion in Pseudomonas aeruginosa (Ronan R. McCarthy, Martina Valentini, Alain Filloux)....Pages 213-224 Semiquantitative Analysis of the Red, Dry, and Rough Colony Morphology of Salmonella enterica Serovar Typhimurium and Escherichia coli Using Congo Red (Annika Cimdins, Roger Simm)....Pages 225-241 Front Matter ....Pages 243-243 Fluorescent 2-Aminopurine c-di-GMP and GpG Analogs as PDE Probes (Jie Zhou, Clement Opoku-Temeng, Herman O. Sintim)....Pages 245-261 Measuring Cyclic Diguanylate (c-di-GMP)-Specific Phosphodiesterase Activity Using the MANT-c-di-GMP Assay (Dorit Eli, Trevor E. Randall, Henrik Almblad, Joe J. Harrison, Ehud Banin)....Pages 263-278 Determining Phosphodiesterase Activity (Radioactive Assay) (Barbara I. Kazmierczak)....Pages 279-283 Determining Diguanylate Cyclase Activity (Radioactive Assay) (Barbara I. Kazmierczak)....Pages 285-289 Front Matter ....Pages 291-291 Detection of c-di-GMP-Responsive DNA Binding (Jacob R. Chambers, Karin Sauer)....Pages 293-302 Use of Nonradiochemical DNAse Footprinting to Analyze c-di-GMP Modulation of DNA-Binding Proteins (Claudine Baraquet, Caroline S. Harwood)....Pages 303-315 Detection of Cyclic di-GMP Binding Proteins Utilizing a Biotinylated Cyclic di-GMP Pull-Down Assay (Jacob R. Chambers, Karin Sauer)....Pages 317-329 Probing Protein–Protein Interactions with Genetically Encoded Photoactivatable Cross-Linkers (Richard B. Cooley, Holger Sondermann)....Pages 331-345 Identification of c-di-AMP-Binding Proteins Using Magnetic Beads (Jan Kampf, Jan Gundlach, Christina Herzberg, Katrin Treffon, Jörg Stülke)....Pages 347-359 Pull-Down with a c-di-GMP-Specific Capture Compound Coupled to Mass Spectrometry as a Powerful Tool to Identify Novel Effector Proteins (Benoît-Joseph Laventie, Timo Glatter, Urs Jenal)....Pages 361-376 Identification of c-di-GMP-Responsive Riboswitches (Johann Peltier, Olga Soutourina)....Pages 377-402 Isothermal Titration Calorimetry to Determine Apparent Dissociation Constants (Kd) and Stoichiometry of Interaction (n) of C-di-GMP Binding Proteins (Bruno Y. Matsuyama, Petya V. Krasteva, Marcos V. A. S. Navarro)....Pages 403-416 Front Matter ....Pages 417-417 Targeting c-di-GMP Signaling, Biofilm Formation, and Bacterial Motility with Small Molecules (Clement Opoku-Temeng, Herman O. Sintim)....Pages 419-430 Discovering Selective Diguanylate Cyclase Inhibitors: From PleD to Discrimination of the Active Site of Cyclic-di-GMP Phosphodiesterases (S. Rinaldo, G. Giardina, F. Mantoni, A. Paiardini, Alessio Paone, Francesca Cutruzzolà)....Pages 431-453 High-Throughput Screening for Compounds that Modulate the Cellular c-di-GMP Level in Bacteria (Julie Groizeleau, Jens Bo Andersen, Michael Givskov, Jens Berthelsen, Tim Tolker-Nielsen)....Pages 455-470 Genetic Tools to Study c-di-GMP-Dependent Signaling in Pseudomonas aeruginosa (Livia Leoni, Sarika Vishnu Pawar, Giordano Rampioni)....Pages 471-480 Back Matter ....Pages 481-486