Bacterial Chemosensing: Methods and Protocols

Description

This volume covers a wide range of up-to-date technologies that have been successfully applied to study the chemosensing behavior of the traditional model species, such as Escherichia coli and Salmonella typhimurium, while being also applicable to a wide spectrum of other species. Beginning with an introduction, the sections of the book explore methods for studying bacterial chemotaxis at the population and whole-cell levels, in vivo analysis of receptor function, cryo-EM methods for studying chemoreceptor structure, as well as intracellular movement of chemosensory proteins, high-throughput methods to screen for novel chemoeffectors, and chemical tools and computer simulations for analyzing chemotaxis. Written for the highly successful Methods in Molecular Biology series, chapters include brief introductions to their topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips for troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Bacterial Chemosensing: Methods and Protocols provides an extensive repertoire of approaches that can be extended to understanding chemotaxis, in particular, and chemosensing, in general, in the context of the enormously varied lifestyles adopted in the larger bacterial world. Front Matter ....Pages i-xiii Front Matter ....Pages 1-1 The Diversity of Bacterial Chemosensing (Michael D. Manson)....Pages 3-6 Transmembrane Signal Transduction in Bacterial Chemosensing (Michael D. Manson)....Pages 7-19 Front Matter ....Pages 21-21 Two Spatial Chemotaxis Assays: The Nutrient-Depleted Chemotaxis Assay and the Agarose-Plug-Bridge Assay (Victoria Korolik, Karen M. Ottemann)....Pages 23-31 Quantification of Bacterial Chemotaxis Responses at the Mouths of Hydrogel Capillaries (Benjamin A. Webb, Timofey D. Arapov, Birgit E. Scharf)....Pages 33-45 A Static Microfluidic Device for Investigating the Chemotaxis Response to Stable, Non-linear Gradients (Nitesh Sule, Daniel Penarete-Acosta, Derek L. Englert, Arul Jayaraman)....Pages 47-59 Visualizing Chemoattraction of Planktonic Cells to a Biofilm (Sneha Jani)....Pages 61-69 Labeling Bacterial Flagella with Fluorescent Dyes (Linda Turner, Howard C. Berg)....Pages 71-76 Front Matter ....Pages 77-77 All-Codon Mutagenesis for Structure-Function Studies of Chemotaxis Signaling Proteins (Peter Ames, John S. Parkinson)....Pages 79-85 Mutational Analysis of Binding Protein–Chemoreceptor Interactions (Andrew L. Seely)....Pages 87-94 In Vitro Assay for Measuring Receptor-Kinase Activity in the Bacillus subtilis Chemotaxis Pathway (Hanna E. Walukiewicz, George W. Ordal, Christopher V. Rao)....Pages 95-105 FRET Analysis of the Chemotaxis Pathway Response (Anja Paulick, Victor Sourjik)....Pages 107-126 Monitoring Two-Component Sensor Kinases with a Chemotaxis Signal Readout (Run-Zhi Lai, John S. Parkinson)....Pages 127-135 Analyzing Protein Domain Interactions in Chemoreceptors by In Vivo PEGylation (Kylie J. Watts, Mark S. Johnson)....Pages 137-145 Tuning Chemoreceptor Signaling by Positioning Aromatic Residues at the Lipid–Aqueous Interface (Rahmi Yusuf, Robert J. Lawrence, Lucy V. Eke, Roger R. Draheim)....Pages 147-158 Analyzing Chemoreceptor Interactions In Vivo with the Trifunctional Cross-Linker TMEA (Claudia A. Studdert, Diego A. Massazza)....Pages 159-170 Front Matter ....Pages 171-171 Use of Cryo-EM to Study the Structure of Chemoreceptor Arrays In Vivo (Wen Yang, Ariane Briegel)....Pages 173-185 Visualizing Chemoreceptor Arrays in Bacterial Minicells by Cryo-Electron Tomography and Subtomogram Analysis (Zhuan Qin, Bo Hu, Jun Liu)....Pages 187-199 Front Matter ....Pages 201-201 Bacterial Chemoreceptor Imaging at High Spatiotemporal Resolution Using Photoconvertible Fluorescent Proteins (Jacopo Solari, Francois Anquez, Katharina M. Scherer, Thomas S. Shimizu)....Pages 203-231 Imaging of Single Dye-Labeled Chemotaxis Proteins in Live Bacteria Using Electroporation (Diana Di Paolo, Richard M. Berry)....Pages 233-246 Fluorescence Anisotropy to Detect In Vivo Stimulus-Induced Changes in Chemoreceptor Packing (Vered Frank, Ady Vaknin)....Pages 247-252 Front Matter ....Pages 253-253 Chemotaxis to Atypical Chemoattractants by Soil Bacteria (Rebecca E. Parales, Jayna L. Ditty)....Pages 255-280 Screening Chemoreceptor–Ligand Interactions by High-Throughput Thermal-Shift Assays (Maximilian K. G. Ehrhardt, Suzanne L. Warring, Monica L. Gerth)....Pages 281-290 High-Throughput Screening to Identify Chemoreceptor Ligands (Matilde Fernández, Álvaro Ortega, Miriam Rico-Jiménez, David Martín-Mora, Abdelali Daddaoua, Miguel A. Matilla et al.)....Pages 291-301 Identification of Specific Ligands for Sensory Receptors by Small-Molecule Ligand Arrays and Surface Plasmon Resonance (Christopher J. Day, Victoria Korolik)....Pages 303-317 Front Matter ....Pages 319-319 Fluorescence Measurement of Kinetics of CheY Autophosphorylation with Small Molecule Phosphodonors (Ruth E. Silversmith, Robert B. Bourret)....Pages 321-335 Synthesis of a Stable Analog of the Phosphorylated Form of CheY: Phosphono-CheY (Daniel B. Lookadoo, Matthew S. Beyersdorf, Christopher J. Halkides)....Pages 337-343 Front Matter ....Pages 345-345 Quantitative Modeling of Flagellar Motor-Mediated Adaptation (Pushkar P. Lele)....Pages 347-352 Molecular Modeling of Chemoreceptor:Ligand Interactions (Asuka A. Orr, Arul Jayaraman, Phanourios Tamamis)....Pages 353-372 Phylogenetic and Protein Sequence Analysis of Bacterial Chemoreceptors (Davi R. Ortega, Igor B. Zhulin)....Pages 373-385 Back Matter ....Pages 387-389