Manson Michael D. (ed.) Bacterial Chemosensing: Methods and Protocols

Humana Press, 2018. — 375 p. — (Methods in Molecular Biology 1729). — ISBN 978-1-4939-7576-1.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.Introduction
The Diversity of Bacterial Chemosensing
Tran smembrane Signal Transduction in Bacterial Chemosensing
Methods for Studying Bacterial Chemotaxis at the Population and Whole-Cell Levels
Two Spatial Chemotaxis Assays:​ The Nutrient-Depleted Chemotaxis Assay and the Agarose-Plug-Bridge Assay
Quantification of Bacterial Chemotaxis Responses at the Mouths of Hydrogel Capillaries
A Static Microfluidic Device for Investigating the Chemotaxis Response to Stable, Non-linear Gradients
Visualizing Chemoattraction of Planktonic Cells to a Biofilm
Labeling Bacterial Flagella with Fluorescent Dyes
In Vivo Analysis of Receptor Function
All-Codon Mutagenesis for Structure-Function Studies of Chemotaxis Signaling Proteins
Mutational Analysis of Binding Protein–Chemoreceptor Interactions
In Vitro Assay for Measuring Receptor-Kinase Activity in the Bacillus subtilis Chemotaxis Pathway
FRET Analysis of the Chemotaxis Pathway Response
Monitoring Two-Component Sensor Kinases with a Chemotaxis Signal Readout
Analyzing Protein Domain Interactions in Chemoreceptors by In Vivo PEGylation
Tuning Chemoreceptor Signaling by Positioning Aromatic Residues at the Lipid–Aqueous Interface
Analyzing Chemoreceptor Interactions In Vivo with the Trifunctional Cross-Linker TMEA
Cryo-EM Methods for Studying Chemoreceptor Structure
Use of Cryo-EM to Study the Structure of Chemoreceptor Arrays In Vivo
Visualizing Chemoreceptor Arrays in Bacterial Minicells by Cryo-Electron Tomography and Subtomogram Analysis
Monitoring the Intracellular Movement of Chemosensory Proteins
Bacterial Chemoreceptor Imaging at High Spatiotemporal Resolution Using Photoconvertible​ Fluorescent Proteins
Imaging of Single Dye-Labeled Chemotaxis Proteins in Live Bacteria Using Electroporation
Fluorescence Anisotropy to Detect In Vivo Stimulus-Induced Changes in Chemoreceptor Packing
High-Throughput Methods for Screening Novel Chemoeffectors
Chemotaxis to Atypical Chemoattractants​ by Soil Bacteria
Screening Chemoreceptor–Ligand Interactions by High-Throughput Thermal-Shift Assays
High-Throughput Screening to Identify Chemoreceptor Ligands
Identification of Specific Ligands for Sensory Receptors by Small-Molecule Ligand Arrays and Surface Plasmon Resonance
Creating Chemical Tools for Studying Chemosensory Signal Transduction
Fluorescence Measurement of Kinetics of CheY Autophosphorylat​ion with Small Molecule Phosphodonors
Synthesis of a Stable Analog of the Phosphorylated Form of CheY:​ Phosphono-CheY
Computer Simulation of Chemotaxis
Quantitative Modeling of Flagellar Motor-Mediated Adaptation
Molecular Modeling of Chemoreceptor:​Ligand Interactions
Phylogenetic and Protein Sequence Analysis of Bacterial Chemoreceptors