Bacterial Chemosensing: Methods and Protocols

ISBN-13: 9781493985265 / Angielski / Miękka / 2019 / 389 str.

Michael D. Manson

Spis treści

Part I: Introduction

1. The Diversity of Bacterial Chemosensing

            Michael D. Manson

2. Transmembrane Signal Transduction in Bacterial Chemosensing

            Michael D. Manson

Part II: Methods for Studying Bacterial Chemotaxis at the Population and Whole-Cell Levels

3. Two Spatial Chemotaxis Assays: The Nutrient-Depleted Chemotaxis Assay and the Agarose-Plug-Bridge Assay

            Victoria Korolik and Karen M. Ottemann

4. Quantification of Bacterial Chemotaxis Responses at the Mouths of Hydrogel Capillaries

            Benjamin A. Webb, Timofey Arapov, and Birgit Scharf

5. A Static Microfluidic Device for Investigating the Chemotaxis Response to Stable, Non-Linear Gradients

            Nitesh Sule, Daniel Penarete-Acosta, Derek L. Englert, and Arul Jayaraman

6. Visualizing Chemoattraction of Planktonic Cells to a Biofilm

            Sneha Jani

7. Labeling Bacterial Flagella with Fluorescent Dyes

            Linda Turner and Howard C. Berg

Part III: In Vivo Analysis of Receptor Function

8. All-Codon Mutagenesis for Structure-Function Studies of Chemotaxis Signaling Proteins

            Peter Ames and John S. Parkinson

9. Mutational Analysis of Binding Protein/Chemoreceptor Interactions

            Andrew L. Seely

10. In Vitro Assay for Measuring Receptor-Kinase Activity in the Bacillus subtilis Chemotaxis Pathway

            Hanna E. Walukiewicz, George W. Ordal, and Christopher V. Rao

11. FRET Analysis of the Chemotaxis Pathway Response

            Anja Paulick and Victor Sourjik

12. Monitoring Two-Component Sensor Kinases with a Chemotaxis Signal Readout

            Run-Zhi Lai and John S. Parkinson

13. Analyzing Protein Domain Interactions in Chemoreceptors by In Vivo PEGylation

            Kylie J. Watts and Mark S. Johnson

14. Tuning Chemoreceptor Signaling by Positioning Aromatic Residues at the Lipid-Aqueous Interface

            Rahmi Yusuf, Robert J. Lawrence, Lucy V. Eke, and Roger R. Draheim

15. Analyzing Chemoreceptor Interactions In Vivo with the Tri-Functional Crosslinker TMEA

            Claudia A. Studdert and Diego A. Massazza

Part IV: Cryo-EM Methods for Studying Chemoreceptor Structure

16. Use of Cryo-EM to Study the Structure of Chemoreceptor Arrays In Vivo

            Wen Yang and Ariane Briegel

17. Visualizing Chemoreceptor Arrays in Bacterial Minicells by Cryo-Electron Tomography and Subtomogram Analysis

            Zhuan Qin, Bo Hu, and Jun Liu

Part V: Monitoring the Intracellular Movement of Chemosensory Proteins

18. Bacterial Chemoreceptor Imaging at High Spatio-Temporal Resolution Using Photoconvertible Fluorescent Proteins

            Jacopo Solari, Francois Anquez, Katharina Scherer, and Thomas S. Shimizu

19. Imaging of Single Dye-Labeled Chemotaxis Proteins in Live Bacteria Using Electroporation

            Diana Di Paolo and Richard M. Berry

20. Fluorescence Anisotropy to Detect In Vivo Stimulus-Induced Changes in Chemoreceptor Packing

            Vered Frank and Ady Vaknin

Part VI: High-Throughput Methods for Screening Novel Chemoeffectors

21. Chemotaxis to Atypical Chemoattractants by Soil Bacteria

            Rebecca E. Parales and Jayna L. Ditty

22. Screening Chemoreceptor–Ligand Interactions by High-Throughput Thermal-Shift Assays

            Maximilian K.G. Ehrhardt, Suzanne L. Warring, and Monica L. Gerth

23. High-Throughput Screening to Identify Chemoreceptor Ligands

            Mathilde Fernández, Álvaro Ortega, Miriam Rico-Jiménez, David Martín-Mora, Abdelali Daddaoua, Miguel. A. Matilla, and Tino Krell

24. Identification of Specific Ligands for Sensory Receptors by Small-Molecule Ligand Arrays and Surface Plasmon Resonance

            Christopher J. Day and Victoria Korolik

Part VII: Creating Chemical Tools for Studying Chemosensory Signal Transduction

25. Fluorescence Measurement of Kinetics of CheY Autophosphorylation with Small Molecule Phosphodonors

            Ruth E. Silversmith and Robert B. Bourret

26. Synthesis of a Stable Analog of the Phosphorylated Form of CheY: Phosphono-CheY

            Daniel B. Lookadoo, Matthew S. Beyersdorf, and Christopher J. Halkides

Part VIII: Computer Simulation of Chemotaxis

27. Quantitative Modeling of Flagellar Motor-Mediated Adaptation

            Pushkar P. Lele

28. Molecular Modeling of Chemoreceptor:Ligand Interactions

            Asuka A. Orr, Arul Jayaraman, and Phanourios Tamamis

29. Phylogenetic and Protein Sequence Analysis of Bacterial Chemoreceptors

            Davi R. Ortega and Igor B. Zhulin

Blurb

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.