Bacterial Chemosensing: Methods and Protocols

375 Pages·2018·12.552 MB·English

by  Michael D. Manson (eds.)

Methods in
Molecular Biology 1729
Michael D. Manson Editor
Bacterial
Chemosensing
Methods and Protocols
M M B
ethods in olecular iology
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire, AL10 9AB, UK
For further volumes:
http://www.springer.com/series/7651
Bacterial Chemosensing
Methods and Protocols
Edited by
Michael D. Manson
Department of Biology, Texas A&M University , College Station, TX, USA
Editor
Michael D. Manson
Department of Biology
Texas A&M University
College Station, TX, USA
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-7576-1 ISBN 978-1-4939-7577-8 (eBook)
https://doi.org/10.1007/978-1-4939-7577-8
Library of Congress Control Number: 2017963360
© Springer Science+Business Media, LLC 2018
This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is
concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction
on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation,
computer software, or by similar or dissimilar methodology now known or hereafter developed.
The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not
imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and
regulations and therefore free for general use.
The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed
to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty,
express or implied, with respect to the material contained herein or for any errors or omissions that may have been
made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Cover Illustration: Artist’s impression of chemoreceptor distribution and mobility, based on data from photoactivation
localization microscopy (PALM) and localized photoactivation single-particle tracking (LPA-SPT) in two E. coli cells
(Chapter 18)
Printed on acid-free paper
This Humana Press imprint is published by Springer Nature
The registered company is Springer Science+Business Media, LLC
The registered company address is: 233 Spring Street, New York, NY 10013, U.S.A.
Preface
The chemosensory behavior of bacteria is the signal transduction system that is best under-
stood at the molecular level. A good part of the reason for that status is the development of
a large and diverse toolkit of both simple and sophisticated methods for the analysis of dif-
ferent aspects of the chemosensory signaling pathways. A large number of these method-
ologies have been developed using the traditional model systems of Escherichia coli and
Salmonella typhimurium, but they are also generally applicable to a wide spectrum of other
species. Interest is turning to other bacteria because of the diversity of chemoattractants
and repellents that they recognize and because of the enormous range of ecological con-
texts in which chemotaxis is an important contributing factor to survival. This volume is
designed to cover a wide range of up-to-date technologies that have been successfully
applied to study the chemosensing behavior of the traditional model species. It is hoped
that this extensive repertoire of approaches can be extended to understand chemotaxis, in
particular, and chemosensing, in general, in the context of the enormously varied lifestyles
adopted in the larger bacterial world.
College Station, TX, USA Michael D. Manson
v
Contents
Preface........................................................... v
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi
Part I IntroductIon
1 The Diversity of Bacterial Chemosensing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Michael D. Manson
2 Transmembrane Signal Transduction in Bacterial Chemosensing. . . . . . . . . . . . 7
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. . . . . . . . . . . . . . . . . . . . 23
Victoria Korolik and Karen M. Ottemann
4 Quantification of Bacterial Chemotaxis Responses at the Mouths
of Hydrogel Capillaries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Benjamin A. Webb, Timofey D. Arapov, and Birgit E. Scharf
5 A Static Microfluidic Device for Investigating the Chemotaxis
Response to Stable, Non-linear Gradients . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Nitesh Sule, Daniel Penarete-Acosta, Derek L. Englert,
and Arul Jayaraman
6 Visualizing Chemoattraction of Planktonic Cells to a Biofilm . . . . . . . . . . . . . . 61
Sneha Jani
7 Labeling Bacterial Flagella with Fluorescent Dyes . . . . . . . . . . . . . . . . . . . . . . . 71
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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Peter Ames and John S. Parkinson
9 Mutational Analysis of Binding Protein–Chemoreceptor Interactions. . . . . . . . . 87
Andrew L. Seely
10 In Vitro Assay for Measuring Receptor-Kinase Activity
in the Bacillus subtilis Chemotaxis Pathway. . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Hanna E. Walukiewicz, George W. Ordal, and Christopher V. Rao
11 FRET Analysis of the Chemotaxis Pathway Response . . . . . . . . . . . . . . . . . . . . 107
Anja Paulick and Victor Sourjik
vii
viii Contents
12 Monitoring Two-Component Sensor Kinases with a Chemotaxis
Signal Readout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Run-Zhi Lai and John S. Parkinson
13 Analyzing Protein Domain Interactions in Chemoreceptors
by In Vivo PEGylation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Kylie J. Watts and Mark S. Johnson
14 Tuning Chemoreceptor Signaling by Positioning Aromatic
Residues at the Lipid–Aqueous Interface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Rahmi Yusuf, Robert J. Lawrence, Lucy V. Eke,
and Roger R. Draheim
15 Analyzing Chemoreceptor Interactions In Vivo
with the Trifunctional Cross-Linker TMEA. . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
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. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
Wen Yang and Ariane Briegel
17 Visualizing Chemoreceptor Arrays in Bacterial Minicells by Cryo-Electron
Tomography and Subtomogram Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
Zhuan Qin, Bo Hu, and Jun Liu
Part v MonItorIng the Intracellular MoveMent
of cheMosensory ProteIns
18 Bacterial Chemoreceptor Imaging at High Spatiotemporal
Resolution Using Photoconvertible Fluorescent Proteins. . . . . . . . . . . . . . . . . . 203
Jacopo Solari, Francois Anquez, Katharina M. Scherer,
and Thomas S. Shimizu
19 Imaging of Single Dye-Labeled Chemotaxis Proteins
in Live Bacteria Using Electroporation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
Diana Di Paolo and Richard M. Berry
20 Fluorescence Anisotropy to Detect In Vivo Stimulus- Induced
Changes in Chemoreceptor Packing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247
Vered Frank and Ady Vaknin
Part vI hIgh-throughPut Methods for screenIng novel
cheMoeffectors
21 Chemotaxis to Atypical Chemoattractants by Soil Bacteria. . . . . . . . . . . . . . . . . 255
Rebecca E. Parales and Jayna L. Ditty
22 Screening Chemoreceptor–Ligand Interactions by High-Throughput
Thermal-Shift Assays. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281
Maximilian K. G. Ehrhardt, Suzanne L. Warring, and Monica L. Gerth
Contents ix
23 High-Throughput Screening to Identify Chemoreceptor Ligands . . . . . . . . . . . 291
Matilde 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 . . . . . . . . . . 303
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. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321
Ruth E. Silversmith and Robert B. Bourret
26 Synthesis of a Stable Analog of the Phosphorylated Form of CheY:
Phosphono-CheY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337
Daniel B. Lookadoo, Matthew S. Beyersdorf, and Christopher J. Halkides
Part vIII coMPuter sIMulatIon of cheMotaxIs
27 Quantitative Modeling of Flagellar Motor-Mediated Adaptation . . . . . . . . . . . . 347
Pushkar P. Lele
28 Molecular Modeling of Chemoreceptor:Ligand Interactions . . . . . . . . . . . . . . . 353
Asuka A. Orr, Arul Jayaraman, and Phanourios Tamamis
29 Phylogenetic and Protein Sequence Analysis of Bacterial Chemoreceptors . . . . . 373
Davi R. Ortega and Igor B. Zhulin
Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 387
Contributors
Peter aMes • Department of Biology, University of Utah, Salt Lake City, UT, USA
francoIs anquez • Laboratoire de Physique des Lasers, Atomes et Molécules, UMR CNRS
8523, Université Lille 1, Villeneuve d’Ascq, France
tIMofey d. araPov • Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
hoWard c. Berg • Departments of Molecular and Cellular Biology and of Physics,
Harvard University, Cambridge, MA, USA; The Rowland Institute at Harvard,
Cambridge, MA, USA
rIchard M. Berry • Berry Group, Clarendon Laboratory, Department of Physics,
University of Oxford, Oxford, UK
MattheW s. Beyersdorf • Department of Chemistry and Biochemistry, The University of
North Carolina, Wilmington, NC, USA
roBert B. Bourret • Department of Microbiology and Immunology, University of North
Carolina, Chapel Hill, NC, USA
arIane BrIegel • Department of Biology, Leiden University, Leiden, The Netherlands
aBdelalI daddaoua • Department of Environmental Protection, Estación Experimental
del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
chrIstoPher J. day • Institute for Glycomics, Griffith University, Southport, QLD, Australia
dIana dI Paolo • Cambridge Healthcare Research, St John’s Innovation Centre,
Cambridge, UK; Biological Physics Research Group, Clarendon Laboratory, Department
of Physics, University of Oxford, Oxford, UK
Jayna l. dItty • Department of Biology, College of Arts and Sciences, University of St .
Thomas, St . Paul, MN, USA
roger r. draheIM • School of Pharmacy and Biomedical Sciences, Institute of Biological
and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
MaxIMIlIan K.g. ehrhardt • Department of Biochemistry, University of Otago,
Dunedin, New Zealand
lucy v. eKe • School of Pharmacy and Biomedical Sciences, Institute of Biological and
Biomedical Sciences, University of Portsmouth, Portsmouth, UK
dereK l. englert • Department of Chemical and Materials Engineering, University of
Kentucky, Paducah, KY, USA
MatIlde fernández • Department of Environmental Protection, Estación Experimental
del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
vered franK • The Racah Institute of Physics, The Hebrew University, Jerusalem, Israel
MonIca l. gerth • Department of Biological Sciences, Victoria University of Wellington,
Wellington, New Zealand
chrIstoPher J. halKIdes • Department of Chemistry and Biochemistry, The University of
North Carolina, Wilmington, NC, USA
Bo hu • Department of Microbiology and Molecular Biology, McGovern Medical School,
The University of Texas, Houston, TX, USA
xi
xii Contributors
sneha JanI • Molecular Foundry, Lawrence Livermore National Laboratory, Berkeley, CA,
USA
arul JayaraMan • Artie McFerrin Department of Chemical Engineering, Texas A&M
University, College Station, TX, USA
MarK s. Johnson • Division of Microbiology and Molecular Genetics, Loma Linda
University, Loma Linda, CA, USA
vIctorIa KorolIK • Institute for Glycomics, Griffith University, Southport, QLD, Australia
tIno Krell • Department of Environmental Protection, Estación Experimental del
Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
run-zhI laI • Department of Biology, University of Utah, Salt Lake City, UT, USA
roBert J. laWrence • School of Pharmacy and Biomedical Sciences, Institute of Biological
and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
PushKar P. lele • Artie McFerrin Department of Chemical Engineering, Texas A&M
University, College Station, TX, USA
Jun lIu • Department of Microbial Pathogenesis and Microbial Sciences Institute,
Yale School of Medicine, Advanced Biosciences Center, New Haven, CT, USA
danIel B. looKadoo • Department of Chemistry and Biochemistry, The University of
North Carolina, Wilmington, NC, USA
MIchael d. Manson • Department of Biology, Texas A&M University, College
Station, TX, USA
davId Martín-Mora • Department of Environmental Protection, Estación Experimental
del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
dIego a. Massazza • Instituto de Investigaciones en Ciencia y Tecnología de Materiales
(INTEMA), Conicet-Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
MIguel a. MatIlla • Department of Environmental Protection, Estación Experimental
del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
george W. ordal • Department of Medical Biochemistry, University of Illinois,
Urbana, IL, USA
asuKa a. orr • Artie McFerrin Department of Chemical Engineering, Texas A&M
University, College Station, TX, USA
álvaro ortega • Department of Environmental Protection, Estación Experimental del
Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
davI r. ortega • Division of Biology and Biological Engineering, California Institute of
Technology, Pasadena, CA, USA
Karen M. otteMann • Department of Microbiology and Environmental Toxicology,
University of California Santa Cruz, Santa Cruz, CA, USA
reBecca e. Parales • Department of Microbiology and Molecular Genetics, College of
Biological Sciences, University of California, Davis, CA, USA
John s. ParKInson • Department of Biology, University of Utah, Salt Lake City, UT, USA
anJa PaulIcK • Max Planck Institute for Terrestrial Microbiology, Marburg, Germany;
LOEWE Research Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
danIel Penarete-acosta • Artie McFerrin Department of Chemical Engineering, Texas
A&M University, College Station, TX, USA
zhuan qIn • Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale
School of Medicine, Advanced Biosciences Center, New Haven, CT, USA
chrIstoPher v. rao • Department of Chemical and Biomolecular Engineering,
University of Illinois at Urbana-Champaign, Urbana, IL, USA