Cellular Microbiology

, by Cossart, Pascale; Boquet, Patrice; Normark, Staffan

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ISBN: 9781555813024 | 155581302X
Cover: Hardcover
Copyright: 1/1/2005

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Institut Pasteur, Paris, France. Reference text contains data on fundamental cell biology and microbiology. Offers five new chapters that cover human pathogen genomes, host cell structure and dynamics, study of prokaryotic biology, cell biology of virus infection, and more. Features new full-color and halftone illustrations, graphs, and charts. Previous edition: c2000.

Contributors

xix

Foreword

xxv

Preface

xxix

Microbial Pathogens: an Overview

(34)

Pascale Cossart

Javier Pizarro-Cerda

Marc Lecuet

Bacteria

(25)

Strict Intracellular Bacteria

(5)

Facultative Intracellular Bacteria (Entry and Multiplication in Phagocytic Cells)

(2)

Facultative Intracellular Bacteria (Entry and Multiplication in Nonphagocytic Cells)

(6)

Nonsporulating Extracellular Bacteria

(11)

Sporulating Extracellular Bacteria

(1)

Parasites

(4)

Yeasts and Molds

(2)

Selected Readings

(3)

Bacterial Human Pathogen Genomes: an Overview

(28)

Stephen Bentley

Mohammed Sebaihia

Nicholas Thomson

Matthew Holden

Lisa Crossman

Kenneth Bell

Ana Cerdeno-Tarraga

Julian ParkHill

Alphaproteobacteria

(4)

Rickettsia prowazekii

(1)

Rickettsia conorii

(1)

Brucella melitensis

(3)

Brucella suis

(1)

Betaproteobacteria

(1)

Neisseria meningitidis

(1)

Gammaproteobacteria

(5)

Haemophilus influenzae

(1)

Vibrio cholerae

(1)

Pseudomonas aeruginosa

(1)

Escherichia coli

(1)

Pasteurella multocida

(1)

Yersinia pestis

(1)

Salmonella enterica Subspecies enterica

(1)

Shigella flexneri

(1)

Epsilonproteobacteria

(1)

Helicobacter pylori

(1)

Campylobacter jejuni

(1)

Firmicutes

(6)

Mycoplasma spp.

(1)

Streptococcus pyogenes

(1)

Staphylococcus aureus

(1)

Streptococcus pneumoniae

(1)

Listeria monocytogenes

(1)

Clostridium perfringens

(1)

Streptococcus agalactiae

(1)

Streptococcus mutans

(1)

Spirochetes

(1)

Borrelia burgdorferi

(1)

Treponema pallidum

(1)

Actinobacteria

(2)

Mycobacterium tuberculosis

(2)

Mycobacterium leprae

(1)

Chlamydiae

(2)

Chlamydia and Chlamydophila spp.

(2)

Fusobacteria

(1)

Fusobacterium nucleatum

(1)

Concluding Remarks

(1)

Selected Readings

(6)

Cell Biology: an Overview

(24)

Dana Philpott

Patrice Boquet

General Cell Organization

(2)

Structure of the Cell Membrane

(1)

Signal Transduction and Cell Regulation

(8)

Detection and Initial Transduction

(1)

Secondary Signal Transduction

(5)

Toll and Toll-Like Receptors

(1)

Secondary Signal Transduction: NF-κB Signaling

(1)

Membrane Traffic

(2)

Organelle Biogenesis

(1)

The Cytoskeleton

(3)

Cell Adhesion and Morphogenesis

(2)

Apoptosis

(1)

Cell Cycle and Organelle Inheritance

(2)

Conclusion

(1)

Selected Readings

(2)

Extracellular Matrix and Host Cell Surfaces: Potential Sites of Pathogen Interaction

(18)

Klaus T. Preissner

G. Singh Chhatwal

Structural and Functional Components of the Extracellular Matrix

(4)

Collagens

(1)

Laminins

(1)

Elastin and Fibrillins

(2)

Proteoglycans and Hyaluronan

(1)

Adhesive Glycoproteins

(6)

Fibronectin

(1)

Vitronectin

(2)

Fibrinogen-Fibrin

(1)

Thrombospondin and Other ``Matricellular'' Proteins

(1)

ECM Degradation

(1)

Cell Surfaces and Bacterial Interactions

(5)

Lectins, Proteoglycans, and Mucins

(1)

Glycolipids

100

(1)

Cell Surface Adhesion Receptors

101

(2)

Conclusion

103

(1)

Selected Readings

104

(1)

Bacterial Adherence to Cell Surfaces and Extracellular Matrix

105

(16)

B. Brett Finlay

Michael Caparon

Gram-Negative Fimbriae

106

(3)

P Pili: a Model Fimbria

106

(2)

Type IV Pili

108

(1)

Curli

108

(1)

Pathogens and Their Nonfimbrial Adhesins

109

(9)

Escherichia coli Afimbrial Adhesins

109

(1)

Helicobacter pylori

110

(1)

Bordetella pertussis

111

(1)

Neisseria Species

111

(1)

Yersinia Species

112

(1)

Haemophilus influenzae

112

(1)

Mycobacterium Species

113

(1)

Staphylococcus and Streptococcus

113

(5)

Role of Adherence in Disease

118

(1)

Selected Readings

119

(2)

Molecular Basis for Cell Adhesion and Adhesion-Mediated Signaling

121

(18)

Benjamin Geiger

Avri Ben-Ze'ev

Eli Zamir

Alexander D. Bershadsky

Structural and Functional Diversity of Cell Adhesions

121

(3)

Transmembrane Interaction of the Extracellular Matrix with the Actin Cytoskeleton

124

(3)

Signaling Components in Matrix Adhesions

127

(2)

Molecular Interactions in Cell-Cell Adherens Junctions

129

(1)

Signaling at Cell-Cell Adherens Junction

130

(3)

Cross Talk between Adhesion-Dependent Signaling and the Rho Family of GTPases

133

(2)

Tension-Dependent Regulation of Adhesion Structure Assembly

135

(1)

Complex Cytoskeletal Cross Talk

136

(1)

Conclusions and Link to Microorganism Invasion

136

(1)

Selected Readings

137

(2)

Bacterial Signaling to Host Cells through Adhesion Molecules and Lipid Rafts

139

(18)

Guy Tran Van Nhieu

Philippe J. Sansonetti

Frank Lafont

Adhesion Molecules as Pathogen Receptors

139

(4)

Receptors' Accessibility and Bacterial Fate

143

(1)

Pathogen Adhesion Determining Host Tissue Tropism

144

(1)

Direct Interaction

144

(1)

Adherence via ECM Proteins: Bridging Mechanism

145

(1)

Signaling via Adhesion Molecules and Bacterial Internalization

145

(3)

Invasin-Mediated Uptake of Yersinia

145

(1)

InIA-Mediated Uptake of Listeria

146

(2)

Bacterial Invasion and Growth Factor Receptor Signaling

148

(1)

Type III Secretion and Bacterial Invasion

148

(2)

Lipid Raft Microdomain Involvement in Pathogen-Host Cell Interactions

150

(2)

Structure-Function of Lipid Rafts

150

(1)

Lipid Rafts and Bacterial Signaling

151

(1)

Route of Internalization and Intracellular Survival within the Macrophage

152

(1)

Pathogen-Induced Up-Regulation of Adhesion Molecules

152

(2)

Future Challenges

154

(1)

Selected Readings

154

(3)

Host Cell Membrane Structure and Dynamics

157

(46)

Lynda M. Pierini

Frederick R. Maxfield

Host Cell Plasma Membrane Organization

157

(18)

Plasma Membrane Lipids

157

(8)

Plasma Membrane Structure

165

(3)

Lateral Plasma Membrane Organization

168

(2)

Physical Properties of Lateral Lipid Domains

170

(5)

Methods for Studying Membrane Organization

175

(15)

Model Membranes

175

(1)

Fluorescent Probes for Studying Membrane Organization and Dynamics

176

(4)

Detergent Sensitivity

180

(1)

Fluorescence Microscopy

181

(1)

Biophysical Characterization

182

(6)

Cholesterol Modulation: Acute and Metabolic Methods

188

(2)

Lipid Organization on Intracellular Membranes

190

(4)

The Biosynthetic Pathway

190

(2)

The Endocytic Pathway

192

(1)

Lipid Sorting and Membrane Traffic

192

(2)

Membrane Domains, Toxin Trafficking, and Microbial Pathogenesis

194

(5)

Toxin Uptake

195

(2)

Bacterial Invasion

197

(1)

Viral Entry and Budding

198

(1)

Conclusion

199

(1)

Selected Readings

200

(3)

Membrane Traffic in the Endocytic Pathway of Eukaryotic Cells

203

(24)

Michela Felberbaum-Corti

Raluca Flukiger-Gagescu

Jean Gruenberg

Membrane Traffic in Eukaryotic Cells

203

(2)

Organelles and Membrane Dynamics

205

(1)

Ways of Entry into the Cell

205

(5)

Endocytic Pathways

205

(4)

Phagocytic Pathways

209

(1)

Endosomes at the Crossroad of Membrane Traffic

210

(2)

Autophagy

211

(1)

Phagocytosis

211

(1)

Endocytic Pathway

212

(3)

Sorting in Early Endosomes

212

(1)

Recycling Pathway

213

(1)

Degradation Pathway

213

(2)

Sorting in Polarized Cells

215

(1)

Specialized Routes of Endocytic Membrane Traffic

216

(1)

Molecular Mechanisms

217

(8)

Coat Proteins and Their Sorting Signals

217

(2)

Ubiquitination and Sorting

219

(1)

Cytoskeleton

219

(1)

Rab Proteins and Their Effectors

220

(1)

SNARE Proteins, NSF, and SNAPs

221

(1)

Membrane Microheterogeneity

222

(3)

Selected Readings

225

(2)

Where To Stay inside the Cell: a Homesteader's Guide to Intracellular Parasitism

227

(28)

David G. Russell

Routes of Invasion

227

Phagocytosis

228

(1)

Induced Endocytosis and Phagocytosis

229

(1)

Active Invasion

229

Selection of an Intracellular Niche

(222)

Intralysosomal Pathogens

232

(3)

Pathogens Sequestered in Modified or Isolated Vacuoles

235

(8)

Pathogens Resident in Host Cell Cytosol

243

(2)

Modulation of Intracellular Compartments by the Host Immune Response

245

(1)

Nutrient Acquisition: Eat In or Order Out?

246

(2)

Cell-Cell Spread (Metastasis) of Intracellular Pathogens

248

(1)

Conclusion

249

(1)

Selected Readings

249

(6)

The Actin Cytoskeleton: Regulation of Actin Filament Assembly and Disassembly

255

(20)

Frederick S. Southwick

Basic Properties of Actin Monomer and Filament

255

(2)

Actin Assembly Kinetics

257

(2)

Modulation of Actin Dynamics by Actin-Binding Proteins

259

(9)

Monomer-Binding Proteins

260

(3)

Actin Filament-Capping Proteins

263

(2)

Actin Filament-Severing Proteins

265

(1)

Actin Filament-Bundling and Cross-Linking Proteins

265

(1)

Actin-Depolymerizing Proteins

266

(1)

Other Actin-Regulatory Proteins

266

(2)

Polymerization Zone Model

268

(3)

Conclusion

271

(1)

Selected Readings

271

(4)

Bacterial Manipulation of the Host Cell Cytoskeleton

275

(24)

Jennifer R. Robbins

David N. Baldwin

Sandra J. McCallum

Julie A. Theriot

Mechanisms of Bacterial Invasion

277

(7)

The Zipper Mechanism of Bacterial Uptake by Nonphagocytic Cells

277

(2)

The Trigger Mechanism of Bacterial Uptake by Nonphagocytic Cells

279

(5)

Preventing Phagocytosis

284

(1)

Yersinia Species

284

(1)

Bacterial Attachment without Invasion

285

(2)

Enteropathogenic Escherichia coli

285

(1)

Helicobacter pylori

286

(1)

Intracellular Motility and Intercellular Spread

287

(9)

Actin-Based Motility: Listeria monocytogenes

288

(4)

Actin-Based Motility: Shigella flexneri

292

(2)

Intercellular Spread by Listeria monocytogenes and Shigella flexneri

294

(2)

Selected Readings

296

(3)

Bacterial Toxins

299

(42)

Mariagrazia Pizza

Vega Masignani

Rino Rappuoli

Extracellular Toxins Acting on the Cell Surface

308

(12)

Superantigens

309

(2)

Binding Domains of A/B Toxins

311

(1)

Toxins Cleaving Cell Surface Molecules

312

(1)

Pore-Forming Toxins

313

(5)

Anthrax Protective Antigen

318

(2)

Extracellular Toxins Acting on Intracellular Targets

320

(12)

Toxins Acting on Protein Synthesis

320

(2)

Toxins Acting on Signal Transduction

322

(6)

Toxins Acting on Intracellular Trafficking

328

(3)

Toxins Acting on the Cytoskeleton

331

(1)

Toxins Directly Delivered by Bacteria into the Cytoplasm of Eukaryotic Cells

332

(7)

Toxins Acting on Signal Transduction

333

(1)

Proteins Acting on the Cytoskeleton

334

(2)

Proteins Altering Inositol Phosphate Metabolism

336

(1)

Apoptosis-Inducing Proteins

336

(1)

Cytotoxins with Unknown Mechanisms of Action

337

(1)

Novel Bacterial Toxins Detected by Genome Mining

338

(1)

Selected Readings

339

(2)

Bacterial Protein Toxins as Tools in Cell Biology and Pharmacology

341

(20)

Klaus Aktories

Toxins as Tools To Study Nucleotide-Binding Proteins

343

(3)

Cholera Toxin, Pertussis Toxin, and Pasteurella multocida Toxin as Tools To Study G-Protein-Mediated Signaling

343

(3)

Toxins as Tools To Study the Regulation of the Actin Cytoskeleton

346

(3)

Actin ADP-Ribosylating Toxins

346

(3)

Toxins That Affect Small GTPases

349

(6)

Rho-Inactivating Toxins

352

(3)

Rho-Activating Toxins

355

(1)

Toxins as Part of a Transmembrane Carrier System

355

(3)

Clostridial Neurotoxins as Tools To Study Exocytosis

356

(1)

Toxins as Tools for Permeabilization of Eukaryotic Cells

356

(2)

Selected Readings

358

(3)

Type III Secretion Systems in Animal- and Plant-Interacting Bacteria

361

(32)

Matthew S. Francis

Kurt Schesser

Ake Forsberg

Hans Wolf-Watz

Type III Secretion Systems

367

(10)

Secreton Assembly

368

(4)

Homologous Components

372

(1)

Substrate Specificity Switch

373

(1)

Secreted Proteins

374

(2)

Chaperone Proteins

376

(1)

Delivery and Effectors

377

(11)

Injection System

377

(2)

Effectors

379

(9)

Common Regulatory Mechanisms

388

(1)

Conclusion

389

(1)

Selected Readings

390

(3)

Bacterial Type IV Secretion Systems: DNA Conjugation Machines Adapted for Export of Virulence Factors

393

(16)

Peter J. Christie

Antonello Covacci

An Expanding Family of Type IV Injectosomes

393

(4)

The A. tumefaciens T-Complex Transfer System as a Paradigm for Assembly of Type IV Secretion Systems

397

(2)

Substrate Recognition and the Export Route

399

(2)

Molecular Biology of Type IV Secretion Systems

401

(1)

The Cell Biology of Effector Molecules

401

(6)

Bordetella pertussis ptl System

401

(1)

Helicobacter pylori cag System

402

(4)

Legionella pneumophila dot/icm System

406

(1)

Conclusion

407

(1)

Selected Readings

408

(1)

Induction of Apoptosis by Microbial Pathogens

409

(16)

Jeremy E. Moss

Ilona Idanpaan-Heikkila

Arturo Zychlinsky

Apoptosis Is Genetically Programmed

410

(1)

Triggering of Apoptosis

411

(1)

Signal Transduction of a Cell Death Signal

411

(1)

Apoptosis and the Cell Cycle

411

(1)

Effector Molecules of Apoptosis

412

(2)

Caspases

412

(1)

Bcl-2 Family

413

(1)

Apoptosis in Diseases

414

(1)

Induction of Apoptosis by Microorganisms

414

(8)

Activation of Host Cell Receptors That Signal for Apoptosis

415

(1)

Induction of Second Messengers

416

(1)

Regulation of Caspase Activity

416

(3)

Inhibition of Apoptosis via Bcl-2

419

(1)

Inhibition of Protein Synthesis

419

(1)

Disruption of the Cytoplasmic Membrane

420

(1)

Alternative Mechanisms

421

(1)

Selected Readings

422

(3)

Interaction of Pathogens with the Innate and Adaptive Immune System

425

(48)

Emil R. Unanue

Ennio De Gregorio

Innate and Adaptive Immunity

425

(1)

Innate Response

426

(1)

Macrophage Response---the Activated Macrophage

427

(7)

Interactions Involving Neutrophils

434

Interaction Involving the NK-Cell Response

432

(1)

Macrophage-NK-Cell Interaction: Lessons from Listeriosis

433

(2)

Symbiosis between the Innate Cellular System and the T-Cell Response---the MHC System

435

(5)

APC-T-Cell Interaction

440

(3)

Interactions with Adhesion Molecules

441

(1)

Interaction of CD40 with CD40L

441

(1)

Pairing of B7-1/B7-2 with CD28/CTLA-4

441

(1)

Role of Cytokines

442

(1)

Apoptosis of Lymphocytes

443

(1)

Pathogen Detection by the Innate Immune System: the Toll-Like Receptors

444

(3)

Selected Readings

447

(5)

Electron Microscopy

Chantal de Chastellier

Basic Conventional Electron Microscopy

452

(3)

Cytochemical Methods To Characterize Bacteria or Host Cells

455

(1)

Methods To Study Intersection with the Endocytic Pathway

455

(9)

Acquisition of Content Markers

455

(4)

Enzyme Cytochemistry Methods: Acquisition of Lysosomal Enzymes by Phagosomes

459

(2)

Acquisition of Membrane Markers and Analysis of Phagosome Membrane Composition

461

(1)

Phagosome Acidification

462

(2)

Methods To Study Intersection with the Endoplasmic Reticulum

464

(1)

Immunoelectron Microscopy

464

(4)

Methods

464

(1)

Crucial Points

465

(3)

Quantitative Immunocytochemistry

468

(1)

Conclusion

468

(1)

Selected Readings

469

(4)

New Tools for Virulence Gene Discovery

473

(16)

Timothy K. McDaniel

Raphael H. Valdivia

Identifying Candidate Virulence Genes by Mutation

474

(3)

Enrichment Strategies

474

(1)

Signature-Tagged Mutagenesis

474

(3)

Identifying Candidate Virulence Genes by Differential Expression

477

(7)

Gene Expression Profiling with DNA Microarrays

477

(2)

Promoter Traps

479

(1)

In Vivo Expression Technology

480

(2)

Differential Fluorescence Induction

482

(2)

Functional Approaches

484

(1)

Comparative Genomics

485

(1)

Conclusion

486

(1)

Selected Readings

487

(2)

Genome-Wide Approaches to Studying Prokaryotic Biology

489

(28)

Su L. Chiang

Stephen Lory

DNA Arrays

490

(12)

Microarray Design and Production

490

(3)

Applications

493

(9)

Proteomics

502

(10)

Mass Spectrometry

502

(1)

Genetic Analysis of Protein Interactions Using ``Two-Hybrid'' Screens

503

(5)

Protein Arrays

508

(4)

Conclusion

512

(1)

Selected Readings

512

(5)

Cell Biology of Virus Infection

517

(26)

Mark Marsh

Virus Organization and Structure

517

(2)

Entry

519

(14)

Receptors

520

(4)

Endocytosis

524

(4)

Fusion

528

(3)

A Role for Raft Domains?

531

(1)

Uncoating

532

(1)

pH-Dependent Entry

532

(1)

Viral Assembly and Egress

533

(3)

Virus Factories

533

(1)

Viral Membrane Protein Synthesis

533

(1)

Formation of Enveloped Viruses

534

(1)

Roles for Raft Domains?

535

(1)

Assembly in the Endocytic Pathway

535

(1)

Cell-to-Cell Transmission

536

(1)

Movement of Viruses within Cells

536

(3)

Involvement of the Cytoskeleton in Virus Entry

536

(2)

Involvement of the Cytoskeleton in Virus Egress

538

(1)

Roles for the Intermediate Filament System

538

(1)

Viral Regulation of Cellular Protein Synthesis and Expression

539

(4)

Signaling

540

(1)

Conclusions

541

(1)

Selected Readings

541

(2)

Use of Simple Nonvertebrate Hosts To Model Mammalian Pathogenesis

543

(22)

Costi D. Sifri

Frederick M. Ausubel

Development of Alternative Host-Pathogen Models

545

(5)

Conservation of Bacterial Virulence Factors

545

(3)

Conservation of Host Innate Immune Factors

548

(2)

Caenorhabditis elegans as a Model Host

550

(4)

Drosophila melanogaster as a Model Host

554

(1)

Arabidopsis thaliana as a Model Host

555

(2)

Galleria mellonella (Wax Moth Caterpillar) as a Model Host

557

(1)

Miscellaneous Hosts

558

(2)

Interactive Host-Pathogen Genetics

560

(1)

Conclusion

561

(1)

Selected Readings

562

(3)

About the Contributors

565

(10)

Index

575

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Cellular Microbiology

Summary

Table of Contents

Supplemental Materials