Cellular Microbiology

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

• ISBN13: 9781555813024
• ISBN10: 155581302X
• Edition: 2nd
• Format: Hardcover
• Copyright: 2005-01-01
• Publisher: Amer Society for Microbiology

Summary

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.

Table of Contents

Contributors	xix
Foreword	xxv
Preface	xxix
Microbial Pathogens: an Overview	1	(34)
Pascale Cossart
Javier Pizarro-Cerda
Marc Lecuet
Bacteria	1	(25)
Strict Intracellular Bacteria	1	(5)
Facultative Intracellular Bacteria (Entry and Multiplication in Phagocytic Cells)	6	(2)
Facultative Intracellular Bacteria (Entry and Multiplication in Nonphagocytic Cells)	8	(6)
Nonsporulating Extracellular Bacteria	14	(11)
Sporulating Extracellular Bacteria	25	(1)
Parasites	26	(4)
Yeasts and Molds	30	(2)
Selected Readings	32	(3)
Bacterial Human Pathogen Genomes: an Overview	35	(28)
Stephen Bentley
Mohammed Sebaihia
Nicholas Thomson
Matthew Holden
Lisa Crossman
Kenneth Bell
Ana Cerdeno-Tarraga
Julian ParkHill
Alphaproteobacteria	35	(4)
Rickettsia prowazekii	35	(1)
Rickettsia conorii	36	(1)
Brucella melitensis	36	(3)
Brucella suis	39	(1)
Betaproteobacteria	39	(1)
Neisseria meningitidis	39	(1)
Gammaproteobacteria	40	(5)
Haemophilus influenzae	40	(1)
Vibrio cholerae	40	(1)
Pseudomonas aeruginosa	41	(1)
Escherichia coli	41	(1)
Pasteurella multocida	42	(1)
Yersinia pestis	43	(1)
Salmonella enterica Subspecies enterica	44	(1)
Shigella flexneri	45	(1)
Epsilonproteobacteria	45	(1)
Helicobacter pylori	45	(1)
Campylobacter jejuni	46	(1)
Firmicutes	46	(6)
Mycoplasma spp.	46	(1)
Streptococcus pyogenes	47	(1)
Staphylococcus aureus	48	(1)
Streptococcus pneumoniae	49	(1)
Listeria monocytogenes	50	(1)
Clostridium perfringens	50	(1)
Streptococcus agalactiae	51	(1)
Streptococcus mutans	51	(1)
Spirochetes	52	(1)
Borrelia burgdorferi	52	(1)
Treponema pallidum	52	(1)
Actinobacteria	52	(2)
Mycobacterium tuberculosis	52	(2)
Mycobacterium leprae	54	(1)
Chlamydiae	54	(2)
Chlamydia and Chlamydophila spp.	54	(2)
Fusobacteria	56	(1)
Fusobacterium nucleatum	56	(1)
Concluding Remarks	56	(1)
Selected Readings	57	(6)
Cell Biology: an Overview	63	(24)
Dana Philpott
Patrice Boquet
General Cell Organization	64	(2)
Structure of the Cell Membrane	66	(1)
Signal Transduction and Cell Regulation	67	(8)
Detection and Initial Transduction	67	(1)
Secondary Signal Transduction	68	(5)
Toll and Toll-Like Receptors	73	(1)
Secondary Signal Transduction: NF-κB Signaling	74	(1)
Membrane Traffic	75	(2)
Organelle Biogenesis	77	(1)
The Cytoskeleton	77	(3)
Cell Adhesion and Morphogenesis	80	(2)
Apoptosis	82	(1)
Cell Cycle and Organelle Inheritance	83	(2)
Conclusion	85	(1)
Selected Readings	85	(2)
Extracellular Matrix and Host Cell Surfaces: Potential Sites of Pathogen Interaction	87	(18)
Klaus T. Preissner
G. Singh Chhatwal
Structural and Functional Components of the Extracellular Matrix	88	(4)
Collagens	89	(1)
Laminins	90	(1)
Elastin and Fibrillins	90	(2)
Proteoglycans and Hyaluronan	92	(1)
Adhesive Glycoproteins	92	(6)
Fibronectin	93	(1)
Vitronectin	93	(2)
Fibrinogen-Fibrin	95	(1)
Thrombospondin and Other ``Matricellular'' Proteins	96	(1)
ECM Degradation	97	(1)
Cell Surfaces and Bacterial Interactions	98	(5)
Lectins, Proteoglycans, and Mucins	99	(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	23	(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