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Helicobacter pylori
Physiology and Genetics
Mobley
Harry L. T.
Mendz
George L.
Hazell
Stuart L.
2001
© 2001
ASM Press
Microbiology
Table of Contents
Contributors
Preface
Acknowledgments
Part I Introduction
Chapter 1 Overview
Harry L. T. Mobley, George L. Mendz, and Stuart L. Hazell
Chapter 2 Epidemiology of Infection
Hazel M. Mitchell
Prevalence of Infection
Natural History of Infection
Conclusion
References
Chapter 3 One Hundred Years of Discovery and Rediscovery of
Helicobacter pylori
and Its Association with Peptic Ulcer Disease
Barry J. Marshall
Spiral Bacteria
Epidemic Gastritis with Hypochlorhydria
The Origin of Gastric Urease
Bismuth Salts for Gastric Disease
Synthesis: Warren and Marshall 1979–84
Questions for the Future
References
Part II Bacteriology
Chapter 4 Basic Bacteriology and Culture
Lief Percival Andersen and Torkel Wadström
Campylobacteriaceae
The Genus
Helicobacter
References
Chapter 5 Taxonomy of the
Helicobacter
Genus
Jay V. Solnick and Peter Vandamme
Introduction
Description of the Genus
Helicobacter
Methods for the Differentiation of
Helicobacter
Species
Validated and Candidate
Helicobacter
Species
Identification of Novel
Helicobacter
Species
Conclusions
Acknowledgment
References
Chapter 6 Morphology and Ultrastructure
Jani O'Rourke and Günter Bode
Morphology of
Helicobacter pylori
Conclusion
References
Chapter 7 Cell Envelope
Paul W. O'Toole and Marguerite Clyne
Peptidoglycan
Fatty Acid and Lipid Composition of
H. pylori
Lipopolysaccharide
Surface Localization of Cytoplasmic Proteins
Outer Membrane Proteins of
H. pylori
Conclusions
Acknowledgments
References
Chapter 8 Molecular Structure, Biosynthesis, and Pathogenic Roles of Lipopolysaccharides
Anthony P. Moran
General Architecture of LPS
Future Outlook
Acknowledgments
References
Chapter 9 Vacuolating Cytotoxin
John C. Atherton, Timothy L. Cover, Emanuele Papini, and John L. Telford
The
vacA
Gene
References
Part III Energy Metabolism and Synthetic Pathways
Chapter 10 Microaerobic Physiology: Aerobic Respiration, Anaerobic Respiration, and Carbon Dioxide Metabolism
David J. Kelly, Nicky J. Hughes, and Robert K. Poole
Modes of Energy Transduction
Aerobic Electron Transport in
H. pylori
Anaerobic Electron Transport in
H. pylori
Microaerophily versus Oxidative Stress
The CO
2
Enigma
Concluding Remarks
Acknowledgments
References
Chapter 11 Nitrogen Metabolism
Hilde De Reuse and Stéphane Skouloubris
Nitrogen Sources for
Helicobacter pylori
Nitrogen Assimilation
Urea Cycle and Arginase
Two Paralogous Amidases
Conclusions
References
Chapter 12 The Citric Acid Cycle and Fatty Acid Biosynthesis
David J. Kelly and Nicky J. Hughes
Diversity and Multiple Roles of the Citric Acid Cycle in Prokaryotes
The CAC in
H. pylori
Fatty Acid Biosynthesis in
H. pylori
Acknowledgments
References
Chapter 13 Nucleotide Metabolism
George L. Mendz
Pyrimidine Ribonucleotides
Purine Nucleotides
Biosynthesis of Deoxyribonucleotides
Conclusions
References
Chapter 14 Biosynthetic Pathways Related to Cell Structure and Function
Partha Krishnamurthy, Suhas H. Phadnis, Cindy R. DeLoney, Raoul S. Rosenthal, and Bruce E. Dunn
Bacterial Peptidoglycans
Biosynthetic Pathway of Peptidoglycan Formation
Conclusions
References
Chapter 15 Evasion of the Toxic Effects of Oxygen
Stuart L. Hazell, Andrew G. Harris, and Mark A. Trend
Oxygen as a Toxic Species
Gene Regulation and Repair Mechanisms
Conclusion
References
Part IV Physiology and Molecular Biology
Chapter 16 Urease
Harry L. T. Mobley
Enzymology
Protein Structure
Genetics
Physiology
Pathogenesis
Detection of
H. pylori
using Urease
Typing Systems Based on Urease Genes
Urease in Vaccines
Acknowledgment
References
Chapter 17 Ion Metabolism and Transport
Arnoud H. M. van Vliet, Stefan Bereswill, and Johannes G. Kusters
Ion Homeostasis
Ion Metabolism
Ion Transport
Conclusions
Acknowledgments
References
Chapter 18 Metabolite Transport
Brendan P. Burns and George L. Mendz
Glucose Transport
Fumarate Transport
Arginine Transport
Urea Transport
Nucleotide Transport
Nickel Transport
Iron Transport
Copper Transport
Novel Drug Transporter Systems
Metabolite Transport and Total Genome Analysis
Conclusions
References
Chapter 19 Protein Export
Dag Ilver, Rino Rappuoli, and John L. Telford
The General Secretory Pathway
Sec-independent Export
Less Conventional Mechanisms for Protein Export
References
Chapter 20 Alternative Mechanisms of Protein Release
Steven R. Blanke and Dan Ye
Type IV Secretion: Adaptation of Conjugative Cellular Machinery
Bacterial Autolysis: An "Altruistic" Mechanism for
H. pylori
Adaptation within a Hostile Environment?
Outer Membrane Vesicles: Bundling Cell Envelope Proteins for Delivery?
Conclusions
Acknowledgments
References
Chapter 21 Motility, Chemotaxis, and Flagella
Gunther Spohn and Vincenzo Scarlato
The Flagella
Chemotaxis
Perspectives
Acknowledgments
References
Chapter 22 Natural Transformation, Recombination, and Repair
Wolfgang Fischer, Dirk Hofreuter, and Rainer Haas
Natural Transformation Competence
Genes Involved in DNA Uptake
Recombination
DNA Repair
References
Chapter 23 Chromosomal Replication, Plasmid Replication, and Cell Division
Hiroaki Takeuchi and Teruko Nakazawa
Chromosomal Replication
Plasmid Replication
Cell Division
Summary and Perspectives
References
Chapter 24 Restriction and Modification Systems
John P. Donahue and Richard M. Peek Jr.
Classification of R-M Systems
Conclusion
Acknowledgments
References
Chapter 25 Regulation of Urease for Acid Habitation
George Sachs, David R. Scott, David L. Weeks, Marina Rektorscheck, and Klaus Melchers
Acid Resistance
The Mechanism of UreI
Conclusions
References
Chapter 26 Transcription and Translation
Sanjib Bhattacharyya, Mae F. Go, Bruce E. Dunn, and Suhas H. Phadnis
Transcription
Translation
Summary
References
Part V Genetics
Chapter 27 The Genome
Richard A. Alm and Brian Noonan
Comparative Analysis of the
H. pylori
Genomes
Genome of
H. pylori
Compared with Other Sequenced Microbial Genomes
Functional Genomes and Understanding the Host-Pathogen Interaction
Future Considerations
Acknowledgments
References
Chapter 28 Genetic Exchange
Dawn A. Israel
Transformation
Conjugation
Transduction
Barriers to Genetic Exchange
Conclusion
Acknowledgments
References
Chapter 29 Gene Regulation
Nicolette de Vries, Arnoud H.M. van Vliet, and Johannes G. Kusters
Gene Regulation in response to Environmental Factors
Regulation of Motility and Chemotaxis
Phase Variation
Other Regulatory Systems
Conclusions
Acknowledgments
References
Chapter 30 Mutagenesis
Agnès Labigne and Peter J. Jenks
Introduction to Mutagenesis
Spontaneous Mutagenesis of
H. pylori
Induced Mutagenesis for
H. pylori
Genetics
Acknowledgment
References
Chapter 31 The
cag
Pathogenicity Island
Markus Stein, Rino Rappuoli, and Antonello Covacci
The
cag
Pathogenicity Island of
H. pylori
Type IV Secretion Systems and Their Functions
Pathogenic Functions of the
cag
Pathogenicity Island
Conclusions
Acknowledgments
References
Chapter 32 Population Genetics
Sebastian Suerbaum and Mark Achtman
Bacterial Population Genetics
Genetic Heterogeneity of
H. pylori
Evidence for Recombination in
H. pylori
Geographic Variation in
H. pylori
Do
H. pylori
Genotypes Reflect Human Migrations?
Microevolution during Chronic Colonization
Acknowledgments
References
Chapter 33 Heterogeneity and Subtyping
Robert J. Owen, Diane E. Taylor, Ge Wang, and Leen-Jan van Doorn
Introduction
Genotyping Based on Multiple Sites throughout the Genome and on Plasmids—Macrodiversity Analysis
Genotyping Based on Known Loci—Microdiversity Analysis
Mechanisms of Genetic Variation in Relation to Genotyping
Conclusions
References
Part VI Bacterial Virulence and Pathogenic Mechanisms
Chapter 34 Adherence and Colonization
Traci L. Testerman, David J. McGee, and Harry L. T. Mobley
Adherence
Bacterial Adhesins and Receptors
Adherence Antagonists
Does Invasion into Host Cells Occur?
Interations of
H. pylori
with Phagocytic Cells
Colonization
Conclusions
References
Chapter 35 Lipopolysaccharide Lewis Antigens
Ben J. Appelmelk and Christina M. J. E. Vandenbroucke-Grauls
Phase Variation in
H. pylori
LPS
The Biological Role of
H. pylori
Lewis Antigen Mimicry
H. pylori
Lewis Antigens as Adhesins
References
Chapter 36 Gastric Autoimmunity
Mathijs P. Bergman, Gerhard Faller, Mario M. D'Elios, Gianfranco Del Prete, Christina M. J. E. Vandenbroucke-Grauls, and Ben J. Appelmelk
H. pylori
Infection induces Autoantibodies to Gastric Mucosal Antigens
AIG/PA and Experimental Autoimmune Gastritis
Gastric T-Cell and Cytokine Responses in
H. pylori
Infection
Gastric Epithelial Cells during
H. pylori
Infection
A Model for the Pathogenesis of
H. pylori
-associated Antigastric Autoimmunity
References
Chapter 37 Vaccines
Jacques Pappo, Steven Czinn, and John Nedrud
The Immune Response against
Helicobacter pylori
: Implications for Vaccination
Preventive and Therapeutic Vaccines
Mechanisms of Immune Protection
Clinical Trials
References
Part VII Pathogenesis in the Host, Diagnosis, and Treatment
Chapter 38 Pathology of Gastritis and Peptic Ulceration
Michael F. Dixon
General Features of
H. pylori
Gastritis
Patterns of
H. pylori
Gastritis
Duodenal Ulceration
Gastric Ulceration
Conclusion
References
Chapter 39 Host Inflammatory Response to Infection
Jide Wang, Thomas G. Blanchard, and Peter B. Ernst
The Interactions between
H. pylori
and the Host Regulate Colonization and Pathogenicity
The Role of the Host Response in the Pathogenesis of Gastroduodenal Disease
Summary
References
Chapter 40 Gastric Cancer
Masahiro Asaka, Antonia R. Sepulveda, Toshiro Sugiyama, and David Y. Graham
Epidemiological Evaluation of the Relationship between
H. pylori
Infection and Gastric Cancer
Molecular Pathogenesis of
H. pylori
and Gastric Cancer
Development of Gastric Cancer in
H. pylori
-infected Animals
Genetic Alterations in Gastric Carcinogenesis
Perspective
References
Chapter 41 Markers of Infection
David Y. Graham and Waqar A. Qureshi
Laboratory Abnormalities
Markers Based on
H. pylori
Enzymes
Markers Based on Anti-
H. pylori
Antibodies
Markers Based on the Presence of
H. pylori
Antigens
Markers Based on the Presence of the Bacterium
References
Chapter 42 Antibiotic Susceptibility and Resistance
Francis Mégraud, Stuart Hazell, and Youri Glupczynski
5-Nitroimidazole Activity and Mechanism of Resistance
Macrolide Activity and Mechanisms of Resistance
Resistance to β-Lactams
Resistance to Other Antibiotics
Antimicrobial Susceptibility Testing
Genomics and Drug Discovery
References
Part VIII Animal Models and Other
Helicobacter
Species
Chapter 43 Enterohepatic
Helicobacter
Species
David B. Schauer
Helicobacter hepaticus
Helicobacter cinaedi
and
Helicobacter fennelliae
Helicobacter canis
Helicobacter pametensis
and
Helicobacter pullorum
Other Urease-negative
Helicobacter
Species from Mice and Hamsters
H. muridarum
"Helicobacter rappini"
H. bilis
H. trogontum
Helicobacter aurati
Enterohepatic
Helicobacter
Species in Human Liver Disease
References
Chapter 44 Other Gastric Helicobacters and Spiral Organisms
Stephen J. Danon and Adrian Lee
History
The Ecology of the Gastric Helicobacters
References
Chapter 45 In Vivo Modeling of
Helicobacter
-associated Gastrointestinal Diseases
Richard L. Ferrero and James G. Fox
Helicobacter
Colonization of Animal Hosts
Bacterial Host Specificity and Gastric Inflammation
Factors Mediating Helicobacter-induced Inflammation and Tissue Damage
Carcinogenesis
Applications of
Helicobacter
Infection Models
Conclusions
Acknowledgments
References
Chapter 46 In Vivo Adaptation to the Host
Richard L. Ferrero and Peter J. Jenks
In Vitro versus In Vivo
Mechanisms of Adaptation to the Host
Selection in the Host
Conclusions and Perspectives
Acknowledgment
References
List of Figures
Copyright © 2001
ASM Press
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