1 . Overview

Yoshio Yamaoka

After the modern discovery of Helicobacter approximately 25 years ago by Robin Warren and Barry J. Marshall, many scientists developed an interest in the unique characteristics of Helicobacter, especially H. pylori, a bacterium proven to be the cause of gastritis and peptic ulcer and the progression to gastric cancer. H. pylori has very unique characteristics, such as microaerophily and nitrogen metabolism; therefore, H. pylori has been the subject of intensive research to unravel the mysteries of its genetics and cellular biology. In fact the number of publications in this field has risen dramatically in recent years making it extremely difficult for even the most diligent reader to stay abreast of progress. This book distils the most important cutting-edge findings in the field to produce a timely and comprehensive review. In this chapter, we described a brief background of the field including the discovery of Helicobacter and the relationship between H. pylori and gastroduodenal diseases. We then briefly summarize each chapter.

2 . Helicobacter pylori Lipopolysaccharides and Lewis Antigens

Anthony P. Moran and M. Stephen Trent

The outer membrane of Helicobacter pylori, like other Gram-negative bacteria, contains lipopolysaccharides (LPSs) which are important for the structure of the bacterial cell envelope and the interaction of the bacterium with its environment. They are a family of phoshorylated lipoglycans, composed of a lipid moiety, termed lipid A, a core oligosaccharide and an O-chain polysaccharide. The present chapter reviews the main biological attributes of H. pylori LPS and the understanding that has been gained into the molecular genetics, structure and contributing properties of this class of molecule to H. pylori pathogenesis. Compared with LPSs of other bacteria, LPS of H. pylori has low immunoactivities, the molecular basis for which is the under-phosphorylation and unusual acylation pattern of the lipid A component that interacts with immune receptors. Important insights have been gained into the biosynthesis and modification pathways that remodel H. pylori lipid A and hence aid persistence of the bacterium in the gastric mucosa. Notwithstanding this, the LPS core exhibits structural properties (i.e., laminin binding and pepsinogen induction) the molecular variation of which may influence the virulence of H. pylori strains. Furthermore, the O-chains of most strains, though not all isolates (i.e., those associated with asymptomatic infection), mimic Lewis and related blood group antigens. The nature of these antigens in H. pylori, their genetic determination and regulation of expression, particularly of the fucosyltransferases required for synthesis, as well as the biological consequences of this mimicry have provided a better understanding of the molecular pathogenesis of H. pylori.

3 . Helicobacter pylori Outer Membrane Proteins

Yoshio Yamaoka and Richard A. Alm

Analysis of the three completed Helicobacter pylori genomes has confirmed the presence of five major outer membrane proteins (OMPs) families. However, there appears to be a trend within the protein families as to which two of the three orthologs are more closely related. H. pylori 26695 and HPAG1 proteins are the most closely related more often as H. pylori J99 and HPAG1 or H. pylori J99 and 26695. Whether this is because both HPAG1 and 26695 were isolated from gastritis patients and J99 from a duodenal ulcer patient is an intriguing, but untested possibility. It has been demonstrated that several OMPs in the largest family act as adhesions, and these include BabA, SabA, OipA, AlpAB and HopZ. This unusual set of specialized OMPs may be a reflection of the adaptation of H. pylori to the unique gastric environment where it is found. Many of these genes undergo phase variation such that not all strains will produce functional proteins, and the stability of expression with passage varied with OipA > BabA > BabB > SabA. In this chapter, as well as describing the general features of the H. pylori OMP families, we describe the well characterized OMPs (BabA, SabA and OipA) in detail. Each OMP appears to have specific functions, and further studies will be necessary for investigating the detailed analyses of these OMPs as well as many unstudied OMPs.

4 . Helicobacter Flagella, Motility and Chemotaxis

Melanie Rust, Tobias Schweinitzer, and Christine Josenhans

All gastric and enterohepatic Helicobacter species are highly motile. Comparative genomic analysis in different Helicobacter species and related bacteria in recent years have facilitated the analysis of genus-, species- and niche-specific properties. The characteristic sheathed flagellar filaments of helicobacters are composed of two copolymerized flagellins, FlaA and FlaB. Experiments in different animal models with Helicobacter pylori, Helicobacter mustelae and Helicobacter felis showed that flagellar motility is essential for Helicobacter species to colonize the gastric mucus. H. pylori has homologs of almost all flagellar structural proteins known from Enterobacteriaceae, but the regulatory network of H. pylori motility genes, which has been investigated in some detail, lacks a flhCD master operon and other regulatory factors, and relies on a three-tiered hierarchical regulatory system with RpoN as the central sigma factor. H. pylori shows taxis (directed motility) towards urea, amino acids, and bicarbonate, and moves away from low pH. Recently, it has been shown in several in vivo systems that chemotaxis in addition to motility is required for colonisation, and that H. pylori and H. felis reside in a very narrow layer of the gastric mucus, close to the gastric epithelium, where they are guided by the mucus pH gradient. So far, the mucus pH gradient seems to be the most important sensing stimulus in vivo for H. pylori orientation. However, it is still not completely clear which combinations of horizontal and vertical chemical gradients are used by H. pylori in vivo to maintain an optimal position in the gastric mucus layer. The chemotaxis systems of H. pylori and H. hepaticus are genetically similar to the Salmonella system as based on genomic analysis, but extensive functional analyses on the proteins involved have just been started. A dominant property of the H. pylori sensing system from recent in vivo and in vitro studies seems to be pH taxis.

5 . Helicobacter pylori Vacuolating Toxin

Steven R. Blanke and Timothy L. Cover

Helicobacter pylori VacA is a protein toxin that is secreted into the extracellular space by a Type V autotransporter mechanism. Specific allelic variants of vacA exhibit different levels of toxin activity in vitro and are associated with different risks of gastroduodenal disease in H. pylori-infected humans. The structural features and the cell-modulating activities of VacA are distinct from those of any other known bacterial toxin. VacA can exert a wide array of effects on gastric epithelial cells, including alteration of endocytic compartments, alteration of mitochondrial membrane permeability, and activation of signal transduction pathways. Moreover, VacA inhibits activation and proliferation of T cells and can have effects on several other types of immune cells. VacA contributes to the ability of H. pylori to colonize the stomach and also contributes to the pathogenesis of H. pylori-associated peptic ulcer disease and gastric cancer. VacA displays both immunosuppressive as well as pro-inflammatory activities in vitro, underscoring the potentially complex role of this toxin in vivo.

6 . Type IV Secretion Systems in Helicobacter pylori

Wolfgang Fischer, Arno Karnholz, Luisa F. Jimenez-Soto and Rainer Haas

Type IV secretion systems are widely distributed in prokaryotes, where they are used to deliver DNA or protein substrates to bacterial or eukaryotic target cells. They are structurally complex molecular machines, typically composed of a cell envelope-spanning translocation channel, three cytoplasmic ATPases, and potentially an extracellular pilus structure. The Agrobacterium tumefaciens VirB/D4 type IV secretion system serves as a prototype system for which detailed structural and functional data are available. In H. pylori, three type IV secretion systems have been identified, the ComB, Cag and Tfs3 systems. The ComB system is found in all H. pylori strains and is involved in DNA uptake during natural transformation competence. The Cag type IV secretion system is restricted to a subset of more pathogenic H. pylori strains and mediates transfer of the effector protein CagA into different cell types of the host. The distribution and function of the Tfs3 system is unknown. This review summarizes recent progress in our understanding of the structure, function and regulation of the different type IV secretion systems in H. pylori.

7 . Gastric Biology of Helicobacter pylori

George Sachs, Yi Wen and David R. Scott

Helicobacter pylori colonizes the highly acidic environment of the gastric mucosa. H. pylori, although a neutralophile, is able to flourish in its acidic gastric niche by buffering its periplasm to near neutrality using the mechanism of acid acclimation. This unique acid acclimation, in contrast to acid resistance or tolerance expressed by other neutralophiles, is dependent on urease activity, a proton gate urea channel, UreI, that enables rapid urea access to cytoplasmic urease, and a periplasmic membrane anchored α-carbonic anhydrase. The genes encoding these proteins increased transcription in acid in vitro and are members of the acid sensing ArsRS regulon that responds to a decline of periplasmic pH. Analysis of the in vivo transcriptome of H. pylori infecting the gerbil stomach also showed up-regulation of 11 of these 12 genes as well as 23 other genes in the ArsRS regulon indicating that the site of infection is indeed acidic, lowering periplasmic pH to < 6.2. Other genes increased transcription in vivo including some for chemotaxis, motility, transport, cell envelope, adhesion, bioenergetics and metabolism providing information as to other requirements for colonization. Therefore although acid acclimation is necessary it may not be sufficient for gastric colonization.

8 . Metal Metabolism and Transport in Helicobacter pylori

Jeroen Stoof, Clara Belzer and Arnoud H.M. van Vliet

The members of the genus Helicobacter are among the most successful colonizers of the mammalian gastrointestinal and hepatobiliary tract, and are thought to have co-evolved during the development of the mammalian digestive system. The best studied Helicobacter species is the human pathogen H. pylori, which colonises the gastric mucosa, and this colonization results in chronic gastritis which may develop into peptic ulcer disease or gastric adenocarcinoma. The longevity of gastric colonization suggests that H. pylori must be able to cope with the different stresses encountered in the gastric mucosa, like low pH and restriction of essential metals like iron and nickel. In this chapter we will review the current knowledge on the role of metal metabolism in the physiology of H. pylori, and discuss the contribution of the regulatory mechanisms involved in controlling metal metabolism in the adaptation of H. pylori to its gastric niche.

9 . Replication, Partitioning, Segregation, and Cell Division in Helicobacter pylori

Teruko Nakazawa and Hiroaki Takeuchi

Chromosome replication and cell division are essential steps for bacterial proliferation. Recent studies in Escherichia coli and some other bacteria have emerged important insights on the whole process. The complete genome sequences of three strains of Helicobacter pylori revealed that homologs of most genes involved in replication and segregation are present, suggesting that the basic mechanisms are common. However, some orthologs for cell division are missing in H. pylori possibly because of its unique niche in gastric mucus as well as the life style. Analysis of the replication machinery of H. pylori has started very recently. The replication origin oriC, the initiator protein DnaA, and the replication helicase DnaB was identified. In addition, the ParABS system for chromosome partitioning was identified. FtsK-dif system for chromosome segregation and FtsZ-ring system for cell division might be functioning in H. pylori like in many other bacteria although further studies are required to elucidate the process.

10 . Molecular Mechanisms of Host-adaptation in Helicobacter

Stephan C. Schuster, Nicola E. Wittekindt and Bodo Linz

Helicobacter pylori has lived in close association with its human host for 100,000s of years. This has resulted in the highly adapted strains, on which today's clinical and molecular research is based. Through the host-jump of a Helicobacter from an early human to large felines, it became possible to study the adaptation process in a genomic comparative analysis. In this chapter we describe the molecular mechanisms that have driven the genomic evolution of Helicobacter in its host and have enabled the enormous plasticity of the bacterium's genome. Based on its unusually high mutation and recombination rate, we propose a 6 step model for host adaptation that also includes Helicobacter's ability for horizontal gene transfer in combination with its natural competence for DNA uptake.

11 . Genomotyping of Helicobacter pylori and its Host: Microarray Based Insights on Gene Variation, Expression and Function

Olivier Humbert, Delia M. Pinto-Santini and Nina R. Salama

Whole genome microarray analysis or genomotyping has been used to query many aspects of Helicobacter pylori biology. Comparative genomic hybridization has yielded new insights into the genome wide extent of genetic diversity both between H. pylori strains from different geographic regions as well as within the bacterial population of single infected hosts. Transcriptional profiling of bacterial RNA has shown that H. pylori has a complex transcriptional response to a variety of environmental stresses encountered in the stomach in spite of having few annotated transcription factors in its genome. Transcriptional profiling of natural (human) and experimental hosts has revealed molecular signatures of disease progression and successful vaccination. Additional microarray based technologies for genetic screens for infectivity, localization of transcription factor binding sites and whole genome mutational analysis are beginning to provide molecular details of the mechanisms by which H. pylori establishes a persistent infection in the human stomach.

12 . The Application of Proteomics Technology to Helicobacter pylori-associated Gastroduodenal Disease: State-of-the-Art and Future Clinical Potentials

Ming-Shiang Wu, Lu-Ping Chow, Jaw-Town Lin and Shyh-Horng Chiou

The current disease paradigm suggests that host genetics and Helicobacter pylori virulence play an important role in modulation of the final outcome. Elucidation of the bidirectional relationship between the host and bacteria is thus essential to clarify pathogenesis and development of new prevention and treatment strategies. Proteomics technology has provided unprecedented opportunity to comprehensively survey a cell's translational landscape and may allow in-depth analyses of host and pathogen interaction, either separately or interactively. Using this high-throughput platform and taking advantage of complete sequences for both the H. pylori and human genome in the database, some promising results and important information have been reported. Among the recent contributions relating to H. pylori, this review focuses on proteomics-based characterization of intrinsic and extrinsic perturbations and strain differences of H. pylori, epithelial cell response to H. pylori infection, identification of diagnostic/prognostic biomarkers, and uncovering of immunogenic proteins for vaccine targets. Future combination of evolving new proteomics technologies with clinical phenotypes and genotypes information will enhance the understanding of disease pathogenesis, lead to a more precise predication of variable outcomes, and facilitate the development of effective biomarkers for diagnosis, treatment and prevention of H. pylori infection.