Differential gene expression from two transcriptional units in the cag pathogenicity island of Helicobacter pylori

Acanthamoeba castellanii supports extracellular survival of Helicobacter pylori in co-culture

This study aimed to demonstrate whether Helicobacter pylori is able to survive in co-culture with a protozoan, Acanthamoeba castellanii, in order to further investigate a possible aqueous environmental mode of transmission. Numbers of H. pylori in co-culture with A castellanii were assessed by colony forming unit (CFU) assay and cell morphology was observed by electron microscopy. Viable and intact H. pylori in co-culture were detected and the number of H. pylori in co-culture with A. castellanii was significantly higher than in bacterial single culture. It was also shown that co-culture of H. pylori with A. castellanii physically separated by a filter membrane negated this survival effect, suggesting that adherence of H. pylori to A. castellanii affects its survival. Scanning electron microscopy revealed helical forms of H. pylori in co-culture with A. castellanii, but not in single culture. These results imply that mutual interaction between H. pylori and A. castellanii in the environment is critical for survival of H. pylori. In addition, the H. pylori gene expression profile was found to differ between single and co-cultured cells using RNA-sequence analysis.

Outer inflammatory protein a (OipA) of Helicobacter pylori is regulated by host cell contact and mediates CagA translocation and interleukin-8 response only in the presence of a functional cag pathogenicity island type IV secretion system

OipA is a phase-variable virulence factor of Helicobacter pylori. Mutations in oipA to turn the gene phase on in a cag pathogenicity island (PAI)-negative strain of H. pylori (J68) or phase off in a cag PAI-positive strain (26695) demonstrated that phase on oipA alleles in both strains had both increased oipA mRNA and human gastric adenocarcinoma (AGS) cell adherence compared to isogenic oipA phase off mutants. An oipA phase off mutant of H. pylori 26695 demonstrated decreased IL-8 secretion by AGS cells and failure to translocate the cag PAI effector CagA. Increased attachment by OipA expressing cag PAI-negative H. pylori J68 failed to alter secreted IL-8 levels. Thus, OipA is necessary but not sufficient for the induction of IL-8; however, it is necessary for translocation of the oncoprotein CagA. Perhaps the nearly invariant phase on status of oipA alleles among cag PAI-positive H. pylori isolates relates to the role of this outer membrane protein in effective translocation of CagA. oipA mRNA comparisons between AGS cell-adherent and non-adherent H. pylori 26695 revealed significantly greater levels in the adherent cells. This may allow H. pylori to adapt to conditions of host cell contact by altering expression of this virulence factor.

Structure-function analyses of metal-binding sites of HypA reveal residues important for hydrogenase maturation in Helicobacter pylori

The nickel-containing enzymes of Helicobacter pylori, urease and hydrogenase, are essential for efficient colonization in the human stomach. The insertion of nickel into urease and hydrogenase is mediated by the accessory protein HypA. HypA contains an N-terminal nickel-binding site and a dynamic structural zinc-binding site. The coordination of nickel and zinc within HypA is known to be critical for urease maturation and activity. Herein, we test the hydrogenase activity of a panel of H. pylori mutant strains containing point mutations within the nickel- and zinc-binding sites. We found that the residues that are important for hydrogenase activity are those that were similarly vital for urease activity. Thus, the zinc and metal coordination sites of HypA play similar roles in urease and hydrogenase maturation. In other pathogenic bacteria, deletion of hydrogenase leads to a loss in acid resistance. Thus, the acid resistance of two strains of H. pylori containing a hydrogenase deletion was also tested. These mutant strains demonstrated wild-type levels of acid resistance, suggesting that in H. pylori, hydrogenase does not play a role in acid resistance.

Patterns of Adherence of Helicobacter pylori Clinical Isolates to Epithelial Cells, and its Association with Disease and with Virulence Factors

BACKGROUND AND AIM

Adherence to the gastric epithelium is one of the most important steps of Helicobacter pylori to remain and cause disease. The aim of this study was to analyze whether H. pylori isolates from patients with different gastroduodenal diseases present differences in the pattern of adherence to gastric epithelial cells (AGS), in the ability to induce IL-8, and in the presence of virulence genes.

METHODS

We tested 75 H. pylori strains isolated from nonatrophic gastritis, gastric cancer, and duodenal ulcer patients. The adhesion pattern and IL-8 induction were determined in AGS cells, and invasion of AGS cells was studied using a gentamicin protection assay. The IL-8 levels induced were determined by ELISA.

RESULTS

Helicobacter pylori strains presented diffuse adherence (DA) and localized (LA) adherence patterns, similar to those described for enteropathogenic E. coli (EPEC), were observed in AGS cells. A DA pattern was observed in 57% and LA in 43% of the strains, and DA was more frequent in isolates from patients with gastric cancer (p = 0.044). Strains with a LA pattern induced higher levels of IL-8 (p = 0.042) in AGS cells.

CONCLUSION

The adherence pattern was not associated with neither invasiveness nor with the presence of virulence genes. Our study shows that H. pylori strains present adherence patterns to AGS cells resembling those observed in EPEC and that these patterns may be associated with disease and with activity on AGS cells.

Dynamic HypA zinc site is essential for acid viability and proper urease maturation in Helicobacter pylori

Helicobacter pylori requires urease activity in order to survive in the acid environment of the human stomach. Urease is regulated in part by nickelation, a process that requires the HypA protein, which is a putative nickel metallochaperone that is generally associated with hydrogenase maturation. However, in H. pylori, HypA plays a dual role. In addition to an N-terminal nickel binding site, HypA proteins also contain a structural zinc site that is coordinated by two rigorously conserved CXXC sequences, which in H. pylori are flanked by His residues. These structural Zn sites are known to be dynamic, converting from Zn(Cys)4 centers at pH 7.2 to Zn(Cys)2(His)2 centers at pH 6.3 in the presence of Ni(ii) ions. In this study, mutant strains of H. pylori that express zinc site variants of the HypA protein are used to show that the structural changes in the zinc site are important for the acid viability of the bacterium, and that a reduction in acid viability in these variants can be traced in large measure to deficient urease activity. This in turn leads to a model that connects the Zn(Cys)4 coordination to urease maturation.

In depth analysis of the Helicobacter pylori cag pathogenicity island transcriptional responses

The severity of symptoms elicited by the widespread human pathogen Helicobacter pylori is strongly influenced by the genetic diversity of the infecting strain. Among the most important pathogen factors that carry an increased risk for gastric cancer are specific genotypes of the cag pathogenicity island (cag-PAI), encoding a type IV secretion system (T4SS) responsible for the translocation of the CagA effector oncoprotein. To date, little is known about the regulatory events important for the expression of a functional cag-T4SS. Here we demonstrate that the cag-PAI cistrons are subjected to a complex network of direct and indirect transcriptional regulations. We show that promoters of cag operons encoding structural T4SS components display homogeneous transcript levels, while promoters of cag operons encoding accessory factors vary considerably in their basal transcription levels and responses. Most cag promoters are transcriptionally responsive to growth-phase, pH and other stress-factors, although in many cases in a pleiotropic fashion. Interestingly, transcription from the Pcagζ promoter controlling the expression of transglycolase and T4SS stabilizing factors, is triggered by co-culture with a gastric cell line, providing an explanation for the increased formation of the secretion system observed upon bacterial contact with host cells. Finally, we demonstrate that the highly transcribed cagA oncogene is repressed by iron limitation through a direct apo-Fur regulation mechanism. Together the results shed light on regulatory aspects of the cag-PAI, which may be involved in relevant molecular and etiological aspects of H. pylori pathogenesis.

Conserved transcriptional unit organization of the cag pathogenicity island among Helicobacter pylori strains

The Helicobacter pyloricag pathogenicity island (cag PAI) encodes a type IV secretion system that is more commonly found in strains isolated from patients with gastroduodenal disease than from those with asymptomatic gastritis. Genome-wide organization of the transcriptional units in H. pylori strain 26695 was recently established using RNA sequence analysis (Sharma et al., 2010). Here we used quantitative reverse-transcription polymerase chain reaction of open reading frames and intergenic regions to identify putative cag PAI operons in H. pylori; these operons were analyzed further by transcript profiling after deletion of selected promoter regions. Additionally, we used a promoter-trap system to identify functional cag PAI promoters. The results demonstrated that expression of genes on the H. pyloricag PAI varies by nearly five orders of magnitude and that the organization of cag PAI genes into transcriptional units is conserved among several H. pylori strains, including, 26695, J99, G27, and J166. We found evidence for 20 transcripts within the cag PAI, many of which likely overlap. Our data suggests that there are at least 11 operons: cag1-4, cag3-4, cag10-9, cag8-7, cag6-5, cag11-12, cag16-17, cag19-18, cag21-20, cag23-22, and cag25-24, as well as five monocistronic genes (cag4, cag13, cag14, cag15, and cag26). Additionally, the location of four of our functionally identified promoters suggests they are directing expression of, in one case, a truncated version of cag26 and in the other three, transcripts that are antisense to cag7, cag17, and cag23. We verified expression of two of these antisense transcripts, those antisense to cag17 and cag23, by reverse-transcription polymerase chain reaction. Taken together, our results suggest that the cag PAI transcriptional profile is generally conserved among H. pylori strains, 26695, J99, G27, and J166, and is likely complex.

Alterations in Helicobacter pylori triggered by contact with gastric epithelial cells

Helicobacter pylori lives within the mucus layer of the human stomach, in close proximity to gastric epithelial cells. While a great deal is known about the effects of H. pylori on human cells and the specific bacterial products that mediate these effects, relatively little work has been done to investigate alterations in H. pylori that may be triggered by bacterial contact with human cells. In this review, we discuss the spectrum of changes in bacterial physiology and morphology that occur when H. pylori is in contact with gastric epithelial cells. Several studies have reported that cell contact causes alterations in H. pylori gene transcription. In addition, H. pylori contact with gastric epithelial cells promotes the formation of pilus-like structures at the bacteria–host cell interface. The formation of these structures requires multiple genes in the cag pathogenicity island, and these structures are proposed to have an important role in the type IV secretion system-dependent process through which CagA enters host cells. Finally, H. pylori contact with epithelial cells can promote bacterial replication and the formation of microcolonies, phenomena that are facilitated by the acquisition of iron and other nutrients from infected cells. In summary, the gastric epithelial cell surface represents an important niche for H. pylori, and upon entry into this niche, the bacteria alter their behavior in a manner that optimizes bacterial proliferation and persistent colonization of the host.

The Helicobacter pylori Ferric Uptake Regulator (Fur) is essential for growth under sodium chloride stress

Epidemiological data and animal models indicate that Helicobacter pylori and dietary NaCl have a synergistic ill effect on gastric maladies. Here we show that the Ferric Uptake Regulator (Fur), which is a crucial regulatory factor required for H. pylori colonization, is essential for growth in the presence of high NaCl concentrations. Moreover, we demonstrate that the transcriptional response induced by sodium chloride stress exhibits similarities to that seen under iron depletion.

Profile of Expression of Helicobacter pylori gamma-glutamyltranspeptidase

BACKGROUND

Helicobacter pylori produces gamma-glutamyltranspeptidase (GGT), a potential virulence factor involved in induction of host cell apoptosis. Regulation of the production of this protein is not known.

METHODS

The transcription start sites were determined by primer extension analysis. Transcription level of the GGT gene was examined by measuring the mRNA by RT-PCR and expression level of GGT protein was examined by Western blot analysis under different conditions.

RESULTS

Two transcription start sites were identified; thymine at 78-bp upstream and adenine at 79-bp upstream from the ATG codon of the GGT gene. There was a possible -10 consensus promoter sequence (ATTAAT), but no apparent -35 consensus sequence was found. The transcription of the mRNA and the expression of the protein were at almost constant level during the course of culture. The mRNA level increased by exposure to low pH; however, the actual protein expression level remained almost constant. Addition of glutamine or glutamate did not affect the mRNA level and the protein expression level to a remarkable degree, nor did co-culture with AGS cells affect the GGT activity level.

CONCLUSION

It was suggested that H. pylori GGT is constitutively expressed under various conditions.

Protein-protein interactions among Helicobacter pylori cag proteins

Many Helicobacter pylori isolates contain a 40-kb region of chromosomal DNA known as the cag pathogenicity island (PAI). The risk for development of gastric cancer or peptic ulcer disease is higher among humans infected with cag PAI-positive H. pylori strains than among those infected with cag PAI-negative strains. The cag PAI encodes a type IV secretion system that translocates CagA into gastric epithelial cells. To identify Cag proteins that are expressed by H. pylori during growth in vitro, we compared the proteomes of a wild-type H. pylori strain and an isogenic cag PAI deletion mutant using two-dimensional difference gel electrophoresis (2D-DIGE) in multiple pH ranges. Seven Cag proteins were identified by this approach. We then used a yeast two-hybrid system to detect potential protein-protein interactions among 14 Cag proteins. One heterotypic interaction (CagY/7 with CagX/8) and two homotypic interactions (involving H. pylori VirB11/ATPase and Cag5) were similar to interactions previously reported to occur among homologous components of the Agrobacterium tumefaciens type IV secretion system. Other interactions involved Cag proteins that do not have known homologues in other bacterial species. Biochemical analysis confirmed selected interactions involving five of the proteins that were identified by 2D-DIGE. Protein-protein interactions among Cag proteins are likely to have an important role in the assembly of the H. pylori type IV secretion apparatus.

Novel plasmids for gene expression analysis and for genetic manipulation in the gastric pathogen Helicobacter pylori

To facilitate gene expression analysis in the human gastric pathogen Helicobacter pylori, we constructed the plasmids pHPLAC-KAN and pHPLAC-CAT containing a promoterless Escherichia coli lacZ gene located upstream from the antibiotic resistance genes aphA-3 or cat, respectively. The suitability of the plasmids for H. pylori mutagenesis and gene expression analysis was evaluated by plasmid integration into the genome of H. pylori strain 1061 by single homologous recombination, using the rpl9 gene encoding ribosomal protein L9 as target. By monitoring beta-galactosidase production from the resulting rpl9::lacZ fusion, it was demonstrated that H. pylori rpl9 displays the classical growth phase-dependent regulation of components of the protein synthesis machinery, as beta-galactosidase production dropped fivefold in the stationary growth phase. The plasmids described in this study extend our methodological repertoire for genetic modification and molecular analysis of H. pylori, and may also be of use for other bacteria, as the resistance cassettes and the lacZ gene are active in the related Campylobacter species.

Strain-specific expression profiles of virulence genes in Helicobacter pylori during infection of gastric epithelial cells and granulocytes

Helicobacter pylori expresses a variety of known virulence-associated factors, whose expression is likely to be dependent on the ecological niche of this pathogen. Here, we compared the temporal changes in the level of virulence-associated gene transcription in H. pylori strains isolated from patients with different pathology. Our aim was to study the coordinated gene expression profiles of these virulence factors during infection of AGS gastric epithelial cells and granulocytes. Using real-time quantitative (TaqMan) RT-PCR, we determined the mRNA expression of cagA, ureA, napA, katA, vacAs1 and vacAs2 alleles in a time course up to 6 h. The expression profiles of the investigated genes vary according to the strain, and were mainly either upregulated or unchanged upon bacterial contact with AGS cells. In contrast, upon contact with granulocytes, the majority of the genes were repressed in H. pylori. The following major results were obtained: (i) genetically diverse H. pylori exhibit different mRNA expression profiles, (ii) the expression patterns were strain-specific and time-dependent and (iii) the regulation of expression profiles was host cell dependent. These data were statistically significant and suggest that contact with target cells leads to an active cross-talk between the pathogen and its host. The use of Taqman-PCR to analyse the expression of mRNA of a bacterial pathogen in response to a changing host environment enabled us to identify variable and strain-specific transcription profiles in a sensitive and reproducible manner.

Promoter analysis of Helicobacter pylori genes with enhanced expression at low pH

To identify Helicobacter pylori genes with expression that is enhanced under low pH conditions, we used subtractive hybridization methodology. We identified 28 acid-induced genes, of which 18 have known or putative functions. Six pairs of genes were co-transcribed. Primer extension analysis identified single or multiple transcriptional start points (tsp) for 14 of the 22 loci. Sequence analysis of the -10 regions upstream of the tsps revealed consensus motifs for multiple RNA polymerase sigma factors present in H. pylori (sigma80, sigma54 and sigma28). No sequences resembling the -35 Escherichia coli consensus sequence (TTGACA) were present upstream of any of the genes. Both increased gene transcription and decreased mRNA decay contribute to the observed increase in H. pylori transcript abundance at acid pH. These studies document the complex response of H. pylori to environmental pH changes, and provide insight into mechanisms used for intragastric survival.

Gene expression profiling of Helicobacter pylori reveals a growth-phase-dependent switch in virulence gene expression

The global pattern of growth-phase-dependent gene expression of Helicobacter pylori during in vitro culture was analyzed by using a high-density DNA microarray. To detect consistent coordinated gene expression in this bacterium, temporal changes in transcription were assessed in two independent time courses. Cluster analysis of the expression profiles highlighted a major switch in gene expression during the late log-to-stationary phase transition that we have termed the Log-Stat switch. Statistical analysis of the genes that were significantly induced or repressed during the Log-Stat switch revealed that many of these genes were related to virulence. Among these, expression of the genes for the neutrophil activating protein (napA) and the major flagellin subunit (flaA) were significantly induced. Additionally, the expression of a number of genes involved in iron homeostasis changed dramatically at this switch; the gene for the iron-storage protein, pfr, was induced, while the genes for two putative iron uptake proteins, fecA and frpB, were significantly repressed. These data suggest that the late log phase may correspond to the most virulent phase of growth in H. pylori and may be intimately related to its pathogenesis. The use of microarrays to analyze the kinetics of the transcriptional response of a bacterial pathogen to a changing environment has enabled the discovery of previously unappreciated relationships between genes by elucidation of coordinated gene expression profiles.

Growth phase-dependent and differential transcriptional control of flagellar genes in Helicobacter pylori

Helicobacter pylori possesses two different flagellin genes, flaA and flaB, which are unlinked on the chromosome and transcribed from sigma(28) and sigma(54) promoters, respectively. Both flagellins are hypothesized to be present in varying amounts in the flagellum, to adapt the physical properties of the flagellar filament to different environmental conditions. The influence of growth phase and environmental conditions on the transcriptional regulation of both flagellin genes has not been investigated so far. Using three different reporter genes as well as Northern blot analyses and RT-PCR, it was determined that both flagellin genes are transcribed in a growth phase-dependent fashion. Growth phase dependency was also found for the flagellar basal body export apparatus gene flhA which is involved in the transcriptional regulation of both flagellin genes. Peak transcription of flaB and flhA occurred earlier during the growth phase than that of flaA, possibly consistent with a hook-proximal localization of the minor flagellin FlaB. Of the reporter gene systems, luciferase fusions reflected best the dynamic regulation patterns of H. pylori flagellin genes. Growth phase in vitro had the strongest influence on transcriptional control of H. pylori flaA and flaB, while differences in supplements to a rich culture medium had only a modest modulatory effect on flagellin gene transcription.

In vivo complementation of ureB restores the ability of Helicobacter pylori to colonize

The objective of this study was to determine (i) if complementation of ureB-negative Helicobacter pylori restores colonization and (ii) if urease is a useful reporter for promoter activity in vivo. Strains used were M6, M6DeltaureB, and 10 recombinant derivatives of M6 or M6DeltaureB in which urease expression was under the control of different H. pylori promoters. Mice were orally inoculated with either the wild type or one of the mutant strains, and colonization, in vivo urease activity, and extent of gastritis were determined. Of eight M6DeltaureB recombinants tested, four colonized mice. Of those, three had the highest in vitro urease activity of any of the recombinants, significantly different from that of the noncolonizing mutants. The fourth colonizing recombinant, with ureB under control of the cag-15 promoter, had in vitro urease activity which did not differ significantly from the noncolonizing strains. In vivo, urease activities of the four colonizing transformants and the wild-type control were indistinguishable. There were no differences in gastritis or epithelial lesions between mice infected with M6 and those infected with the transformants. These results demonstrate that recovery of urease activity can restore colonizing ability to urease-negative H. pylori. They also suggest that cag-15 is upregulated in vivo, as was previously suggested by demonstrating that it is upregulated upon contact with epithelial cells. Finally, our results suggest that total urease activity and colonization density do not contribute to gastritis due to H. pylori.