Regulation of transcription in Helicobacter pylori: simple systems or complex circuits?

Insights into the Allosteric Response to Acidity by the Helicobacter pylori NikR Transcription Factor

Helicobacter pylori NikR (HpNikR) is a nickel-responsive transcription factor that regulates genes involved in nickel homeostasis, which is essential for the survival of this pathogen within the acidic human stomach. HpNikR also responds to drops in pH and regulates genes controlling acid acclimation of the bacteria, independently of nickel. We previously showed that nickel binding biases the conformational ensemble of HpNikR to the more DNA-binding competent states via an allosteric network of residues encompassing the nickel binding sites and the interface between the metal- and DNA-binding domains. Here, we examine how acidity promotes this response using 19F-NMR, mutagenesis, and DNA-binding studies. 19F-NMR revealed that a drop in pH from 7.6 to 6.0 does little to shift the conformational ensemble of HpNikR to the DNA binding-compatible cis conformer. Nevertheless, DNA-binding affinities of apo-HpNikR at pH 6.0 and Ni(II)-HpNikR at pH 7.6 are comparable for the ureA promoter. Histidine residues of the nickel binding sites were shown to be important for pH-dependent DNA binding and thus likely impart positive charge to the protein, initiating long-range electrostatic interactions with DNA that induce DNA complexation. The results point to a different DNA-binding mechanism in response to acidity compared to the conformational selection mechanism in response to nickel and overall provide new insights into the influence of pH on HpNikR activity, which contributes to H. pylori viability.

Mechanistic insights into the nickel-dependent allosteric response of the Helicobacter pylori NikR transcription factor

In Helicobacter pylori, the nickel-responsive NikR transcription factor plays a key role in regulating intracellular nickel concentrations, which is an essential process for survival of this pathogen in the acidic human stomach. Nickel binding to H. pylori NikR (HpNikR) allosterically activates DNA binding to target promoters encoding genes involved in nickel homeostasis and acid adaptation, to either activate or repress their transcription. We previously showed that HpNikR adopts an equilibrium between an open conformation and DNA-binding competent cis and trans states. Nickel binding slows down conformational exchange between these states and shifts the equilibrium toward the binding-competent states. The protein then becomes stabilized in a cis conformation upon binding the ureA promoter. Here, we investigate how nickel binding creates this response and how it is transmitted to the DNA-binding domains. Through mutagenesis, DNA-binding studies, and computational methods, the allosteric response to nickel was found to be propagated from the nickel-binding sites to the DNA-binding domains via the β-sheets of the metal-binding domain and a network of residues at the inter-domain interface. Our computational results suggest that nickel binding increases protein rigidity to slow down the conformational exchange. A thymine base in the ureA promoter sequence, known to be critical for high affinity DNA binding by HpNikR, was also found to be important for the allosteric response, while a modified version of this promoter further highlighted the importance of the DNA sequence in modulating the response. Collectively, our results provide insights into regulation of a key protein for H. pylori survival.

Insights into the Orchestration of Gene Transcription Regulators in Helicobacter pylori

Bacterial pathogens employ a general strategy to overcome host defenses by coordinating the virulence gene expression using dedicated regulatory systems that could raise intricate networks. During the last twenty years, many studies of Helicobacter pylori, a human pathogen responsible for various stomach diseases, have mainly focused on elucidating the mechanisms and functions of virulence factors. In parallel, numerous studies have focused on the molecular mechanisms that regulate gene transcription to attempt to understand the physiological changes of the bacterium during infection and adaptation to the environmental conditions it encounters. The number of regulatory proteins deduced from the genome sequence analyses responsible for the correct orchestration of gene transcription appears limited to 14 regulators and three sigma factors. Furthermore, evidence is accumulating for new and complex circuits regulating gene transcription and H. pylori virulence. Here, we focus on the molecular mechanisms used by H. pylori to control gene transcription as a function of the principal environmental changes.

Multiple regulatory mechanisms for pH homeostasis in the gastric pathogen, Helicobacter pylori

Acid-resistance in gastric pathogen Helicobacter pylori requires the coordination of four essential processes to regulate urease activity. Firstly, urease expression above a base level needs to be finely tuned at different ambient pH. Secondly, as nickel is needed to activate urease, nickel homeostasis needs to be maintained by proteins that import and export nickel ions, and sequester, store and release nickel when needed. Thirdly, urease accessary proteins that activate urease activity by nickel insertion need to be expressed. Finally, a reliable source of urea needs to be maintained by both intrinsic and extrinsic sources of urea. Two-component systems (arsRS and flgRS), as well as a nickel response regulator (NikR), sense the change in pH and act on a variety of genes to accomplish the function of acid resistance without causing cellular overalkalization and nickel toxicity. Nickel storage proteins also feature built-in switches to store nickel at neutral pH and release nickel at low pH. This review summarizes the current status of H. pylori research and highlights a number of hypotheses that need to be tested.

Definition of the Binding Architecture to a Target Promoter of HP1043, the Essential Master Regulator of Helicobacter pylori

HP1043 is an essential orphan response regulator of Helicobacter pylori orchestrating multiple crucial cellular processes. Classified as a member of the OmpR/PhoB family of two-component systems, HP1043 exhibits a highly degenerate receiver domain and evolved to function independently of phosphorylation. Here, we investigated the HP1043 binding mode to a target sequence in the hp1227 promoter (P_hp1227). Scanning mutagenesis of HP1043 DNA-binding domain and consensus sequence led to the identification of residues relevant for the interaction of the protein with a target DNA. These determinants were used as restraints to guide a data-driven protein-DNA docking. Results suggested that, differently from most other response regulators of the same family, HP1043 binds in a head-to-head conformation to the P_hp1227 target promoter. HP1043 interacts with DNA largely through charged residues and contacts with both major and minor grooves of the DNA are required for a stable binding. Computational alanine scanning on molecular dynamics trajectory was performed to corroborate our findings. Additionally, in vitro transcription assays confirmed that HP1043 positively stimulates the activity of RNA polymerase.

Kinetic and catalytic properties of M.HpyAXVII, a phase-variable DNA methyltransferase from Helicobacter pylori

The bacterium Helicobacter pylori is one of the most common infectious agents found in the human stomach. H. pylori has an unusually large number of DNA methyltransferases (MTases), prompting speculation that they may be involved in the cancerization of epithelial cells. The mod-4a/4b locus, consisting of the hp1369 and hp1370 ORFs, encodes for a truncated and inactive MTase in H. pylori strain 26695. However, slipped-strand synthesis within the phase-variable polyguanine tract in hp1369 results in expression of an active HP1369-1370 fusion N ⁶-adenine methyltransferase, designated M.HpyAXVII. Sequence analysis of the mod-4a/4b locus across 74 H. pylori strain genomes has provided insights into the regulation of M.HpyAXVII expression. To better understand the role of M.HpyAXVII in the H. pylori biology, here we cloned and overexpressed the hp1369-70 fusion construct in Escherichia coli BL21(DE3) cells. Results from size-exclusion chromatography and multi-angle light scattering (MALS) analyses suggested that M.HpyAXVII exists as a dimer in solution. Kinetic studies, including product and substrate inhibition analyses, initial velocity dependence between substrates, and isotope partitioning, suggested that M.HpyAXVII catalyzes DNA methylation in an ordered Bi Bi mechanism in which the AdoMet binding precedes DNA binding and AdoMet's methyl group is then transferred to an adenine within the DNA recognition sequence. Altering the highly conserved catalytic motif (DPP(Y/F)) as well as the AdoMet-binding motif (FXGXG) by site-directed mutagenesis abolished the catalytic activity of M.HpyAXVII. These results provide insights into the enzyme kinetic mechanism of M.HpyAXVII. We propose that AdoMet binding conformationally "primes" the enzyme for DNA binding.

The Helicobacter pylori Heat-Shock Repressor HspR: Definition of Its Direct Regulon and Characterization of the Cooperative DNA-Binding Mechanism on Its Own Promoter

The ability of pathogens to perceive environmental conditions and modulate gene expression accordingly is a crucial feature for bacterial survival. In this respect, the heat-shock response, a universal cellular response, allows cells to adapt to hostile environmental conditions and to survive during stress. In the major human pathogen Helicobacter pylori the expression of chaperone-encoding operons is under control of two auto-regulated transcriptional repressors, HrcA and HspR, with the latter acting as the master regulator of the regulatory circuit. To further characterize the HspR regulon in H. pylori, we used global transcriptome analysis (RNA-sequencing) in combination with Chromatin Immunoprecipitation coupled with deep sequencing (ChIP-sequencing) of HspR genomic binding sites. Intriguingly, these analyses showed that HspR is involved in the regulation of different crucial cellular functions through a limited number of genomic binding sites. Moreover, we further characterized HspR-DNA interactions through hydroxyl-radical footprinting assays. This analysis in combination with a nucleotide sequence alignment of HspR binding sites, revealed a peculiar pattern of DNA protection and highlighted sequence conservation with the HAIR motif (an HspR-associated inverted repeat of Streptomyces spp.). Site-directed mutagenesis demonstrated that the HAIR motif is fundamental for HspR binding and that additional nucleotide determinants flanking the HAIR motif are required for complete binding of HspR to its operator sequence spanning over 70 bp of DNA. This finding is compatible with a model in which possibly a dimer of HspR recognizes the HAIR motif overlapping its promoter for binding and in turn cooperatively recruits two additional dimers on both sides of the HAIR motif.

ArsRS-Dependent Regulation of homB Contributes to Helicobacter pylori Biofilm Formation

One elusive area in the Helicobacter pylori field is an understanding of why some infections result in gastric cancer, yet others persist asymptomatically for the life-span of the individual. Even before the genomic era, the high level of intraspecies diversity of H. pylori was well recognized and became an intriguing area of investigation with respect to disease progression. Of interest in this regard is the unique repertoire of over 60 outer membrane proteins (OMPs), several of which have been associated with disease outcome. Of these OMPs, the association between HomB and disease outcome varies based on the population being studied. While the molecular roles for some of the disease-associated OMPs have been evaluated, little is known about the role that HomB plays in the H. pylori lifecycle. Thus, herein we investigated homB expression, regulation, and contribution to biofilm formation. We found that in H. pylori strain G27, homB was expressed at a relatively low level until stationary phase. Furthermore, homB expression was suppressed at low pH in an ArsRS-dependent manner; mutation of arsRS resulted in increased homB transcript at all tested time-points. ArsRS regulation of homB appeared to be direct as purified ArsR was able to specifically bind to the homB promoter. This regulation, combined with our previous finding that ArsRS mutations lead to enhanced biofilm formation, led us to test the hypothesis that homB contributes to biofilm formation by H. pylori. Indeed, subsequent biofilm analysis using a crystal-violet quantification assay and scanning electron microscopy (SEM) revealed that loss of homB from hyper-biofilm forming strains resulted in reversion to a biofilm phenotype that mimicked wild-type. Furthermore, expression of homB in trans from a promoter that negated ArsRS regulation led to enhanced biofilm formation even in strains in which the chromosomal copy of homB had been deleted. Thus, homB is necessary for hyper-biofilm formation of ArsRS mutant strains and aberrant regulation of this gene is sufficient to induce a hyper-biofilm phenotype. In summary, these data suggest that the ArsRS-dependent regulation of OMPs such as HomB may be one mechanism by which ArsRS dictates biofilm development in a pH responsive manner.

Insight into the essential role of the Helicobacter pylori HP1043 orphan response regulator: genome-wide identification and characterization of the DNA-binding sites

Many bacterial regulatory genes appear to be dispensable, as they can be deleted from the genome without loss of bacterial functionalities. In Helicobacter pylori, the hp1043 gene, also known as hsrA, is one of the transcriptional regulator that is essential for cell viability. This gene could not be deleted, nor the amount of protein modulated, supporting the hypothesis that HP1043 could be involved in the regulation of crucial cellular processes. Even though detailed structural data are available for the HP1043 protein, its targets are still ill-defined. Using Chromatin Immunoprecipitation-sequencing (ChIP-seq), one of the most powerful approaches to characterize protein-DNA interactions in vivo, we were able to identify genome-wide several new HP1043 binding sites. Moreover, in vitro DNA binding assays enabled precise mapping of the HP1043 binding sites on the new targets, revealing the presence of a conserved nucleotide sequence motif. Intriguingly, a significant fraction of the newly identified binding sites overlaps promoter regions controlling the expression of genes involved in translation. Accordingly, when protein translation was blocked, a significant induction of almost all HP1043 target genes was detected. These observations prompted us to propose HP1043 as a key regulator in H. pylori, likely involved in sensing and in coordinating the response to environmental conditions that provoke an arrest of protein synthesis. The essential role of HP1043 in coordinating central cellular processes is discussed.

Characterization of Key Helicobacter pylori Regulators Identifies a Role for ArsRS in Biofilm Formation

Helicobacter pylori must be able to rapidly respond to fluctuating conditions within the stomach. Despite this need for constant adaptation, H. pylori encodes few regulatory proteins. Of the identified regulators, the ferric uptake regulator (Fur), the nickel response regulator (NikR), and the two-component acid response system (ArsRS) are each paramount to the success of this pathogen. While numerous studies have individually examined these regulatory proteins, little is known about their combined effect. Therefore, we constructed a series of isogenic mutant strains that contained all possible single, double, and triple regulatory mutations in Fur, NikR, and ArsS. A growth curve analysis revealed minor variation in growth kinetics across the strains; these were most pronounced in the triple mutant and in strains lacking ArsS. Visual analysis showed that strains lacking ArsS formed large aggregates and a biofilm-like matrix at the air-liquid interface. Biofilm quantification using crystal violet assays and visualization via scanning electron microscopy (SEM) showed that all strains lacking ArsS or containing a nonphosphorylatable form of ArsR (ArsR-D52N mutant) formed significantly more biofilm than the wild-type strain. Molecular characterization of biofilm formation showed that strains containing mutations in the ArsRS pathway displayed increased levels of cell aggregation and adherence, both of which are key to biofilm development. Furthermore, SEM analysis revealed prevalent coccoid cells and extracellular matrix formation in the ArsR-D52N, ΔnikR ΔarsS, and Δfur ΔnikR ΔarsS mutant strains, suggesting that these strains may have an exacerbated stress response that further contributes to biofilm formation. Thus, H. pylori ArsRS has a previously unrecognized role in biofilm formation.

IMPORTANCE

Despite a paucity of regulatory proteins, adaptation is key to the survival of H. pylori within the stomach. While prior studies have focused on individual regulatory proteins, such as Fur, NikR, and ArsRS, few studies have examined the combined effect of these factors. Analysis of isogenic mutant strains that contained all possible single, double, and triple regulatory mutations in Fur, NikR, and ArsS revealed a previously unrecognized role for the acid-responsive two-component system ArsRS in biofilm formation.

The cag-pathogenicity island encoded CncR1 sRNA oppositely modulates Helicobacter pylori motility and adhesion to host cells

Small regulatory RNAs (sRNAs) are emerging as key post-transcriptional regulators in many bacteria. In the human pathobiont Helicobacter pylori a plethora of trans- and cis-encoded sRNAs have been pinpointed by a global transcriptome study. However, only two have been studied in depth at the functional level. Here we report the characterization of CncR1, an abundant and conserved sRNA encoded by the virulence-associated cag pathogenicity island (cag-PAI) of H. pylori. Growth-phase dependent transcription of CncR1 is directed by the PcagP promoter, which resulted to be a target of the essential transcriptional regulator HsrA (HP1043). We demonstrate that the 213 nt transcript arising from this promoter ends at an intrinsic terminator, few bases upstream of the annotated cagP open reading frame, establishing CncR1 as the predominant gene product encoded by the cagP (cag15) locus. Interestingly, the deletion of the locus resulted in the deregulation en masse of σ(54)-dependent genes, linking CncR1 to flagellar functions. Accordingly, the enhanced motility recorded for cncR1 deletion mutants was complemented by ectopic reintroduction of the allele in trans. In silico prediction identified fliK, encoding a flagellar checkpoint protein, as likely regulatory target of CncR1. The interaction of CncR1 with the fliK mRNA was thus further investigated in vitro, demonstrating the formation of strand-specific interactions between the two RNA molecules. Accordingly, the full-length translational fusions of fliK with a lux reporter gene were induced in a cncR1 deletion mutant in vivo. These data suggest the involvement of CncR1 in the post-transcriptional modulation of H. pylori motility functions through down-regulation of a critical flagellar checkpoint factor. Concurrently, the cncR1 mutant revealed a decrease of transcript levels for several H. pylori adhesins, resulting in a phenotypically significant impairment of bacterial adhesion to a host gastric cell line. The data presented support a model in which the cag-PAI encoded CncR1 sRNA is able to oppositely modulate bacterial motility and adhesion to host cells.

Nickel-responsive regulation of two novel Helicobacter pylori NikR-targeted genes

Nickel is an essential transition metal for the survival of Helicobacter pylori in the acidic human stomach. The nickel-responsive transcriptional regulator HpNikR is important for maintaining healthy cytosolic nickel concentrations through the regulation of multiple genes, but its complete regulon and role in nickel homeostasis are not well understood. To investigate potential gene targets of HpNikR, ChIP sequencing was performed using H. pylori grown at neutral pH in nickel-supplemented media and this experiment identified HPG27_866 (frpB2) and HPG27_1499 (ceuE). These two genes are annotated to encode a putative iron transporter and a nickel-binding, periplasmic component of an ABC transporter, respectively. In vitro DNA-binding assays revealed that HpNikR binds both gene promoter sequences in a nickel-responsive manner with affinities on the order of ∼10(-7) M. The recognition sites of HpNikR were identified and loosely correlate with the HpNikR pseudo-consensus sequence (TATTATT-N11-AATAATA). Quantitative PCR experiments revealed that HPG27_866 and HPG27_1499 are transcriptionally repressed following growth of H. pylori G27 in nickel-supplemented media, and that this response is dependent on HpNikR. In contrast, iron supplementation results in activation of HPG27_1499, but no impact on the expression of HPG27_866 was observed. Metal analysis of the Δ866 strain revealed that HPG27_866 has an impact on nickel accumulation. These studies demonstrate that HPG27_866 and HPG27_1499 are both direct targets of HpNikR and that HPG27_866 influences nickel uptake in H. pylori.

A repetitive DNA element regulates expression of the Helicobacter pylori sialic acid binding adhesin by a rheostat-like mechanism

During persistent infection, optimal expression of bacterial factors is required to match the ever-changing host environment. The gastric pathogen Helicobacter pylori has a large set of simple sequence repeats (SSR), which constitute contingency loci. Through a slipped strand mispairing mechanism, the SSRs generate heterogeneous populations that facilitate adaptation. Here, we present a model that explains, in molecular terms, how an intergenically located T-tract, via slipped strand mispairing, operates with a rheostat-like function, to fine-tune activity of the promoter that drives expression of the sialic acid binding adhesin, SabA. Using T-tract variants, in an isogenic strain background, we show that the length of the T-tract generates multiphasic output from the sabA promoter. Consequently, this alters the H. pylori binding to sialyl-Lewis x receptors on gastric mucosa. Fragment length analysis of post-infection isolated clones shows that the T-tract length is a highly variable feature in H. pylori. This mirrors the host-pathogen interplay, where the bacterium generates a set of clones from which the best-fit phenotypes are selected in the host. In silico and functional in vitro analyzes revealed that the length of the T-tract affects the local DNA structure and thereby binding of the RNA polymerase, through shifting of the axial alignment between the core promoter and UP-like elements. We identified additional genes in H. pylori, with T- or A-tracts positioned similar to that of sabA, and show that variations in the tract length likewise acted as rheostats to modulate cognate promoter output. Thus, we propose that this generally applicable mechanism, mediated by promoter-proximal SSRs, provides an alternative mechanism for transcriptional regulation in bacteria, such as H. pylori, which possesses a limited repertoire of classical trans-acting regulatory factors.

Structure of CbpA J-domain bound to the regulatory protein Cbpm explains its specificity and suggests evolutionary link between Cbpm and transcriptional regulators

CbpA is one of the six E. coli DnaJ/Hsp40 homologues of DnaK co-chaperones and the only one that is additionally regulated by a small protein CbpM, conserved in γ-proteobacteria. CbpM inhibits the co-chaperone and DNA binding activities of CbpA. This regulatory function of CbpM is accomplished through reversible interaction with the N-terminal J-domain of CbpA, which is essential for the interaction with DnaK. CbpM is highly specific for CbpA and does not bind DnaJ despite the high degree of structural and functional similarity between the J-domains of CbpA and DnaJ. Here we report the crystal structure of the complex of CbpM with the J-domain of CbpA. CbpM forms dimers and the J-domain of CbpA interacts with both CbpM subunits. The CbpM-binding surface of CbpA is highly overlapping with the CbpA interface for DnaK, providing a competitive model for regulation through forming mutually exclusive complexes. The structure also provides the explanation for the strict specificity of CbpM for CbpA, which we confirmed by making mutants of DnaJ that became regulated by CbpM. Interestingly, the structure of CbpM reveals a striking similarity to members of the MerR family of transcriptional regulators, suggesting an evolutionary connection between the functionally distinct bacterial co-chaperone regulator CbpM and the transcription regulator HspR.

The 2.2-Å structure of the HP0958 protein from Helicobacter pylori reveals a kinked anti-parallel coiled-coil hairpin domain and a highly conserved ZN-ribbon domain

We have determined the 2.2-Å structure of the HP0958 protein from the human gastric pathogen Helicobacter pylori. HP0958 is essential for flagellum formation and motility. It functions as a chaperone for RpoN (σ(54)) and also controls the stability and translation of mRNA for the major flagellin subunit FlaA. The protein is composed of a highly elongated and kinked coiled-coil hairpin domain (residues 1-170), followed by a C(4) Zn-ribbon domain (residues 174-238). The Zn-ribbon domain is rich in aromatic and positively charged amino acid residues. Electrophoretic mobility shift assays identified residues in a positively charged region of the Zn-ribbon domain of HP0958 whose mutation alters the mobility of an HP0958-flaA mRNA complex. Mutation of surface residues in the coiled-coil domain did not result in an observable change in the mobility of the HP0958-flaA transcript complex. The data thus suggest the arrangement of HP0958 into distinct structural and functional domains.

Built shallow to maintain homeostasis and persistent infection: insight into the transcriptional regulatory network of the gastric human pathogen Helicobacter pylori

Transcriptional regulatory networks (TRNs) transduce environmental signals into coordinated output expression of the genome. Accordingly, they are central for the adaptation of bacteria to their living environments and in host-pathogen interactions. Few attempts have been made to describe a TRN for a human pathogen, because even in model organisms, such as Escherichia coli, the analysis is hindered by the large number of transcription factors involved. In light of the paucity of regulators, the gastric human pathogen Helicobacter pylori represents a very appealing system for understanding how bacterial TRNs are wired up to support infection in the host. Herein, we review and analyze the available molecular and "-omic" data in a coherent ensemble, including protein-DNA and protein-protein interactions relevant for transcriptional control of pathogenic responses. The analysis covers approximately 80% of the annotated H. pylori regulators, and provides to our knowledge the first in-depth description of a TRN for an important pathogen. The emerging picture indicates a shallow TRN, made of four main modules (origons) that process the physiological responses needed to colonize the gastric niche. Specific network motifs confer distinct transcriptional response dynamics to the TRN, while long regulatory cascades are absent. Rather than having a plethora of specialized regulators, the TRN of H. pylori appears to transduce separate environmental inputs by using different combinations of a small set of regulators.

Regulatory circuits in Helicobacter pylori : network motifs and regulators involved in metal-dependent responses

The ability of Helicobacter pylori, one of the most successful human bacterial pathogens, to colonize the acidic gastric niche persistently, depends on the proper homeostasis of intracellular metal ions, needed as cofactors of essential metallo-proteins involved in acid acclimation, respiration and detoxification. This fundamental task is controlled at the transcriptional level mainly by the regulators Fur and NikR, involved in iron homeostasis and nickel response, respectively. Herein, we review the molecular mechanisms that underlie the activity of these key pleiotropic regulators. In addition, we will focus on their involvement in the transcriptional regulatory network of the bacterium, pinpointing a surprising complexity of network motifs that interconnects them and their gene targets. These motifs appear to confer versatile dynamics of metal-dependent responses by extensive horizontal connections between the regulators and feedback control of metal-cofactor availability.

The HP0256 gene product is involved in motility and cell envelope architecture of Helicobacter pylori

BACKGROUND

Helicobacter pylori is the causative agent for gastritis, and peptic and duodenal ulcers. The bacterium displays 5-6 polar sheathed flagella that are essential for colonisation and persistence in the gastric mucosa. The biochemistry and genetics of flagellar biogenesis in H. pylori has not been fully elucidated. Bioinformatics analysis suggested that the gene HP0256, annotated as hypothetical, was a FliJ homologue. In Salmonella, FliJ is a chaperone escort protein for FlgN and FliT, two proteins that themselves display chaperone activity for components of the hook, the rod and the filament.

RESULTS

Ablation of the HP0256 gene in H. pylori significantly reduced motility. However, flagellin and hook protein synthesis was not affected in the HP0256 mutant. Transmission electron transmission microscopy revealed that the HP0256 mutant cells displayed a normal flagellum configuration, suggesting that HP0256 was not essential for assembly and polar localisation of the flagella in the cell. Interestingly, whole genome microarrays of an HP0256 mutant revealed transcriptional changes in a number of genes associated with the flagellar regulon and the cell envelope, such as outer membrane proteins and adhesins. Consistent with the array data, lack of the HP0256 gene significantly reduced adhesion and the inflammatory response in host cells.

CONCLUSIONS

We conclude that HP0256 is not a functional counterpart of FliJ in H. pylori. However, it is required for full motility and it is involved, possibly indirectly, in expression of outer membrane proteins and adhesins involved in pathogenesis and adhesion.

Effect of FliK mutation on the transcriptional activity of the {sigma}54 sigma factor RpoN in Helicobacter pylori

Helicobacter pylori is a motile Gram-negative bacterium that colonizes and persists in the human gastric mucosa. The flagellum gene regulatory circuitry of H. pylori is unique in many aspects compared with the Salmonella/Escherichia coli paradigms, and some regulatory checkpoints remain unclear. FliK controls the hook length during flagellar assembly. Microarray analysis of a fliK-null mutant revealed increased transcription of genes under the control of the sigma(54) sigma factor RpoN. This sigma factor has been shown to be responsible for transcription of the class II flagellar genes, including flgE and flaB. No genes higher in the flagellar hierarchy had altered expression, suggesting specific and localized FliK-dependent feedback on the RpoN regulon. FliK thus appears to be involved in three processes: hook-length control, export substrate specificity and control of RpoN transcriptional activity.

Growth phase and metal-dependent transcriptional regulation of the fecA genes in Helicobacter pylori

Balancing metal uptake is essential for maintaining a proper intracellular metal concentration. Here, we report the transcriptional control exerted by the two metal-responsive regulators of Helicobacter pylori, Fur (iron-dependent ferric uptake regulator) and NikR (nickel-responsive regulator), on the three copies of the fecA genes present in this species. By monitoring the patterns of transcription throughout growth and in response to nickel, iron, and a metal chelator, we found that the expression of the three fecA genes is temporally regulated, responds to metals in different ways, and is selectively controlled by either one of the two regulators. fecA1 is expressed at a constant level throughout growth, and its expression is iron sensitive; the expression of fecA2 is mainly off, with minor expression coming up in late exponential phase. In contrast, the expression of fecA3 is maximal in early exponential phase, gradually decreases with time, and is repressed by nickel. The direct roles of Fur and NikR were studied both in vitro, by mapping the binding sites of each regulator on the promoter regions via DNase I footprinting analysis, and in vivo, by using primer extension analyses of the fecA transcripts in fur and nikR deletion strains. Overall, the results show that the expression of each fecA gene is finely tuned in response to metal availability, as well as during the bacterial growth phase, suggesting specific and dedicated functions for the three distinct FecA homologues.

Identification of small noncoding RNAs in Helicobacter pylori by a bioinformatics-based approach

Small noncoding RNAs (sRNAs) are a group of regulatory RNA molecules normally without a protein-coding function. In recent years, the importance of sRNAs as mediators of gene expression in bacteria has begun to be recognized. More than 70 sRNAs have been known in Escherichia coli. However, little is known about sRNAs in Helicobacter pylori, a human pathogen associated with gastric diseases. Here, we systematically identified sRNAs in the H. pylori genome by a computational approach based on gene location, sequence conservation, promoter and terminator search, and secondary structure. Among a total of six candidate sRNAs initially predicted, two novel sRNAs (IG-443 and IG-524) were confirmed by Northern blot and reverse transcription-polymerase chain reaction (RT-PCR). Virtually, they were a class of natural antisense transcripts, which were complementary to partial sequences of the following genes: flagellar motor switch gene (fliM) and fumarase (fumC). Taken together, the results indicate that there exist novel sRNAs in H. pylori and these RNAs might play a potential role in regulating gene expression.

Posttranscriptional regulation of flagellin synthesis in Helicobacter pylori by the RpoN chaperone HP0958

The Helicobacter pylori protein HP0958 is essential for flagellum biogenesis. It has been shown that HP0958 stabilizes the sigma(54) factor RpoN. The aim of this study was to further investigate the role of HP0958 in flagellum production in H. pylori. Global transcript analysis identified a number of flagellar genes that were differentially expressed in an HP0958 mutant strain. Among these, the transcription of the major flagellin gene flaA was upregulated twofold, suggesting that HP0958 was a negative regulator of the flaA gene. However, the production of the FlaA protein was significantly reduced in the HP0958 mutant, and this was not due to the decreased stability of the FlaA protein. RNA stability analysis and binding assays indicated that HP0958 binds and destabilizes flaA mRNA. The HP0958 mutant was successfully complemented, confirming that the mutant phenotype described was due to the lack of HP0958. We conclude that HP0958 is a posttranscriptional regulator that modulates the amount of the flaA message available for translation in H. pylori.

Acid-responsive gene regulation in the human pathogen Helicobacter pylori

Helicobacter pylori is a human gastric pathogen which is extremely well adapted to the low pH environment of the stomach, since it has evolved mechanisms to survive both severe acid shocks and to grow under mildly acidic conditions. Central to the acid resistance of H. pylori is the enzyme urease whose function is to maintain the cytoplasmic and periplasmic pH of the bacterium near neutrality. Substantial progress has been made recently in unravelling the complex regulation of urease expression and the expression of additional genes involved in the acid adaptation of H. pylori. Acid-responsive gene regulation involves the two-component system ArsRS and the metal responsive pleiotropic transcriptional regulators NikR and Fur which control partially overlapping regulons. Here we review our current understanding of the mechanisms of transcriptional regulation governing the acid response of H. pylori.

The stringent response is required for Helicobacter pylori survival of stationary phase, exposure to acid, and aerobic shock

The gastric pathogen Helicobacter pylori must adapt to fluctuating conditions in the harsh environment of the human stomach with the use of a minimal number of transcriptional regulators. We investigated whether H. pylori utilizes the stringent response, involving signaling through the alarmone (p)ppGpp, as a survival strategy during environmental stresses. We show that the H. pylori homologue of the bifunctional (p)ppGpp synthetase and hydrolase SpoT is responsible for all cellular (p)ppGpp production in response to starvation conditions. Furthermore, the H. pylori spoT gene complements the growth defect of Escherichia coli mutants lacking (p)ppGpp. An H. pylori spoT deletion mutant is impaired for stationary-phase survival and undergoes a premature transformation to a coccoid morphology. In addition, the spoT deletion mutant is unable to survive specific environmental stresses, including aerobic shock and acid exposure, which are likely to be encountered by this bacterium during infection and transmission.

Pathogenesis of Helicobacter pylori Infection

SUMMARY

Helicobacter pylori is the first formally recognized bacterial carcinogen and is one of the most successful human pathogens, as over half of the world's population is colonized with this gram-negative bacterium. Unless treated, colonization usually persists lifelong. H. pylori infection represents a key factor in the etiology of various gastrointestinal diseases, ranging from chronic active gastritis without clinical symptoms to peptic ulceration, gastric adenocarcinoma, and gastric mucosa-associated lymphoid tissue lymphoma. Disease outcome is the result of the complex interplay between the host and the bacterium. Host immune gene polymorphisms and gastric acid secretion largely determine the bacterium's ability to colonize a specific gastric niche. Bacterial virulence factors such as the cytotoxin-associated gene pathogenicity island-encoded protein CagA and the vacuolating cytotoxin VacA aid in this colonization of the gastric mucosa and subsequently seem to modulate the host's immune system. This review focuses on the microbiological, clinical, immunological, and biochemical aspects of the pathogenesis of H. pylori .

Pathogenesis of Helicobacter pylori Infection

SUMMARY

Helicobacter pylori is the first formally recognized bacterial carcinogen and is one of the most successful human pathogens, as over half of the world's population is colonized with this gram-negative bacterium. Unless treated, colonization usually persists lifelong. H. pylori infection represents a key factor in the etiology of various gastrointestinal diseases, ranging from chronic active gastritis without clinical symptoms to peptic ulceration, gastric adenocarcinoma, and gastric mucosa-associated lymphoid tissue lymphoma. Disease outcome is the result of the complex interplay between the host and the bacterium. Host immune gene polymorphisms and gastric acid secretion largely determine the bacterium's ability to colonize a specific gastric niche. Bacterial virulence factors such as the cytotoxin-associated gene pathogenicity island-encoded protein CagA and the vacuolating cytotoxin VacA aid in this colonization of the gastric mucosa and subsequently seem to modulate the host's immune system. This review focuses on the microbiological, clinical, immunological, and biochemical aspects of the pathogenesis of H. pylori .

Pathogenesis of Helicobacter pylori Infection

SUMMARY

Helicobacter pylori is the first formally recognized bacterial carcinogen and is one of the most successful human pathogens, as over half of the world's population is colonized with this gram-negative bacterium. Unless treated, colonization usually persists lifelong. H. pylori infection represents a key factor in the etiology of various gastrointestinal diseases, ranging from chronic active gastritis without clinical symptoms to peptic ulceration, gastric adenocarcinoma, and gastric mucosa-associated lymphoid tissue lymphoma. Disease outcome is the result of the complex interplay between the host and the bacterium. Host immune gene polymorphisms and gastric acid secretion largely determine the bacterium's ability to colonize a specific gastric niche. Bacterial virulence factors such as the cytotoxin-associated gene pathogenicity island-encoded protein CagA and the vacuolating cytotoxin VacA aid in this colonization of the gastric mucosa and subsequently seem to modulate the host's immune system. This review focuses on the microbiological, clinical, immunological, and biochemical aspects of the pathogenesis of H. pylori .

Pathogenesis of Helicobacter pylori infection

Helicobacter pylori is the first formally recognized bacterial carcinogen and is one of the most successful human pathogens, as over half of the world's population is colonized with this gram-negative bacterium. Unless treated, colonization usually persists lifelong. H. pylori infection represents a key factor in the etiology of various gastrointestinal diseases, ranging from chronic active gastritis without clinical symptoms to peptic ulceration, gastric adenocarcinoma, and gastric mucosa-associated lymphoid tissue lymphoma. Disease outcome is the result of the complex interplay between the host and the bacterium. Host immune gene polymorphisms and gastric acid secretion largely determine the bacterium's ability to colonize a specific gastric niche. Bacterial virulence factors such as the cytotoxin-associated gene pathogenicity island-encoded protein CagA and the vacuolating cytotoxin VacA aid in this colonization of the gastric mucosa and subsequently seem to modulate the host's immune system. This review focuses on the microbiological, clinical, immunological, and biochemical aspects of the pathogenesis of H. pylori.

Crystallization and preliminary X-ray crystallographic study of HP1043, a Helicobacter pylori orphan response regulator

The HP1043 protein of Helicobacter pylori is related to the two-component system that regulates prokaryotic transcription in response to environmental changes. The HP1043 gene encodes an orphan response regulator (RR). The N-terminal domain of HP1043 (HP1043N) was purified by affinity-column chromatography. The purified protein was crystallized by hanging drop vapor diffusion at 293 K. The crystal belongs to primitive orthorhombic space group P2(1)2(1)2 with cell dimensions of a=89.0, b=41.3, and c=31.7 A. Assuming the presence of one molecule per asymmetric unit, the solvent content was estimated to be about 45%. A complete data set was collected at 1.8 A resolution.

Repeated sequence motifs in the Helicobacter pylori P1408 promoter do not affect its transcription

The ArsRS two-component system controls the pH-dependent transcription of several target genes involved in the acid resistance of Helicobacter pylori. In its phosphorylated form the response regulator ArsR activates transcription of the urease genes and it has been reported that ArsR approximately P binds to a 26 bp consensus motif which is present in the promoter regions of the ORFs hp1408, hp119 and hp1432 encoding proteins of unknown function. Here we show that the upstream region of ORF hp1408 exhibits considerable sequence variation in different isolates of H. pylori. By the construction of fusions of the P(1408) promoter from different H. pylori strains to the reporter gene gfp in the genetic background of H. pylori G27 we demonstrate that these sequence variations do not significantly affect acid-induced transcription. Furthermore, we show that a P(1408) core promoter comprising only the -10 promoter element and the 26 bp ArsR binding site overlapping the -35 region is sufficient for eliciting the normal acid response of ORF hp1408.

The Helicobacter pylori CrdRS two-component regulation system (HP1364/HP1365) is required for copper-mediated induction of the copper resistance determinant CrdA

Here we describe that the Helicobacter pylori sensor kinase produced by HP1364 and the response regulator produced by HP1365 and designated CrdS and CrdR, respectively, are both required for transcriptional induction of the H. pylori copper resistance determinant CrdA by copper ions. CrdRS-deficient mutants lacked copper induction of crdA expression and were copper sensitive. A direct role of CrdR in transcriptional regulation of crdA was confirmed by in vitro binding of CrdR to the crdA upstream region. A 21-nucleotide sequence located near the crdA promoter was shown to be required for CrdR binding.

NikR-mediated regulation of Helicobacter pylori acid adaptation

Nickel is the cofactor of the Helicobacter pylori urease enzyme, a factor essential for the chronic colonization of the acidic hostile environment in the human stomach. The NikR regulatory protein directly controls urease expression and regulates the uptake of nickel, and is also able to regulate the expression of other regulatory proteins including the iron-responsive regulator Fur. Through regulatory crosstalk and overlapping regulons, the NikR protein controls the expression of many systems important for colonization and acid adaptation. Despite the paucity of regulatory proteins, this enables H. pylori to optimally adapt to conditions in the stomach, making it one of the most successful human pathogens.

Growth phase-dependent regulation of target gene promoters for binding of the essential orphan response regulator HP1043 of Helicobacter pylori

Helicobacter pylori encodes three two-component systems and two orphan response regulators (RRs) that are predicted to be involved in transcriptional regulation. The HP1043 gene encodes an essential OmpR-like RR, 1043RR, for which no histidine kinase has been identified. Gel filtration and cross-linking experiments on the purified 1043RR protein reveals that this protein is a dimer and in vivo dimerization assays localize the dimerization to the N-terminal regulatory domain. DNA-binding studies have revealed two targets for specific binding of the 1043RR protein and moreover, phosphorylation of the protein was not needed for the activation of binding. Footprinting analysis demonstrated that the 1043RR protein binds to its own promoter, P(1043), overlapping the -35 promoter element from positions -17 to -45, suggesting that this protein is autoregulatory. In addition, it binds at a similar location, spanning nucleotides from positions -22 to -51 at the promoter of the methyl-accepting chemotaxis tlpB gene, P(tlpB). A possible inverted repeat was identified in the binding sites of both promoters. In an attempt to overexpress 1043RR in H. pylori, the 10-fold induction in transcription of a second copy of HP1043 with use of an inducible promoter failed to increase cellular levels of the RR protein, suggesting that 1043RR is tightly regulated at a posttranscriptional level. The P(1043) and P(tlpB) promoters were demonstrated to be coordinately regulated in response to growth phase in H. pylori. The essential role of HP1043 in encoding a cell cycle regulator is discussed.

Essential role of ferritin Pfr in Helicobacter pylori iron metabolism and gastric colonization

The reactivity of the essential element iron necessitates a concerted expression of ferritins, which mediate iron storage in a nonreactive state. Here we have further established the role of the Helicobacter pylori ferritin Pfr in iron metabolism and gastric colonization. Iron stored in Pfr enabled H. pylori to multiply under severe iron starvation and protected the bacteria from acid-amplified iron toxicity, as inactivation of the pfr gene restricted growth of H. pylori under these conditions. The lowered total iron content in the pfr mutant, which is probably caused by decreased iron uptake rates, was also reflected by an increased resistance to superoxide stress. Iron induction of Pfr synthesis was clearly diminished in an H. pylori feoB mutant, which lacked high-affinity ferrous iron transport, confirming that Pfr expression is mediated by changes in the cytoplasmic iron pool and not by extracellular iron. This is well in agreement with the recent discovery that iron induces Pfr synthesis by abolishing Fur-mediated repression of pfr transcription, which was further confirmed here by the observation that iron inhibited the in vitro binding of recombinant H. pylori Fur to the pfr promoter region. The functions of H. pylori Pfr in iron metabolism are essential for survival in the gastric mucosa, as the pfr mutant was unable to colonize in a Mongolian gerbil-based animal model. In summary, the pfr phenotypes observed give new insights into prokaryotic ferritin functions and indicate that iron storage and homeostasis are of extraordinary importance for H. pylori to survive in its hostile natural environment.

Molecular microbiology and pathogenesis of Helicobacter and Campylobacter updated: a meeting report of the 11th conference on Campylobacter, Helicobacter and related organisms

The genome analysis of the gastrointestinal pathogens Helicobacter and Campylobacter has stimulated a wealth of new research activities, which are presented every 2 years at the international conferences on Campylobacter, Helicobacter and Related Organisms (CHRO). Both organisms represent excellent models for the identification of new molecular mechanisms involved in pathogenesis, host response and physiological adaptation in course of acute and chronic infectious diseases. The investigation of their global distribution, pronounced genetic and antigenic diversity as well as the molecular mechanisms allowing long-term persistence in hostile and unusual microbial habitats, is a challenge for scientists of many different disciplines world-wide. With a focus on the molecular microbiology aspects, this review summarizes recent trends in Helicobacter and Campylobacter research by highlighting selected presentations at the 11th CHRO conference. The topics include the discovery of new virulence factors, functional analysis of protein secretion systems, host signalling pathways, adaptation to stress conditions, global gene regulation, and genetic variability.