Proteomic analysis of proteins expressed by Helicobacter pylori under oxidative stress

Changes in Fecal Pellet Microbiome of the Cold-Adapted Antarctic Copepod Tigriopus kingsejongensis at Different Temperatures and Developmental Stages

Tigriopus kingsejongensis, a copepod species reported from the King Sejong Station, Antarctica, serves as a valuable food resource in ecosystems. We cultured T. kingsejongensis at three different temperatures (2 °C, 8 °C, and 15 °C) in a laboratory to observe the changes in its fecal pellet microbiome depending on the cultivation temperatures and developmental stages. We observed that the fecal pellet microbiome of the copepod changed with temperature: a lower microbial diversity, higher abundance of the aquatic bacterium Vibrio, and lower abundance of the psychrophilic bacterium Colwellia were noted at higher temperatures. In addition, the fecal pellet microbiome of the copepod changed according to the developmental stage: a lower microbial diversity was noted in egg-attached copepods than in nauplii at 8 °C. We further analyzed three shotgun metagenomes from the fecal pellet samples of T. kingsejongensis at different temperatures and obtained 44 metagenome-assembled genomes (MAGs). We noted that MAGs of V. splendidus D contained glycosyl hydrolases (GHs) encoding chitinases and virulence factors at a higher relative abundance at 15 °C than at lower temperatures. These results indicate that increasing temperature affects the fecal pellet microbiome and the development of copepods. The findings are helpful to understand the changes in cold-adapted copepods and the effect of temperature on their growth.

Oxidative responses and defense mechanism of hyperpigmented P. aeruginosa as characterized by proteomics and metabolomics

Pseudomonas aeruginosa is known to produce multiple types of pigment which are involved in its pathogenicity and survival in certain environments. Herein, we reported the identification of P. aeruginosa dark-brown hyperpigmented (HP) strains which have been isolated from clinical samples. In order to study the role of these dark-brown containing secretions, alterations of metabolic processes and cellular responses under microenvironment of this bacterial pathogen, two-dimensional gel electrophoresis (2-DE) in conjunction with peptide mass fingerprinting (PMF) were performed. Protein spots showing the most significant differences and high spot optical density values were selected for further characterization. Fold difference of protein expression levels among those spots were calculated. Three major groups of proteins including anti-oxidant enzyme such as catalase, alkyl hydroperoxide reductase and also iron-superoxide dismutase (Fe-SOD), transmembrane proteins as well as proteins involved in energy metabolism such as ATP synthase and pyruvate/2-oxoglutarate dehydrogenase were significantly decreased in P. aeruginosa HP. Whereas, malate syntase and isocitrate lyase, the key enzyme in glyoxylate cycle as well as alcohol dehydrogenase were significantly increased in P. aeruginosa HP, as compared to the reference strain ATCC 27853. Moreover, the HP exerted SOD-like activity with its IC₅₀ equal to 0.26 mg/ml as measured by NBT assay. Corresponding to secretomic metabolome identification, elevated amounts of anti-oxidant compounds are detected in P. aeruginosa HP than those observed in ATCC 27853. Our findings indicated successful use of proteomics and metabolomics for understanding cell responses and defense mechanisms of P. aeruginosa dark-brown hyperpigmented strains upon surviving in its microenvironment.

Acid-regulated gene expression of Helicobacter pylori: Insight into acid protection and gastric colonization

BACKGROUND

The pathogen Helicobacter pylori encounters many stressors as it transits to and infects the gastric epithelium. Gastric acidity is the predominate stressor encountered by the bacterium during initial infection and establishment of persistent infection. H. pylori initiates a rapid response to acid to maintain intracellular pH and proton motive force appropriate for a neutralophile. However, acid sensing by H. pylori may also serve as a transcriptional trigger to increase the levels of other pathogenic factors needed to subvert host defenses such as acid acclimation, antioxidants, flagellar synthesis and assembly, and CagA secretion.

MATERIALS AND METHODS

Helicobacter pylori were acid challenged at pH 3.0, 4.5, 6.0 vs nonacidic pH for 4 hours in the presence of urea, followed by RNA-seq analysis and qPCR. Cytoplasmic pH was monitored under the same conditions.

RESULTS

About 250 genes were induced, and an equal number were repressed at acidic pHs. Genes encoding for antioxidant proteins, flagellar structural proteins, particularly class 2 genes, T4SS/Cag-PAI, F_o F₁ -ATPase, and proteins involved in acid acclimation were highly expressed at acidic pH. Cytoplasmic pH decreased from 7.8 at pH_out of 8.0 to 6.0 at pH_out of 3.0.

CONCLUSIONS

These results suggest that increasing extracellular or intracellular acidity or both are detected by the bacterium and serve as a signal to initiate increased production of protective and pathogenic factors needed to counter host defenses for persistent infection. These changes are dependent on degree of acidity and time of acid exposure, triggering a coordinated response to the environment required for colonization.

Application of proteomics to the study of Helicobacter pylori and implications for the clinic

INTRODUCTION

Helicobacter pylori (H. pylori) is a gram-negative bacterium that colonizes the gastric epithelium and mucous layer of more than half the world's population. H. pylori is a primary human pathogen, responsible for the development of chronic gastritis, peptic ulceration and gastric cancer. Proteomics is impacting several aspects of medical research: understanding the molecular basis of infection and disease manifestation, identification of therapeutic targets and discovery of clinically relevant biomarkers. Areas covered: The main aim of the present review is to provide a comprehensive overview of the contribution of proteomics to the study of H. pylori infection pathophysiology. In particular, we focused on the role of the bacterium and its most important virulence factor, CagA, in the progression of gastric cells transformation and cancer progression. We also discussed the proteomic approaches aimed at the investigation of the host response to bacterial infection. Expert commentary: In the field of proteomics of H. pylori, comprehensive analysis of clinically relevant proteins (functional proteomics) rather than entire proteomes will result in important medical outcomes. Finally, we provided an outlook on the potential development of proteomics in H. pylori research.

Oxidative and nitrosative stress defences of Helicobacter and Campylobacter species that counteract mammalian immunity

Helicobacter and Campylobacter species are Gram-negative microaerophilic host-associated heterotrophic bacteria that invade the digestive tract of humans and animals. Campylobacter jejuni is the major worldwide cause of foodborne gastroenteritis in humans, while Helicobacter pylori is ubiquitous in over half of the world's population causing gastric and duodenal ulcers. The colonisation of the gastrointestinal system by Helicobacter and Campylobacter relies on numerous cellular defences to sense the host environment and respond to adverse conditions, including those imposed by the host immunity. An important antimicrobial tool of the mammalian innate immune system is the generation of harmful oxidative and nitrosative stresses to which pathogens are exposed during phagocytosis. This review summarises the regulators, detoxifying enzymes and subversion mechanisms of Helicobacter and Campylobacter that ultimately promote the successful infection of humans.

GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes

Although the number of sequenced prokaryotic genomes is growing rapidly, experimentally verified annotation of prokaryotic genome remains patchy and challenging. To facilitate genome annotation efforts for prokaryotes, we developed an open source software called GAPP for genome annotation and global profiling of post-translational modifications (PTMs) in prokaryotes. With a single command, it provides a standard workflow to validate and refine predicted genetic models and discover diverse PTM events. We demonstrated the utility of GAPP using proteomic data from Helicobacter pylori, one of the major human pathogens that is responsible for many gastric diseases. Our results confirmed 84.9% of the existing predicted H. pylori proteins, identified 20 novel protein coding genes, and corrected four existing gene models with regard to translation initiation sites. In particular, GAPP revealed a large repertoire of PTMs using the same proteomic data and provided a rich resource that can be used to examine the functions of reversible modifications in this human pathogen. This software is a powerful tool for genome annotation and global discovery of PTMs and is applicable to any sequenced prokaryotic organism; we expect that it will become an integral part of ongoing genome annotation efforts for prokaryotes. GAPP is freely available at https://sourceforge.net/projects/gappproteogenomic/.

Clinical proteomics identifies potential biomarkers in Helicobacter pylori for gastrointestinal diseases

The development of gastrointestinal diseases has been found to be associated with Helicobacter pylori (H. pylori) infection and various biochemical stresses in stomach and intestine. These stresses, such as oxidative, osmotic and acid stresses, may bring about bi-directional effects on both hosts and H. pylori, leading to changes of protein expression in their proteomes. Therefore, proteins differentially expressed in H. pylori under various stresses not only reflect gastrointestinal environment but also provide useful biomarkers for disease diagnosis and prognosis. In this regard, proteomic technology is an ideal tool to identify potential biomarkers as it can systematically monitor proteins and protein variation on a large scale of cell’s translational landscape, permitting in-depth analyses of host and pathogen interactions. By performing two-dimensional polyacrylamide gel electrophoresis (2-DE) followed by liquid chromatography-nanoESI-mass spectrometry (nanoLC-MS/MS), we have successfully pinpointed alkylhydroperoxide reductase (AhpC), neutrophil-activating protein and non-heme iron-binding ferritin as three prospective biomarkers showing up-regulation in H. pylori under oxidative, osmotic and acid stresses, respectively. Further biochemical characterization reveals that various environmental stresses can induce protein structure change and functional conversion in the identified biomarkers. Especially salient is the antioxidant enzyme AhpC, an abundant antioxidant protein present in H. pylori. It switches from a peroxide reductase of low-molecular-weight (LMW) oligomers to a molecular chaperone of high-molecular-weight (HMW) complexes under oxidative stress. Different seropositivy responses against LMW or HMW AhpC in H. pylori-infected patients faithfully match the disease progression from disease-free healthy persons to patients with gastric ulcer and cancer. These results has established AhpC of H. pylori as a promising diagnostic marker for gastrointestinal maladies, and highlight the utility of clinical proteomics for identifying disease biomarkers that can be uniquely applied to disease-oriented translational medicine.

Proteomic analysis of Fusarium graminearum treated by the fungicide JS399-19

JS399-19 (2-cyano-3-amino-3-phenylancryic acetate), a novel cyanoacrylate fungicide, has powerful inhibition against Fusarium species, especially to Fusarium graminearum. Treated with JS399-19, mycelium of F. graminearum was distorted and swelled. The embranchment increased. In order to investigate the effect of JS399-19 on protein expression of F. graminearum, total protein of F. graminearum cultured in normal condition and that treated with 0.5 μg/mL (EC90 value) JS399-19 were extracted respectively and proteomic analysis was performed using two-dimensional gel electrophoresis. The expression levels of 38 proteins varied quantitatively at least twofold. 33 proteins out of the 38 were successfully identified by MALDI-TOF-MS/MS and MASCOT. According to the classification of physiological functions from Conserved Domain Database analysis, 19, 5, 2, 3, 2 and 2 proteins were respectively associated with metabolism, regulation, motility, defense, signal transduction, and unknown function, which indicated that energy metabolism, the synthesis and transport of proteins and DNA of F. graminearum were inhibited by JS399-19 in different degrees. The expression levels of the genes were further confirmed by quantitative real-time PCR analyses. This study represents the first proteomic analysis of F. graminearum treated by JS399-19 and will provide some useful information to find the mode of action of the fungicide against F. graminearum.

Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics

Correct annotation of protein coding genes is the basis of conventional data analysis in proteomic studies. Nevertheless, most protein sequence databases almost exclusively rely on gene finding software and inevitably also miss protein annotations or possess errors. Proteogenomics tries to overcome these issues by matching MS data directly against a genome sequence database. Here we report an in-depth proteogenomics study of Helicobacter pylori strain 26695. MS data was searched against a combined database of the NCBI annotations and a six-frame translation of the genome. Database searches with Mascot and X! Tandem revealed 1115 proteins identified by at least two peptides with a peptide false discovery rate below 1%. This represents 71% of the predicted proteome. So far this is the most extensive proteome study of Helicobacter pylori. Our proteogenomic approach unambiguously identified four previously missed annotations and furthermore allowed us to correct sequences of six annotated proteins. Since secreted proteins are often involved in pathogenic processes we further investigated signal peptidase cleavage sites. By applying a database search that accommodates the identification of semi-specific cleaved peptides, 63 previously unknown signal peptides were detected. The motif LXA showed to be the predominant recognition sequence for signal peptidases.

BIOLOGICAL SIGNIFICANCE

The results of MS-based proteomic studies highly rely on correct annotation of protein coding genes which is the basis of conventional data analysis. However, the annotation of protein coding sequences in genomic data is usually based on gene finding software. These tools are limited in their prediction accuracy such as the problematic determination of exact gene boundaries. Thus, protein databases own partly erroneous or incomplete sequences. Additionally, some protein sequences might also be missing in the databases. Proteogenomics, a combination of proteomic and genomic data analyses, is well suited to detect previously not annotated proteins and to correct erroneous sequences. For this purpose, the existing database of the investigated species is typically supplemented with a six-frame translation of the genome. Here, we studied the proteome of the major human pathogen Helicobacter pylori that is responsible for many gastric diseases such as duodenal ulcers and gastric cancer. Our in-depth proteomic study highly reliably identified 1115 proteins (FDR<0.01%) by at least two peptides (FDR<1%) which represent 71% of the predicted proteome deposited at NCBI. The proteogenomic data analysis of our data set resulted in the unambiguous identification of four previously missed annotations, the correction of six annotated proteins as well as the detection of 63 previously unknown signal peptides. We have annotated proteins of particular biological interest like the ferrous iron transport protein A, the coiled-coil-rich protein HP0058 and the lipopolysaccharide biosynthesis protein HP0619. For instance, the protein HP0619 could be a drug target for the inhibition of the LPS synthesis pathway. Furthermore it has been proven that the motif "LXA" is the predominant recognition sequence for the signal peptidase I of H. pylori. Signal peptidases are essential enzymes for the viability of bacterial cells and are involved in pathogenesis. Therefore signal peptidases could be novel targets for antibiotics. The inclusion of the corrected and new annotated proteins as well as the information of signal peptide cleavage sites will help in the study of biological pathways involved in pathogenesis or drug response of H. pylori.

Proteomic analysis of the function of spot in Helicobacter pylori anti-oxidative stress in vitro and colonization in vivo

As a microaerobe, Helicobacter pylori employs the global regulator SpoT for defending against oxidative stress in vitro. However, the mechanisms how SpoT affects bacterial gene expression is still unknown. Moreover, the function of SpoT in H. pylori colonization in the host is remaining undetermined. To explore the functions of the SpoT in H. pylori pathogenesis, we constructed H. pylori 26695 spoT-deficient mutant (ΔspoT). While grown in ambient atmosphere, protein expression profile of the ΔspoT was analyzed with 2D gel electrophoresis and real-time PCR. Compared to the wild type, the spoT-deficient strain downregulated its transcription of the oxidative-induced genes, as well as the genes responsible for protein degradation and that related to energy metabolism. Meanwhile, the colonization ability of ΔspoT strains in Mongolian gerbil was tested, the results demonstrated a decayed colonization in the mouse stomach with ΔspoT than the wild type. As a matter of facts, the AGS cells infected with the ΔspoT strains excreted increased level of the gastric inflammation cytokines IL-8, and the ΔspoT strains showed poor survival ability when treated with reactive oxygen stress (sodium nitroprusside). The elevated capacity of stimulating cytokines and fragility to reactive oxygen stress may be contribute to decreased colonization of the spoT-deficient mutant in the mouse stomach. Conclusively, we speculate that spoT is a key regulator of the genes for H. pylori spreading in the air and colonization in host stomach.

Up-regulation of neutrophil activating protein in Helicobacter pylori under high-salt stress: structural and phylogenetic comparison with bacterial iron-binding ferritins

It is generally accepted that most gastrointestinal diseases are probably caused by the bacterial pathogen Helicobacter pylori (H. pylori). In this study we have focused on the comparison of protein expression profiles of H. pylori grown under normal and high-salt conditions by a proteomics approach. We have identified about 190 proteins whose expression levels changed after growth at high salt concentration. Among these proteins, neutrophil-activating protein (NapA) was found to be consistently up-regulated under osmotic stress brought by high salts. We have investigated the effect of high salt on secondary and tertiary structures of NapA by circular dichroism spectroscopy followed by analytical ultracentrifugation to monitor the change of quaternary structure of recombinant NapA with increasing salt concentration. The loss of iron-binding activity of NapA coupled with noticeable energetic variation in protein association of NapA as revealed by isothermal titration calorimetry was found under high salt condition. The phylogenetic tree analysis based on sequence comparison of 16 protein sequences encompassing NapA proteins and ferritin of H. pylori and other prokaryotic organisms pointed to the fact that all H. pylori NapA proteins of human origin are more homologous to NapA of Helicobacter genus than to other bacterial NapA. Based on computer modeling, NapA proteins from H. pylori of human isolates are found more similar to ferritin from H. pylori than to NapA from other species of bacteria. Taken together, these results suggested that divergent evolution of NapA and ferritin possessing dissimilar and diverse sequences follows a path distinct from that of convergent evolution of NapA and ferritin with similar dual functionality of iron-binding and ferroxidase activities.

Helicobacter pylori defense against oxidative attack

Helicobacter pylori is a microaerophilic, gram-negative pathogen of the human stomach. Despite the chronic active gastritis that develops following colonization, H. pylori is able to persist unharmed in the stomach for decades. Much of the damage caused by gastric inflammation results from the accumulation of reactive oxygen/nitrogen species within the stomach environment, which can induce oxidative damage in a wide range of biological molecules. Without appropriate defenses, this oxidative damage would be able to rapidly kill nearby H. pylori, but the organism employs a range of measures, including antioxidant enzymes, biological repair systems, and inhibitors of oxidant generation, to counter the attack. Despite the variety of measures employed to defend against oxidative injury, these processes are intimately interdependent, and any deficiency within the antioxidant system is generally sufficient to cause substantial impairment of H. pylori viability and persistence. This review provides an overview of the development of oxidative stress during H. pylori gastritis and examines the methods the organism uses to survive the resultant damage.

Oxidative stress response in the opportunistic oral pathogen Fusobacterium nucleatum

The anaerobic, Gram-negative bacillus Fusobacterium nucleatum plays a vital role in oral biofilm formation and the development of periodontal disease. The organism plays a central bridging role between early and late colonizers within dental plaque and plays a protective role against reactive oxygen species. Using a two-dimensional gel electrophoresis and mass spectrometry approach, we have annotated 78 proteins within the proteome of F. nucleatum subsp. nucleatum and identified those proteins whose apparent intracellular concentrations change in response to either O(2)- or H(2)O(2)-induced oxidative stress. Three major protein systems were altered in response to oxidative stress: (i) proteins of the alkyl hydroperoxide reductase/thioredoxin reductase system were increased in intracellular concentration; (ii) glycolytic enzymes were modified by oxidation (i.e. D-glyceraldehyde 3-phosphate dehydrogenase, and fructose 6-phosphate aldolase) or increased in intracellular concentration, with an accompanying decrease in ATP production; and (iii) the intracellular concentrations of molecular chaperone proteins and related proteins (i.e. ClpB, DnaK, HtpG, and HrcA) were increased.

Identification of S-nitrosylation of proteins of Helicobacter pylori in response to nitric oxide stress

Innate and adaptive immune responses are activated in humans when Helicobacter pylori invades the gastric mucosa. Nitric oxide (NO) and reactive nitrogen species are important immune effectors, which can exert their functions through oxidation and S-nitrosylation of proteins. S-nitrosoglutathione and sodium nitroprus-side were used as NO donors and H. pylori cells were incubated with these compounds to analyze the inhibitory effect of NO. The suppressing effect of NO on H. pylori has been shown in vitro. Furthermore, the proteins modified by S-nitrosylation in H. pylori were identified through the biotin switch method in association with matrix-assisted laser desorption ionization/time-of-flight tandem mass spectrometry (MALDI-TOF-MS/MS). Five S-nitrosylated proteins identified were a chaperone and heat-shock protein (GroEL), alkyl hydroperoxide reductase (TsaA), urease alpha subunit (UreA), HP0721, and HP0129. Importantly, S-nitrosylation of TsaA and UreA were confirmed using purified recombinant proteins. Considering the importance of these enzymes in antioxidant defenses, adherence, and colonization, NO may exert its antibacterial actions by targeting enzymes through S-nitrosylation. Identification of protein S-nitrosylation may contribute to an understanding of the antibacterial actions of NO. Our findings provide an insight into potential targets for the development of novel therapeutic agents against H. pylori infection.

Clinical proteomics: current status, challenges, and future perspectives

This account will give an overview and evaluation of the current advances in mass spectrometry (MS)-based proteomics platforms and technology. A general review of some background information concerning the application of these methods in the characterization of molecular sizes and related protein expression profiles associated with different types of cells under varied experimental conditions will be presented. It is intended to provide a concise and succinct overview to those clinical researchers first exposed to this foremost powerful methodology in modern life sciences of postgenomic era. Proteomic characterization using highly sophisticated and expensive instrumentation of MS has been used to characterize biological samples of complex protein mixtures with vastly different protein structure and composition. These systems are then used to highlight the versatility and potential of the MS-based proteomic strategies for facilitating protein expression analysis of various disease-related organisms or tissues of interest. Major MS-based strategies reviewed herein include (1) matrix-assisted laser desorption ionization-MS and electron-spray ionization proteomics; (2) one-dimensional or two-dimensional gel-based proteomics; (3) gel-free shotgun proteomics in conjunction with liquid chromatography/tandem MS; (4) Multiple reaction monitoring coupled tandem MS quantitative proteomics and; (5) Phosphoproteomics based on immobilized metal affinity chromatography and liquid chromatography-MS/MS.

A novel compound from celery seed with a bactericidal effect against Helicobacter pylori

Objectives

The aim was to purify and characterise an antimicrobial component from celery (Apium graveolens) seeds, which have been used for centuries as a herbal medicine with reported antibacterial effects.

Methods

A crude alcoholic extract of celery seeds was fractionated by organic solvent extractions, column chromatography and HPLC. Fractions were assayed for antimicrobial activity against the gastric pathogen Helicobacter pylori and other bacteria. The purified antibacterial component was characterised via MS and NMR. Preliminary investigation of its mechanism of action included morphological studies, incorporation of macromolecular precursors, membrane integrity and two-dimensional protein electrophoresis.

Key findings

The purified component, termed ‘compound with anti-Helicobacter activity’ (CAH), had potent bactericidal effects against H. pylori; the minimum inhibitory concentration and minimum bactericidal concentration were 3.15 μg/ml and 6.25–12.5 μg/ml, respectively. CAH (Mr = 384.23; empirical formula C24H32O4) had specific inhibitory effects on H. pylori and was not active against Campylobacter jejuni or Escherichia coli. MS and NMR data were consistent with a dimeric phthalide structure. The results appeared to rule out mechanisms that operated solely by loss of membrane integrity or inhibition of protein or nucleic acid synthesis.

Conclusions

CAH may be suitable for further investigation as a potent agent for treating H. pylori infections.

Upregulation of a non-heme iron-containing ferritin with dual ferroxidase and DNA-binding activities in Helicobacter pylori under acid stress

Helicobacter pylori is a spiral Gram-negative microaerophilic bacterium. It is unique and distinctive among various bacterial pathogens for its ability to persist in the extreme acidic environment of human stomachs. To address and identify changes in the proteome of H. pylori in response to low pH, we have used a proteomic approach to study the protein expression of H. pylori under neutral (pH 7) and acidic (pH 5) conditions. Global protein-expression profiles of H. pylori under acid stress were analysed by two-dimensional polyacrylamide gel electrophoresis (2-DE) followed by liquid chromatography (LC)-nanoESI-mass spectrometry (MS)/MS and bioinformatics database analysis. Among the proteins differentially expressed under acidic condition, a non-heme iron-containing ferritin of H. pylori (HP-ferritin) was found to be consistently upregulated at pH 5 as compared to pH 7. It was also found that HP-ferritin can switch from an iron-storage protein with ferroxidase activity to a DNA-binding/protection function under in vitro conditions upon exposure to acidic environment. Prokaryotic ferritins, such as non-heme iron-binding HP-ferritin with dual functionality reported herein, may play a significant urease-independent role in the acid adaptation of H. pylori under physiological conditions in vivo.

Tetracycline treatment targeting Wolbachia affects expression of an array of proteins in Brugia malayi parasite

Wolbachia is an intracellular endosymbiont of Brugia malayi parasite whose presence is essential for the survival of the parasite. Treatment of B. malayi-infected jirds with tetracycline eliminates Wolbachia, which affects parasite survival and fitness. In the present study we have tried to identify parasite proteins that are affected when Wolbachia is targeted by tetracycline. For this Wolbachia depleted parasites (B. malayi) were obtained by tetracycline treatment of infected Mongolian jirds (Meriones unguiculatus) and their protein profile after 2-DE separation was compared with that of untreated parasites harboring Wolbachia. Approximately 100 protein spots could be visualized followed by CBB staining of 2-D gel and included for comparative analysis. Of these, 54 showed differential expressions, while two new protein spots emerged (of 90.3 and 64.4 kDa). These proteins were subjected to further analysis by MALDI-TOF for their identification using Brugia coding sequence database composed of both genomic and EST sequences. Our study unravels two crucial findings: (i) the parasite or Wolbachia proteins, which disappeared/down-regulated appear be essential for parasite survival and may be used as drug targets and (ii) tetracycline treatment interferes with the regulatory machinery vital for parasites cellular integrity and defense and thus could possibly be a molecular mechanism for the killing of filarial parasite. This is the first proteomic study substantiating the wolbachial genome integrity with its nematode host and providing functional genomic data of human lymphatic filarial parasite B. malayi.

Helicobacter pylori proteins response to nitric oxide stress

Helicobacter pylori is a highly pathogenic microorganism with various strategies to evade human immune responses. Nitric oxide (NO) and reactive nitrogen species (RNS) generated via nitric oxide synthase pathway are important effectors during the innate immune response. However, the mechanisms of H. pylori to survive the nitrosative stress are not clear. Here the proteomic approach has been used to define the adaptive response of H. pylori to nitrosative stress. Proteomic analysis showed that 38 protein spots were regulated by NO donor, sodium nitroprusside (SNP). These proteins were involved in protein processing, anti-oxidation, general stress response, and virulence, as well as some unknown functions. Particularly, some of them were participated in iron metabolism, potentially under the control of ferric uptake regulator (Fur). Real time PCR revealed that fur was induced under nitrosative stress, consistent with our deduction. One stress-related protein up-regulated under nitrosative conditions was thioredoxin reductase (TrxR). Inactivation of fur or trxR can lead to increased susceptivity to nitrosative stress respectively. These studies described the adaptive response of H. pylori to nitric oxide stress, and analyzed the relevant role of Fur regulon and TrxR in nitrosative stress management.

Proteomic identification of biomarkers related to Helicobacter pylori-associated gastroduodenal disease: challenges and opportunities

Helicobacter pylori colonize the stomach of over half the world's population. While 80-90% H. pylori-infected individuals have clinically asymptomatic gastritis, 10-15% develop peptic ulcer, and 1-2% gastric malignancies. These variable clinical outcomes have led to an interest in prognostic indicators. The current disease paradigm suggests that host genetics and bacterial virulence both play important roles in modulating the final outcome of H. pylori infection. Elucidation of the interaction between host and bacterium is essential to clarify pathogenesis and to develop new strategies for prevention and treatment. Proteomic technology is a powerful tool for simultaneously monitoring proteins and protein variation on a large scale in biological samples. It has provided an unprecedented opportunity to survey a cell's translational landscape comprehensively, and the results may allow in-depth analyses of host and pathogen interactions. Using this high-throughput platform and taking advantage of complete sequences for both the H. pylori and the human genome in available databases, we have identified several crucial proteins that have pathogenic and prognostic potential. Among them, antibodies to AhpC and GroEs of H. pylori could be utilized for identification of patients who are at high risk of disease complications after H. pylori infection. Evolving proteomic technologies, together with appropriate clinical phenotyping and genotype information should enhance understanding of disease pathogenesis and lead to more precise prediction of variable disease outcomes. It will also facilitate development of biomarkers for diagnosis, treatment, and prevention of H. pylori infection.

Exploration of intraclonal adaptation mechanisms of Pseudomonas brassicacearum facing cadmium toxicity

Pseudomonas brassicacearum forms phenotypic variants in vitro as well as in planta during root colonization under natural conditions, leading to subpopulations (phase I and II cells) that differ in colony morphology and production of exoenzymes/secondary metabolites. The maximal concentration of cadmium allowing both variants growth was 25 μM; however, phase II cells accumulated fivefold higher Cd than phase I cells, even though both variants showed the same growth rate and kinetics, comprising a long stasis period (50 h). The whole transcriptome analysis of both variants in response to Cd was investigated using the home-made DNA microarrays. This analysis revealed completely different adaptation mechanisms developed by each variant to withstand and grow in the presence of the toxic. A re-organization of the cell wall to limit Cd entrance was noticed for phase I cells, as genes encoding levan exopolymers were downregulated at the expense of an upregulation of genes encoding alginate, and an upregulation of transporters such as cadA, and a downregulation of copper transporters. Phase II cells were unable to prevent Cd entrance and recruited genes under the control of oxyR and soxR regulation to face osmotic and oxidant stresses generated by Cd. Putrescine and spermidine metabolism appeared to play a central role in Cd tolerance. Microarray data were validated by biological analyses such as motility, oxidative stress assay, metabolite profiling with ICR-FT/MS and UPLC, capillary electrophoresis analysis of biogenic amines.

Urease activity and urea gene sequencing of coccoid forms of H. pylori induced by different factors

Helicobacter pylori exists in two morphologic forms: spiral shaped and coccoid. The nonculturable coccoid forms were believed to be the morphologic manifestations of cell death for a long time. However, recent studies indicate the viability of such forms. This form of H. pylori is now suspected to play a role in the transmission of the bacteria and is partly responsible for relapse of infection after antimicrobial treatment. Urease activity of H. pylori is an important maintenance factor. Determination of urease activity and possible mutations in the DNA sequences of coccoid bacteria will hence contribute to the understanding of pathogenesis of infections, which these forms might be responsible for. In this study, our aim was to analyze the urease activity and investigate the urease gene sequences of coccoid H. pylori forms induced by different factors with respect to the spiral form. For this purpose, the urease activities of H. pylori NCTC 11637 standard strain and two clinical isolates were examined before and after transformation of the cells to coccoid forms by different methods such as exposure to amoxicillin, aerobiosis, cold starvation, and aging. The effects of these conditions on the urease gene were examined by the amplification of 411-bp ureA gene and 115-bp ureB gene regions by PCR technique and sequencing of the ureA gene. The urease activities of coccoid cells were found to be lower than those of the spiral form. ureA and ureB gene regions were amplified in all coccoid cells by PCR. Inducing the change to coccoid form by different methods was found to have no effect on the nucleotide sequence of the ureA gene. These results show that the urease gene region of coccoid H. pylori is highly protected under various mild environmental conditions.

Improved in vitro model systems for gastrointestinal infection by choice of cell line, pH, microaerobic conditions, and optimization of culture conditions

BACKGROUND

Commonly used in vitro infection cultures do not mimic the human gastrointestinal tract with regard to pH and microaerobic conditions. Furthermore, despite the importance of mucin-Helicobacter interactions, the cell lines used have not been selected for appropriate mucin expression. To make in vitro studies more applicable to human disease, we have developed coculture methods taking these factors into account.

MATERIALS AND METHODS

Nine human gastrointestinal epithelial cell lines (MKN1, MKN7, MKN28, MKN45, KATO3, HFE145, PCAA/C11 Caco-2, and LS513) were investigated. Expression and glycosylation of mucins (MUC1, 2, 3, 4, 5AC, 5B, 6, 12, 13, and 16) were determined by immunohistochemistry. We analyzed the effect of microaerobic conditions and acidic pH on cell proliferation, viability, and apoptosis.

RESULTS

Microaerobic culture, which is more physiological for the bacteria, did not adversely affect mammalian cell viability, proliferation, or induce apoptosis The cell lines varied in mucin expression, with MKN7 and MKN45 being most similar to gastric mucosa and Caco-2 and LS513 to intestinal mucosa, although none exactly matched normal mucosa. However, changes in culture conditions did not cause major changes in the mucin expression within cell lines.

CONCLUSIONS

Culture conditions mimicking the natural environment and allowing the bacterial cells to thrive had no effect on cell viability or apoptosis, and very little influence on mucin expression of human gastrointestinal cells. Thus, it is feasible, using the simple methods we present here, to substantially improve bacterial-mammalian cell in vitro coculture studies to make them more reflective of human infection.

Crucial role of antioxidant proteins and hydrolytic enzymes in pathogenicity of Penicillium expansum: analysis based on proteomics approach

Penicillium expansum, a widespread filamentous fungus, is a major causative agent of fruit decay and may lead to the production of mycotoxin that causes harmful effects on human health. In this study, we compared the cellular and extracellular proteomes of P. expansum in the absence and presence of borate, which affects the virulence of the fungal pathogen. The differentially expressed proteins were identified using ESI-Q-TOF-MS/MS. Several proteins related to stress response (glutathione S-transferase, catalase, and heat shock protein 60) and basic metabolism (glyceraldehyde-3-phosphate dehydrogenase, dihydroxy-acid dehydratase, and arginase) were identified in the cellular proteome. Catalase and glutathione S-transferase, the two antioxidant enzymes, exhibited reduced levels of expression upon exposure to borate. Because catalase and glutathione S-transferase are related to oxidative stress response, we further investigated the reactive oxygen species (ROS) levels and oxidative protein carbonylation (damaged proteins) in P. expansum. Higher amounts of ROS and carbonylated proteins were observed after borate treatment, indicating that catalase and glutathione S-transferase are important in scavenging ROS and protecting cellular proteins from oxidative damage. Additionally to find secretory proteins that contribute to the virulence, we studied the extracellular proteome of P. expansum under stress condition with reduced virulence. The expression of three protein spots were repressed in the presence of borate and identified as the same hydrolytic enzyme, polygalacturonase.

The diverse antioxidant systems of Helicobacter pylori

The gastric pathogen Helicobacter pylori induces a strong inflammatory host response, yet the bacterium maintains long-term persistence in the host. H. pylori combats oxidative stress via a battery of diverse activities, some of which are unique or newly described. In addition to using the well-studied bacterial oxidative stress resistance enzymes superoxide dismutase and catalase, H. pylori depends on a family of peroxiredoxins (alkylhydroperoxide reductase, bacterioferritin co-migratory protein and a thiol-peroxidase) that function to detoxify organic peroxides. Newly described antioxidant proteins include a soluble NADPH quinone reductase (MdaB) and an iron sequestering protein (NapA) that has dual roles - host inflammation stimulation and minimizing reactive oxygen species production within H. pylori. An H. pylori arginase attenuates host inflammation, a thioredoxin required as a reductant for many oxidative stress enzymes is also a chaperon, and some novel properties of KatA and AhpC were discovered. To repair oxidative DNA damage, H. pylori uses an endonuclease (Nth), DNA recombination pathways and a newly described type of bacterial MutS2 that specifically recognizes 8-oxoguanine. A methionine sulphoxide reductase (Msr) plays a role in reducing the overall oxidized protein content of the cell, although it specifically targets oxidized Met residues. H. pylori possess few stress regulator proteins, but the key roles of a ferric uptake regulator (Fur) and a post-transcriptional regulator CsrA in antioxidant protein expression are described. The roles of all of these antioxidant systems have been addressed by a targeted mutant analysis approach and almost all are shown to be important in host colonization. The described antioxidant systems in H. pylori are expected to be relevant to many bacterial-associated diseases, as genes for most of the enzymes carrying out the newly described roles are present in a number of pathogenic bacteria.

The antioxidant protein alkylhydroperoxide reductase of Helicobacter pylori switches from a peroxide reductase to a molecular chaperone function

Helicobacter pylori, an oxygen-sensitive microaerophilic bacterium, contains many antioxidant proteins, among which alkylhydroperoxide reductase (AhpC) is the most abundant. The function of AhpC is to protect H. pylori from a hyperoxidative environment by reduction of toxic organic hydroperoxides. We have found that the sequence of AhpC from H. pylori is more homologous to mammalian peroxiredoxins than to eubacterial AhpC. We have also found that the protein structure of AhpC could shift from low-molecular-weight oligomers with peroxide-reductase activity to high-molecular-weight complexes with molecular-chaperone function under oxidative stresses. Time-course study by following the quaternary structural change of AhpC in vivo revealed that this enzyme changes from low-molecular-weight oligomers under normal microaerobic conditions or short-term oxidative shock to high-molecular-weight complexes after severe long-term oxidative stress. This study revealed that AhpC of H. pylori acts as a peroxide reductase in reducing organic hydroperoxides and as a molecular chaperone for prevention of protein misfolding under oxidative stress.