Potential for proteomic profiling of Helicobacter pylori and other Helicobacter spp. using a ProteinChip array

Comparative genomics analysis to differentiate metabolic and virulence gene potential in gastric versus enterohepatic Helicobacter species

Background

The genus Helicobacter are gram-negative, microaerobic, flagellated, mucus-inhabiting bacteria associated with gastrointestinal inflammation and classified as gastric or enterohepatic Helicobacter species (EHS) according to host species and colonization niche. While there are over 30 official species, little is known about the physiology and pathogenic mechanisms of EHS, which account for most in the genus, as well as what genetic factors differentiate gastric versus EHS, given they inhabit different hosts and colonization niches. The objective of this study was to perform a whole-genus comparative analysis of over 100 gastric versus EHS genomes in order to identify genetic determinants that distinguish these Helicobacter species and provide insights about their evolution/adaptation to different hosts, colonization niches, and mechanisms of virulence.

Results

Whole-genome phylogeny organized Helicobacter species according to their presumed gastric or EHS classification. Analysis of orthologs revealed substantial heterogeneity in physiological and virulence-related genes between gastric and EHS genomes. Metabolic reconstruction predicted that unlike gastric species, EHS appear asaccharolytic and dependent on amino/organic acids to fuel metabolism. Additionally, gastric species lack de novo biosynthetic pathways for several amino acids and purines found in EHS and instead rely on environmental uptake/salvage pathways. Comparison of virulence factor genes between gastric and EHS genomes identified overlapping yet distinct profiles and included canonical cytotoxins, outer membrane proteins, secretion systems, and survival factors.

Conclusions

The major differences in predicted metabolic function suggest gastric species and EHS may have evolved for survival in the nutrient-rich stomach versus the nutrient-devoid environments, respectively. Contrasting virulence factor gene profiles indicate gastric species and EHS may utilize different pathogenic mechanisms to chronically infect hosts and cause inflammation and tissue damage. The findings from this study provide new insights into the genetic differences underlying gastric versus EHS and support the need for future experimental studies to characterize these pathogens.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5171-2) contains supplementary material, which is available to authorized users.

Differential proteomics of Helicobacter pylori associated with autoimmune atrophic gastritis

Atrophic autoimmune gastritis (AAG) is a condition of chronic inflammation and atrophy of stomach mucosa, for which development can be partially triggered by the bacterial pathogen Helicobacter pylori (HP). HP can cause a variety of gastric diseases, such as duodenal ulcer (DU) or gastric cancer (GC). In this study, a comparative proteomic approach was used by two-dimensional fluorescence difference gel electrophoresis (DIGE) to identify differentially expressed proteins of HP strains isolated from patients with AAG, to identify markers of HP strain associated with AAG. Proteome profiles of HP isolated from GC or DU were used as a reference to compare proteomic levels. Proteomics analyses revealed 27 differentially expressed spots in AAG-associated HP in comparison with GC, whereas only 9 differential spots were found in AAG-associated HP profiles compared with DU. Proteins were identified after matrix-assisted laser desorption ionization (MALDI)-TOF and peptide mass fingerprinting. Some AAG-HP differential proteins were common between DU- and GC-HP (peroxiredoxin, heat shock protein 70 [HSP70], adenosine 5'-triphosphate [ATP] synthase subunit α, flagellin A). Our results presented here may suggest that comparative proteomes of HP isolated from AAG and DU share more common protein expression than GC and provide subsets of putative AAG-specific upregulated or downregulated proteins that could be proposed as putative markers of AAG-associated HP. Other comparative studies by two-dimensional maps integrated with functional genomics of candidate proteins will undoubtedly contribute to better decipher the biology of AAG-associated HP strains.

Comparative proteomics of Helicobacter species: the discrimination of gastric and enterohepatic Helicobacter species

Helicobacter pylori is a major human pathogen that infects the gastric mucosa and is responsible for a range of infections including gastritis and gastric carcinoma. Although other bacteria within the Helicobacter genus can also infect the gastric mucosa, there are Helicobacter species that infect alternative sites within the gastrointestinal (GI) tract. Two-dimensional gel electrophoresis was used to compare the cellular proteomes of seven non-pylori Helicobacters (H. mustelae, H. felis, H. cinaedi, H. hepaticus, H. fennelliae, H. bilis and H. cholecystus) against the more extensively characterised H. pylori. The different Helicobacter species showed distinctive 2D protein profiles, it was possible to combine them into a single dataset using Progenesis SameSpots software. Principal Component Analysis was used to search for correlations between the bacterial proteomes and their sites of infection. This approach clearly discriminated between gastric (i.e. those which infect in the gastric mucosa) and enterohepatic Helicobacter species (i.e. those bacteria that infect the small intestine and hepatobillary regions of the GI tract). Selected protein spots showing significant differences in abundance between these two groups of bacteria were identified by LC-MS. The data provide an initial insight into defining those features of the bacterial proteome that influence the sites of bacterial infection.

BIOLOGICAL SIGNIFICANCE

This study demonstrated that representative members of the Helicobacter genus were readily discriminated from each other on the basis of their in vitro whole cell proteomes determined using 2D gel electrophoresis. Despite the intra-species heterogeneity observed it was possible, to demonstrate that the enterohepatic (represented by H. bilis, H. hepaticus, H. fennelliae, H. cinaedi and H. cholecystus) and gastric (represented by H. pylori, H. mustelae, and H. felis) Helicobacters formed discrete groups based on their 2D protein profiles. A provisional proteomic signature was identified that correlated with the typical sites of colonisation of these members of the Helicobacter genus. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.

Helicobacter pylori immunoproteomics in gastric cancer and gastritis of the carcinoma phenotype

Helicobacter pylori infection is linked to the development of gastric cancer. Atrophic body gastritis is considered the first important step in the histogenesis of such neoplasia. H. pylori infection is involved in the induction of atrophic body gastritis, but documentation of H. pylori infection is difficult because of the progressive disappearance of the bacterium. Host-pathogen interactions may be investigated by means of immunoproteomics, which provides global information regarding the host humoral response to H. pylori infection and allows the identification of relevant specific and nonspecific antigens, and can be used for diagnostic or prognostic purposes. In the present review, we describe how several research groups used H. pylori immunoproteomics to investigate highly immunoreactive bacterial antigens related to the development of gastric cancer.

Proteomic Helicobacter pylori biomarkers discriminating between duodenal ulcer and gastric cancer

Protein patterns of 129 Helicobacter pylori strains isolated from Korean and Colombian patients suffering from duodenal ulcer or gastric cancer were analyzed by the high-throughput methodology SELDI-TOF-MS. Eighteen statistically significant candidate biomarkers discriminating between the two clinical outcomes were selected by using the Mann-Whitney test. Three biomarker proteins were purified and identified as a neutrophil-activating protein NapA (HU HPAG1_0821), a RNA-binding protein (HPAG1_0813), and a DNA-binding histone-like protein HU, respectively (jhp0228). These novel biomarkers can be used for development of diagnostic assays predicting the evolution to gastric cancer in H. pylori-infected patients.

Bacterial outer membrane protein analysis by electrophoresis and microchip technology

Outer membrane proteins are indispensable components of bacterial cells and participate in several relevant functions of the microorganisms. Changes in the outer membrane protein composition might alter antibiotic sensitivity and pathogenicity. Furthermore, the effects of various factors on outer membrane protein expression, such as antibiotic treatment, mutation, changes in the environment, lipopolysaccharide modification and biofilm formation, have been analyzed. Traditionally, the outer membrane protein profile determination was performed by sodium dodecyl sulfate polyacrylamide gel electrophoresis. Converting this technique to capillary electrophoresis format resulted in faster separation, lower sample consumption and automation. Coupling capillary electrophoresis with mass spectrometry enabled the fast identification of bacterial proteins, while immediate quantitative analysis permitted the determination of up- and downregulation of certain outer membrane proteins. Adapting capillary electrophoresis to microchip format ensured a further ten- to 100-fold decrease in separation time. Application of different separation techniques combined with various sensitive detector systems has ensured further opportunities in the field of high-throughput bacterial protein analysis. This review provides an overview using selected examples of outer membrane proteins and the development and application of the electrophoretic and microchip technologies for the analysis of these proteins.

Two-dimensional blue native/SDS gel electrophoresis of multiprotein complexes from Helicobacter pylori

The study of protein interactions constitutes an important domain to understand the physiology and pathogenesis of microorganisms. The two-dimensional blue native/SDS-PAGE was initially reported to analyze membrane protein complexes. In this study, both cytoplasmic and membrane complexes of a bacterium, the strain J99 of the gastric pathogen Helicobacter pylori, were analyzed by this method. It was possible to identify 34 different proteins grouped in 13 multiprotein complexes, 11 from the cytoplasm and two from the membrane, either previously reported partially or totally in the literature. Besides complexes involved in H. pylori physiology, this method allowed the description of interactions involving known pathogenic factors such as (i) urease with the heat shock protein GroEL or with the putative ketol-acid reductoisomerase IlvC and (ii) the cag pathogenicity island CagA protein with the DNA gyrase GyrA as well as insight on the partners of TsaA, a peroxide reductase/stress-dependent molecular chaperone. The two-dimensional blue native/SDS-PAGE combined with mass spectrometry is a potential tool to study the differences in complexes isolated in various situations and also to study the interactions between bacterial and eucaryotic cell proteins.

Analysis of differential protein expression in Acidithiobacillus ferrooxidans grown under different energy resources respectively using SELDI-ProteinChip technologies

Surface-enhanced laser desorption/ionization (SELDI)-time of flight is an affinity-based mass spectrometric method in which proteins of interest are selectively absorbed to a chemically modified surface on a chip, which allows proteomic analysis with limited material requirements. This characteristic makes it a valuable technique for microbiologists handling problematic samples, such as low cell number cultures. In this study, we explored differential-expressed proteome of Acidithiobacillus ferrooxidans cultivated with Fe(2+) and elemental sulfur separately by adopting the protein biochip SELDI approach. The cell lysates of A. ferrooxidans were applied onto Ciphergen ProteinChip WCX2, SAX2 and IMAC-Cu arrays. Proteins bound to the chips were analyzed on a ProteinChip Reader Model PBS II. A summary of the molecular masses of the differentially regulated proteins found on WCX2, IMAC-Cu and SAX2 was obtained and 28 differentially expressed proteins were found on the molecular weight range of 5.0 to 25 kDa.

Novel therapeutic targets in Helicobacter pylori

The failure of current regimens to treat the gastric pathogen Helicobacter pylori is a growing problem. Responsible for gastritis and peptic ulcer disease, and designated as a Class 1 carcinogen, its presence in up to 90% of the population of the developing world makes its treatment a primary concern. The use of genomic, proteomic and transcriptomic data to determine essential gene products as targets for novel therapeutic agents is of key interest in this research. This review describes how such data can be obtained, evaluated and eventually used as a basis for the development of both vaccine and novel anti-helicobacter agents. It indicates both past successes and possible new avenues to exploit the increased availability of such data, whilst also examining the limitations of such approaches.

Analysis of differential protein expression in Actinobacillus pleuropneumoniae by Surface Enhanced Laser Desorption Ionisation—ProteinChip™ (SELDI) technology

Actinobacillus pleuropneumoniae (APP) is the aetiological agent of porcine pleuropneumonia. An increased understanding of its molecular basis of pathogenicity and vaccine development will be facilitated by the availability of sequence data from a complete genome which, by analogy to other bacteria, is predicted to encode many proteins in the molecular mass range 3-20kDa. However, conventional techniques to study bacterial protein expression, such as SDS-PAGE and 2-dimensional electrophoresis, typically focus on the 15-200kDa range. In this study we have evaluated Surface Enhanced Laser Desorption Ionisation-ProteinChip (SELDI) technology for the analysis of protein expression, in particular those of <20kDa, of APP grown under different environmental conditions. Cytoplasmic/periplasmic and outer membrane protein fractions were obtained from the APP wildtype serotype 1 strain 4074 grown in Brain Heart Infusion (BHI) broth (+different concentrations of NAD), BHI containing pig serum or defined medium. Optimum conditions for SELDI profiles included a sample size of 1 microg and the use of sinapinic acid as the energy absorbing matrix. In the <20kDa range, the SELDI profiles obtained from wild-type bacteria grown in rich medium plus 33-66% pig serum were most similar to those grown in defined medium. The SELDI profiles of extracts of the wild-type and of an rpoE mutant were similar although there were clear differences. The results suggest that SELDI is a useful complementary approach to conventional proteomic analytical methods with APP, and presumably other bacterial pathogens, being particularly suited for analysis of proteins in the <20kDa mass range.

Helicobacter pylori and extragastric diseases -- other helicobacters

The role of Helicobacter pylori infection is explored in more and more extragastric diseases without definite proof in most of the studies, except possibly some hematologic diseases. In cardiovascular diseases, including stroke, the presence of CagA positive strains may be involved. The possible role of helicobacters in hepatobiliary diseases goes beyond that of H. pylori to involve enterohepatic helicobacters. New Helicobacter species are regularly described and molecular methods are developed to improve their detection. Helicobacter felis remains the major species to be used in animal models of Helicobacter infection.