MudPIT analysis of released proteins in Pseudomonas aeruginosa laboratory and clinical strains in relation to pro-inflammatory effects.
ABSTRACT Pseudomonas aeruginosa (Pa) is the most common virulent pathogen contributing to the pathogenesis of cystic fibrosis (CF). During bacterial lung colonization, the products of its metabolism are released in the extracellular space contributing to the pathogenic events associated with its presence. To gain insights on the mechanisms involved in the Pa pathogenesis we focused our attention on proteins released by Pa using a MudPIT approach combined with cell biology assays. Conditioned medium (CM) collected under aerobic and microaerobic conditions from Pa clinical strains (in early and late colonization), unlike the laboratory strain, induced expression of IL-8 mRNA in CF airway epithelial cells. We have identified proteins released by clinically relevant Pa strains, focusing on the pro-inflammatory effects as metalloproteases (MMPs). In fact, their expression pattern was associated with the highest pro-inflammatory activity measured in the early clinically isolated strain. The relation was further supported by the result of the analysis of a larger and independent set of Pa isolates derived from sporadically and chronically infected CF patients: 76% of sporadic samples expressed protease activity (n = 44), while only 27% scored positive in the chronically infected individuals (n = 38, p < 0.0001, Fisher's exact test). Finally, looking for a possible mechanism of action of bacterial MMPs, we found that CM from early clinical isolates can cleave CXCR1 on the surface of human neutrophils, suggesting a potential role for the bacterially released MMPs in the protection of the pathogen from the host's response.
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ABSTRACT: BACKGROUND: Mass spectrometry is an important analytical tool for clinical proteomics. Primarily employed forbiomarker discovery, it is increasingly used for developing methods which may help to provideunambiguous diagnosis of biological samples. In this context, we investigated the classification ofphenotypes by applying support vector machine (SVM) on experimental data obtained by MudPITapproach. In particular, we compared the performance capabilities of SVM by using twoindependent collection of complex samples and different data-types, such as mass spectra (m/z), peptides and proteins. RESULTS: Globally, protein and peptide data allowed a better discriminant informative content thanexperimental mass spectra (overall accuracy higher than 87% in both collection 1 and 2). Theseresults indicate that sequencing of peptides and proteins reduces the experimental noise affecting theraw mass spectra, and allows the extraction of more informative features available for the effectiveclassification of samples. In addition, proteins and peptides features selected by SVM matched for80% with the differentially expressed proteins identified by the MAProMa software. CONCLUSIONS: These findings confirm the availability of the most label-free quantitative methods based onprocessing of spectral count and SEQUEST-based SCORE values. On the other hand, it stresses theusefulness of MudPIT data for a correct grouping of sample phenotypes, by applying bothsupervised and unsupervised learning algorithms. This capacity permit the evaluation of actualsamples and it is a good starting point to translate proteomic methodology to clinical application.Journal of clinical bioinformatics. 01/2013; 3(1):1.
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ABSTRACT: The halophyte Mesembryanthemum crystallinum adapts to salt stress by salt uptake and switching from C3 photosynthesis to Crassulacean Acid Metabolism (CAM). An important role in this process is played by transport proteins in the tonoplast of the central vacuole. Here we examine dynamic changes in protein composition during salt-stress adaptation in microsomes from M. crystallinum leaves. Plants challenged with 400 mM NaCl accumulate salt already at day 4 of treatment and malic acid only at day 12; a switching to CAM hence follows any initial steps of salt adaptation with a delay. With a label-free and semi-quantitative approach, we identified here the most dramatic changes between the proteome of control plants and plants harvested at 12 days of the treatment; the abundance of 14 proteins was significantly affected. The proteome data reveal the majority of subunits of the vacuolar H+-ATPase holoenzyme (V-ATPase). The salt treatment somewhat decreases the abundance of all subunits in the short-term (4 days). Long-term adaptation, including the switching to CAM, goes together with a strong increase in the representation of all detectable subunits. Because this increase is subunit-specific, with the highest rise occurring for subunits E and c, the data suggests that long-term adaptation to salt stress correlates with a change in V-ATPase subunit stoichiometry and point out the structural plasticity of this holoenzyme.Biochemical Journal 12/2012; · 4.65 Impact Factor