Proteomic network of antibiotic-induced outer membrane vesicles released by extensively drug-resistant Elizabethkingia anophelis
Ontology highlight
ABSTRACT:
INSTRUMENT(S): LTQ Orbitrap Elite
ORGANISM(S): Elizabethkingia Anophelis
TISSUE(S): Blood, Macrophage
DISEASE(S): Pneumonia
SUBMITTER: 
Ming-Hsien Chiang
LAB HEAD: Ming-Hsien Chiang
PROVIDER: PXD033858 | Pride | 2022-07-11
REPOSITORIES: Pride
Similar Datasets
Project description:This project aims to analyse the proteins of outer membrane vesicles (OMVs) released by a Serratia bacteria strain Su_YN1, which is isolated from field-caught mosquito gut. Su_YN1 produces massive OMVs under host serum induction. The data contain LC-MSMS results of the OMVs released without serum induction (WT-), and serum induced OMVs of WT strain (WT+) and several gene disruption strains (disruption of the ABC transporter genes ABC1 and ABC2). This project was conducted by CEMPS lab and Shanghai hoogen biotech co.ltd. The CEMPS lab prepared the purified OMV samples and Shanghai hoogen biotech co.ltd conducted the LC-MSMS analysis.
2023-08-02 | PXD042831 | Pride
Project description:The continuing reports of plastic pollution in various ecosystems highlight the threat posed by the ever-increasing consumption of synthetic polymers. Therefore, Pseudomonas capeferrum TDA1, a strain recently isolated from a plastic dump site, was examined further regarding its ability to degrade polyurethane (PU) compounds. The previously reported degradation pathway for 2,4-toluene diamine (2,4-TDA), a precursor and degradation intermediate of PU, could be confirmed by RNA-seq in this organism. In addition, different cell fractions of cells grown on a PU oligomer were tested for extracellular hydrolytic activity using a standard assay. Strikingly, purified outer membrane vesicles (OMV) of P. capeferrum TDA1 grown on a PU oligomer showed higher esterase activity than cell pellets. Hydrolases in the OMV fraction possibly involved in extracellular PU degradation were identified by mass spectrometry. On this basis, we propose a model for extracellular degradation of polyester-based PUs by P. capeferrum TDA1 involving the role of OMVs in synthetic polymer degradation.
2022-02-22 | PXD029164 | Pride
Project description:Francisella tularensis is a Gram-negative bacteria responsible for tularemia, a disease for which the high prevalence of failure and relapses is a main concern. Directed evolution experiments carried out in presence of antibiotics revealed that acquisition of fluoroquinolones (FQ) resistance was not exclusively related to mutations in DNA gyrase genes which are the first targets of these molecules. Here, using F. tularensis LVS as model, we investigated the role of FupA/B (Fer-Utilization Protein), whose possible contribution to FQ resistance was suggested by genomic analysis of resistant isolates. Using trans-complementation/mutagenesis approaches we definitely connected FupA/B expression to FQ sensitivity. Furthermore, we showed that the virulent strain F. tularensis subsp. tularensis SCHU S4, lacking the homologous FupA protein, exhibited a lower FQ susceptibility. Importantly, the deletion of this lipoprotein promoted an increased secretion of outer membrane vesicles (OMVs). Mass spectrometry-based quantitative proteomic characterization of OMVs from LVS and LVS-∆fupA/B strains led to the identification of 801 proteins among which a subset of 23 proteins exhibited a differential abundance between OMVs from both strains and may therefore contribute to the observed increased FQ susceptibility. We finally demonstrated that OMVs are structural key elements of F. tularensis LVS biofilms providing protection against FQ. Taken together, these results showed that mutations targeting FupA/B contribute to antimicrobial resistance through quantitative and qualitative modulations of OMV biogenesis and biofilm formation, providing new basis for understanding and fighting against Francisella antibiotic resistance and/or persistence.
2019-11-12 | PXD010305 | Pride
Project description:Aggregatibacter actinomycetemcomitans is an oral and systemic pathogen associated with aggressive forms of periodontitis, and with endocarditis. Outer membrane vesicles (OMVs) released by this species have been demonstrated to deliver effector proteins such as cytolethal distending toxin (CDT) and leukotoxin (LtxA) into human host cells, and to act as triggers of innate immunity upon carriage of NOD1- and NOD2-active pathogen-associated molecular patterns (PAMPs). To improve our understanding of the pathogenicity-associated functions that A. actinomycetemcomitans exports via OMVs, we have used liquid chromatography-tandem mass spectrometry (LC-MS/MS) to characterize the OMV-associated proteome of a rough-colony type clinical isolate, strain 173 (serotype e). This yielded identification of 151 proteins overlapping in three out of four independent experiments, using density gradient-purified OMVs. Further to confirming the vesicle-associated release of LtxA, and of several proteins earlier demonstrated to act as immunoreactive antigens in the human host, we identified numerous additional putative virulence-related proteins in the A. actinomycetemcomitans OMV proteome, including proteins involved in immune evasion, drug targeting, and iron/nutrient acquisition. In summary our findings are consistent with an OMV-associated proteome that exhibits several offensive and defensive functions, and they provide a comprehensive basis to further disclose roles of A. actinomycetemcomitans OMVs in periodontal and systemic disease.
2015-09-21 | PXD002509 | Pride
Project description:Glioblastoma (GBM) remains among the deadliest of human malignancies, and the emergence of the cancer stem cell (CSC) phenotype represents a major challenge to durable treatment response. Because the environmental and lifestyle factors that impact CSC populations are not clear, we sought to understand the consequences of diet on CSC enrichment. We evaluated disease progression in mice fed an obesity-inducing high-fat diet (HFD) versus a low-fat, control diet. HFD resulted in hyper-aggressive disease accompanied by CSC enrichment and shortened survival. HFD drove intracerebral accumulation of saturated fats, which inhibited the production of the cysteine metabolite and gasotransmitter, hydrogen sulfide (H2S). H2S functions principally through protein S-sulfhydration and regulates multiple programs including bioenergetics and metabolism. Inhibition of H2S increased proliferation and chemotherapy resistance, whereas treatment with H2S donors led to death of cultured GBM cells and stasis of GBM tumors in vivo. GBM specimens present an overall reduction in protein S-sulfhydration, primarily associated with proteins regulating cellular metabolism. These findings provide new evidence that diet modifiable H2S signaling serves to suppress GBM by restricting metabolic fitness, while its loss triggers CSC enrichment and disease acceleration. Interventions augmenting H2S bioavailability concurrent with GBM standard of care may improve outcomes for GBM patients.
2021-05-25 | PXD023685 | Pride
Project description:Large-scale production of bacterial extracellular vesicles is a hurdle for their development as novel cancer immunotherapeutic agents. Here, we developed manufacturing processes for mass production of Escherichia coli EVs known as outer membrane vesicles (OMVs). We present a comprehensive proteome of mass-produced E. coli OMVs.
2023-10-24 | PXD043119 | Pride
Project description:Number of publications show that intestinal microflora vesicles secretion is essential for the maintaining homeostasis. Conducted comprehensive genomic, transcriptomic and proteomic studies of vesicles determine the nature and the basic mechanisms of bacterial influence to the host. The role of the vesicles to a greater extent is defined as carriers of virulence factors or enzymes determining the nutritional function. In addition some bacterial vesicles have a special mission. B.fragilis vesicles are providing anti-inflammatory effect on the colon immune cells. However there is no information about possible role of vesicles secreted by ETBF, contributing bowel disease development and colon cancer. To determine possible effects of ETBF vesicles to the host compared with NTBF, we performed comprehensive proteome and for the first time metabolome analysis and reconstructed pathways for vesicles of both strains with subsequent confirmation of the activity of one of the main pathway by fluxome analysis. A detailed analysis of the vesicles allowed us to discover a new quality of ETBF vesicles as intelligent systems capable of absorbing and processing of exogenous substrates. We believe that this property allows them to maintain stability for a long time and implement mechanisms of pathogenicity.
2017-11-13 | PXD005255 | Pride
Project description:An important question for the use of the mouse as a model for studying human disease is the degree of functional conservation of genetic control pathways from human to mouse. The human and mouse placenta show structural similarities but there have been no systematic attempt to assess their molecular similarities or differences. We built a comprehensive database of protein and microarray data for the highly vascular exchange region micro-dissected from the human and mouse placenta near-term. Abnormalities in this region are associated with two of the most common and serious complications of human pregnancy, maternal preeclampsia (PE) and fetal intrauterine growth restriction (IUGR), each disorder affecting ~5% of all pregnancies. Over 7,000 orthologs were detected with 70% co-expressed and over 80% of genes known to cause placental phenotypes in mouse were co-expressed. These genes form a tight protein-protein interaction network with novel candidate genes likely to be important in placental structure and/or function. The entire data is available as a web-accessible database to guide the informed development of mouse models to study human disease This experiment is now fully represented in NCBI Peptidome database with accession PSE115; http://www.ncbi.nlm.nih.gov/peptidome/search/index.shtml?acc=PSE115 Microdissection of human villous trees and mouse placental labyrinth. Tissues were split for microarray and protein analysis. For protein analysis samples were first fractionated by differential sucrose gradients into mitochrondria, cytosol, microsomes and nuclei. Mitochrondira and neuclei were each extracted by two different methods for soluble and insoluble material. Each subcellular fraction for each tissue was analysed in quintuplet by 9 step 2 dimensional LC/MSMS. This generated a total of 270 mzXML files for each tissue.
2009-06-29 | E-GEOD-13299 | biostudies-arrayexpress
Project description:This study is the first to show transfer of regulatory bacterial sRNAs from bacterial OMVs to host cells. Demonstration of transfer of bacterial sRNA from Pseudomonas aeruginosa OMVs to host cells in two cell types. RNA isolated from PA14 OMV exposed primary human bronchial epithelial cells or CFBE41o- bronchial epithelial cells as well as unexposed control cells was analyzed by small RNA-Seq. Primary cell exposures were performed on two donors and exposures of CFBE41o- cells were done in triplicate.
2016-05-13 | E-GEOD-80421 | biostudies-arrayexpress
Project description:We present a functional characterisation of two members of the IDA-LIKE (IDL) peptide family in Arabidopsis thaliana, IDL6 and IDL7. They are processed both C- and N-terminally to produce active peptides. Structure analyses of synthesized IDL6 and IDL7 peptides indicate that they lack secondary structure elements. Localisation studies suggest that the peptides require a signal peptide and C-terminally processing to be correctly transported out of the cell. Treatment of plants with synthetic IDL6 and IDL7 peptides resulted in down-regulation of a broad range of stress-responsive genes, including early stress-responsive transcripts, dominated by a large group of ZINC FINGER PROTEINS (ZFPs), WRKYs and genes encoding calcium-dependent proteins. idl6 and idl7 mutants were more tolerant to salt, whereas the respective overexpression lines displayed increased sensitivity to both salt and oxidative stress. Taken together, our results suggest that the putative peptide ligands IDL6 and IDL7 act as suppressors of abiotic stress responses in Arabidopsis. Two weeks old seedlings were treated either with 100 nM IDL6 or IDL7 peptide (treated) or 100 nM mock peptide (control) and whole rosettes were harvested 2 hours after treatment. 4 biological replicaes per treatment. Two color microarray. Biological replicas are dye-swapped between slides.
2016-03-31 | E-GEOD-77467 | biostudies-arrayexpress