Browse
Submit Data
Databases
API
Help

Dataset Information

433 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The zinc repository of Cupriavidus metallidurans

ABSTRACT: Zinc is a central player in the metalloproteomes of prokaryotes and eukaryotes. We used a top-down quantitative proteomic approach to reveal the repository of the zinc pools in the proteobacterium Cupriavidus metallidurans. About 60% of the theoretical proteome of C. metallidurans were identified, quantified, and compared between a ΔzupT mutant defect in zinc allocation and its parent strain. In both strains, the number of zinc-binding proteins and their binding sites exceeded that of the zinc ions per cell, indicating that the totality of the zinc proteome provides empty binding sites for incoming zinc ions. This zinc repository plays a central role in zinc homeostasis in C. metallidurans and probably also in other organisms.

INSTRUMENT(S): Synapt MS

ORGANISM(S): Cupriavidus Metallidurans

TISSUE(S): Prokaryotic Cell

SUBMITTER: Sacha Baginsky

LAB HEAD: Baginsky, Sacha

PROVIDER: PXD001356 | Pride | 2016-05-04

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	MH1_120917_001.raw.zip	Raw
	MH1_120917_001.zip	Other
	MH1_120917_003.raw.zip	Raw
	MH1_120917_003.zip	Other
	MH1_120917_004.raw.zip	Raw

Items per page:

1 - 5 of 84

Publications

The zinc repository of Cupriavidus metallidurans.

Herzberg Martin M Dobritzsch Dirk D Helm Stefan S Baginsky Sacha S Nies Dietrich H DH

Metallomics : integrated biometal science 20141101 11

Zinc is a central player in the metalloproteomes of prokaryotes and eukaryotes. We used a bottom-up quantitative proteomic approach to reveal the repository of the zinc pools in the proteobacterium Cupriavidus metallidurans. About 60% of the theoretical proteome of C. metallidurans was identified, quantified, and the defect in zinc allocation was compared between a ΔzupT mutant and its parent strain. In both strains, the number of zinc-binding proteins and their binding sites exceeded that of th ...[more]

PMID: 25315396

Similar Datasets

Mass spectrometry based quantitative proteome analyses for the import mutants ppi2 and tic56-1 as well as for spectinomycin treated Arabidopsis thalian plants

Project description:We acquired quantitative proteomics data from eight week old ppi2 and tic56-1 mutants as well as from wild type treated with 60 µg/ml spectinomycin and related them to their respective wildtype reference. Protein identification and quantification was performed by data-independent MSE acquisition on a Synapt G2S mass spectrometer (Waters). Quantification was based on the Hi3 method (Silva et al., 2006). Silva, J.C., Gorenstein, M.V., Li, G.Z., Vissers, J.P., and Geromanos, S.J. (2006). Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Molecular & cellular proteomics : MCP 5, 144-156.

2016-12-14 | PXD004125 | Pride

Fonsecaea pedrosoi response to zinc deprivation

Project description:Fungal diseases significantly impact human mortality and morbidity. However, despite the number of annual deaths caused by fungi exceeding 1.6 million, these microorganisms are often neglected. Fonsecaea pedrosoi is the main etiologic agent of chromoblastomycosis (CBM), a chronic mycosis that affects the skin and subcutaneous tissue that, in 2017, was included in the WHO list of neglected tropical diseases. It is essentially an occupational disease that affects individuals in poverty, causing significant morbidity and mortality. CBM is a disease of global distribution, and most cases are described in tropical and subtropical regions of America, Africa and Asia. Despite its importance in the etiology of the disease, the molecular mechanisms involved in the interaction of F. pedrosoi with the host are still poorly explored. During the infectious process, the host limits the availability of zinc to fungal pathogens in order to contain the infection, a process called nutritional immunity. In this work, we show that F. pedrosoi is able to grow in a wide range of zinc concentration and that genes related to zinc uptake are induced in zinc-limiting conditions. Proteomic analysis revealed that after 48 h of exposure to zinc scarcity synthesis of fatty acid and the pentose-phosphate pathway are up-regulated. On the other hand, protein synthesis is repressed. Additionally, glucan increases while chitin content is reduced in the cell wall under zinc limitation, demonstrating that cell wall remodeling is important for adaptation to this stress condition.

2024-01-29 | PXD048714 | Pride

Paenibacillus sp. GKG secreted proteins LC-MSMS

Project description:The advances of next-generation sequencing technologies enabled the continuous growth in the number of gene sequences deposited into the CAZy database, meanwhile, the number of biochemically characterized CAZymes is growing at a much slower rate. The biochemical characterization of discovered enzymes is important because of the industrially relevant properties such as high thermal stability or cold-adaptivity that these enzymes may possess. The aim of our project is to screen for up-to-date biochemically uncharacterized CAZymes. We screen for microorganisms that are able to produce extracellular CAZymes. We use LC-MSMS proteomics to identify extracellular enzymes produced by the selected microorganisms.

2022-10-20 | PXD036565 | Pride

Identification of YqfB enzyme expressed in colorectal cancer cell line HCT116 using LC-MS/MS proteomics

Project description:Gene-directed enzyme prodrug therapy is an emerging strategy for cancer treatment based on the delivery of a gene that encodes an enzyme that is able to convert a prodrug into a potent cytotoxin exclusively in target cancer cells. The aim of this study is to determine the capability of bacterial amidohydrolases to activate novel prodrugs and the effect such system has on the viability of eukaryotic cancer cells. HCT116 cancer cell line was subjected to LC-MS/MS proteomic analysis to confirm bacterial YqfB amidohydrolase expression at protein level.

2024-01-26 | PXD045918 | Pride

Marine Synechococcus sp. strain WH7803 shows specific adaptative responses to assimilate nanomolar concentrations of nitrate

Project description:Marine Synechococcus, together with Prochlorococcus, contribute to a significant proportion of the primary production on Earth. The spatial distribution of these two groups of marine picocyanobacteria depends on different factors such as nutrients availability or temperature. Some Synechococcus ecotypes thrive in mesotrophic and moderately oligotrophic waters, where they exploit both oxidized and reduced forms of nitrogen. Here, we present a comprehensive study, which includes transcriptomic and proteomic analyses of the response of Synechococcus sp. strain WH7803 to nanomolar concentrations of nitrate, compared to ammonium or nitrogen starvation. We found that Synechococcus has a specific response to nanomolar nitrate concentration that differs to the response showed under nitrogen starvation or the presence of standard concentrations of either ammonium or nitrate. This fact suggests that the particular response to the uptake of nanomolar concentration of nitrate could be an evolutionary advantage for marine Synechococcus against Prochlorococcus in the natural field.

2022-07-11 | PXD031142 | Pride

Bovine Longissimus thoracis muscle HDMSE with differents ultimate pH

Project description:The purpose of this research was to investigate the causes and consequences of pHu variations in beef cattle. For that, were evaluated 176 Nellore beef cattle, and classified into two different pHu groups: High (≥6.0, N=17) and Normal (<5.8, N=159). Plasma concentrations of cortisol and adrenocorticotropic hormone, lactate and glycogen muscular content, meat color, shear force and Longissimus thoracis muscle proteomic profile were evaluated and compared between pHu groups. Muscle glycogen content, meat color and shear force statistically differed between pHu groups. Label-free quantitative proteomic analysis revealed ten differentially abundant proteins between pHu groups, involved in metabolic processes and muscle contraction. Thirty-six and 31 proteins were exclusively present in Normal and High pHu group, respectively, which were related to TCA cycle, cortisol production, calcium regulation, and antioxidant function. The MYH7, UGP2, and VDAC3 were identified as potential indicators of pHu variations. CALM and NNT appeared to be interesting proteins to better understand the metabolic pathways behind pHu.

2018-07-11 | PXD009320 | Pride

Determination of allergen levels, isoforms and their hydroxyproline modifications among peanut genotypes by mass spectrometry

Project description:The recently published genome of peanut enables detailed molecular description of seed storage proteins, particularly allergens, which make up the peanut seed proteome. A detailed description of the allergenic proteome was produced using peanuts of different genetic backgrounds to increase the coverage of potentially expressed proteins and additionally allows for analysis of protein variability. Using relative quantification by mass spectrometry, minor variation of some allergenic proteins was observed but total levels of Ara h 1, 2, 3 and 6 were relatively consistent among genotypes. The isoform compositions of Ara h 1, 2 and 6 were similar. Three Ara h 3 isoforms were variable among genotypes and contributed to a large proportion of total Ara h 3 when present. The immunologically relevant amino acid modification hydroxyproline, previously thought to be present only on Ara h 2, was detected on Ara h 1 and 3 in consistent proportions given when the associated isoforms were present. The relevance of the data was evaluated in terms of food allergy regarding applications to reference materials, diagnostic and immunotherapeutic use, detection of peanuts in food, and risk assessment. The data can be used to design targeted mass spectrometry methods to permit analytical control of such materials.

2022-08-11 | PXD028086 | Pride

Fibrosis associated changes detected in the proteome of surface epithelium overlying Crohn’s Disease Strictures

Project description:Background and aims: Intestinal fibrosis is a common complication of Crohn’s disease (CD). It is characterised by an excessive accumulation of fibroblasts differentiating into activated myofibroblasts secreting excessive extracellular matrix. The potential role of the intestinal epithelium in this fibrotic process remains poorly defined. Methods: A total of 113 CD and control subjects were studied. We performed a pilot proteomic study comparing the proteome of surface epithelium isolated by laser capture microdissection in normal and fibrotic zones of resected ileal CD strictures (n=5). Selected proteins were validated by immunohistochemistry (IHC) in colonic and ileal samples of stricturing CD patients (n=44), pure inflammatory CD (n=29) and control subjects (n=40). Functional assays with cell lines cultures and a fibroblast to myofibroblast differentiation model were used to assess the role of the highlighted epithelial proteins in CD fibrosis. Results: Proteomic study revealed an endoplasmic reticulum (ER) stress and unfolded protein response (UPR) markers increase in the epithelium overlying ileal fibrotic strictures, involving Anterior gradient protein 2 homolog (AGR2) and Binding immunoglobulin protein (BiP). This was confirmed by IHC. The ER stress induction in intestinal epithelial cells increased AGR2 as well as BiP expression and led to an extracellular secreted AGR2. A fibroblast to myofibroblast differentiation was obtained with the supernatant of intestinal epithelial cells pre-conditioned by ER stress and with recombinant AGR2. Conclusions: AGR2 and other ER stress markers are increased within the intestinal epithelium overlying fibrotic strictures and might contribute to profibrotic signals involved in CD fibrosis.

2022-04-04 | PXD022214 | Pride

Direct and Absolute Quantification of over 1800 Yeast Proteins via Selected Reaction Monitoring HUB_MAN C4PR_LIV

Project description:Defining intracellular protein concentration is critical in molecular systems biology. Although strategies for determining relative protein changes are available, defining robust absolute values in copies per cell has proven significantly more challenging. Here we present a reference dataset quantifying over 1800 S. cerevisiae proteins by direct means using protein-specific stable-isotope labelled internal standards and selected reaction monitoring (SRM) mass spectrometry, far exceeding any previous study. This was achieved by careful design of over 100 QconCAT recombinant proteins as standards, defining 1167 proteins in terms of copies per cell and upper limits on a further 668, with robust CVs routinely less than 20%. The SRM-derived proteome is compared with existing quantitative data sets, highlighting the disparities between methodologies. Coupled with a quantification of the transcriptome by RNA-seq taken from the same cells, these data enable revised estimates of several fundamental molecular parameters: a total protein count of ~100 million molecules-per-cell, a median of ~1000 proteins-per-transcript, and a linear model of protein translation explaining 70% of the variance in translation rate. This work contributes a ‘gold-standard’ reference yeast proteome (including 531 proteins with high quality, dual peptide quantification) that can be widely used in systems models and for other comparative studies.

2015-12-11 | PXD002694 | Pride

Detection of Cell-Cell Interactions via Photocatalytic Cell Tagging

Project description:The growing appreciation of immune cell-cell interactions within disease environments has led to significant efforts to develop highly effective protein- and cell-based immunotherapies. However, characterizing these complex cell-cell interfaces in high resolution remains challenging. Thus, technologies that can leverage therapeutic-based modalities to profile intercellular environments offer the opportunity to study cell-cell interactions with molecular-level insight. To address this, we introduce Photocatalytic Cell Tagging (PhoTag), a platform for profiling cell-cell interactions utilizing a single domain antibody (VHH) conjugated to a photoactivatable flavin-based cofactor. Upon irradiation with visible light, the tethered flavin photocatalyst generates phenoxy radical tags for targeted labeling within cell-cell contact regions. Using anti-PD-1 or anti-PD-L1 VHH flavin conjugates, we demonstrate that PhoTag achieves highly selective synaptic labeling in antigen presenting cell-T cell co-culture systems. By combining the high resolution transcellular biotinylation capability of PhoTag with multi-omics single cell sequencing, we interrogated transient interactions between peripheral blood mononuclear cell (PBMC) populations and Raji PD-L1 B cells and discovered that specific T cell subtypes can transiently interact more efficiently than others. We envision that the spatiotemporal and modular nature of PhoTag will enable its broad utilization for detailed profiling of intercellular interactions across different biological systems.

2022-06-03 | PXD032203 | Pride