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A combined N-terminomics and shotgun proteomics approach to investigate the responses of human cells to rapamycin and zinc at the mitochondrial level

ABSTRACT: This study aims investigating the impact of rapamycin and zinc at subtoxic doses on the human mitochondrial proteome. Experiments were performed on U397 monocytic cells. A dN-TOP strategy, combining shotgun proteomics and N-terminomics, was applied to study both internal and N-terminal peptides of the mitochondrial proteins.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Monocyte, Cell Culture

SUBMITTER: Joanna Bons

LAB HEAD: Christine Carapito

PROVIDER: PXD010572 | Pride | 2019-05-14

REPOSITORIES: Pride

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			Action	DRS
	F012812.dat	Other
	F012812.pride.mgf.gz	Mgf
	F012812.pride.mztab.gz	Mztab
	F012812.xml.gz	Xml
	F012813.dat	Other

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Publications

A Combined N-terminomics and Shotgun Proteomics Approach to Investigate the Responses of Human Cells to Rapamycin and Zinc at the Mitochondrial Level.

Bons Joanna J Macron Charlotte C Aude-Garcia Catherine C Vaca-Jacome Sebastian Alvaro SA Rompais Magali M Cianférani Sarah S Carapito Christine C Rabilloud Thierry T

Molecular & cellular proteomics : MCP 20190315 6

All but thirteen mammalian mitochondrial proteins are encoded by the nuclear genome, translated in the cytosol and then imported into the mitochondria. For a significant proportion of the mitochondrial proteins, import is coupled with the cleavage of a presequence called the transit peptide, and the formation of a new N-terminus. Determination of the neo N-termini has been investigated by proteomic approaches in several systems, but generally in a static way to compile as many N-termini as possi ...[more]

PMID: 31154437

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A combined N-terminomics and shotgun proteomics approach to investigate the responses of human cells to rapamycin and zinc at the mitochondrial level

Project description:This study aims at investigating the impact of rapamycin and zinc at subtoxic doses on the human mitochondrial proteome. Experiments were performed on U397 monocytic cells. A dN-TOP strategy, combining shotgun proteomics and N-terminomics, was applied to study both internal and N-terminal peptides of the mitochondrial proteins.

2019-05-14 | PXD010220 | Pride

Human “free-N-terminome” analysis

Project description:The high throughput characterization of protein N-termini is becoming an emerging challenge in the proteomics and proteogenomics fields. The present study describes the N-terminal oriented analysis of human mitochondria enriched samples by the trimethoxyphenyl phosphonium (TMPP) labeling approach (N-TOP and dN-TOP approaches (Gallien et al, 2009, Bertaccini et al. 2013)). The dN-TOP strategy based on a double light/heavy TMPP labeling has been optimized in order to improve and automate the workflow for efficient, fast and reliable high throughput N-terminome analysis.

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Human “free-N-terminome” analysis

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Rhesus macaque cecal CD45+ leukocytes

Project description:10X transcriptomics + B cell V(D)J sequencing of CD45+ leukocytes

2024-04-30 | E-MTAB-13902 | biostudies-arrayexpress

In vivo proteolytic profiling of the type I and type II metacaspases in Chlamydomonas reinhardtii exposed to salt stress

Project description:Metacaspases are cysteine proteases present in plants, fungi and protists. While the association of metacaspases with cell death is studied in a range of organisms, their native substrates are largely unknown. Here, we explored the in vivo proteolytic landscape of the two metacaspases, CrMCA-I and CrMCA-II, present in the green freshwater alga Chlamydomonas reinhardtii, using N-terminal peptide labelling and enrichment during standard conditions and salt stress. Comparison between the cleavage events of CrMCA-I and CrMCA-II in metacaspase mutants revealed unique cleavage preferences and substrate specificity. Degradome analysis demonstrated relevance of the predicted metacaspase substrates to the physiology of Chlamydomonas reinhardtii cells and its adaptation during salt stress. Functional enrichment analysis indicated an involvement of CrMCA-I in photosynthesis and translation, while CrMCA-II seems to be important during the catabolism of carboxylic acids. Altogether, our findings suggest distinct cellular functions of the two metacaspases in C. reinhardtii during salt stress response.

2024-06-11 | PXD051835 | Pride

Translational microarray analysis of liver samples treated with PredTox hepatotoxic compound FP014SC

Project description:Liver samples were lysed (15 mM Tris-HCl (pH 8.0), 300 mM NaCl and 15 mM MgCl2, plus inhibitors (1 mg/ml heparin 100 Âµg/ml cycloheximide and 80 U RNAsin)), added to a 10-50% sucrose gradient and ultracentrifuged at 182,000x g for 2 hours. The gradient was aliquotted into 16 1ml fractions and added to Tri reagent (Sigma). RNA was extracted as per the manufacturer's instructions and then sub-pooled into fractions corresponding to monosomes, light polysomes, medium polysomes and heavy polysomes, according to ribosomal density (more ribosomal occupancy = higher translational activity = heavier, and therefore, located in the more dense fractions). Microarray analysis was performed by hybridising control (vehicle treated) monosomes against test (high-dose treated) monosomes on one microarray, control light polysomes against test light polysomes on a second microarray, and so forth for each sub-pool of fractions. Following microarray analysis there were a maximum of four values for each mRNA, corresponding to the proportional representation of that mRNA within each sub-pool of fractions. By calculating the change in values, i.e. degree of slope, across the monosomal region, the light polysomal region, the medium polysomal region and the dense polysomal region it was possible to determine any translational change in activity. In addition, the overall transcriptional change could be analysed for each mRNA. Dual colour microarrays performed on n = 3 samples, implementing a dye swap design. Control samples were treated with vehicle only. The treated samples had 1120mg/kg of the compound (Tetraethyl[(3-hydroxy-2-pyridyl)amino]-methanediphosphonate) for 15 days.

2012-06-20 | E-GEOD-38807 | biostudies-arrayexpress

Analysis of ageing-dependent thiol oxidation reveals early oxidation of proteins involved in core proteostasis functions

Project description:Oxidants have a profound impact on biological systems in physiology and under pathological conditions. Oxidative post-translational modifications of protein thiols are well-recognized as a readily occurring alteration of proteins. Changes in protein thiol redox state can modify the function of proteins and thus can control cellular processes. However, chronic oxidative stress causes oxidative damage to proteins with detrimental consequences for cellular function and organismal health. The development of techniques enabling the site-specific and quantitative assessment of protein thiol oxidation on a proteome-wide scale significantly expanded the number of known oxidation-sensitive protein thiols. However, lacking behind are large-scale data on the redox state of proteins during ageing, a physiological process accompanied by increased levels of endogenous oxidants. Here, we present the landscape of protein thiol oxidation in chronologically aged wild-type Saccharomyces cerevisiae in a time-dependent manner. Our data determine early oxidation targets in key biological processes governing the de novo production of proteins, folding, and protein degradation. Comparison to existing datasets reveals evolutionary conservation of early oxidation targets. To facilitate accessibility and cross-species comparison of the experimental data obtained, we created the OxiAge Database, a free online tool for the research community that integrates current datasets on thiol redoxomes in aged yeast, nematode Caenorhabditis elegans, fruit fly Drosophila melanogaster, and mouse Mus musculus.

2024-02-07 | PXD042047 | Pride

Gene expression profile of TRAIL-sensitive and -resistant H460 cells

Project description:We generated H460 cells with acquired TRAIL resistance by exposing the parental sentisitve cells to subtoxic concentrations of TRAIL for 6 months. Then we compared the gene expression profile of the sensitive versus the resistant cells. We generated acquired TRAIL-resistant H460 cells from the sentisitve cells by treating subtoxic range of TRAIL for 6 month. And we tried to compare the expressional profile of the genes between two cell types to isolate genes regulating acquired TRAIL-resistance H460 cells were treated with subtoxic concentrations of TRAIL for 6 month. After confirmation of the resistance, the RNA was extracted and the gene expression profile was analyzed.

2014-09-01 | E-GEOD-55859 | biostudies-arrayexpress

Gene expression profile of TRAIL-sensitive and -resistant H460 cells

2014-09-01 | GSE55859 | GEO