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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 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.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Monocyte, Cell Culture

SUBMITTER: Joanna Bons

LAB HEAD: Christine CARAPITO

PROVIDER: PXD010220 | Pride | 2019-05-14

REPOSITORIES: Pride

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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

Similar Datasets

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 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 | PXD010572 | 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.

2015-06-02 | PXD001521 | Pride

Human “free-N-terminome” analysis

2015-06-02 | PXD001522 | Pride

Responses of macrophages to repeated exposures to different forms of amorphous silica

Project description:Synthetic amorphous silica (SAS) is a nanomaterial used in a wide variety of applications, including the use as a food additive. Two types of SAS are commonly employed as a powder additive, precipitated silica and fumed silica. Numerous studies have investigated the effects of synthetic amorphous silica on mammalian cells. However, most of them have used an exposure scheme based on a single dose of SAS. In this study, we have used instead a repeated 10-days exposure scheme, closer to the occupational exposure encountered in daily life. As a biological model we have used the murine macrophage cell line J774A.1, as macrophages are very important innate immune cells in the response to particulate materials. In order to get a better appraisal of the macrophage responses to this repeated exposure to SAS, we have used proteomics as a wide-scale approach. Furthermore, some of the biological pathways detected as modulated by the exposure to SAS by the proteomic experiments have been validated through targeted experiments. Overall, proteomics showed that precipitated SAS induced a more important macrophage response than fumed SAS at equal dose. Nevertheless, validation experiments showed that most of the responses detected by proteomics are indeed adaptive, as the cellular homeostasis appeared to be maintained at the end of the exposure. For example, the intracellular glutathione levels or the mitochondrial transmembrane potential at the end of the 10 days exposure were similar for SAS-exposed cells and for unexposed cells. Nevertheless, important functions of macrophages such as phagocytosis, TNF and interleukin-6 secretion were up-modulated after exposure, as was the expression of important membrane proteins such as the scavenger receptor or the MAC-1 receptor. These results suggest that repeated exposure to low doses of SAS slightly modulates the immune functions of macrophages, which may alter the homeostasis of the immune system.

2022-06-09 | PXD030002 | Pride

Effect of xenosiderophores on Pseudomonas aeruginosa proteome

Project description:P. aeruginosa was described to sense xenosiderophores in the extracellular environment, leading to a regulation of genes encoding the siderophore uptake proteins. Data presented here allowed to characterize the proteomic response of P. aeruginosa in presence of different xenosiderophores. PAO1 strain was grown under iron-starvation conditions with or without addition of xenosiderophores. Proteomic analyses were performed on bacterial lysates in biological triplicates.

2020-02-17 | PXD011950 | Pride

Identification of potential chemical signals in the European water vole Arvicola terrestris

Project description:The water vole Arvicola terrestris (= Arvicola amphibious L.) is endemic in Europe where its outbreak generates severe economic losses for farmers. Our project aimed at deciphering the modalities of chemical communication in this species, to develop new sustainable methods for populations control. The water vole, as well as other rodents, uses specific urination sites as territorial and sex pheromone markers, the chemical and biochemical identification of which is still unknown. Lateral scent glands and urine samples were collected from wild males and females caught in the field, at different periods of the year. Volatile signals were searched in urine by SPME/GC-MS, and in lateral scent glands by solvent extraction followed by GC-MS. The volatile composition of urine was analysed for each individual and not on pooled samples, showing no significant difference between males and females. Lateral scent glands contained some volatile components (pyrazines, alcohols, terpenes), and mostly long chain fatty acid esters, again without quantitative and qualitative differences between sexes. Conversely, the urinary protein content, analysed by 1D- and 2D-electrophoresis is different, as only males secrete high levels of lipocalins, whatever the reproduction period. The proteins were identified by mass spectrometry and “de novo” analysis (Orbitrap), which provided specific information to design primers for PCR amplification of cDNA sequences. Thus, urinary proteins were characterized by direct amplification from liver RNA. The identified protein sequences are closed to those of Myodes glareolus, a closely related species of Cricetidae, and to hamster Aphrodisin.

2019-12-11 | PXD013803 | Pride

Extended investigation of tube-gel sample preparation: a versatile and simple choice for high throughput quantitative proteomics

Project description:We investigated the compatibility of tube-gel with alternatives to SDS-based buffers allowing notably the extraction of proteins in various pH conditions. We also explored the use of photopolymerization to extend the number of possibilities, as it is compatible with a wide range of pH and is non-oxydative. To achieve this goal, we compared six extraction buffers in combination with two polymerization conditions to further optimize tube-gel protocol and evaluate its versatility.

2018-06-06 | PXD008656 | Pride

Effect of rapamycin on murine subcutaneous MC38 tumor cell populations

Project description:To determine differential metabolic gene expression in distinct cell populations from subcutaneous MC38 tumors at baseline and in response to rapamycin, tumors from mice treated with vehicle or rapamycin were harvested, reconstituted to single cell suspensions, and flow sorted into cancer cell (CD45-), tumor-associated macrophage (TAM, CD45+ CD11b+ Ly6G- Ly6C lo F4/80 hi), monocytic myeloid-derived suppressor cell (M-MDSC, CD45+ CD11b+ Ly6G- Ly6C hi), CD8 T cell (CD45+ CD3+ CD8a+), and CD4 T cell (CD45+ CD3+ CD8a-) populations. RNA was extracted and transcripts were quantified by the NanoString nCounter Metabolic Pathways Panel.

2021-02-26 | GSE165223 | GEO

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

MicroRNA expression profile in 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 microRNA expression profile in the sensitive versus resistant cells. H460 cells were treated with subtoxic concentrations of TRAIL for 6 month. After confirmation of the resistance, the RNA was extracted and the microRNA expression profile was analyzed using the NanoString technology.

2014-09-01 | E-GEOD-55821 | biostudies-arrayexpress

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