Browse
Submit Data
Databases
API
Help

Dataset Information

282 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Draft of the mitochondrial landscape, OM/IM

ABSTRACT: The mitochondrial subcompartment proteomes revealed by quantitative MS.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

TISSUE(S): Cell Culture

SUBMITTER: René Zahedi

LAB HEAD: René Zahedi

PROVIDER: PXD005463 | Pride | 2017-08-24

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Landscape of submitochondrial protein distribution.

Vögtle F-Nora FN Burkhart Julia M JM Gonczarowska-Jorge Humberto H Kücükköse Cansu C Taskin Asli Aras AA Kopczynski Dominik D Ahrends Robert R Mossmann Dirk D Sickmann Albert A Zahedi René P RP Meisinger Chris C

Nature communications 20170818 1

The mitochondrial proteome comprises ~1000 (yeast)-1500 (human) different proteins, which are distributed into four different subcompartments. The sublocalization of these proteins within the organelle in most cases remains poorly defined. Here we describe an integrated approach combining stable isotope labeling, various protein enrichment and extraction strategies and quantitative mass spectrometry to produce a quantitative map of submitochondrial protein distribution in S. cerevisiae. This qua ...[more]

PMID: 28819139

Similar Datasets

Draft of the mitochondrial landscape

Project description:The mitochondrial subcompartment proteomes revealed by quantitative MS.

2017-11-15 | PXD005541 | Pride

Towards biorecycling of polyurethanes: Strategies of Pseudomonas capeferrum TDA1 for extra- and intracellular degradation

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

Expression of Cell Cycle related genes in developing mouse cerebellum

Project description:The goal of the study was to analize expression of cell cycle related genes during postnatal development of Ts65Dn (Down syndrome mouse model) and control mice cerebellum. Keywords: Gene expression study in mouse model of disease RNA from 3 controls and 3 Ts65Dn postnatal day 2 cerebellum were analized on separate arrays.

2008-05-18 | E-GEOD-9216 | biostudies-arrayexpress

Proteins of outer membrane vesicles of Bordetella pertussis

Project description:proteome analysis OMV extracted from B. pertussis Tohama I wildtype

2023-05-03 | PXD033489 | Pride

Identification of immunoreactive proteins in murine sera after immunization with outer membrane vesicles isolated from Francisella tularensis subsp. holarctica strain FSC200

Project description:Secretion of outer membrane vesicles (OMV) presents an important phenomenon in Gram-negative bacteria and they play multiple roles in their lifestyle including virulence and host-pathogen interaction. Francisella tularensis secretes unusually shaped tubular OMV filled with immunoreactive material and virulence factors. Mice were immunized with OMV isolated from Francisella tularensis subsp. holarctica, fully virulent strain FSC200. Their sera were then used for detection of immunoreactive proteins.

2024-02-22 | PXD047830 | Pride

Large-Scale Analysis of Breast Cancer-Related Conformational Changes in Proteins using Limited Proteolysis

Project description:Conformational changes in proteins can lead to disease. Thus, methods for identifying conformational changes in proteins can further improve our understanding and facilitate detection of disease states. Here we combine limited proteolysis (LiP) with Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) to characterize breast cancer-related conformational changes in proteins on the proteomic scale. Studied here are the conformational properties of proteins in two cell culture models of breast cancer, including the MCF-10A and MCF-7 cell lines. The SILAC-LiP approach described here identified ~200 proteins with cell-line dependent conformational changes, as determined by their differential susceptibility to proteolytic digestion using the non-specific protease, proteinase K. The protease susceptibility profiles of the proteins in these cell lines were compared to thermodynamic stability and expression level profiles previously generated for proteins in these same breast cancer cell lines. The comparisons revealed that there was little overlap between the proteins with protease susceptibility changes and the proteins with thermodynamic stability and/or expression level changes. Thus, the large-scale conformational analysis described here provides unique insight into the molecular basis of the breast cancer phenotypes in this study.

2016-12-23 | PXD005210 | Pride

A landscape of mouse mitochondrial small non-coding RNAs

Project description:Small noncoding RNAs (ncRNAs), particularly miRNAs, play key roles in a plethora of biological processes both in health and disease. Although largely operative in the cytoplasm, emerging data indicate their shuttling in different subcellular compartments. Given the central role of mitochondria in cellular homeostasis, here we systematically profiled their small ncRNAs content across mouse tissues that largely rely on mitochondria functioning. The ubiquitous presence of piRNAs in mitochondria (mitopiRNA) of somatic tissues is reported for the first time, supporting the idea of a strong and general connection between mitochondria biology and piRNA pathways. Then, we found groups of tissue-shared and tissue-specific mitochondrial miRNAs (mitomiRs), potentially related to the “basic” or “cell context dependent” biology of mitochondria. Overall, this large data platform will be useful to deepen the knowledge about small ncRNAs processing and their governed regulatory networks contributing to mitochondria functions.

2023-09-01 | E-MTAB-12911 | biostudies-arrayexpress

Cardiac and Soleus muscles following exposure of rats to heat acclimation and exercise training

Project description:The processes of adaptation to environmental heat and aerobic exercise training improve efficiency in various body systems and bring about acclimatory homeostasis. In order to examine the global genomic responses of the soleus and heart following exposure of rats to these stressors, nylon cDNA Atlas Array was used. Male rats were exposed to one of the following stressors: heat acclimation, aerobic training (treadmill), and combined heat acclimation and aerobic training for short (2, 3 days) and long (1 mo) time period. The study comprised seven experimental groups: Controls-untreated. Heat acclimated groups (2dac, Acc)â exposure to environmental heat at 34C for 2 or 30 days. Exercise groups (3dex, Ex)â graduated training protocol under normothermic conditions for 3 and 30 days at 24C. Exercise training and heat acclimation â (3dexac, ExAc)- exposed to both environmental heat and aerobic exercise as above. The Series data tables appended below: 1) Heart - normalized log2 ratio of geomeans defined as treatment/control 2) Soleus - normalized log2 ratio of geomeans defined as treatment/control 21 samples, 3 pool each, of: 1)Â Control untreated rats 2)Â Long-term heat acclimated rats 3)Â Long-term aerobic-exercised trained rats. 4)Â Rats exposed to long-term heat acclimation and exercise training. 5)Â Short term heat acclimated rats. 6)Â Short term aerobic exercised trained rats 7)Â Rats exposed to short-term heat acclimation and exercise training.

2010-05-27 | E-GEOD-7799 | biostudies-arrayexpress

2DE images and LC-MS/MS of smooth and rough strains of Salmonella Gallinarum

Project description:Antigens of SG002, field isolated Salmonella Gallinarum in Korea, were tested against antiserum of SG002 and SR2-N6 (rough mutant of SG002) using 2DE western blotting. Different blots obtained were analyzed using LC-MS/MS. Outer membrane protein extracts of SR2-N6 were also tested against the antiserum of SR2-N6 using 2DE western blotting. Spots were analyzed with LC-MS/MS.

2020-10-20 | PXD022024 | Pride

Transcription profiling of human proximal tubular epithelial cells inclubated with 5% plasma from septic patients or healthy volunteers

Project description:proximal tubular epithelial cell apoptosis were incubated with 5% plasma of septic patients or healthy volunteers diluited in RPMI 1640

2008-03-15 | E-MEXP-1510 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data