Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Definition and characterization of the mitochondrial proteome of human cells (MitoCoP)

ABSTRACT: Aim of this project was the definition and characterization of the mitochondrial proteome of human cells, referred to as MitoCoP. To this end, we combined the complementary strengths of subtractive proteomics, ImportOmics and subcellular protein profiling in a global multidimensional classification approach. This multifaceted human mitochondria-centered analysis was expanded to a functional characterization of the mitochondrial proteome. The association of proteins with mitochondrial membranes was assessed by quantitative proteomic and single-protein studies. Protein copy numbers per mitochondrial unit were determined followed by a thorough compilation and functional classification of a high-quality human mitochondrial proteome. We further examined the organization of mitochondrial proteins in large functional assemblies by Blue Native (BN) complexome profiling and characterized functional protein networks of so far not described mitochondrial constituents by quantitative affinity purification mass spectrometry (q-AP-MS) and biochemical analysis. And finally, we systematically studied mitochondrial proteome dynamics and established a comprehensive subunit-resolved turnover map of large membrane protein machineries and central biosynthesis pathways of human mitochondria.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

SUBMITTER: Friedel Drepper

LAB HEAD: Bettina Warscheid

PROVIDER: PXD016924 | Pride | 2021-11-25

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ELITE-RSLC011436.raw	Raw
	ELITE-RSLC011437.raw	Raw
	ELITE-RSLC011438.raw	Raw
	ELITE-RSLC011439.raw	Raw
	ELITE-RSLC011440.raw	Raw

Items per page:

1 - 5 of 1254

Similar Datasets

Characterization of the mitochondrial proteome of human cells (MitoCoP)

Project description:The overall aim of the project is the definition and characterization of the mitochondrial proteome of human cells, referred to as MitoCoP. To this end, we combined the complementary strengths of subtractive proteomics, ImportOmics and subcellular protein profiling in a global multidimensional classification approach (see dataset PXD016924). In this part of the project, we (1) performed subtractive proteomics experiments of gradient-purified versus crude mitochondrial fractions prepared from multiple cell lines (multi-cell lines pM-vs-cM experiments), (2) studied the organization of mitochondrial proteins in large functional assemblies by Blue Native (BN) complexome profiling, and (3) analyzed the effect of LYRM9 knockout on mitochondrial protein complexes by BN-PAGE (LYRM9KO-vs-control experiment) to complement the characterization of MitoCoP.

2021-11-25 | PXD028149 | Pride

Definition of a high-confidence mitochondrial proteome at quantitative scale_pure versus crude mitochondria

Project description:Mitochondria perform central functions in cellular bioenergetics, metabolism and signaling and their malfunction has been linked to numerous diseases. The available studies cover only part of the mitochondrial proteome and a separation of core mitochondrial proteins from associated fractions has not been achieved. We developed an integrative, quantitative MS-based experimental approach to define the high confidence proteome of yeast mitochondria and to identify new mitochondrial proteins. The analysis includes protein abundance under fermentable and non-fermentable growth, submitochondrial localization, single-protein analysis and subcellular classification of mitochondria-associated fractions. We identified novel mitochondrial interactors of respiratory chain supercomplexes, ATP synthase, AAA proteases, the mitochondrial contact site and cristae organizing system (MICOS) and coenzyme Q biosynthesis cluster as well as new mitochondrial proteins with dual cellular localization. The integrative proteome provides a high confidence source for the characterization of physiological and pathophysiological functions of mitochondria and their integration into the cellular environment.

2017-06-29 | PXD006151 | Pride

The non-canonical mitochondrial inner membrane presequence translocase of trypanosomatids contains two essential rhomboid-like proteins

Project description:Mitochondrial protein import is essential for all eukaryotes. Here we show that the early diverging eukaryote Trypanosoma brucei has a non-canonical inner membrane (IM) protein translocation machinery. Besides TbTim17, the single member of the Tim17/22/23 family in trypanosomes, the presequence translocase contains nine subunits that co-purify in reciprocal immunoprecipitations and with a presequence-containing substrate that is trapped in the translocation channel. Two of the newly discovered subunits are rhomboid-like proteins, which are essential for growth and mitochondrial protein import. Rhomboid-like proteins were proposed to form the protein translocation pore of the ER-associated degradation system, suggesting that they may contribute to pore formation in the presequence translocase of T. brucei. Pulldown of import-arrested mitochondrial carrier protein shows that the carrier translocase shares eight subunits with the presequence translocase. This indicates that T. brucei may have a single IM translocase that with compositional variations mediates import of presequence-containing and carrier proteins.

2016-12-20 | PXD005484 | Pride

Release of a nuclear ubiquitin-like protein activates proteasomal degradation of mislocalized hydrophobic mitochondrial proteins in trypanosomes

Project description:Mitochondrial protein import in the parasitic protozoan Trypanosoma brucei is mediated by the atypical outer membrane translocase, ATOM. It consists of seven subunits including ATOM69, the import receptor for hydrophobic proteins. Ablation of ATOM69, but not of any other subunit, triggers a unique quality control pathway resulting in the proteasomal degradation of non-imported mitochondrial proteins. The process requires a protein of unknown function, an E3 ubiquitin ligase and the ubiquitin-like protein (TbUbL1), which all are recruited to the mitochondrion upon ATOM69 depletion. TbUbL1 is a nuclear protein, a fraction of which is released to the cytosol upon triggering of the pathway. Nuclear release is essential since cytosolic TbUbL1 can bind mislocalized mitochondrial proteins and likely transfers them to the proteasome. Mitochondrial quality control has previously been studied in yeast and metazoans. Finding such a pathway in the highly diverged trypanosomes suggests such pathways are an obligate feature of all mitochondria.

2022-05-04 | PXD027739 | Pride

Amplicons of a ND5 mRNA segment to detect m1A1374 levels in HEK APPwt and Ctl cells

Project description:This experiment was set up to quantify m1A methylation levels at position 1374 of the mitochondrial encoded ND5 mRNA. To investigate the relevance of this methylation in Alzheimer's disease two cell lines were compared. HEK APPwt cells, transfected with a plasmid encoding the wild-type Amyloid-Precursor-protein and untransfected control cells were used. In the first step a RT was performed with SuperScript-IV (SS-IV) and a ND5 specific RT primer. Afterwards a PCR was conducted to amplify the sequence around the m1A position. The amplicon is about 100 bp length and was sequenced in an Illumina Sequencing was performed in a MiSeq 2x75 PE run. For both cell lines the m1A analysis method was conducted with 4 biological replicates of total RNA and 2 biological replicates of RNA isolated from mitochondrial extracts.

2023-07-21 | E-MTAB-12033 | biostudies-arrayexpress

A technique to identify context-based protein biomarkers: Application to a mouse liver cancer model

Project description:To date, most proteomic analyses towards cancer biomarker discovery have been based on protein quantification. However, proteins function in association with other proteins to form modules that are localized in specific subcellular compartments. Cellular mislocalization of proteins has in fact been detected as a key feature in a variety of cancer cells1,2. Here, we describe a strategy for biomarker detection based on a mitochrondrial enrichment score (mtES), which is sensitive to protein abundance as well as protein translocation between mitochondria and cytosol. The mtES score integrates protein expression data from total cellular lysates and enriched mitochondrial fractions and provides important information for the classification of cancer samples, which is not apparent from conventional quantitative protein measurements. We apply the new strategy to a panel of wild-type and mutant mice that are either healthy or present liver cancer. We show that proteome changes based on mtES scores outperform protein abundance measurements in discriminating liver cancer from healthy liver tissue and that they are uniquely robust against strong genetic perturbation. Overall, our method provides a more sensitive approach to cancer biomarker discovery that takes into account contextual information of tested proteins.

2019-05-09 | PXD008758 | Pride

Definition and characterization of the mitochondrial proteome of human cells (MitoCoP): Relation between MS analysis time, sample fractionation, proteases, replicates and number of proteins identified/quantified

Project description:Aim of the overall project was the definition and characterization of the mitochondrial proteome of human cells, referred to as MitoCoP. To this end, we combined the complementary strengths of subtractive proteomics, ImportOmics and subcellular protein profiling in a global multidimensional classification approach. In this part of the project, we analyzed the correlation between MS analysis time, sample fractionation, use of multiple proteases and replicates on the number of proteins identified and quantified in mitochondrial fractions applying the subtractive proteomics approach.

2021-11-25 | PXD029242 | Pride

RNA-seq of total and polysomal RNA of clk-1(qm30) mutants in Caenorhabditis elegans

Project description:This study uses total and polysomal RNA-sequencing to show that the translational efficiencies of specific mRNAs change depending on the mitochondrial activity in longer-lived C. elegans.

2018-09-05 | E-MTAB-7166 | biostudies-arrayexpress

DNA-seq of mitochondrial DNA from mouse heart that is both heart SOD2 knockout and deficient for mitochondrial DNA repair

Project description:To study whether increase in mitochondrial oxidative stress (SOD2 removal) and decrease in mitochondrial DNA repair (Ogg1 dMTS) results into increase in mitochondrial DNA mutation load. Oxidative stress has been suggested to induce mutations in mtDNA. To verify this, we extracted and sequenced (Illumina) mitochondrial DNA from heart Sod2 knockout animals that were also deficient for mitochondrial base-excision repair. The repair deficiency was induced by removing the genomic region encoding for the predicted mitochondrial targeting sequence from endogenous OGG1 (L2 to W23) called Ogg1 dMTS mice, thus excluding the protein from mitochondria. OGG1 is a DNA glycosylase that recognizes and repairs 8-oxo-dG damage from DNA. Oxidative stress can induce 8-oxo-dG lesions, thus we removed the mitochondrial matrix localized superoxide dismutase (SOD2) from these mice to increase the level of oxidative stress. 8-oxo-dG lesion can be mutagenic because some DNA repair polymerases are known to erroneously incorporate adenosine opposite to 8-oxo-dG during replication leading to GC>TA transversion mutations.

2018-07-13 | E-MTAB-6533 | biostudies-arrayexpress

DNA-seq of mitochondrial DNA from liver of OGG1 and MUTYH deficient mice that have been bred for five consecutive generations

Project description:Studying whether removal of base-excision repair from mitochondria will result into increase in mitochondrial DNA (mtDNA) mutation load. The endogenous genes of OGG1 and MUTYH DNA glycosylases were modified to lack the genomic region encoding for the predicted mitochondrial targeting sequence. The mouse lines used: A mouse line that lacks the region encoding for the mitochondrial targeting sequence (L2 to W23) of OGG1 (Ogg1 dMTS mice). A mouse line that lacks the region encoding the mitochondrial targeting sequence (K2 to P33) of MUTYH (Mutyh dMTS mice). To accumulate mutations to the mitochondrial DNA these mice were bred double homozygous Mutyh dMTS x Ogg1 dMTS mice as a maternal lineage for five consecutive generations and mitochondrial DNA from liver was extracted from the offspring and sequenced with Illumina. OGG1 and MUTYH are involved in repair of 8-oxo-dG from DNA. 8-oxo-dG can be a mutagenic lesion because some DNA repair polymerases are known to erroneously incorporate adenosine opposite to 8-oxo-dG during replication leading to GC>TA transversion mutations.

2018-07-13 | E-MTAB-6532 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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