PXD002425-1

PXD002425 is an original dataset announced via ProteomeXchange.

Title	An impaired respiratory electron chain triggers down-regulation of the energy metabolism and de-ubiquitination of solute carrier amino acid transporters
Description	We integrated metabolome and proteome profiles of the parental cell line 143B.TK- versus ρ0, including PTM analyses such as phosphorylation and ubiquitination to characterize the impact of the absence of mtDNA for the entire cell. For quantitative proteome profiling, we used a shotgun LC-MS/MS approach including the classical SILAC labeling. For comprehensive metabolome profiling, we applied a targeted LC-MS approach, based on multiple reaction monitoring (MRM). Our study revealed that mtDNA depletion leads to a non-uniform down-regulation of the mitochondrial energy metabolism in ρ0 cells on the proteome level. Metabolites of the TCA cycle were highly dysregulated which in turn had an impact on the amino acid levels, which were up regulated. Perturbation of the mitochondrial energy metabolism could lead to an activation of the retrograde response, indicated by sets of up-regulated signaling pathways in ρ0 cells, further supported by altered phosphorylation in signaling pathways and the cytoskeleton as well as de-ubiquitination of SLC transporters.
HostingRepository	PRIDE
AnnounceDate	2016-02-08
AnnouncementXML	Submission_2016-02-08_08:37:37.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ina Gielisch
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; ubiquitination signature dipeptidyl lysine
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-06-25 01:40:25	ID requested
⏵ 1	2016-02-08 08:37:38	announced
2	2024-10-22 04:06:01	announced	2024-10-22: Updated project metadata.

Aretz I, Hardt C, Wittig I, Meierhofer D, An Impaired Respiratory Electron Chain Triggers Down-regulation of the Energy Metabolism and De-ubiquitination of Solute Carrier Amino Acid Transporters. Mol Cell Proteomics, 15(5):1526-38(2016) [pubmed]

curator keyword: Biomedical, Biological

submitter keyword: ρ0 cells, OXPHOS deficiency, metabolome profiling, proteome profiling, mass spectrometry, ubiquitination, retrograde response

David Meierhofer
contact affiliation	Max Planck Institute for Molecular Genetics, Ihnestrasse 63-72, 14195 Berlin, Germany
contact email	meierhof@molgen.mpg.de
lab head
Ina Gielisch
contact affiliation	MPIMG
contact email	gielisch@molgen.mpg.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/02/PXD002425

PRIDE project URI

• PRIDE
  1. PXD002425
     1. Label: PRIDE project
     2. Name: An impaired respiratory electron chain triggers down-regulation of the energy metabolism and de-ubiquitination of solute carrier amino acid transporters