PXD027586

PXD027586 is an original dataset announced via ProteomeXchange.

Title	Temporal Analysis of Protein Ubiquitylation and Phosphorylation During Parkin-dependent Mitophagy
Description	Mitophagy, the selective degradation of mitochondria by autophagy, affects defective mitochondria following damage or stress. At the onset of mitophagy, parkin ubiquitylates proteins on mitochondrial outer membrane (MOM). While the role of parkin at the onset of mitophagy is well understood, less is known about its activity during later stages of the process. Here we used HeLa cells expressing catalytically active or inactive parkin to perform temporal analysis of the proteome, ubiquitylome and phosphoproteome during 18 hours after induction of mitophagy by mitochondrial uncoupler CCCP. Abundance profiles of proteins downregulated in parkin-dependent manner revealed a stepwise, “outside-in” directed degradation of mitochondrial subcompartments. While ubiquitylation of MOM proteins was enriched among early parkin-dependent targets, numerous mitochondrial inner membrane, matrix and cytosolic proteins were also found ubiquitinated at later stages of mitophagy. Phosphoproteome analysis revealed a possible cross-talk between phosphorylation and ubiquitylation during mitophagy on several key parkin targets, such as VDAC1/2.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:52:55.342.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nicolas Nalpas
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	ubiquitinylated lysine; phosphorylated residue
Instrument	Q Exactive HF; Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-27 07:26:32	ID requested
1	2022-01-17 02:33:17	announced
⏵ 2	2023-11-14 08:52:55	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: Quantitative proteomics, Mitochondria, Mitophagy, Ubiquitin,Parkin

Prof. Dr. Boris Macek
contact affiliation	Chair, Quantitative Proteomics Director, Proteome Center Tuebingen Interfaculty Institute for Cell Biology University of Tuebingen Auf der Morgenstelle 15 72076 Tuebingen Germany
contact email	boris.macek@uni-tuebingen.de
lab head
Nicolas Nalpas
contact affiliation	Tuebingen University
contact email	nalpas.nicolas@gmail.com
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/2022/01/PXD027586

PRIDE project URI

• PRIDE
  1. PXD027586
     1. Label: PRIDE project
     2. Name: Temporal Analysis of Protein Ubiquitylation and Phosphorylation During Parkin-dependent Mitophagy