Quantitative proteomic analysis of Parkin substrates in Drosophila neurons.

TitleQuantitative proteomic analysis of Parkin substrates in Drosophila neurons.
Publication TypeJournal Article
Year of Publication2017
AuthorsMartinez, A, Lectez, B, Ramirez, J, Popp, O, Sutherland, JD, Urbé, S, Dittmar, G, Clague, MJ, Mayor, U
JournalMol Neurodegener
Volume12
Issue1
Pagination29
Date Published2017 04 11
ISSN1750-1326
KeywordsAnimals, Cell Line, Tumor, Drosophila melanogaster, Humans, Mitochondria, Mitochondrial Proteins, Mutation, Neuroblastoma, Neurons, Protein Kinases, Protein Transport, Proteomics, Substrate Specificity, Ubiquitin-Protein Ligases, Ubiquitination
Abstract

BACKGROUND: Parkin (PARK2) is an E3 ubiquitin ligase that is commonly mutated in Familial Parkinson's Disease (PD). In cell culture models, Parkin is recruited to acutely depolarised mitochondria by PINK1. PINK1 activates Parkin activity leading to ubiquitination of multiple proteins, which in turn promotes clearance of mitochondria by mitophagy. Many substrates have been identified using cell culture models in combination with depolarising drugs or proteasome inhibitors, but not in more physiological settings.

METHODS: Here we utilized the recently introduced BioUb strategy to isolate ubiquitinated proteins in flies. Following Parkin Wild-Type (WT) and Parkin Ligase dead (LD) expression we analysed by mass spectrometry and stringent bioinformatics analysis those proteins differentially ubiquitinated to provide the first survey of steady state Parkin substrates using an in vivo model. We further used an in vivo ubiquitination assay to validate one of those substrates in SH-SY5Y cells.

RESULTS: We identified 35 proteins that are more prominently ubiquitinated following Parkin over-expression. These include several mitochondrial proteins and a number of endosomal trafficking regulators such as v-ATPase sub-units, Syx5/STX5, ALiX/PDCD6IP and Vps4. We also identified the retromer component, Vps35, another PD-associated gene that has recently been shown to interact genetically with parkin. Importantly, we validated Parkin-dependent ubiquitination of VPS35 in human neuroblastoma cells.

CONCLUSIONS: Collectively our results provide new leads to the possible physiological functions of Parkin activity that are not overtly biased by acute mitochondrial depolarisation.

DOI10.1186/s13024-017-0170-3
Alternate JournalMol Neurodegener
Citation Key10.1186/s13024-017-0170-3
PubMed ID28399880
PubMed Central IDPMC5387213