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Quantitative mass spectrometry to discover interactors of parkin E3 ubiquitin ligase, a protein implicated in early-onset Parkinson's disease Pu, Christopher Hao

Abstract

Ubiquitylation is a major post-translational modification based on a network of about six hundred E3 ubiquitin ligases in human. It is involved in several processes such as proteolysis, vesicle trafficking and DNA damage response. Mutations in PARK2, which encode parkin E3 ubiquitin ligase, account for half of autosomal recessive juvenile Parkinsonism cases, an early onset form of Parkinson’s disease. Multiple PARK2 mutations underlie the RING domain, which contains ligase activity. This finding suggests an inability for substrate ubiquitylation may trigger neurodegeneration. We used a quantitative proteomics approach to seek identifying parkin substrates and interactors. We first developed and tested new methods to enrich for ubiquitylated proteins that could potentially be used to study the influence of parkin on the ubiquitin proteome. In our first approach, ubiquitin conjugates were purified from SH-SY5Y neuroblastoma expressing His8-biotin-ubiquitin by tandem affinity purification. A second approach to purify ubiquitylated proteins was based on affinity chromatography using S5a proteasome receptor that bound to poly-ubiquitylated proteins. We determined that both approaches were not adequate for identifying low abundance parkin substrates. We then sought to identify which proteins were associated with parkin. Parkin interactors were enriched from SH-SY5Y expressing FLAG-parkin versus endogenous parkin by anti-FLAG immunoprecipitation in the context of SILAC. Proteins from the neuroendocrine chromogranin-secretogranin family were highly enriched suggesting a potential granin vesicle trafficking role for parkin. CCCP, a mitochondrial uncoupling agent was also employed to investigate parkin ligase interactors during mitochondrial stress since parkin localizes to mitochondria to promote mitophagy upon a reduction in mitochondrial membrane potential. Several actin related proteins were enriched from FLAG-parkin cells treated with CCCP including non-muscle unconventional signaling myosin suggesting a potential role for these proteins during parkin-mediated mitophagy.

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