Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization

By Shireen A. Sarraf, Malavika Raman, Virginia Guarani‐Pereira, M. Sowa, L. Edward, Huttlin, Steven P. Gygi, J. Harper. Nature, 2013

1,011 citations recorded by the source corpus.

The PARKIN ubiquitin ligase (also known as PARK2) and its regulatory kinase PINK1 (also known as PARK6), often mutated in familial early-onset Parkinson’s disease, have central roles in mitochondrial homeostasis and mitophagy. Whereas PARKIN is recruited to the mitochondrial outer membrane (MOM) upon depolarization via PINK1 action and can ubiquitylate porin, mitofusin and Miro proteins on the MOM, the full repertoire of PARKIN substrates—the PARKIN-dependent ubiquitylome—remains poorly defined. Here we use quantitative diGly capture proteomics (diGly) to elucidate the ubiquitylation site specificity and topology of PARKIN-dependent target modification in response to mitochondrial depolarization. Hundreds of dynamically regulated ubiquitylation sites in dozens of proteins were identified, with strong enrichment for MOM proteins, indicating that PARKIN dramatically alters the ubiquitylation status of the mitochondrial proteome. Using complementary interaction proteomics, we found depolarization-dependent PARKIN association with numerous MOM targets, autophagy receptors, and the proteasome. Mutation of the PARKIN active site residue C431, which has been found mutated in Parkinson’s disease patients, largely disrupts these associations. Structural and topological analysis revealed extensive conservation of PARKIN-dependent ubiquitylation sites on cytoplasmic domains in vertebrate and Drosophila melanogaster MOM proteins. These studies provide a resource for understanding how the PINK1–PARKIN pathway re-sculpts the proteome to support mitochondrial homeostasis.

Subfields: Epidemiology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/88aa784eb7905fda325f418566de8c1ba4464068

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Citations in the corpus

Prohibitin 2 Is an Inner Mitochondrial Membrane Mitophagy Receptor (2016, neutral): “PHB2 ubiquitination was also noted in proteomics analyses of mammalian cells undergoing Parkin-dependent mitophagy, although no validation studies were performed to assess whether it is a bona fide Parkin substrate (Bingol et al., 2014; Sarraf et al., 2013).”
Deciphering the Molecular Signals of PINK1/Parkin Mitophagy. (2016, background): “Five different autophagy receptors translocate to mitochondria during PINK1/Parkin mitophagy: Optineurin, nuclear dot protein 52 (NDP52), p62, neighbor of BRCA1 gene 1 (NBR1), and Tax1-binding protein 1 (TAX1BP1) [30,31].”
The PINK1-PARKIN mitochondrial ubiquitylation pathway drives a program of TBK1 activation and recruitment of OPTN and NDP52 to promote mitophagy (2015, methodology): “We previously identified eight major ubiquitylation sites in MFN2 (K406, K416, K420, K460, K719, K720, K730 and K737) (Sarraf et al., 2013), the replacement of which to arginine largely blocked PARKIN and PINK1-dependent MFN2 ubiquitylation (Figure 1A).”
Quantitative proteomics reveal a feed-forward model for mitochondrial PARKIN translocation and UB chain synthesis (2014, positive): “When PARKIN encounters activated PINK1 associated with the TOM complex on damaged mitochondria (Lazarou et al., 2012; Sarraf et al., 2013), it becomes phosphorylated on S65 (Figure 7E), leading to activation of its UB chain assembly function by more than 2,000-fold based on our quantitative…”
The BioGRID interaction database: 2015 update (2014, methodology): “In addition, we carried out the systematic annotation of ubiquitination sites detected by high-throughput mass-spectrometry-based approaches (64–66).”
Metabolic regulation of mitochondrial dynamics (2016, background): “Activated Parkin results in widespread ubiquitination of mitochondrial outer-membrane proteins, whose degradation by the 26S proteasome (Chan et al., 2011; Sarraf et al., 2013) is required for targeting of the mitochondrion to autophagic membranes.”