USP30 and parkin homeostatically regulate atypical ubiquitin chains on mitochondria

Christian N Cunningham; Joshua M Baughman; Lilian Phu; Joy S Tea; Christine Yu; Mary Coons; Donald S Kirkpatrick; Baris Bingol; Jacob E Corn

doi:10.1038/ncb3097

USP30 and parkin homeostatically regulate atypical ubiquitin chains on mitochondria

Nat Cell Biol. 2015 Feb;17(2):160-9. doi: 10.1038/ncb3097. Epub 2015 Jan 26.

Authors

Christian N Cunningham¹, Joshua M Baughman², Lilian Phu², Joy S Tea³, Christine Yu⁴, Mary Coons⁴, Donald S Kirkpatrick², Baris Bingol³, Jacob E Corn¹

Affiliations

¹ Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA.
² Department of Protein Chemistry, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA.
³ Department of Neuroscience, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA.
⁴ Department of Structural Biology, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA.

PMID: 25621951
DOI: 10.1038/ncb3097

Abstract

Multiple lines of evidence indicate that mitochondrial dysfunction is central to Parkinson's disease. Here we investigate the mechanism by which parkin, an E3 ubiquitin ligase, and USP30, a mitochondrion-localized deubiquitylase, regulate mitophagy. We find that mitochondrial damage stimulates parkin to assemble Lys 6, Lys 11 and Lys 63 chains on mitochondria, and that USP30 is a ubiquitin-specific deubiquitylase with a strong preference for cleaving Lys 6- and Lys 11-linked multimers. Using mass spectrometry, we show that recombinant USP30 preferentially removes these linkage types from intact ubiquitylated mitochondria and counteracts parkin-mediated ubiquitin chain formation in cells. These results, combined with a series of chimaera and localization studies, afford insights into the mechanism by which a balance of ubiquitylation and deubiquitylation regulates mitochondrial homeostasis, and suggest a general mechanism for organelle autophagy.

MeSH terms

Carbonyl Cyanide m-Chlorophenyl Hydrazone / pharmacology
Catalytic Domain
Cell Extracts
Gene Knockdown Techniques
Green Fluorescent Proteins / metabolism
HEK293 Cells
HeLa Cells
Homeostasis* / drug effects
Humans
Hydrogen-Ion Concentration / drug effects
Lysine / metabolism
Mass Spectrometry
Membrane Potential, Mitochondrial / drug effects
Mitochondria / drug effects
Mitochondria / metabolism*
Mitochondrial Proteins / chemistry
Mitochondrial Proteins / metabolism*
Mitophagy / drug effects
Models, Biological
Peroxisomes / drug effects
Peroxisomes / metabolism
Substrate Specificity / drug effects
Thiolester Hydrolases / chemistry
Thiolester Hydrolases / metabolism*
Ubiquitin / metabolism*
Ubiquitin-Protein Ligases / metabolism*
Ubiquitin-Specific Proteases / metabolism
Ubiquitination / drug effects

Substances

Cell Extracts
Mitochondrial Proteins
Ubiquitin
Usp30 protein, human
Green Fluorescent Proteins
Carbonyl Cyanide m-Chlorophenyl Hydrazone
Ubiquitin-Protein Ligases
parkin protein
Thiolester Hydrolases
Ubiquitin-Specific Proteases
Lysine