Article | Published:

USP30 and parkin homeostatically regulate atypical ubiquitin chains on mitochondria

Nature Cell Biology volume 17, pages 160169 (2015) | Download Citation

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.

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Acknowledgements

The authors wish to acknowledge C. Balakarski, A. Decker and W. Forrest for assistance with bioinformatic tools and statistical analyses, Y. Franke for assistance with construct design and creation and E. Dueber, J. Lill and D. Vucic for critical reading of the manuscript. PTMScan is carried out at Genentech under limited license from Cell Signaling Technologies.

Author information

Author notes

    • Joshua M. Baughman
    •  & Lilian Phu

    These authors contributed equally to this work.

    • Jacob E. Corn

    Present address: Innovative Genomics Initiative, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.

Affiliations

  1. Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA

    • Christian N. Cunningham
    •  & Jacob E. Corn
  2. Department of Protein Chemistry, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA

    • Joshua M. Baughman
    • , Lilian Phu
    •  & Donald S. Kirkpatrick
  3. Department of Neuroscience, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA

    • Joy S. Tea
    •  & Baris Bingol
  4. Department of Structural Biology, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA

    • Christine Yu
    •  & Mary Coons

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Contributions

C.N.C., J.M.B., L.P., J.S.T., B.B. and J.E.C. were responsible for the experimental work. C.N.C., D.S.K., B.B. and J.E.C. planned the project and designed the experiments. C.N.C., J.M.B., L.P., D.S.K., B.B. and J.E.C. analysed the data. C.Y. and M.C. provided materials and reagents. C.N.C. and J.E.C. wrote the manuscript with help from all authors.

Competing interests

The authors declare competing financial interests. C.N.C., J.M.B., L.P., C.Y., M.C., D.S.K. and B.B. are all employees of Genentech, Inc.

Corresponding authors

Correspondence to Donald S. Kirkpatrick or Baris Bingol or Jacob E. Corn.

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https://doi.org/10.1038/ncb3097

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