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

Sarraf, Shireen A., Raman, Malavika, Guarani-Pereira, Virginia, Sowa, Mathew E., Huttlin, Edward L., Gygi, Steven P., Harper, J. Wade·2013·Nature
DOI 10.1038/nature12043PMC PMC3641819
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Crossref · 10.1038/nature12043

Cites

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  • These chains appear to be conjugated to K27, K48, and K76 in the parkin Ubl domain.

    “These chains appear to be conjugated to K27, K48, and K76 in the parkin Ubl domain”

    From USP8 regulates mitophagy by removing K6‐linked ubiquitin conjugates from parkin (2014) · cites this paper as Sarraf et al, 2013

    The passage labeled Abstract (page unavailable) identifies K27 and K48 as regulated ubiquitylation sites in parkin’s UBL domain. Our copy does not identify K76 as a UBL ubiquitylation site or establish that the chains in the claim are conjugated at those sites. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

  • Parkin ubiquitinates a number of mitochondrial proteins in addition to ubiquitinating itself.

    “where it ubiquitinates a number of mitochondrial proteins (Chan et al, 2011;Sarraf et al, 2013), in addition to ubiquitinating itself (Matsuda et al, 2010;Lazarou et al, 2013).”

    From USP8 regulates mitophagy by removing K6‐linked ubiquitin conjugates from parkin (2014) · cites this paper as Sarraf et al, 2013

  • USP8 has little effect on the ubiquitination or stability of other known mitochondrial substrates of parkin.

    “Moreover, we find that USP8 preferentially removes K6-linked Ub conjugates from parkin but has little effect on the ubiquitination or stability of other known mitochondrial substrates of parkin.”

    From USP8 regulates mitophagy by removing K6‐linked ubiquitin conjugates from parkin (2014) · cites this paper as Sarraf et al, 2013

    The Abstract identifies mitochondrial substrates of PARKIN and describes their ubiquitylation, but it does not assess USP8’s effect on their ubiquitylation or stability. Searches for USP8 and the claimed effect returned no relevant passage in our copy. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

  • Following CCCP treatment, ubiquitination at K27, K48, and K76 and phosphorylation at S65 are identified by LC-MS/MS, all within the parkin Ubl domain.

    “Following treatment with CCCP, ubiquitination at three sites, K27, K48, and K76, and phosphorylation at S65 were identified by LC-MS/MS, all within the parkin Ubl domain (Fig 5B) and consistent with previous findings (Kondapalli et al, 2012;Sarraf et al, 2013).”

    From USP8 regulates mitophagy by removing K6‐linked ubiquitin conjugates from parkin (2014) · cites this paper as Sarraf et al, 2013

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Cites

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Research works printed but not linked: 26

  1. Narendra, D., Walker, J. E. & Youle, R. Mitochondrial quality control mediated by PINK1 and Parkin: links to parkinsonism. Cold Spring Harb. Perspect. Biol. 4, a011338 (2012) · DOI
  2. Dawson, T. M. & Dawson, V. L. The role of parkin in familial and sporadic Parkinson’s disease. Mov. Disord. 25 (Suppl 1). S32–S39 (2010) · DOI
  3. Chan, N. C. et al. Broad activation of the ubiquitin-proteasome system by Parkin is critical for mitophagy. Hum. Mol. Genet. 20, 1726–1737 (2011) · DOI · Paper page
  4. Glauser, L., Sonnay, S., Stafa, K. & Moore, D. J. Parkin promotes the ubiquitination and degradation of the mitochondrial fusion factor mitofusin 1. J. Neurochem. 118, 636–645 (2011) · DOI · Paper page
  5. Ziviani, E., Tao, R. N. & Whitworth, A. J. Drosophila parkin requires PINK1 for mitochondrial translocation and ubiquitinates mitofusin. Proc. Natl Acad. Sci. USA 107, 5018–5023 (2010) · DOI · Paper page
  6. Sun, Y., Vashisht, A. A., Tchieu, J., Wohlschlegel, J. A. & Dreier, L. VDACs recruit Parkin to defective mitochondria to promote mitochondrial autophagy. J. Biol. Chem. 287, 40652–40660 (2012) · DOI
  7. Wang, X. et al. PINK1 and Parkin target Miro for phosphorylation and degradation to arrest mitochondrial motility. Cell 147, 893–906 (2011) · DOI
  8. Kim, W. et al. Systematic and quantitative assessment of the ubiquitin-modified proteome. Mol. Cell 44, 325–340 (2011) · DOI
  9. Wagner, S. A. et al. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Mol. Cell Proteomics 10, M111.013284 (2011) · DOI
  10. Wenzel, D. M., Lissounov, A., Brzovic, P. S. & Klevit, R. E. UbcH7-reactivity profile reveals Parkin and HHARI to be RING/HECT hybrids. Nature 474, 105–108 (2011) · DOI
  11. Joselin, A. P. et al. ROS-dependent regulation of Parkin and DJ-1 localization during oxidative stress in neurons. Hum. Mol. Genet. 21, 4888–4903 (2012) · DOI
  12. Lazarou, M., Jin, S. M., Kane, L. A. & Youle, R. J. Role of PINK1 binding to the TOM complex and alternate intracellular membranes in recruitment and activation of the E3 ligase Parkin. Dev. Cell 22, 320–333 (2012) · DOI · Paper page
  13. Kondapalli, C. et al. PINK1 is activated by mitochondrial membrane potential depolarization and stimulates Parkin E3 ligase activity by phosphorylating Serine 65. Open Biol. 2, 120080 (2012) · DOI · Paper page
  14. Sha, D., Chin, L. S. & Li, L. Phosphorylation of parkin by Parkinson disease-linked kinase PINK1 activates parkin E3 ligase function and NF-κB signaling. Hum. Mol. Genet. 19, 352–363 (2010) · DOI
  15. Lazarou, M. et al. PINK1 drives Parkin self-association and HECT-like E3 activity upstream of mitochondrial binding. J. Cell Biol. 200, 163–172 (2013) · DOI · Paper page
  16. Sowa, M. E., Bennett, E. J., Gygi, S. P. & Harper, J. W. Defining the human deubiquitinating enzyme interaction landscape. Cell 138, 389–403 (2009) · DOI
  17. Chaugule, V. K. et al. Autoregulation of Parkin activity through its ubiquitin-like domain. EMBO J. 30, 2853–2867 (2011) · DOI · Paper page
  18. Narendra, D., Kane, L. A., Hauser, D. N., Fearnley, I. M. & Youle, R. J. p62/SQSTM1 is required for Parkin-induced mitochondrial clustering but not mitophagy; VDAC1 is dispensable for both. Autophagy 6, 1090–1106 (2010) · DOI
  19. Onoue, K. et al. Fis1 acts as mitochondrial recruitment factor for TBC1D15 that is involved in regulation of mitochondrial morphology. J. Cell Sci.. http://dx.doi.org/10.1242/jcs.111211 (2012) · DOI
  20. von Muhlinen, N. et al. LC3C, bound selectively by a noncanonical LIR motif in NDP52, is required for antibacterial autophagy. Mol. Cell 48, 329–342 (2012) · DOI · Paper page
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Cited by

Sorted by citations

Authors
Sarraf, S. A., Raman, M., Guarani-Pereira, V., Sowa, M. E., Huttlin, E. L., Gygi, S. P., & Harper, J. W.
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2013-03-17
Volume
496
Issue
7445
Pages
372-376
ISSN
  • 0028-0836
  • 1476-4687
DOI
10.1038/nature12043
PMC
PMC3641819
Cited by
1,010
References
7
Language
en
Licence
www.springer.com/tdm (tdm)

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