Table of Contents
International Journal of Proteomics
Volume 2013 (2013), Article ID 857918, 12 pages
http://dx.doi.org/10.1155/2013/857918
Research Article

A Novel Peptide-Based SILAC Method to Identify the Posttranslational Modifications Provides Evidence for Unconventional Ubiquitination in the ER-Associated Degradation Pathway

1Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3200, USA
2Department of Protein Chemistry, Genentech Inc., South San Francisco, CA 94080, USA

Received 6 September 2012; Accepted 13 December 2012

Academic Editor: Mu Wang

Copyright © 2013 Veronica G. Anania et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. B. Meusser, C. Hirsch, E. Jarosch, and T. Sommer, “ERAD: the long road to destruction,” Nature Cell Biology, vol. 7, no. 8, pp. 766–772, 2005. View at Publisher · View at Google Scholar · View at Scopus
  2. C. M. Pickart, “Mechanisms underlying ubiquitination,” Annual Review of Biochemistry, vol. 70, pp. 503–533, 2001. View at Publisher · View at Google Scholar · View at Scopus
  3. A. Mogk, R. Schmidt, and B. Bukau, “The N-end rule pathway for regulated proteolysis: prokaryotic and eukaryotic strategies,” Trends in Cell Biology, vol. 17, no. 4, pp. 165–172, 2007. View at Publisher · View at Google Scholar · View at Scopus
  4. K. Cadwell and L. Coscoy, “Biochemistry: ubiquitination on nonlysine residues by a viral E3 ubiquitin ligase,” Science, vol. 309, no. 5731, pp. 127–130, 2005. View at Publisher · View at Google Scholar · View at Scopus
  5. X. Wang, R. A. Herr, W. J. Chua, L. Lybarger, E. J. H. J. Wiertz, and T. H. Hansen, “Ubiquitination of serine, threonine, or lysine residues on the cytoplasmic tail can induce ERAD of MHC-I by viral E3 ligase mK3,” Journal of Cell Biology, vol. 177, no. 4, pp. 613–624, 2007. View at Publisher · View at Google Scholar · View at Scopus
  6. C. Williams, M. Van Den Berg, R. R. Sprenger, and B. Distel, “A conserved cysteine is essential for Pex4p-dependent ubiquitination of the peroxisomal import receptor Pex5p,” The Journal of Biological Chemistry, vol. 282, no. 31, pp. 22534–22543, 2007. View at Publisher · View at Google Scholar · View at Scopus
  7. S. W. G. Tait, E. De Vries, C. Maas, A. M. Keller, C. S. D'Santos, and J. Borst, “Apoptosis induction by Bid requires unconventional ubiquitination and degradation of its N-terminal fragment,” Journal of Cell Biology, vol. 179, no. 7, pp. 1453–1466, 2007. View at Publisher · View at Google Scholar · View at Scopus
  8. R. J. Deshaies and C. A. P. Joazeiro, “RING domain E3 ubiquitin ligases,” Annual Review of Biochemistry, vol. 78, pp. 399–434, 2009. View at Publisher · View at Google Scholar · View at Scopus
  9. H. Yu, G. Kaung, S. Kobayashi, and R. R. Kopito, “Cytosolic degradation of T-cell receptor α chains by the proteasome,” Journal of Biological Chemistry, vol. 272, no. 33, pp. 20800–20804, 1997. View at Publisher · View at Google Scholar · View at Scopus
  10. H. Yu and R. R. Kopito, “The role of multiubiquitination in dislocation and degradation of the α subunit of the T cell antigen receptor,” The Journal of Biological Chemistry, vol. 274, no. 52, pp. 36852–36858, 1999. View at Publisher · View at Google Scholar · View at Scopus
  11. S. Tiwari and A. M. Weissman, “Endoplasmic reticulum (ER)-associated degradation of T cell receptor subunits: involvement of ER-associated ubiquitin-conjugating enzymes (E2s),” The Journal of Biological Chemistry, vol. 276, no. 19, pp. 16193–16200, 2001. View at Publisher · View at Google Scholar · View at Scopus
  12. M. Kikkert, R. Doolman, M. Dai et al., “Human HRD1 Is an E3 ubiquitin ligase involved in degradation of proteins from the endoplasmic reticulum,” The Journal of Biological Chemistry, vol. 279, no. 5, pp. 3525–3534, 2004. View at Publisher · View at Google Scholar · View at Scopus
  13. Y. Shimizu, Y. Okuda-Shimizu, and L. M. Hendershot, “Ubiquitylation of an ERAD substrate occurs on multiple types of amino acids,” Molecular Cell, vol. 40, no. 6, pp. 917–926, 2010. View at Publisher · View at Google Scholar · View at Scopus
  14. S. Ishikura, A. M. Weissman, and J. S. Bonifacino, “Serine residues in the cytosolic tail of the T-cell antigen receptor α-chain mediate ubiquitination and endoplasmic reticulum-associated degradation of the unassembled protein,” The Journal of Biological Chemistry, vol. 285, no. 31, pp. 23916–23924, 2010. View at Publisher · View at Google Scholar · View at Scopus
  15. S. Tanner, H. Shu, A. Frank et al., “InsPecT: identification of posttranslationally modified peptides from tandem mass spectra,” Analytical Chemistry, vol. 77, no. 14, pp. 4626–4639, 2005. View at Publisher · View at Google Scholar · View at Scopus
  16. L. Phu, A. Izrael-Tomasevic, M. L. Matsumoto et al., “Improved quantitative mass spectrometry methods for characterizing complex ubiquitin signals,” Molecular & Cellular Proteomics, vol. 10, no. 5, Article ID M110.003756, 2011. View at Publisher · View at Google Scholar
  17. M. J. Eddins, C. M. Carlile, K. M. Gomez, C. M. Pickart, and C. Wolberger, “Mms2-Ubc13 covalently bound to ubiquitin reveals the structural basis of linkage-specific polyubiquitin chain formation,” Nature Structural and Molecular Biology, vol. 13, no. 10, pp. 915–920, 2006. View at Publisher · View at Google Scholar · View at Scopus
  18. D. S. Grenda, M. Murakami, J. Ghatak et al., “Mutations of the ELA2 gene found in patients with severe congenital neutropenia induce the unfolded protein response and cellular apoptosis,” Blood, vol. 110, no. 13, pp. 4179–4187, 2007. View at Publisher · View at Google Scholar · View at Scopus
  19. K. Cadwell and L. Coscoy, “The specificities of kaposi's sarcoma-associated herpesvirus-encoded E3 ubiquitin ligases are determined by the positions of lysine or cysteine residues within the intracytoplasmic domains of their targets,” Journal of Virology, vol. 82, no. 8, pp. 4184–4189, 2008. View at Publisher · View at Google Scholar · View at Scopus
  20. C. Soto, “Protein misfolding and disease; protein refolding and therapy,” FEBS Letters, vol. 498, no. 2-3, pp. 204–207, 2001. View at Publisher · View at Google Scholar · View at Scopus
  21. M. Horwitz, F. Q. Li, D. Albani et al., “Leukemia in severe congenital neutropenia: defective proteolysis suggests new pathways to malignancy and opportunities for therapy,” Cancer Investigation, vol. 21, no. 4, pp. 579–587, 2003. View at Publisher · View at Google Scholar · View at Scopus
  22. Y. Ichimura, T. Kirisako, T. Takao et al., “A ubiquitin-like system mediates protein lipidation,” Nature, vol. 408, no. 6811, pp. 488–492, 2000. View at Publisher · View at Google Scholar · View at Scopus