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A membrane protein complex mediates retro-translocation from the ER lumen into the cytosol

Abstract

Elimination of misfolded proteins from the endoplasmic reticulum (ER) by retro-translocation is an important physiological adaptation to ER stress. This process requires recognition of a substrate in the ER lumen and its subsequent movement through the membrane by the cytosolic p97 ATPase. Here we identify a p97-interacting membrane protein complex in the mammalian ER that links these two events. The central component of the complex, Derlin-1, is a homologue of Der1, a yeast protein whose inactivation prevents the elimination of misfolded luminal ER proteins. Derlin-1 associates with different substrates as they move through the membrane, and inactivation of Derlin-1 in C. elegans causes ER stress. Derlin-1 interacts with US11, a virally encoded ER protein that specifically targets MHC class I heavy chains for export from the ER, as well as with VIMP, a novel membrane protein that recruits the p97 ATPase and its cofactor.

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Figure 1: Identification of the Derlin-1/VIMP complex.
Figure 2: In vitro association of VIMP with p97 complexes.
Figure 3: VIMP mediates p97 binding to hDerlin-1.
Figure 4: Derlin-1/VIMP associates with MHC class I heavy chains and US11.
Figure 5: Derlin-1/VIMP associates with misfolded proteins and Derlin-1 depletion causes ER stress.
Figure 6: Model for US11-mediated retro-translocation of MHC class I heavy chains.

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References

  1. Ellgaard, L. & Helenius, A. ER quality control: towards an understanding at the molecular level. Curr. Opin. Cell Biol. 13, 431–437 (2001)

    Article  CAS  Google Scholar 

  2. Tsai, B., Ye, Y. & Rapoport, T. A. Retro-translocation of proteins from the endoplasmic reticulum into the cytosol. Nature Rev. Mol. Cell Biol. 3, 246–255 (2002)

    Article  CAS  Google Scholar 

  3. Wiertz, E. J. H. J. et al. The human cytomegalovirus US11 gene product dislocates MHC class I heavy chains from the endoplasmic reticulum to the cytosol. Cell 84, 769–779 (1996)

    Article  CAS  Google Scholar 

  4. Aridor, M. & Balch, W. E. Integration of endoplasmic reticulum signaling in health and disease. Nature Med. 5, 745–751 (1999)

    Article  CAS  Google Scholar 

  5. Meyer, H. H., Shorter, J. G., Seemann, J., Pappin, D. & Warren, G. A complex of mammalian ufd1 and npl4 links the AAA-ATPase, p97, to ubiquitin and nuclear transport pathways. EMBO J. 19, 2181–2192 (2000)

    Article  CAS  Google Scholar 

  6. Ye, Y., Meyer, H. H. & Rapoport, T. A. Function of the p97-Ufd1-Npl4 complex in retrotranslocation from the ER to the cytosol: dual recognition of nonubiquitinated polypeptide segments and polyubiquitin chains. J. Cell Biol. 162, 71–84 (2003)

    Article  CAS  Google Scholar 

  7. Langer, T. AAA proteases: cellular machines for degrading membrane proteins. Trends Biochem. Sci. 25, 247–251 (2000)

    Article  CAS  Google Scholar 

  8. Bays, N. W., Wilhovsky, S. K., Goradia, A., Hodgkiss-Harlow, K. & Hampton, R. Y. HRD4/NPL4 is required for the proteasomal processing of ubiquitinated ER proteins. Mol. Biol. Cell 12, 4114–4128 (2001)

    Article  CAS  Google Scholar 

  9. Ye, Y., Meyer, H. H. & Rapoport, T. A. The AAA ATPase Cdc48/p97 and its partners transport proteins from the ER into the cytosol. Nature 414, 652–656 (2001)

    Article  CAS  ADS  Google Scholar 

  10. Jarosch, E. et al. Protein dislocation from the ER requires polyubiquitination and the AAA-ATPase Cdc48. Nature Cell Biol. 4, 134–139 (2002)

    Article  CAS  Google Scholar 

  11. Rabinovich, E., Kerem, A., Frohlich, K. U., Diamant, N. & Bar-Nun, S. AAA-ATPase p97/Cdc48p, a cytosolic chaperone required for endoplasmic reticulum-associated protein degradation. Mol. Cell. Biol. 22, 626–634 (2002)

    Article  CAS  Google Scholar 

  12. Wang, Q. & Chang, A. Substrate recognition in ER-associated degradation mediated by Eps1, a member of the protein disulfide isomerase family. EMBO J. 22, 3792–3802 (2003)

    Article  CAS  Google Scholar 

  13. Story, C. M., Furman, M. H. & Ploegh, H. L. The cytosolic tail of class I MHC heavy chain is required for its dislocation by the human cytomegalovirus US2 and US11 gene products. Proc. Natl Acad. Sci. USA 96, 8516–8521 (1999)

    Article  CAS  ADS  Google Scholar 

  14. Gillece, P., Luz, J. M., Lennarz, W. J., de La Cruz, F. J. & Romisch, K. Export of a cysteine-free misfolded secretory protein from the endoplasmic reticulum for degradation requires interaction with protein disulfide isomerase. J. Cell Biol. 147, 1443–1456 (1999)

    Article  CAS  Google Scholar 

  15. Nishikawa, S. I., Fewell, S. W., Kato, Y., Brodsky, J. L. & Endo, T. Molecular chaperones in the yeast endoplasmic reticulum maintain the solubility of proteins for retrotranslocation and degradation. J. Cell Biol. 153, 1061–1070 (2001)

    Article  CAS  Google Scholar 

  16. Tsai, B., Rodighiero, C., Lencer, W. I. & Rapoport, T. A. Protein disulfide isomerase acts as a redox-dependent chaperone to unfold cholera toxin. Cell 104, 937–948 (2001)

    Article  CAS  Google Scholar 

  17. Molinari, M., Calanca, V., Galli, C., Lucca, P. & Paganetti, P. Role of EDEM in the release of misfolded glycoproteins from the calnexin cycle. Science 299, 1397–1400 (2003)

    Article  CAS  Google Scholar 

  18. Oda, Y., Hosokawa, N., Wada, I. & Nagata, K. EDEM as an acceptor of terminally misfolded glycoproteins released from calnexin. Science 299, 1394–1397 (2003)

    Article  CAS  Google Scholar 

  19. Knop, M., Finger, A., Braun, T., Hellmuth, K. & Wolf, D. H. Der1, a novel protein specifically required for endoplasmic reticulum degradation in yeast. EMBO J. 15, 753–763 (1996)

    Article  CAS  Google Scholar 

  20. Vashist, S. & Ng, D. T. Misfolded proteins are sorted by a sequential checkpoint mechanism of ER quality control. J. Cell Biol. 165, 41–52 (2004)

    Article  CAS  Google Scholar 

  21. Travers, K. J. et al. Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation. Cell 101, 249–258 (2000)

    Article  CAS  Google Scholar 

  22. Hitt, R. & Der Wolf, D. H. 1p, a protein required for degradation of malfolded soluble proteins of the endoplasmic reticulum: topology and Der1-like proteins. FEMS Yeast Res. 4, 721–729 (2004)

    Article  CAS  Google Scholar 

  23. Kryukov, G. V. et al. Characterization of mammalian selenoproteomes. Science 300, 1439–1443 (2003)

    Article  CAS  ADS  Google Scholar 

  24. DeLaBarre, B. & Brunger, A. T. Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains. Nature Struct. Biol. 10, 856–863 (2003)

    Article  CAS  Google Scholar 

  25. Flierman, D., Ye, Y., Dai, M., Chau, V. & Rapoport, T. A. Polyubiquitin serves as a recognition signal, rather than a ratcheting molecule, during retrotranslocation of proteins across the endoplasmic reticulum membrane. J. Biol. Chem. 278, 34774–34782 (2003)

    Article  CAS  Google Scholar 

  26. Wiertz, E. J. H. J. et al. Sec61-mediated transfer of a membrane protein from the endoplasmic reticulum to the proteasome for destruction. Nature 384, 432–438 (1996)

    Article  CAS  ADS  Google Scholar 

  27. Lilley, B. N., Tortorella, D. & Ploegh, H. L. Dislocation of a type I membrane protein requires interactions between membrane-spanning segments within the lipid bilayer. Mol. Biol. Cell 14, 3690–3698 (2003)

    Article  CAS  Google Scholar 

  28. Braakman, I., Helenius, J. & Helenius, A. Manipulating disulfide bond formation and protein folding in the endoplasmic reticulum. EMBO J. 11, 1717–1722 (1992)

    Article  CAS  Google Scholar 

  29. Calfon, M. et al. IRE1 couples endoplasmic reticulum load to secretory capacity by processing the XBP-1 mRNA. Nature 415, 92–96 (2002)

    Article  CAS  ADS  Google Scholar 

  30. Plemper, R. K. et al. Genetic interactions of Hrd3p and Der3p/Hrd1p with Sec61p suggest a retro-translocation complex mediating protein transport for ER degradation. J. Cell Sci. 112, 4123–4134 (1999)

    CAS  PubMed  Google Scholar 

  31. Gardner, R. G. et al. Endoplasmic reticulum degradation requires lumen to cytosol signaling. Transmembrane control of Hrd1p by Hrd3p. J. Cell Biol. 151, 69–82 (2000)

    Article  CAS  Google Scholar 

  32. Frand, A. R. & Kaiser, C. A. The ERO1 gene of yeast is required for oxidation of protein dithiols in the endoplasmic reticulum. Mol. Cell 1, 161–170 (1998)

    Article  CAS  Google Scholar 

  33. Pollard, M. G., Travers, K. J. & Weissman, J. S. Ero1p: a novel and ubiquitous protein with an essential role in oxidative protein folding in the endoplasmic reticulum. Mol. Cell 1, 171–182 (1998)

    Article  CAS  Google Scholar 

  34. Gao, Y. et al. Regulation of the selenoprotein SelS by glucose deprivation and endoplasmic reticulum stress—SelS is a novel glucose-regulated protein. FEBS Lett. 563, 185–190 (2004)

    Article  CAS  Google Scholar 

  35. Akiyama, Y. & Ito, K. Reconstitution of membrane proteolysis by FtsH. J. Biol. Chem. 278, 18146–18153 (2003)

    Article  CAS  Google Scholar 

  36. Timmons, L., Court, D. L. & Fire, A. Ingestion of bacterially expressed dsRNAs can produce specific and potent genetic interference in Caenorhabditis elegans. Gene 263, 103–112 (2001)

    Article  CAS  Google Scholar 

  37. Urano, F. et al. A survival pathway for Caenorhabditis elegans with a blocked unfolded protein response. J. Cell Biol. 158, 639–646 (2002)

    Article  CAS  Google Scholar 

  38. Harding, H. P. et al. An integrated stress response regulates amino acid metabolism and resistance to oxidative stress. Mol. Cell 11, 619–633 (2003)

    Article  CAS  Google Scholar 

  39. Shamu, C. E., Story, C. M., Rapoport, T. A. & Ploegh, H. L. The pathway of US11-dependent degradation of MHC class I heavy chains involves a ubiquitin-conjugated intermediate. J. Cell Biol. 147, 45–58 (1999)

    Article  CAS  Google Scholar 

  40. Lilley, B. N. & Ploegh, H. L. A membrane protein required for dislocation of misfolded proteins from the ER. Nature (this issue)

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Acknowledgements

We thank R. Prywes for ATF6 plasmid, the Taplin Mass Spectrometry facility (Harvard Medical School) for protein identification, and the Nikon imaging facility (Harvard Medical School) for assistance in microscopy. We thank E. Hartmann for help with sequence analysis, D. Flierman for help with the Derlin-1 immunoprecipitation, and C. Shamu, D. Finley and K. Cannon for critical reading of the manuscript. Y.Y. is supported by a Helen Hay Whitney fellowship and T.A.R. by an NIH grant. C.Y is supported by an NIH fellowship and D.R. by NIH grants and the Ellison Medical Foundation. T.A.R. is a Howard Hughes Medical Institute investigator.

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Correspondence to Tom A. Rapoport.

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The authors declare that they have no competing financial interests.

Supplementary information

Supplementary Figure S1

Phylogenetic analysis of Der1/Derlin family members. (JPG 60 kb)

Supplementary Figure S2

Amino acid sequence of VIMP. (DOC 19 kb)

Supplementary Figure S3

Specificity of the Derlin-1 and VIMP antibodies. (JPG 58 kb)

Supplementary Figure S4

VIMP associates with p97 in transfected cells. (JPG 64 kb)

Supplementary Figure S5

Gel filtration of the purified cytosolic domain of VIMP (VIMPc). (JPG 23 kb)

Supplementary Figure S6

US11 and Derlin-1 co-localize in transfected COS cells. (JPG 246 kb)

Supplementary Figure S7

Overexpression of VIMP alters ER morphology. (JPG 203 kb)

Supplementary Figure Legends (DOC 23 kb)

Supplementary Table 1

Identification of p97-interacting proteins (DOC 19 kb)

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Ye, Y., Shibata, Y., Yun, C. et al. A membrane protein complex mediates retro-translocation from the ER lumen into the cytosol. Nature 429, 841–847 (2004). https://doi.org/10.1038/nature02656

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