An unstructured initiation site is required for efficient proteasome-mediated degradation (original) (raw)

References

  1. Glickman, M.H. & Ciechanover, A. The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction. Physiol. Rev. 82, 373–428 (2002).
    Article CAS Google Scholar
  2. Baumeister, W., Walz, J., Zühl, F. & Seemüller, E. The proteasome: paradigm of a self-compartmentalizing protease. Cell 92, 367–380 (1998).
    Article CAS Google Scholar
  3. Groll, M. et al. Structure of 20S proteasome from yeast at 2.4 Å resolution. Nature 386, 463–471 (1997).
    Article CAS Google Scholar
  4. Groll, M. et al. A gated channel into the proteasome core particle. Nat. Struct. Biol. 7, 1062–1067 (2000).
    Article CAS Google Scholar
  5. Wenzel, T. & Baumeister, W. Conformational constraints in protein degradation by the 20S proteasome. Nat. Struct. Biol. 2, 199–204 (1995).
    Article CAS Google Scholar
  6. Johnston, J.A., Johnson, E.S., Waller, P.R.H. & Varshavsky, A. Methotrexate inhibits proteolysis of dihydrofolate reductase by the N-end rule pathway. J. Biol. Chem. 270, 8172–8178 (1995).
    Article CAS Google Scholar
  7. Deveraux, Q., Ustrell, V., Pickart, C. & Rechsteiner, M. A 26S protease subunit that binds ubiquitin conjugates. J. Biol. Chem. 269, 7059–7061 (1994).
    CAS PubMed Google Scholar
  8. Lam, Y.A., Lawson, T.G., Velayutham, M., Zweier, J.L. & Pickart, C.M. A proteasomal ATPase subunit recognizes the polyubiquitin degradation signal. Nature 416, 763–767 (2002).
    Article CAS Google Scholar
  9. Braun, B.C. et al. The base of the proteasome regulatory particle exhibits chaperone-like activity. Nat. Cell Biol. 1, 221–226 (1999).
    Article CAS Google Scholar
  10. Lee, C., Schwartz, M.P., Prakash, S., Iwakura, M. & Matouschek, A. ATP-dependent proteases degrade their substrates by processively unraveling them from the degradation signal. Mol. Cell 7, 627–637 (2001).
    Article CAS Google Scholar
  11. Kenniston, J.A., Baker, T.A., Fernandez, J.M. & Sauer, R.T. Linkage between ATP consumption and mechanical unfolding during the protein processing reactions of an AAA+ degradation machine. Cell 114, 511–520 (2003).
    Article CAS Google Scholar
  12. Breitschopf, K., Bengal, E., Ziv, T., Admon, A. & Ciechanover, A. A novel site for ubiquitination: the N-terminal residue, and not internal lysines of MyoD, is essential for conjugation and degradation of the protein. EMBO J. 17, 5964–5973 (1998).
    Article CAS Google Scholar
  13. Pickart, C.M. Mechanisms underlying ubiquitination. Annu. Rev. Biochem. 70, 503–533 (2001).
    Article CAS Google Scholar
  14. Thrower, J.S., Hoffman, L., Rechsteiner, M. & Pickart, C.M. Recognition of the polyubiquitin proteolytic signal. EMBO J. 19, 94–102 (2000).
    Article CAS Google Scholar
  15. Verma, R. et al. Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science 298, 611–615 (2002).
    Article CAS Google Scholar
  16. Petroski, M.D. & Deshaies, R.J. Context of multiubiquitin chain attachment influences the rate of Sic1 degradation. Mol. Cell 11, 1435–1444 (2003).
    Article CAS Google Scholar
  17. Hoskins, J.R., Yanagihara, K., Mizuuchi, K. & Wickner, S. ClpAP and ClpXP degrade proteins with tags located in the interior of the primary sequence. Proc. Natl. Acad. Sci. USA 99, 11037–11042 (2002).
    Article CAS Google Scholar
  18. Kihara, A., Akiyama, Y. & Ito, K. Dislocation of membrane proteins in FtsH-mediated proteolysis. EMBO J. 18, 2970–2981 (1999).
    Article CAS Google Scholar
  19. Reid, B.G., Fenton, W.A., Horwich, A.L. & Weber-Ban, E.U. ClpA mediates directional translocation of the substrate proteins into the ClpP protease. Proc. Natl. Acad. Sci. USA 98, 3768–3772 (2001).
    Article CAS Google Scholar
  20. Herman, C., Prakash, S., Lu, C.Z., Matouschek, A. & Gross, C.A. Lack of a robust unfoldase activity confers a unique level of substrate specificity to the universal AAA protease FtsH. Mol. Cell 11, 659–669 (2003).
    Article CAS Google Scholar
  21. Bachmair, A., Finley, D. & Varshavsky, A. In vivo half-life of a protein is a function of its amino-terminal residue. Science 234, 179–186 (1986).
    Article CAS Google Scholar
  22. Orian, A. et al. Structural motifs involved in ubiquitin-mediated processing of the NF-κB precursor p105: roles of the glycine-rich region and a downstream ubiquitination domain. Mol. Cell Biol. 19, 3664–3673 (1999).
    Article CAS Google Scholar
  23. Orlowski, M. & Wilk, S. Ubiquitin-independent proteolytic functions of the proteasome. Arch. Biochem. Biophys. 415, 1–5 (2003).
    Article CAS Google Scholar
  24. Flynn, J.M., Neher, S.B., Kim, Y.I., Sauer, R.T. & Baker, T.A. Proteomic discovery of cellular substrates of the ClpXP protease reveals five classes of ClpX-recognition signals. Mol. Cell 11, 671–683 (2003).
    Article CAS Google Scholar
  25. Uversky, V.N. What does it mean to be natively unfolded? Eur. J. Biochem. 269, 2–12 (2002).
    Article CAS Google Scholar
  26. Viitanen, P.V., Donaldson, G.K., Lorimer, G.H., Lubben, T.H. & Gatenby, A.A. Complex interactions between the chaperonin 60 molecular chaperone and dihydrofolate reductase. Biochemistry 30, 9716–9723 (1991).
    Article CAS Google Scholar
  27. Bachmair, A. & Varshavsky, A. The degradation signal in a short-lived protein. Cell 56, 1019–1032 (1989).
    Article CAS Google Scholar
  28. Stack, J.H., Whitney, M., Rodems, S.M. & Pollok, B.A. A ubiquitin-based tagging system for controlled modulation of protein stability. Nat. Biotechnol. 18, 1298–1302 (2000).
    Article CAS Google Scholar
  29. Liu, C.W., Corboy, M.J., DeMartino, G.N. & Thomas, P.J. Endoproteolytic activity of the proteasome. Science 299, 408–411 (2003).
    Article CAS Google Scholar
  30. Peng, J. et al. A proteomics approach to understanding protein ubiquitination. Nat. Biotechnol. 21, 921–926 (2003).
    Article CAS Google Scholar
  31. Scherer, D.C., Brockman, J.A., Chen, Z., Maniatis, T. & Ballard, D.W. Signal-induced degradation of IkBa requires site-specific ubiquitination. Proc. Natl. Acad. Sci. USA 92, 11259–11263 (1995).
    Article CAS Google Scholar
  32. Glotzer, M., Murray, A.W. & Kirschner, M.W. Cyclin is degraded by the ubiquitin pathway. Nature 349, 132–138 (1991).
    Article CAS Google Scholar
  33. Rodriguez, M.S., Desterro, J.M., Lain, S., Lane, D.P. & Hay, R.T. Multiple C-terminal lysine residues target p53 for ubiquitin-proteasome–mediated degradation. Mol. Cell Biol. 20, 8458–8467 (2000).
    Article CAS Google Scholar
  34. Hoppe, T. et al. Activation of a membrane-bound transcription factor by regulated ubiquitin/proteasome-dependent processing. Cell 102, 577–586 (2000).
    Article CAS Google Scholar
  35. Delagoutte, E. & von Hippel, P.H. Helicase mechanisms and the coupling of helicases within macromolecular machines. Part I: Structures and properties of isolated helicases. Q. Rev. Biophys. 35, 431–478 (2002).
    Article CAS Google Scholar
  36. Tsu, C.A., Kossen, K. & Uhlenbeck, O.C. The Escherichia coli DEAD protein DbpA recognizes a small RNA hairpin in 23S rRNA. RNA 7, 702–709 (2001).
    Article CAS Google Scholar
  37. Levchenko, I., Seidel, M., Sauer, R.T. & Baker, T.A. A specificity-enhancing factor for the ClpXP degradation machine. Science 289, 2354–2356 (2000).
    Article CAS Google Scholar
  38. Neher, S.B., Sauer, R.T. & Baker, T.A. Distinct peptide signals in the UmuD and UmuD′ subunits of UmuD/D′ mediate tethering and substrate processing by the ClpXP protease. Proc. Natl. Acad. Sci. USA 100, 13219–13224 (2003).
    Article CAS Google Scholar
  39. Elsasser, S. et al. Proteasome subunit Rpn1 binds ubiquitin-like protein domains. Nat. Cell Biol. 4, 725–730 (2002).
    Article CAS Google Scholar
  40. Alberti, S. et al. Ubiquitylation of BAG-1 suggests a novel regulatory mechanism during the sorting of chaperone substrates to the proteasome. J. Biol. Chem. 277, 45920–45927 (2002).
    Article CAS Google Scholar
  41. Rao, H. & Sastry, A. Recognition of specific ubiquitin conjugates is important for the proteolytic functions of the ubiquitin-associated domain proteins Dsk2 and Rad23. J. Biol. Chem. 277, 11691–11695 (2002).
    Article CAS Google Scholar
  42. Raasi, S. & Pickart, C.M. Rad23 ubiquitin-associated domains (UBA) inhibit 26S proteasome-catalyzed proteolysis by sequestering lysine 48–linked polyubiquitin chains. J. Biol. Chem. 278, 8951–8959 (2003).
    Article CAS Google Scholar
  43. Kleijnen, M.F., Alarcon, R.M. & Howley, P.M. The ubiquitin-associated domain of hPLIC-2 interacts with the proteasome. Mol. Biol. Cell 14, 3868–3875 (2003).
    Article CAS Google Scholar
  44. Bateman, A. et al. The Pfam protein families database. Nucleic Acids Res. 32 (Database issue), D138–D141 (2004).
    Article CAS Google Scholar
  45. Dai, R.M., Chen, E., Longo, D.L., Gorbea, C.M. & Li, C.C. Involvement of valosin-containing protein, an ATPase co-purified with IκBα and 26 S proteasome, in ubiquitin-proteasome–mediated degradation of IκBα. J. Biol. Chem. 273, 3562–3573 (1998).
    Article CAS Google Scholar
  46. Lam, Y.A., Xu, W., DeMartino, G.N. & Cohen, R.E. Editing of ubiquitin conjugates by an isopeptidase in the 26S proteasome. Nature 385, 737–740 (1997).
    Article CAS Google Scholar
  47. Leggett, D.S. et al. Multiple associated proteins regulate proteasome structure and function. Mol. Cell 10, 495–507 (2002).
    Article CAS Google Scholar
  48. Hartley, R.W. A two state conformational transition of the extracellular ribonuclease of Bacillus amyloliquefaciens (barnase) induced by sodium dodecyl sulfate. Biochemistry 14, 2367–2370 (1975).
    Article CAS Google Scholar
  49. Rood, J.I., Laird, A.J. & Williams, J.W. Cloning of the Escherichia coli K-12 dihydrofolate reductase gene following mu-mediated transposition. Gene 8, 255–265 (1980).
    Article CAS Google Scholar
  50. Iwakura, M., Nakamura, T., Yamane, C. & Maki, K. Systematic circular permutation of an entire protein reveals essential folding elements. Nat. Struct. Biol. 7, 580–585 (2000).
    Article CAS Google Scholar
  51. Varshavsky, A. The N-end rule. Cell 69, 725–735 (1992).
    Article CAS Google Scholar
  52. Matouschek, A. et al. Active unfolding of precursor proteins during mitochondrial protein import. EMBO J. 16, 6727–6736 (1997).
    Article CAS Google Scholar
  53. Gonda, D.K. et al. Universality and structure of the N-end rule. J. Biol. Chem. 264, 16700–16712 (1989).
    CAS PubMed Google Scholar
  54. Larsen, C.N. & Finley, D. Protein translocation channels in the proteasome and other proteases. Cell 91, 431–434 (1997).
    Article CAS Google Scholar

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