Defining the geometry of the two-component proteasome degron (original) (raw)

References

  1. Pickart, C.M. Back to the future with ubiquitin. Cell 116, 181–190 (2004).
    Article CAS Google Scholar
  2. Prakash, S., Tian, L., Ratliff, K.S., Lehotzky, R.E. & Matouschek, A. An unstructured initiation site is required for efficient proteasome-mediated degradation. Nat. Struct. Mol. Biol. 11, 830–837 (2004).
    Article CAS Google Scholar
  3. Takeuchi, J., Chen, H. & Coffino, P. Proteasome substrate degradation requires association plus extended peptide. EMBO J. 26, 123–131 (2007).
    Article CAS Google Scholar
  4. Schrader, E.K., Harstad, K.G. & Matouschek, A. Targeting proteins for degradation. Nat. Chem. Biol. 5, 815–822 (2009).
    Article CAS Google Scholar
  5. 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
  6. Deveraux, Q., Ustrell, V., Pickart, C. & Rechsteiner, M. A 26 S protease subunit that binds ubiquitin conjugates. J. Biol. Chem. 269, 7059–7061 (1994).
    CAS Google Scholar
  7. 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
  8. Husnjak, K. et al. Proteasome subunit Rpn13 is a novel ubiquitin receptor. Nature 453, 481–488 (2008).
    Article CAS Google Scholar
  9. Elsasser, S. & Finley, D. Delivery of ubiquitinated substrates to protein-unfolding machines. Nat. Cell Biol. 7, 742–749 (2005).
    Article CAS Google Scholar
  10. Finley, D. Recognition and processing of ubiquitin-protein conjugates by the proteasome. Annu. Rev. Biochem. 78, 477–513 (2009).
    Article CAS Google Scholar
  11. Hiyama, H. et al. Interaction of hHR23 with S5a. The ubiquitin-like domain of hHR23 mediates interaction with S5a subunit of 26 S proteasome. J. Biol. Chem. 274, 28019–28025 (1999).
    Article CAS Google Scholar
  12. Elsasser, S. et al. Proteasome subunit Rpn1 binds ubiquitin-like protein domains. Nat. Cell Biol. 4, 725–730 (2002).
    Article CAS Google Scholar
  13. Saeki, Y., Sone, T., Toh-e, A. & Yokosawa, H. Identification of ubiquitin-like protein-binding subunits of the 26S proteasome. Biochem. Biophys. Res. Commun. 296, 813–819 (2002).
    Article CAS Google Scholar
  14. Prakash, S., Inobe, T., Hatch, A.J. & Matouschek, A. Substrate selection by the proteasome during degradation of protein complexes. Nat. Chem. Biol. 5, 29–36 (2009).
    Article CAS Google Scholar
  15. Johnson, E.S., Gonda, D.K. & Varshavsky, A. _cis_-trans recognition and subunit-specific degradation of short-lived proteins. Nature 346, 287–291 (1990).
    Article CAS Google Scholar
  16. Hochstrasser, M. & Varshavsky, A. In vivo degradation of a transcriptional regulator: the yeast alpha 2 repressor. Cell 61, 697–708 (1990).
    Article CAS Google Scholar
  17. Klotzbücher, A., Stewart, E., Harrison, D. & Hunt, T. The 'destruction box' of cyclin A allows B-type cyclins to be ubiquitinated, but not efficiently destroyed. EMBO J. 15, 3053–3064 (1996).
    Article Google Scholar
  18. Verma, R., McDonald, H., Yates, J.R. & Deshaies, R.J. Selective degradation of ubiquitinated Sic1 by purified 26S proteasome yields active S phase cyclin-Cdk. Mol. Cell 8, 439–448 (2001).
    Article CAS Google Scholar
  19. 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
  20. Komander, D. et al. Molecular discrimination of structurally equivalent Lys 63-linked and linear polyubiquitin chains. EMBO Rep. 10, 466–473 (2009).
    Article CAS Google Scholar
  21. Saeki, Y. et al. Lysine 63-linked polyubiquitin chain may serve as a targeting signal for the 26S proteasome. EMBO J. 28, 359–371 (2009).
    Article CAS Google Scholar
  22. Watkins, J.F., Sung, P., Prakash, L. & Prakash, S. The Saccharomyces cerevisiae DNA repair gene RAD23 encodes a nuclear protein containing a ubiquitin-like domain required for biological function. Mol. Cell. Biol. 13, 7757–7765 (1993).
    Article CAS Google Scholar
  23. Schauber, C. et al. Rad23 links DNA repair to the ubiquitin/proteasome pathway. Nature 391, 715–718 (1998).
    Article CAS Google Scholar
  24. Johnston, J.A., Johnson, E.S., Waller, P.R. & 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
  25. Verhoef, L.G. et al. Minimal length requirement for proteasomal degradation of ubiquitin-dependent substrates. FASEB J. 23, 123–133 (2009).
    Article CAS Google Scholar
  26. Politou, A.S., Gautel, M., Pfuhl, M., Labeit, S. & Pastore, A. Immunoglobulin-type domains of titin: same fold, different stability? Biochemistry 33, 4730–4737 (1994).
    Article CAS Google Scholar
  27. Rief, M., Gautel, M., Oesterhelt, F., Fernandez, J.M. & Gaub, H.E. Reversible unfolding of individual titin immunoglobulin domains by AFM. Science 276, 1109–1112 (1997).
    Article CAS Google Scholar
  28. Improta, S., Politou, A.S. & Pastore, A. Immunoglobulin-like modules from titin I-band: extensible components of muscle elasticity. Structure 4, 323–337 (1996).
    Article CAS Google Scholar
  29. von Castelmur, E. et al. A regular pattern of Ig super-motifs defines segmental flexibility as the elastic mechanism of the titin chain. Proc. Natl. Acad. Sci. USA 105, 1186–1191 (2008).
    Article CAS Google Scholar
  30. Yang, T.T., Cheng, L. & Kain, S.R. Optimized codon usage and chromophore mutations provide enhanced sensitivity with the green fluorescent protein. Nucleic Acids Res. 24, 4592–4593 (1996).
    Article CAS Google Scholar
  31. Adams, S.R. et al. New biarsenical ligands and tetracysteine motifs for protein labeling in vitro and in vivo: synthesis and biological applications. J. Am. Chem. Soc. 124, 6063–6076 (2002).
    Article CAS Google Scholar
  32. Beskow, A. et al. A conserved unfoldase activity for the p97 AAA-ATPase in proteasomal degradation. J. Mol. Biol. 394, 732–746 (2009).
    Article CAS Google Scholar
  33. Tian, L., Holmgren, R.A. & Matouschek, A. A conserved processing mechanism regulates the activity of transcription factors Cubitus interruptus and NF-κB. Nat. Struct. Mol. Biol. 12, 1045–1053 (2005).
    Article CAS Google Scholar
  34. Larsen, C.N. & Finley, D. Protein translocation channels in the proteasome and other proteases. Cell 91, 431–434 (1997).
    Article CAS Google Scholar
  35. 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
  36. Keiler, K.C., Waller, P.R. & Sauer, R.T. Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science 271, 990–993 (1996).
    Article CAS Google Scholar
  37. Gottesman, S., Roche, E., Zhou, Y. & Sauer, R.T. The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system. Genes Dev. 12, 1338–1347 (1998).
    Article CAS Google Scholar
  38. 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
  39. Gonzalez, M., Frank, E.G., Levine, A.S. & Woodgate, R. Lon-mediated proteolysis of the Escherichia coli UmuD mutagenesis protein: in vitro degradation and identification of residues required for proteolysis. Genes Dev. 12, 3889–3899 (1998).
    Article CAS Google Scholar
  40. Yamada-Inagawa, T., Okuno, T., Karata, K., Yamanaka, K. & Ogura, T. Conserved pore residues in the AAA protease FtsH are important for proteolysis and its coupling to ATP hydrolysis. J. Biol. Chem. 278, 50182–50187 (2003).
    Article CAS Google Scholar
  41. Hinnerwisch, J., Fenton, W.A., Furtak, K.J., Farr, G.W. & Horwich, A.L. Loops in the central channel of ClpA chaperone mediate protein binding, unfolding, and translocation. Cell 121, 1029–1041 (2005).
    Article CAS Google Scholar
  42. Martin, A., Baker, T.A. & Sauer, R.T. Diverse pore loops of the AAA+ ClpX machine mediate unassisted and adaptor-dependent recognition of ssrA-tagged substrates. Mol. Cell 29, 441–450 (2008).
    Article CAS Google Scholar
  43. Zhang, F. et al. Mechanism of substrate unfolding and translocation by the regulatory particle of the proteasome from Methanocaldococcus jannaschii. Mol. Cell 34, 485–496 (2009).
    Article CAS Google Scholar
  44. Djuranovic, S. et al. Structure and activity of the N-terminal substrate recognition domains in proteasomal ATPases. Mol. Cell 34, 580–590 (2009).
    Article CAS Google Scholar
  45. Miller, W.G. & Goebel, C.V. Dimensions of protein random coils. Biochemistry 7, 3925–3935 (1968).
    Article CAS Google Scholar
  46. Heessen, S., Masucci, M.G. & Dantuma, N.P. The UBA2 domain functions as an intrinsic stabilization signal that protects Rad23 from proteasomal degradation. Mol. Cell 18, 225–235 (2005).
    Article CAS Google Scholar
  47. Levchenko, I., Grant, R.A., Flynn, J.M., Sauer, R.T. & Baker, T.A. Versatile modes of peptide recognition by the AAA+ adaptor protein SspB. Nat. Struct. Mol. Biol. 12, 520–525 (2005).
    Article CAS Google Scholar
  48. McGinness, K.E., Bolon, D.N., Kaganovich, M., Baker, T.A. & Sauer, R.T. Altered tethering of the SspB adaptor to the ClpXP protease causes changes in substrate delivery. J. Biol. Chem. 282, 11465–11473 (2007).
    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. Saeki, Y., Isono, E. & Toh-E, A. Preparation of ubiquitinated substrates by the PY motif-insertion method for monitoring 26S proteasome activity. Methods Enzymol. 399, 215–227 (2005).
    Article CAS Google Scholar

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