Defining the geometry of the two-component proteasome degron

Nature Chemical Biology

Volumn 7, Issue 3, 2011, Pages 161-167

  Inobe, Tomonao ^a,c   Fishbain, Susan ^a,b   Prakash, Sumit ^a,b   Matouschek, Andreas ^a,b  

^a NORTHWESTERN UNIVERSITY   (United States)

^b NORTHWESTERN UNIVERSITY   (United States)

^c RIKEN BRAIN SCIENCE INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DIHYDROFOLATE REDUCTASE; POLYUBIQUITIN; PROTEASOME; UBIQUITIN;

ARTICLE; EUKARYOTE; GEOMETRY; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN DOMAIN;

EUKARYOTA;

EID: 79951850741     PISSN: 15524450     EISSN: 15524469     Source Type: Journal    
DOI: 10.1038/nchembio.521     Document Type: Article

References (50)

1. Pickart, C.M. Back to the future with ubiquitin. Cell 116, 181-190 (2004). (Pubitemid 38167311)
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). (Pubitemid 39128798)
3. Takeuchi, J., Chen, H. & Coffino, P. Proteasome substrate degradation requires association plus extended peptide. EMBO J. 26, 123-131 (2007). (Pubitemid 46094705)
4. Schrader, E.K., Harstad, K.G. & Matouschek, A. Targeting proteins for degradation. Nat. Chem. Biol. 5, 815-822 (2009).
5. Thrower, J.S., Hoffman, L., Rechsteiner, M. & Pickart, C.M. Recognition of the polyubiquitin proteolytic signal. EMBO J. 19, 94-102 (2000). (Pubitemid 30009229)
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). (Pubitemid 24217884)
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). (Pubitemid 34429155)
8. Husnjak, K. et al. Proteasome subunit Rpn13 is a novel ubiquitin receptor. Nature 453, 481-488 (2008). (Pubitemid 351733317)
9. Elsasser, S. & Finley, D. Delivery of ubiquitinated substrates to protein-unfolding machines. Nat. Cell Biol. 7, 742-749 (2005). (Pubitemid 41079042)
10. Finley, D. Recognition and processing of ubiquitin-protein conjugates by the proteasome. Annu. Rev. Biochem. 78, 477-513 (2009).
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).
12. Elsasser, S. et al. Proteasome subunit Rpn1 binds ubiquitin-like protein domains. Nat. Cell Biol. 4, 725-730 (2002). (Pubitemid 34993711)
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).
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).
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).
16. Hochstrasser, M. & Varshavsky, A. In vivo degradation of a transcriptional regulator: the yeast alpha 2 repressor. Cell 61, 697-708 (1990).
17. Klotzb'cher, 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). (Pubitemid 26187753)
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). (Pubitemid 32831560)
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).
20. Komander, D. et al. Molecular discrimination of structurally equivalent Lys 63-linked and linear polyubiquitin chains. EMBO Rep. 10, 466-473 (2009).
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).
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). (Pubitemid 23354300)
23. Schauber, C. et al. Rad23 links DNA repair to the ubiquitin/proteasome pathway. Nature 391, 715-718 (1998). (Pubitemid 28113221)
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).
25. Verhoef, L.G. et al. Minimal length requirement for proteasomal degradation of ubiquitin-dependent substrates. FASEB J. 23, 123-133 (2009).
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). (Pubitemid 24145124)
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). (Pubitemid 27218118)
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).
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). (Pubitemid 351397028)
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). (Pubitemid 26388650)
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). (Pubitemid 34552852)
32. Beskow, A. et al. A conserved unfoldase activity for the p97 AAA-ATPase in proteasomal degradation. J. Mol. Biol. 394, 732-746 (2009).
33. Tian, L., Holmgren, R.A. & Matouschek, A. A conserved processing mechanism regulates the activity of transcription factors Cubitus interruptus and NF-B. Nat. Struct. Mol. Biol. 12, 1045-1053 (2005). (Pubitemid 41746774)
34. Larsen, C.N. & Finley, D. Protein translocation channels in the proteasome and other proteases. Cell 91, 431-434 (1997). (Pubitemid 27508230)
35. Baumeister, W., Walz, J., Z'hl, F. & Seem'ller, E. The proteasome: paradigm of a self-compartmentalizing protease. Cell 92, 367-380 (1998). (Pubitemid 28093014)
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). (Pubitemid 26066397)
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). (Pubitemid 28213409)
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). (Pubitemid 36388762)
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). (Pubitemid 29024851)
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). (Pubitemid 37548857)
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). (Pubitemid 40894633)
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). (Pubitemid 351282539)
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).
44. Djuranovic, S. et al. Structure and activity of the N-terminal substrate recognition domains in proteasomal ATPases. Mol. Cell 34, 580-590 (2009).
45. Miller, W.G. & Goebel, C.V. Dimensions of protein random coils. Biochemistry 7, 3925-3935 (1968).
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).
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). (Pubitemid 43085882)
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). (Pubitemid 47100752)
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). (Pubitemid 10099889)
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). (Pubitemid 41772731)