Crossref journal-article
American Society for Cell Biology (ASCB)
Molecular Biology of the Cell (1076)
Abstract

The mechanism underlying the delivery of ubiquitylated substrates to the proteasome is poorly understood. Rad23 is a putative adaptor molecule for this process because it interacts with ubiquitin chains through its ubiquitin-associated motifs (UBA) and with the proteasome through a ubiquitin-like element (UBL). Here, we demonstrate that the UBL motif of Rad23 also binds Ufd2, an E4 enzyme essential for ubiquitin chain assembly onto its substrates. Mutations in the UBL of Rad23 alter its interactions with Ufd2 and the proteasome, and impair its function in the UFD proteolytic pathway. Furthermore, Ufd2 and the proteasome subunit Rpn1 compete for the binding of Rad23, suggesting that Rad23 forms separate complexes with them. Importantly, we also find that the ability of other UBL/UBA proteins to associate with Ufd2 correlates with their differential involvement in the UFD pathway, suggesting that UBL-mediated interactions may contribute to the substrate specificity of these adaptors. We propose that the UBL motif, a protein-protein interaction module, may be used to facilitate coupling between substrate ubiquitylation and delivery, and to ensure the orderly handoff of the substrate from the ubiquitylation machinery to the proteasome.

Bibliography

Kim, I., Mi, K., & Rao, H. (2004). Multiple Interactions of Rad23 Suggest a Mechanism for Ubiquitylated Substrate Delivery Important in Proteolysis. Molecular Biology of the Cell, 15(7), 3357–3365.

Authors 3
  1. Ikjin Kim (first)
  2. Kaixia Mi (additional)
  3. Hai Rao (additional)
References 41 Referenced 139
  1. Baumeister, W., Walz, J., Zühl, F., and Seemüller, E. (1998). The proteasome: paradigm of a self-compartmentalizing protease.Cell92, 367-380. (10.1016/S0092-8674(00)80929-0)
  2. Bertolaet, B.L., Clarke, D.J., Wolff, M., Watson, M.H., Henze, M., Divita, G., and Reed, S.I. (2001). UBA domains of DNA damage-inducible proteins interact with ubiquitin.Nat. Struct. Biol.8, 417-422. (10.1038/87575)
  3. Biggins, S., Ivanovska, I., and Rose, M.D. (1996). Yeast ubiquitin-like genes are involved in duplication of the microtubule organizing center.J. Cell Biol.133, 1331-1346. (10.1083/jcb.133.6.1331)
  4. Chen, L., and Madura, K. (2002). Rad23 promotes the targeting of proteolytic substrates to the proteasome.Mol. Cell. Biol.22, 4902-4913. (10.1128/MCB.22.13.4902-4913.2002)
  5. DeMartino, G.N., and Slaughter, C.A. (1999). The proteasome, a novel protease regulated by multiple mechanisms.J. Biol. Chem.274, 22123-22126. (10.1074/jbc.274.32.22123)
  6. Elsasser, S., Gali, R.R., Schwickart, M., Larsen, C.N., Leggett, D.S., Muller, B., Feng, M.T., Tubing, F., Dittmar, G.A., and Finley, D. (2002). Proteasome subunit Rpn1 binds ubiquitin-like protein domains.Nat. Cell Biol.4, 725-730. (10.1038/ncb845)
  7. Finley, D. (2001). Signal transduction. An alternative to destruction.Nature412,283, 285-286.
  8. Gasser, T. (1998). Genetics of Parkinson's disease.Clin. Genet54, 259-265. (10.1034/j.1399-0004.1998.5440401.x)
  9. Gillette, T.G., Huang, W., Russell, S.J., Reed, S.H., Johnston, S.A., and Friedberg, E.C. (2001). The 19S complex of the proteasome regulates nucleotide excision repair in yeast.Genes Dev.15, 1528-1539. (10.1101/gad.869601)
  10. Glickman, M.H., Rubin, D.M., Fried, V.A., and Finley, D. (1998). The regulatory particle of the Saccharomyces cerevisiae proteasome.Mol. Cell. Biol.18, 3149-3162. (10.1128/MCB.18.6.3149)
  11. Gottesman, S., Wickner, S., and Maurizi, M.R. (1997). Protein quality control: triage by chaperones and proteases.Genes Dev.11, 815-823. (10.1101/gad.11.7.815)
  12. Grossman, S.R., Deato, M.E., Brignone, C., Chan, H.M., Kung, A.L., Tagami, H., Nakatani, Y., and Livingston, D.M. (2003). Polyubiquitination of p53 by a ubiquitin ligase activity of p300.Science300, 342-344. (10.1126/science.1080386)
  13. Ho, Y.et al. (2002). Systematic identification of protein complexes inSaccharomyces cerevisiaeby mass spectrometry.Nature415, 180-183. (10.1038/415180a)
  14. Hofmann, R.M., and Pickart, C.M. (2001). In vitro assembly and recognition of Lys-63 polyubiquitin chains.J. Biol. Chem.276, 27936-27943. (10.1074/jbc.M103378200)
  15. Johnson, E.S., Ma, P.C.M., Ota, I.M., and Varshavsky, A. (1995). A proteolytic pathway that recognizes ubiquitin as a degradation Signal.J. Biol. Chem.270, 17442-17456. (10.1074/jbc.270.29.17442)
  16. Kleijnen, M.F., Shih, A.H., Zhou, P., Kumar, S., Soccio, R.E., Kedersha, N.L., Gill, G., and Howley, P.M. (2000). The hPLIC proteins may provide a link between the ubiquitination machinery and the proteasome.Mol. Cell.6, 409-419. (10.1016/S1097-2765(00)00040-X)
  17. Koegl, M., Hoppe, T., Schlenker, S., Ulrich, H.D., Mayer, T.U., and Jentsch, S. (1999). A novel ubiquitination factor, E4, is involved in multiubiquitin chain assembly.Cell96, 635-644. (10.1016/S0092-8674(00)80574-7)
  18. Krona, C., Ejeskar, K., Abel, F., Kogner, P., Bjelke, J., Bjork, E., Sjoberg, R.M., and Martinsson, T. (2003). Screening for gene mutations in a 500 kb neuroblastoma tumor suppressor candidate region in chromosome 1p; mutation and stage-specific expression in UBE4B/UFD2.Oncogene22, 2343-2351. (10.1038/sj.onc.1206324)
  19. Lam, Y.A., Lawson, T.G., Velayutham, M., Zweier, J.L., and Pickart, C.M. (2002). A proteasomal ATPase subunit recognizes the polyubiquitin degradation signal.Nature416, 763-767. (10.1038/416763a)
  20. Lambertson, D., Chen, L., and Madura, K. (1999). Pleiotropic defects caused by loss of the proteasome-interacting factors Rad23 and Rpn10 ofSaccharomyces cerevisiae.Genetics153, 69-79. (10.1093/genetics/153.1.69)
  21. Levchenko, I., Grant, R.A., Wah, D.A., Sauer, R.T., and Baker, T.A. (2003). Structure of a delivery protein for an AAA+ protease in complex with a peptide degradation tag.Mol. Cell.12, 365-372. (10.1016/j.molcel.2003.08.014)
  22. Lindsten, K., de Vrij, F.M., Verhoef, L.G., Fischer, D.F., van Leeuwen, F.W., Hol, E.M., Masucci, M.G., and Dantuma, N.P. (2002). Mutant ubiquitin found in neurodegenerative disorders is a ubiquitin fusion degradation substrate that blocks proteasomal degradation.J. Cell Biol.157, 417-427. (10.1083/jcb.200111034)
  23. Lustgarten, V., and Gerst, J.E. (1999). Yeast VSM1 encodes a v-SNARE binding protein that may act as a negative regulator of constitutive exocytosis.Mol. Cell. Biol.19, 4480-4494. (10.1128/MCB.19.6.4480)
  24. Matsumoto, M., Yada, M., Hatakeyama, S., Ishimoto, H., Tanimura, T., Tsuji, S., Kakizuka, A., Kitagawa, M., and Nakayama, K.I. (2004). Molecular clearance of ataxin-3 is regulated by a mammalian E4.EMBO J.23, 659-669. (10.1038/sj.emboj.7600081)
  25. Mumberg, D., Muller, R., and Funk, M. (1994). Regulatable promoters ofSaccharomyces cerevisiae—comparison of transcriptional activity and their use for heterologous expression.Nucleic Acids Res.22, 5767-5768. (10.1093/nar/22.25.5767)
  26. Pickart, C.M. (2001). Mechanisms underlying ubiquitination.Annu. Rev. Biochem.70, 503-533. (10.1146/annurev.biochem.70.1.503)
  27. Raasi, S., and Pickart, C.M. (2003). Rad23 ubiquitin-associated domains (UBA) inhibit 26 S proteasome-catalyzed proteolysis by sequestering lysine 48-linked polyubiquitin chains.J. Biol. Chem.278, 8951-8959. (10.1074/jbc.M212841200)
  28. Rao, H., and Sastry, A. (2002). 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. (10.1074/jbc.M200245200)
  29. Rao, H., Uhlmann, F., Nasmyth, K., and Varshavsky, A. (2001). Degradation of a cohesin subunit by the N-end rule pathway is essential for chromosome stability.Nature410, 955-959. (10.1038/35073627)
  30. Saeki, Y., Saitoh, A., Toh-e, A., and Yokosawa, H. (2002a). Ubiquitin-like proteins and Rpn10 play cooperative roles in ubiquitin-dependent proteolysis.Biochem. Biophys. Res. Commun.293, 986-992. (10.1016/S0006-291X(02)00340-6)
  31. Saeki, Y., Sone, T., Toh-e, A., and Yokosawa, H. (2002b). Identification of ubiquitin-like protein-binding subunits of the 26S proteasome.Biochem. Biophys. Res. Commun.296, 813-819. (10.1016/S0006-291X(02)02002-8)
  32. Schwartz, D.C., and Hochstrasser, M. (2003). A superfamily of protein tags: ubiquitin, SUMO and related modifiers.Trends Biochem. Sci.28, 321-328. (10.1016/S0968-0004(03)00113-0)
  33. Seeger, M., Hartmann-Petersen, R., Wilkinson, C.R., Wallace, M., Samejima, I., Taylor, M.S., and Gordon, C. (2003). Interaction of the anaphase-promoting complex/cyclosome and proteasome protein complexes with multiubiquitin chain-binding proteins.J. Biol. Chem.278, 16791-16796. (10.1074/jbc.M208281200)
  34. Takayama, S., Kochel, K., Irie, S., Inazawa, J., Abe, T., Sato, T., Druck, T., Huebner, K., and Reed, J.C. (1996). Cloning of cDNAs encoding the human BAG1 protein and localization of the human BAG1 gene to chromosome 9p12.Genomics35, 494-498. (10.1006/geno.1996.0389)
  35. Verma, R., Aravind, L., Oania, R., McDonald, W.H., Yates, J.R., 3rd, Koonin, E.V., and Deshaies, R.J. (2002). Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome.Science298, 611-615. (10.1126/science.1075898)
  36. Walters, K.J., Kleijnen, M.F., Goh, A.M., Wagner, G., and Howley, P.M. (2002). Structural studies of the interaction between ubiquitin family proteins and proteasome subunit S5a.Biochemistry41, 1767-1777. (10.1021/bi011892y)
  37. Watkins, J.F., Sung, P., Prakash, L., and Prakash, S. (1993). TheSaccharomyces cerevisiaeDNA repair geneRAD23encodes a nuclear protein containing a ubiquitin-like domain required for biological function.Mol. Cell. Biol.13, 7757-7765. (10.1128/MCB.13.12.7757)
  38. Weissman, A.M. (2001). Themes and variations on ubiquitylation.Nat. Rev. Mol. Cell. Biol.2, 169-178. (10.1038/35056563)
  39. Wilkinson, C.R.M., Seeger, M., Hartmann-Petersen, R., Stone, M., Wallace, M., Semple, C., and Gordon, C. (2001). Proteins containing the UBA domain are able to bind to multi-ubiquitin chains.Nat. Cell Biol.3, 939-943. (10.1038/ncb1001-939)
  40. Yao, T., and Cohen, R.E. (2002). A cryptic protease couples deubiquitination and degradation by the proteasome.Nature419, 403-407. (10.1038/nature01071)
  41. Zhu, Q., Wani, G., Wani, M.A., and Wani, A.A. (2001). Human homologue of yeast Rad23 protein A interacts with p300/cyclic AMP-responsive element binding (CREB)-binding protein to down-regulate transcriptional activity of p53.Cancer Res.61, 64-70.
Dates
Type When
Created 21 years, 3 months ago (May 3, 2004, 8:58 p.m.)
Deposited 4 years, 2 months ago (June 17, 2021, 3:54 a.m.)
Indexed 4 months ago (April 24, 2025, 3:24 a.m.)
Issued 21 years, 1 month ago (July 1, 2004)
Published 21 years, 1 month ago (July 1, 2004)
Published Print 21 years, 1 month ago (July 1, 2004)
Funders 0

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@article{Kim_2004, title={Multiple Interactions of Rad23 Suggest a Mechanism for Ubiquitylated Substrate Delivery Important in Proteolysis}, volume={15}, ISSN={1939-4586}, url={http://dx.doi.org/10.1091/mbc.e03-11-0835}, DOI={10.1091/mbc.e03-11-0835}, number={7}, journal={Molecular Biology of the Cell}, publisher={American Society for Cell Biology (ASCB)}, author={Kim, Ikjin and Mi, Kaixia and Rao, Hai}, year={2004}, month=jul, pages={3357–3365} }