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How the ubiquitin–proteasome system controls transcription

Muratani, Masafumi, Tansey, William P.·2003·Nature Reviews Molecular Cell Biology
DOI 10.1038/nrm1049
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Abstract

Gene transcription and ubiquitin-mediated proteolysis are two processes that have seemingly nothing in common: transcription is the first step in the life of any protein and proteolysis the last. Despite the disparate nature of these processes, a growing body of evidence indicates that ubiquitin and the proteasome are intimately involved in gene control. Here, we discuss the deep mechanistic connections between transcription and the ubiquitin-proteasome system, and highlight how the intersection of these processes tightly controls expression of the genetic information.

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  1. Varshavsky, A. The ubiquitin system. Trends Biochem. Sci. 22, 383–387 (1997). · DOI
  2. Terrell, J., Shih, S., Dunn, R. & Hicke, L. A function for monoubiquitination in the internalization of a G protein-coupled receptor. Mol. Cell 1, 193–202 (1998). · DOI
  3. Spence, J. et al. Cell cycle-regulated modification of the ribosome by a variant multiubiquitin chain. Cell 102, 67–76 (2000). · DOI
  4. Russell, S. J., Reed, S. H., Huang, W., Friedberg, E. C. & Johnston, S. A. The 19S regulatory complex of the proteasome functions independently of proteolysis in nucleotide excision repair. Mol. Cell 3, 687–695 (1999). · DOI
  5. Goldknopf, I. L. et al. Isolation and characterization of protein A24, a 'histone-like' non-histone chromosomal protein. J. Biol. Chem. 250, 7182–7187 (1975). · DOI
  6. Goldknopf, I. L. & Busch, H. Isopeptide linkage between nonhistone and histone 2A polypeptides of chromosomal conjugate-protein A24. Proc. Natl Acad. Sci. USA 74, 864–868 (1977). · DOI
  7. Hunt, L. T. & Dayhoff, M. O. Amino-terminal sequence identity of ubiquitin and the nonhistone component of nuclear protein A24. Biochem. Biophys. Res. Commun. 74, 650–655 (1977). · DOI
  8. Levinger, L. & Varshavsky, A. Selective arrangement of ubiquitinated and D1 protein-containing nucleosomes within the Drosophila genome. Cell 28, 375–385 (1982). · DOI
  9. Nickel, B. E., Allis, C. D. & Davie, J. R. Ubiquitinated histone H2B is preferentially located in transcriptionally active chromatin. Biochemistry 28, 958–963 (1989). · DOI
  10. Davie, J. R. & Murphy, L. C. Level of ubiquitinated histone H2B in chromatin is coupled to ongoing transcription. Biochemistry 29, 4752–4757 (1990). · DOI
  11. Davie, J. R., Lin, R. & Allis, C. D. Timing of the appearance of ubiquitinated histones in developing new macronuclei of Tetrahymena thermophila. Biochem. Cell Biol. 69, 66–71 (1991). · DOI
  12. Vavra, K. J., Allis, C. D. & Gorovsky, M. A. Regulation of histone acetylation in Tetrahymena macro- and micronuclei. J. Biol. Chem. 257, 2591–2598 (1982). · DOI
  13. Huang, S. Y. et al. The active immunoglobulin κ chain gene is packaged by non-ubiquitin-conjugated nucleosomes. Proc. Natl Acad. Sci. USA 83, 3738–3742 (1986). · DOI
  14. Pham, A. D. & Sauer, F. Ubiquitin-activating/conjugating activity of TAFII250, a mediator of activation of gene expression in Drosophila. Science 289, 2357–2360 (2000). · DOI
  15. Chen, H. Y., Sun, J. M., Zhang, Y., Davie, J. R. & Meistrich, M. L. Ubiquitination of histone H3 in elongating spermatids of rat testes. J. Biol. Chem. 273, 13165–13169 (1998). · DOI
  16. Robzyk, K., Recht, J. & Osley, M. A. Rad6-dependent ubiquitination of histone H2B in yeast. Science 287, 501–504 (2000). Identified Rad6 as a Ub-conjugating enzyme for histone H2B in budding yeast and opened the way for genetic analysis of histone ubiquitylation. · DOI
  17. Turner, S. D. et al. The E2 ubiquitin conjugase Rad6 is required for the ArgR/Mcm1 repression of ARG1 transcription. Mol. Cell. Biol. 22, 4011–4019 (2002). · DOI
  18. Sun, Z. W. & Hampsey, M. A general requirement for the Sin3-Rpd3 histone deacetylase complex in regulating silencing in Saccharomyces cerevisiae. Genetics 152, 921–932 (1999). · DOI
  19. Huang, H., Kahana, A., Gottschling, D. E., Prakash, L. & Liebman, S. W. The ubiquitin-conjugating enzyme Rad6 (Ubc2) is required for silencing in Saccharomyces cerevisiae. Mol. Cell. Biol. 17, 6693–6699 (1997). · DOI
  20. Bryk, M. et al. Transcriptional silencing of Ty1 elements in the RDN1 locus of yeast. Genes Dev. 11, 255–269 (1997). · DOI
  21. Ricci, A. R., Genereaux, J. & Brandl, C. J. Components of the SAGA histone acetyltransferase complex are required for repressed transcription of ARG1 in rich medium. Mol. Cell. Biol. 22, 4033–4042 (2002). · DOI
  22. Sun, Z. W. & Allis, C. D. Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature 418, 104–108 (2002). Established that histone ubiquitylation is required for subsequent histone modifications that are important in gene silencing. · DOI
  23. Briggs, S. D. et al. Gene silencing: Trans-histone regulatory pathway in chromatin. Nature 418, 498 (2002). · DOI
  24. Rice, J. C. & Allis, C. D. Histone methylation versus histone acetylation: new insights into epigenetic regulation. Curr. Opin. Cell Biol. 13, 263–273 (2001). · DOI
  25. Strahl, B. D. & Allis, C. D. The language of covalent histone modifications. Nature 403, 41–45 (2000). · DOI · Paper page
  26. Seale, R. L. Rapid turnover of the histone-ubiquitin conjugate, protein A24. Nucleic Acids Res. 9, 3151–3158 (1981). · DOI
  27. Wu, R. S., Kohn, K. W. & Bonner, W. M. Metabolism of ubiquitinated histones. J. Biol. Chem. 256, 5916–5920 (1981). · DOI
  28. Haas, A., Reback, P. M., Pratt, G. & Rechsteiner, M. Ubiquitin-mediated degradation of histone H3 does not require the substrate-binding ubiquitin protein ligase, E3, or attachment of polyubiquitin chains. J. Biol. Chem. 265, 21664–21669 (1990). · DOI
  29. Hook, S. S., Orian, A., Cowley, S. M. & Eisenman, R. N. Histone deacetylase 6 binds polyubiquitin through its zinc finger (PAZ domain) and copurifies with deubiquitinating enzymes. Proc. Natl Acad. Sci. USA 99, 13425–13430 (2002). · DOI
  30. Chen, J. L., Attardi, L. D., Verrijzer, C. P., Yokomori, K. & Tjian, R. Assembly of recombinant TFIID reveals differential coactivator requirements for distinct transcriptional activators. Cell 79, 93–105 (1994). · DOI
  31. Moazed, D. & Johnson, D. A deubiquitinating enzyme interacts with SIR4 and regulates silencing in S. cerevisiae. Cell 86, 667–677 (1996). · DOI
  32. Sanders, S. L., Garbett, K. A. & Weil, P. A. Molecular characterization of Saccharomyces cerevisiae TFIID. Mol. Cell. Biol. 22, 6000–6013 (2002). · DOI
  33. Lee, K. B., Wang, D., Lippard, S. J. & Sharp, P. A. Transcription-coupled and DNA damage-dependent ubiquitination of RNA polymerase II in vitro. Proc. Natl Acad. Sci. USA 99, 4239–4244 (2002). Provided biochemical evidence that DNA-damage-dependent ubiquitylation of RNA polymerase II is coupled to transcription. · DOI
  34. Beaudenon, S. L., Huacani, M. R., Wang, G., McDonnell, D. P. & Huibregtse, J. M. Rsp5 ubiquitin-protein ligase mediates DNA damage-induced degradation of the large subunit of RNA polymerase II in Saccharomyces cerevisiae. Mol. Cell. Biol. 19, 6972–6979 (1999). · DOI
  35. Huibregtse, J. M., Yang, J. C. & Beaudenon, S. L. The large subunit of RNA polymerase II is a substrate of the Rsp5 ubiquitin-protein ligase. Proc. Natl Acad. Sci. USA 94, 3656–3661 (1997). · DOI
  36. Komarnitsky, P., Cho, E. J. & Buratowski, S. Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14, 2452–2460 (2000). · DOI
  37. Mitsui, A. & Sharp, P. A. Ubiquitination of RNA polymerase II large subunit signaled by phosphorylation of carboxyl-terminal domain. Proc. Natl Acad. Sci. USA 96, 6054–6059 (1999). · DOI
  38. Imhof, M. O. & McDonnell, D. P. Yeast RSP5 and its human homolog hRPF1 potentiate hormone-dependent activation of transcription by human progesterone and glucocorticoid receptors. Mol. Cell. Biol. 16, 2594–2605 (1996). · DOI
  39. Woudstra, E. C. et al. A Rad26-Def1 complex coordinates repair and RNA pol II proteolysis in response to DNA damage. Nature 415, 929–933 (2002). · DOI
  40. Darnell, J. E., Jr. STATs and gene regulation. Science 277, 1630–1635 (1997). · DOI · Paper page
  41. Brown, M. S., Ye, J., Rawson, R. B. & Goldstein, J. L. Regulated intramembrane proteolysis: a control mechanism conserved from bacteria to humans. Cell 100, 391–398 (2000). · DOI · Paper page
  42. Palombella, V. J., Rando, O. J., Goldberg, A. L. & Maniatis, T. The ubiquitin-proteasome pathway is required for processing the NF-κB1 precursor protein and the activation of NF-κB. Cell 78, 773–785 (1994). · DOI
  43. Hoppe, T. et al. Activation of a membrane-bound transcription factor by regulated ubiquitin/proteasome-dependent processing. Cell 102, 577–586 (2000). · DOI
  44. Rape, M. et al. Mobilization of processed, membrane-tethered SPT23 transcription factor by CDC48(UFD1/NPL4), a ubiquitin-selective chaperone. Cell 107, 667–677 (2001). · DOI
  45. Borden, K. L. Pondering the promyelocytic leukemia protein (PML) puzzle: possible functions for PML nuclear bodies. Mol. Cell. Biol. 22, 5259–5269 (2002). · DOI
  46. Muller, S., Matunis, M. J. & Dejean, A. Conjugation with the ubiquitin-related modifier SUMO-1 regulates the partitioning of PML within the nucleus. EMBO J. 17, 61–70 (1998). · DOI
  47. Sachdev, S. et al. PIASy, a nuclear matrix-associated SUMO E3 ligase, represses LEF1 activity by sequestration into nuclear bodies. Genes Dev. 15, 3088–3103 (2001). Established a solid connection between SUMO-modification of a transcription factor, transcriptional regulation and PML-body formation. · DOI
  48. Ross, S., Best, J. L., Zon, L. I. & Gill, G. SUMO-1 modification represses Sp3 transcriptional activation and modulates its subnuclear localization. Mol. Cell 10, 831–842 (2002). · DOI
  49. Sapetschnig, A. et al. Transcription factor Sp3 is silenced through SUMO modification by PIAS1. EMBO J. 21, 5206–5215 (2002). · DOI
  50. Bies, J., Markus, J. & Wolff, L. Covalent attachment of the SUMO-1 protein to the negative regulatory domain of the c-Myb transcription factor modifies its stability and transactivation capacity. J. Biol. Chem. 277, 8999–9009 (2002). · DOI
  51. Nishida, T. & Yasuda, H. PIAS1 and PIASxα function as SUMO-E3 ligases toward androgen receptor and repress androgen receptor-dependent transcription. J. Biol. Chem. 277, 41311–41317 (2002). · DOI
  52. Schmidt, D. & Muller, S. Members of the PIAS family act as SUMO ligases for c-Jun and p53 and repress p53 activity. Proc. Natl Acad. Sci. USA 99, 2872–2877 (2002). · DOI
  53. Kim, J., Cantwell, C. A., Johnson, P. F., Pfarr, C. M. & Williams, S. C. Transcriptional activity of CCAAT/enhancer-binding proteins is controlled by a conserved inhibitory domain that is a target for sumoylation. J. Biol. Chem. 277, 38037–38044 (2002). · DOI
  54. Ostendorff, H. P. et al. Ubiquitination-dependent cofactor exchange on LIM homeodomain transcription factors. Nature 416, 99–103 (2002). · DOI
  55. Kaiser, P., Flick, K., Wittenberg, C. & Reed, S. I. Regulation of transcription by ubiquitination without proteolysis: Cdc34/SCF(Met30)-mediated inactivation of the transcription factor Met4. Cell 102, 303–314 (2000). · DOI
  56. Rouillon, A., Barbey, R., Patton, E. E., Tyers, M. & Thomas, D. Feedback-regulated degradation of the transcriptional activator Met4 is triggered by the SCFMet30 complex. EMBO J. 19, 282–294 (2000). · DOI
  57. Kuras, L. et al. Dual regulation of the met4 transcription factor by ubiquitin-dependent degradation and inhibition of promoter recruitment. Mol. Cell 10, 69–80 (2002). Showed that the yeast transcription factor Met4 can be either inactivated or destroyed by Met30-dependent ubiquitylation, depending on nutrients. · DOI
  58. Aberle, H., Bauer, A., Stappert, J., Kispert, A. & Kemler, R. β-catenin is a target for the ubiquitin-proteasome pathway. EMBO J. 16, 3797–3804 (1997). · DOI
  59. Yost, C. et al. The axis-inducing activity, stability, and subcellular distribution of β-catenin is regulated in Xenopus embryos by glycogen synthase kinase 3. Genes Dev. 10, 1443–1454 (1996). · DOI
  60. Maxwell, P. H. et al. The tumour suppressor protein VHL targets hypoxia-inducible factors for oxygen-dependent proteolysis. Nature 399, 271–275 (1999). · DOI · Paper page
  61. Ma, Q. & Baldwin, K. T. 2,3,7,8-tetrachlorodibenzo-p-dioxin-induced degradation of aryl hydrocarbon receptor (AhR) by the ubiquitin-proteasome pathway. Role of the transcription activation and DNA binding of AhR. J. Biol. Chem. 275, 8432–8438 (2000). · DOI
  62. Lo, R. S. & Massague, J. Ubiquitin-dependent degradation of TGF-β-activated Smad2. Nature Cell Biol. 1, 472–478 (1999). · DOI
  63. Kim, T. K. & Maniatis, T. Regulation of interferon-γ-activated STAT1 by the ubiquitin-proteasome pathway. Science 273, 1717–1719 (1996). · DOI
  64. Bertani, D., Oppenheim, A. B. & Narberhaus, F. An internal region of the RpoH heat shock transcription factor is critical for rapid degradation by the FtsH protease. FEBS Lett. 493, 17–20 (2001). · DOI
  65. Becker, G., Klauck, E. & Hengge-Aronis, R. Regulation of RpoS proteolysis in Escherichia coli: the response regulator RssB is a recognition factor that interacts with the turnover element in RpoS. Proc. Natl Acad. Sci. USA 96, 6439–6444 (1999). · DOI
  66. Salghetti, S. E., Kim, S. Y. & Tansey, W. P. Destruction of Myc by ubiquitin-mediated proteolysis: cancer-associated and transforming mutations stabilize Myc. EMBO J. 18, 717–726 (1999). · DOI
  67. Salghetti, S. E., Muratani, M., Wijnen, H., Futcher, B. & Tansey, W. P. Functional overlap of sequences that activate transcription and signal ubiquitin-mediated proteolysis. Proc. Natl Acad. Sci. USA 97, 3118–3123 (2000). · DOI
  68. Molinari, E., Gilman, M. & Natesan, S. Proteasome-mediated degradation of transcriptional activators correlates with activation domain potency in vivo. EMBO J. 18, 6439–6447 (1999). · DOI
  69. Brower, C. S. et al. Mammalian mediator subunit mMED8 is an Elongin BC-interacting protein that can assemble with Cul2 and Rbx1 to reconstitute a ubiquitin ligase. Proc. Natl Acad. Sci. USA 99, 10353–10358 (2002). Established that Ub-ligase activity is directly associated with the RNA polymerase II holoenzyme. · DOI
  70. Chi, Y. et al. Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase. Genes Dev. 15, 1078–1092 (2001). Showed that the yeast transcription factor GCN4 is marked for destruction by a kinase that is present in the RNA polymerase II holoenzyme. · DOI
  71. Liao, S. M. et al. A kinase-cyclin pair in the RNA polymerase II holoenzyme. Nature 374, 193–196 (1995). · DOI
  72. Tansey, W. P. Transcriptional activation: risky business. Genes Dev. 15, 1045–1050 (2001). · DOI
  73. Thomas, D. & Tyers, M. Kamikaze activators. Curr. Biol. 10, R341–R343 (2000). · DOI
  74. Salghetti, S. E., Caudy, A. A., Chenoweth, J. G. & Tansey, W. P. Regulation of transcriptional activation domain function by ubiquitin. Science 293, 1651–1653 (2001). Showed that ubiquitylation of a transcription factor bearing the prototypical VP16 activation domain can be required for transcriptional activation. · DOI
  75. Xie, Y. & Varshavsky, A. RPN4 is a ligand, substrate, and transcriptional regulator of the 26S proteasome: a negative feedback circuit. Proc. Natl Acad. Sci. USA 98, 3056–3061 (2001). · DOI · Paper page
  76. Voges, D., Zwickl, P. & Baumeister, W. The 26S proteasome: a molecular machine designed for controlled proteolysis. Annu. Rev. Biochem. 68, 1015–1068 (1999). · DOI · Paper page
  77. Swaffield, J. C., Bromberg, J. F. & Johnston, S. A. Alterations in a yeast protein resembling HIV Tat-binding protein relieve requirement for an acidic activation domain in GAL4. Nature 357, 698–700 (1992). · DOI
  78. Russell, S. J., Sathyanarayana, U. G. & Johnston, S. A. Isolation and characterization of SUG2. A novel ATPase family component of the yeast 26 S proteasome. J. Biol. Chem. 271, 32810–32817 (1996). · DOI
  79. Swaffield, J. C., Melcher, K. & Johnston, S. A. A highly conserved ATPase protein as a mediator between acidic activation domains and the TATA-binding protein. Nature 374, 88–91 (1995). · DOI
  80. Masuyama, H. & MacDonald, P. N. Proteasome-mediated degradation of the vitamin D receptor (VDR) and a putative role for SUG1 interaction with the AF-2 domain of VDR. J. Cell. Biochem. 71, 429–440 (1998). · DOI
  81. vom Baur, E. et al. Differential ligand-dependent interactions between the AF-2 activating domain of nuclear receptors and the putative transcriptional intermediary factors mSUG1 and TIF1. EMBO J. 15, 110–124 (1996). · DOI
  82. Wang, W., Chevray, P. M. & Nathans, D. Mammalian Sug1 and c-Fos in the nuclear 26S proteasome. Proc. Natl Acad. Sci. USA 93, 8236–8240 (1996). · DOI
  83. Melcher, K. & Johnston, S. A. GAL4 interacts with TATA-binding protein and coactivators. Mol. Cell. Biol. 15, 2839–2848 (1995). · DOI
  84. Makino, Y. et al. Multiple mammalian proteasomal ATPases, but not proteasome itself, are associated with TATA-binding protein and a novel transcriptional activator, TIP120. Genes Cells 4, 529–539 (1999). · DOI
  85. Weeda, G. et al. The XPB subunit of repair/transcription factor TFIIH directly interacts with SUG1, a subunit of the 26S proteasome and putative transcription factor. Nucleic Acids Res. 25, 2274–2283 (1997). · DOI
  86. Kim, Y. J., Bjorklund, S., Li, Y., Sayre, M. H. & Kornberg, R. D. A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 77, 599–608 (1994). · DOI
  87. Russell, S. J. & Johnston, S. A. Evidence that proteolysis of Gal4 cannot explain the transcriptional effects of proteasome ATPase mutations. J. Biol. Chem. 276, 9825–9831 (2001). · DOI
  88. Ferdous, A., Gonzalez, F., Sun, L., Kodadek, T. & Johnston, S. A. The 19S regulatory particle of the proteasome is required for efficient transcription elongation by RNA polymerase II. Mol. Cell 7, 981–991 (2001). · DOI
  89. Blau, J. et al. Three functional classes of transcriptional activation domain. Mol. Cell. Biol. 16, 2044–2055 (1996). · DOI
  90. Verma, R. et al. Proteasomal proteomics: identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes. Mol. Biol. Cell 11, 3425–3439 (2000). · DOI
  91. Myers, L. C. et al. The Med proteins of yeast and their function through the RNA polymerase II carboxy-terminal domain. Genes Dev. 12, 45–54 (1998). · DOI
  92. Makino, Y. et al. SUG1, a component of the 26 S proteasome, is an ATPase stimulated by specific RNAs. J. Biol. Chem. 272, 23201–23205 (1997). · DOI
  93. Albert, T. K. et al. Identification of a ubiquitin-protein ligase subunit within the CCR4-NOT transcription repressor complex. EMBO J. 21, 355–364 (2002). · DOI
  94. Aso, T., Lane, W. S., Conaway, J. W. & Conaway, R. C. Elongin (SIII): a multisubunit regulator of elongation by RNA polymerase II. Science 269, 1439–1443 (1995). · DOI
  95. Mueller, C. L. & Jaehning, J. A. Ctr9, Rtf1, and Leo1 are components of the Paf1/RNA polymerase II complex. Mol. Cell. Biol. 22, 1971–1980 (2002). · DOI
  96. Huibregtse, J. M., Scheffner, M., Beaudenon, S. & Howley, P. M. A family of proteins structurally and functionally related to the E6-AP ubiquitin-protein ligase. Proc. Natl Acad. Sci. USA 92, 2563–2567 (1995). · DOI
  97. Saleh, A. et al. TOM1p, a yeast hect–domain protein which mediates transcriptional regulation through the ADA/SAGA coactivator complexes. J. Mol. Biol. 282, 933–946 (1998). · DOI

Cited by

Metadata

Authors
Muratani, M., & Tansey, W. P.
Venue
Nature Reviews Molecular Cell Biology
Publisher
Springer Science and Business Media LLC
Published
2003-03-01
Volume
4
Issue
3
Pages
192-201
ISSN
  • 1471-0072
  • 1471-0080
DOI
10.1038/nrm1049
Cited by
693
References
5
Language
en
Licence

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