Malleable machines in transcription regulation: The Mediator complex

PLoS Computational Biology

Volumn 4, Issue 12, 2008, Pages

  Tóth Petróczy, Ágnes ^a   Oldfield, Christopher J ^b   Simon, István ^a   Takagi, Yuichiro ^b   Dunker, A Keith ^b   Uversky, Vladimir N ^b,c   Fuxreiter, Monika ^a  

^a INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

^b INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c INSTITUTE FOR BIOLOGICAL INSTRUMENTATION   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; MACHINERY; PROTEINS; TRANSCRIPTION;

CONFORMATIONAL CHANGE; CRYO-ELECTRON MICROSCOPY; HOMO SAPIENS; INTRINSICALLY DISORDERED REGIONS; MEDIATOR COMPLEX; MODULAR ARCHITECTURES; RECOGNITION FEATURES; REGULATORY PROTEIN; RNA POLYMERASE II; TRANSCRIPTION REGULATIONS;

YEAST;

MULTIPROTEIN COMPLEX; RNA POLYMERASE II; TRANSACTIVATOR PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; CONFORMATIONAL TRANSITION; CRYOELECTRON MICROSCOPY; HUMAN; MEDIATOR; MOLECULAR RECOGNITION; NONHUMAN; PREVALENCE; PROTEIN ASSEMBLY; PROTEIN INTERACTION; PROTEIN STRUCTURE; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION; YEAST; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; GENETICS; TRANSCRIPTION INITIATION;

HOMO SAPIENS; SACCHAROMYCES CEREVISIAE;

COMPUTER SIMULATION; GENE EXPRESSION REGULATION; MODELS, GENETIC; TRANS-ACTIVATORS; TRANSCRIPTION FACTORS; TRANSCRIPTIONAL ACTIVATION;

EID: 58149163281     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000243     Document Type: Article

References (82)

1. Kornberg RD (2005) Mediator and the mechanism of transcriptional activation. Trends Biochem Sci 30: 235-239.
2. Takagi Y, Kornberg RD (2006) Mediator as a general transcription factor. J Biol Chem 281: 80-89.
3. Park JM, Gim BS, Kim JM, Yoon JH, Kim HS, et al. (2001) Drosophila Mediator complex is broadly utilized by diverse gene-specific transcription factors at different types of core promoters. Mol Cell Biol 21: 2312-2323.
4. Kuras L, Borggrefe T, Kornberg RD (2003) Association of the Mediator complex with enhancers of active genes. Proc Natl Acad Sci U S A 100: 13887-13891.
5. Cosma MP, Panizza S, Nasmyth K (2001) Cdk1 triggers association of RNA polymerase to cell cycle promoters only after recruitment of the mediator by SBF. Mol Cell 7: 1213-1220.
6. Pokholok DK, Hannett NM, Young RA (2002) Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo. Mol Cell 9: 799-809.
7. Svejstrup JQ, Li Y, Fellows J, Gnatt A, Bjorklund S, et al. (1997) Evidence for a mediator cycle at the initiation of transcription. Proc Natl Acad Sci U S A 94: 6075-6078.
8. Yudkovsky N, Ranish JA, Hahn S (2000) A transcription reinitiation intermediate that is stabilized by activator. Nature 408: 225-229.
9. Davis JA, Takagi Y, Kornberg RD, Asturias FA (2002) Structure of the yeast RNA polymerase II holoenzyme: Mediator conformation and polymerase interaction. Mol Cell 10: 409-415.
10. Asturias FJ (2004) RNA polymerase II structure, and organization of the preinitiation complex. Curr Opin Struct Biol 14: 121-129.
11. Taatjes DJ, Naar AM, Andel F 3rd, Nogales E, Tjian R (2002) Structure, function, and activator-induced conformations of the CRSP coactivator. Science 295: 1058-1062.
12. Taatjes DJ, Schneider-Poetsch T, Tjian R (2004) Distinct conformational states of nuclear receptor-bound CRSP-Med complexes. Nat Struct Mol Biol 11: 664-671.
13. Chadick JZ, Asturias FJ (2005) Structure of eukaryotic Mediator complexes. Trends Biochem Sci 30: 264-271.
14. Asturias FJ, Jiang YW, Myers LC, Gustafsson CM, Kornberg RD (1999) Conserved structures of mediator and RNA polymerase II holoenzyme. Science 283: 985-987.
15. Myers LC, Gustafsson CM, Hayashibara KC, Brown PO, Kornberg RD (1999) Mediator protein mutations that selectively abolish activated transcription. Proc Natl Acad Sci U S A 96: 67-72.
16. Kang JS, Kim SH, Hwang MS, Han SJ, Lee YC, et al. (2001) The structural and functional organization of the yeast mediator complex. J Biol Chem 276: 42003-42010.
17. Takagi Y, Calero G, Komori H, Brown JA, Ehrensberger AH, et al. (2006) Head module control of mediator interactions. Mol Cell 23: 355-364.
18. Elmlund H, Baraznenok V, Lindahl M, Samuelsen CO, Koeck PJ, et al. (2006) The cyclin-dependent kinase 8 module sterically blocks Mediator interactions with RNA polymerase II. Proc Natl Acad Sci U S A 103: 15788-15793.
19. Borggrefe T, Davis R, Erdjument-Bromage H, Tempst P, Kornberg RD (2002) A complex of the Srb8, -9, -10, and -11 transcriptional regulatory proteins from yeast. J Biol Chem 277: 44202-44207.
20. Lorch Y, Beve J, Gustafsson CM, Myers LC, Kornberg RD (2000) Mediator-nucleosome interaction. Mol Cell 6: 197-201.
21. Boube M, Joulia L, Cribbs DL, Bourbon HM (2002) Evidence for a mediator of RNA polymerase II transcriptional regulation conserved from yeast to man. Cell 110: 143-151.
22. Brehm A, Tufteland KR, Aasland R, Becker PB (2004) The many colours of chromodomains. Bioessays 26: 133-140.
23. Tamkun JW, Deuring R, Scott MP, Kissinger M, Pattatucci AM, et al. (1992) brahma: a regulator of Drosophila homeotic genes structurally related to the yeast transcriptional activator SNF2/SWI2. Cell 68: 561-572.
24. Dotson MR, Yuan CX, Roeder RG, Myers LC, Gustafsson CM, et al. (2000) Structural organization of yeast and mammalian mediator complexes. Proc Natl Acad Sci U S A 97: 14307-14310.
25. Obradovic Z, Peng K, Vucetic S, Radivojac P, Brown CJ, et al. (2003) Predicting intrinsic disorder from amino acid sequence. Proteins 53(Suppl 6): 566-572.
26. Dosztanyi Z, Csizmok V, Tompa P, Simon I (2005) The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J Mol Biol 347: 827-839.
27. Baumli S, Hoeppner S, Cramer P (2005) A conserved mediator hinge revealed in the structure of the MED7.MED21 (Med7.Srb7) heterodimer. J Biol Chem 280: 18171-18178.
28. Lariviere L, Geiger S, Hoeppner S, Rother S, Strasser K, et al. (2006) Structure and TBP binding of the Mediator head subcomplex Med8-Med18-Med20. Nat Struct Mol Biol 13: 895-901.
29. Sickmeier M, Hamilton JA, LeGall T, Vacic V, Cortese MS, et al. (2007) DisProt: the Database of Disordered Proteins. Nucleic Acids Res 35: D786-D793.
30. Dyson HJ, Wright PE (2002) Coupling of folding and binding for unstructured proteins. Curr Opin Struct Biol 12: 54-60.
31. Romero P, Obradovic Z, Li X, Garner EC, Brown CJ, et al. (2001) Sequence complexity of disordered protein. Proteins 42: 38-48.
32. Vacic V, Uversky VN, Dunker AK, Lonardi S (2007) Composition Profiler: a tool for discovery and visualization of amino acid composition differences. BMC Bioinformatics 8: 211.
33. Iakoucheva LM, Radivojac P, Brown CJ, O'Connor TR, Sikes JG, et al. (2004) The importance of intrinsic disorder for protein phosphorylation. Nucleic Acids Res 32: 1037-1049.
34. Kim DH, Kim GS, Yun CH, Lee YC (2008) Functional conservation of the glutamine-rich domains of yeast Gal11 and human SRC-1 in the transactivation of glucocorticoid receptor Tau 1 in Saccharomyces cerevisiae. Mol Cell Biol 28: 913-925.
35. Tompa P (2003) Intrinsically unstructured proteins evolve by repeat expansion. Bioessays 25: 847-855.
36. Xie H, Vucetic S, Iakoucheva LM, Oldfield CJ, Dunker AK, et al. (2007) Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J Proteome Res 6: 1882-1898.
37. Tompa P (2005) The interplay between structure and function in intrinsically unstructured proteins. FEBS Lett 579: 3346-3354.
38. Iakoucheva L, Brown C, Lawson J, Obradovic Z, Dunker A (2002) Intrinsic Disorder in Cell-signaling and Cancer-associated Proteins. J Mol Biol 323: 573-584.
39. Liu J, Perumal NB, Oldfield CJ, Su EW, Uversky VN, et al. (2006) Intrinsic disorder in transcription factors. Biochemistry 45: 6873-6888.
40. Minezaki Y, Homma K, Kinjo AR, Nishikawa K (2006) Human transcription factors contain a high fraction of intrinsically disordered regions essential for transcriptional regulation. J Mol Biol 359: 1137-1149.
41. Hegyi H, Schad E, Tompa P (2007) Structural disorder promotes assembly of protein complexes. BMC Struct Biol 7: 65.
42. Fuxreiter M, Simon I, Friedrich P, Tompa P (2004) Preformed structural elements feature in partner recognition by intrinsically unstructured proteins. J Mol Biol 338: 1015-1026.
43. Mohan A, Oldfield CJ, Radivojac P, Vacic V, Cortese MS, et al. (2006) Analysis of molecular recognition features (MoRFs). J Mol Biol 362: 1043-1059.
44. Csizmok V, Bokor M, Banki P, Klement E, Medzihradszky KF, et al. (2005) Primary contact sites in intrinsically unstructured proteins: the case of calpastatin and microtubule-associated protein 2. Biochemistry 44: 3955-3964.
45. Neduva V, Russell RB (2005) Linear motifs: evolutionary interaction switches. FEBS Lett 579: 3342-3345.
46. Fuxreiter M, Tompa P, Simon I (2007) Local structural disorder imparts plasticity on linear motifs. Bioinformatics 23: 950-956.
47. Cheng Y, Oldfield CJ, Meng J, Romero P, Uversky VN, et al. (2007) Mining alpha-helix-forming molecular recognition features with cross species sequence alignments. Biochemistry 46: 13468-13477.
48. Kussie PH, Gorina S, Marechal V, Elenbaas B, Moreau J, et al. (1996) Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science 274: 948-953.
49. Vise P, Baral B, Stancik A, Lowry DF, Daughdrill GW (2007) Identifying long-range structure in the intrinsically unstructured transactivation domain of p53. Proteins 67: 526-530.
50. Mark WY, Liao JC, Lu Y, Ayed A, Laister R, et al. (2005) Characterization of segments from the central region of BRCA1: an intrinsically disordered scaffold for multiple protein-protein and protein-DNA interactions? J Mol Biol 345: 275-287.
51. Han SJ, Lee JS, Kang JS, Kim YJ (2001) Med9/Cse2 and Gal11 modules are required for transcriptional repression of distinct group of genes. J Biol Chem 276: 37020-37026.
52. Guglielmi B, van Berkum NL, Klapholz B, Bijma T, Boube M, et al. (2004) A high resolution protein interaction map of the yeast Mediator complex. Nucleic Acids Res 32: 5379-5391.
53. Hidalgo P, Ansari AZ, Schmidt P, Hare B, Simkovich N, et al. (2001) Recruitment of the transcriptional machinery through GAL11P: structure and interactions of the GAL4 dimerization domain. Genes Dev 15: 1007-1020.
54. Liu HY, Chiang YC, Pan J, Chen J, Salvadore C, et al. (2001) Characterization of CAF4 and CAF16 reveals a functional connection between the CCR4-NOT complex and a subset of SRB proteins of the RNA polymerase II holoenzyme. J Biol Chem 276: 7541-7548.
55. Guidi BW, Bjornsdottir G, Hopkins DC, Lacomis L, Erdjument-Bromage H, et al. (2004) Mutual targeting of mediator and the TFIIH kinase Kin28. J Biol Chem 279: 29114-29120.
56. Brower CS, Sato S, Tomomori-Sato C, Kamura T, Pause A, et al. (2002) 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 U S A 99: 10353-10358.
57. Brown CJ, Takayama S, Campen AM, Vise P, Marshall TW, et al. (2002) Evolutionary rate heterogeneity in proteins with long disordered regions. J Mol Evol 55: 104-110.
58. Daughdrill GW, Narayanaswami P, Gilmore SH, Belczyk A, Brown CJ (2007) Dynamic behavior of an intrinsically unstructured linker domain is conserved in the face of negligible amino acid sequence conservation. J Mol Evol 65: 277-288.
59. Tóth-Petróczy A, Meszaros B, Simon I, Dunker AK, Uversky VN, et al. (2008) Assessing conservation of disordered regions in proteins. Open Proteomics J 1: 46-53.
60. Zemla A, Venclovas C, Fidelis K, Rost B (1999) A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment. Proteins 34: 220-223.
61. Goodman RH, Smolik S (2000) CBP/p300 in cell growth, transformation, and development. Genes Dev 14: 1553-1577.
62. Fuxreiter M, Tompa P, Simon I, Uversky VN, Hansen JC, et al. (2008) Malleable machines take shape in eukaryotic transcription regulation. Nat Chem Biol submitted for publication.
63. Hansen JC, Lu X, Ross ED, Woody RW (2006) Intrinsic protein disorder, amino acid composition, and histone terminal domains. J Biol Chem 281: 1853-1856.
64. Sigler PB (1988) Transcriptional activation. Acid blobs and negative noodles. Nature 333: 210-212.
65. Proudfoot NJ, Furger A, Dye MJ (2002) Integrating mRNA processing with transcription. Cell 108: 501-512.
66. Tompa P, Fuxreiter M (2008) Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions. Trends Biochem Sci 33: 2-8.
67. Wada O, Oishi H, Takada I, Yanagisawa J, Yano T, et al. (2004) BRCA1 function mediates a TRAP/DRIP complex through direct interaction with TRAP220. Oncogene 23: 6000-6005.
68. Albers M, Kranz H, Kober I, Kaiser C, Klink M, et al. (2005) Automated yeast two-hybrid screening for nuclear receptor-interacting proteins. Mol Cell Proteomics 4: 205-213.
69. Dyson HJ, Wright PE (2005) Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol 6: 197-208.
70. Oldfield CJ, Meng J, Yang JY, Yang MQ, Uversky VN, et al. (2008) Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners. BMC Genomics 9 (Suppl 1): S1.
71. Smith JL, Freebern WJ, Collins I, De Siervi A, Montano I, et al. (2004) Kinetic profiles of p300 occupancy in vivo predict common features of promoter structure and coactivator recruitment. Proc Natl Acad Sci U S A 101: 11554-11559.
72. Galea CA, Nourse A, Wang Y, Sivakolundu SG, Heller WT, et al. (2008) Role of intrinsic flexibility in signal transduction mediated by the cell cycle regulator, p27 Kip1. J Mol Biol 376: 827-838.
73. Kriwacki RW, Hengst L, Tennant L, Reed SI, Wright PE (1996) Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk2-bound state: conformational disorder mediates binding diversity. Proc Natl Acad Sci U S A 93: 11504-11509.
74. Tompa P, Szasz C, Buday L (2005) Structural disorder throws new light on moonlighting. Trends Biochem Sci 30: 484-489.
75. van de Peppel J, Kettelarij N, van Bakel H, Kockelkorn TT, van Leenen D, et al. (2005) Mediator expression profiling epistasis reveals a signal transduction pathway with antagonistic submodules and highly specific downstream targets. Mol Cell 19: 511-522.
76. Hermoso A, Aguilar D, Aviles FX, Querol E (2004) TrSDB: a proteome database of transcription factors. Nucleic Acids Res 32: D171-173.
77. Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22: 1658-1659.
78. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
79. Bourbon HM, Aguilera A, Ansari AZ, Asturias FJ, Berk AJ, et al. (2004) A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II. Mol Cell 14: 553-557.
80. Sato S, Tomomori-Sato C, Parmely TJ, Florens L, Zybailov B, et al. (2004) A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology. Mol Cell 14: 685-691.
81. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, et al. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31: 3497-3500.
82. Karlin S, Burge C (1996) Trinucleotide repeats and long homopeptides in genes and proteins associated with nervous system disease and development. Proc Natl Acad Sci U S A 93: 1560-1565.