Structure-system correlation identifies a gene regulatory Mediator submodule

Genes and Development

Volumn 22, Issue 7, 2008, Pages 872-877

  Larivière, Laurent ^a   Seizl, Martin ^a   Van Wageningen, Sake ^b   Röther, Susanne ^a   Van De Pasch, Loes ^b   Feldmann, Heidi ^a   Sträßer, Katja ^a   Hahn, Steve ^c   Holstege, Frank C P ^b   Cramer, Patrick ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^c Fred Hutchinson Cancer Research Center   (United States)

Author keywords

Mediator of transcriptional regulation; Molecular systems biology; Multiprotein coactivator complex; RNA polymerase II transcription; Structure function analysis

Indexed keywords

PROTEIN; PROTEIN MED18; PROTEIN MED20; PROTEIN MED8C; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; BINDING KINETICS; CHEMICAL ANALYSIS; COMPARATIVE STUDY; CORRELATION ANALYSIS; CRYSTALLOGRAPHY; DISSOCIATION; DOWN REGULATION; GENE CONTROL; GENE DELETION; GENE REGULATORY NETWORK; GENE STRUCTURE; GENETIC TRANSCRIPTION; IN VIVO STUDY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DETERMINATION; PROTEIN DOMAIN; TRANSCRIPTION REGULATION; TWO HYBRID SYSTEM;

ELECTROPHORESIS, POLYACRYLAMIDE GEL; GENE DELETION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; MASS SPECTROMETRY; MODELS, BIOLOGICAL; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 41649112169     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.465108     Document Type: Article

References (28)

1. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., et al. 2000. Gene ontology: Tool for the unification of biology. Nat. Genet. 25: 25-29.
2. Backstrom, S., Elfving, N., Nilsson, R., Wingsle, G., and Bjorklund, S. 2007. Purification of a plant mediator from Arabidopsis thaliana identifies PFT1 as the Med25 subunit. Mol. Cell 26: 717-729.
3. Beve, J., Hu, G.Z., Myers, L.C., Balciunas, D., Werngren, O., Hultenby, K., Wibom, R., Ronne, H., and Gustafsson, C.M. 2005. The structural and functional role of Med5 in the yeast Mediator tail module. J. Biol. Chem. 280: 41366-41372.
4. Bjorklund, S. and Gustafsson, C.M. 2005. The yeast Mediator complex and its regulation. Trends Biochem. Sci. 30: 240-244.
5. Boube, M., Joulia, L., Cribbs, D.L., and Bourbon, H.-M. 2002. Evidence for a mediator of RNA polymerase II transcriptional regulation conserved from yeast to man. Cell 110: 143-151.
6. Dotson, M.R., Yuan, C.X., Roeder, R.G., Myers, L.C., Gustafsson, C.M., Jiang, Y.W., Li, Y., Kornberg, R.D., and Asturias, F.J. 2000. Structural organization of yeast and mammalian mediator complexes. Proc. Natl. Acad. Sci. 97: 14307-14310.
7. Enyenihi, A.H. and Saunders, W.S. 2003. Large-scale functional genomic analysis of sporulation and meiosis in Saccharomyces cerevisiae. Genetics 163: 47-54.
8. Gavin, A.C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J.M., Michon, A.M., Cruciat, C.M., et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147.
9. Gavin, A.C., Aloy, P., Grandi, P., Krause, R., Boesche, M., Marzioch, M., Rau, C., Jensen, L.J., Bastuck, S., Dumpelfeld, B., et al. 2006. Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631-636.
10. Guglielmi, B., van Berkum, N.L., Klapholz, B., Bijma, T., Boube, M., Boschiero, C., Bourbon, H.-M., Holstege, F.C.P., and Werner, M. 2004. A high resolution protein interaction map of the yeast Mediator complex. Nucleic Acids Res. 32: 5379-5391.
11. Holstege, F.C., Jennings, E.G., Wyrick, J.J., Lee, T.I., Hengartner, C.J., Green, M.R., Golub, T.R., Lander, E.S., and Young, R.A. 1998. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95: 717-728.
12. Kang, J.S., Kim, S.H., Hwang, M.S., Han, S.J., Lee, Y.C., and Kim, Y.J. 2001. The structural and functional organization of the yeast mediator complex. J. Biol. Chem. 276: 42003-42010.
13. Koleske, A.J., Buratowski, S., Nonet, M., and Young, R.A. 1992. A novel transcription factor reveals a functional link between the RNA polymerase II CTD and TFIID. Cell 69: 883-894.
14. Kornberg, R.D. 2005. Mediator and the mechanism of transcriptional activation. Trends Biochem. Sci. 30: 235-239.
15. Krogan, N.J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A.P., et al. 2006. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-643.
16. Lariviere, L., Geiger, S., Hoeppner, S., Rother, S., Strasser, K., and Cramer, P. 2006. Structure and TBP binding of the Mediator head subcomplex Med8-Med18-Med20. Nat. Struct. Mol. Biol. 13: 895-901.
17. Lee, Y.C., Park, J.M., Min, S., Han, S.J., and Kim, Y.J. 1999. An activator binding module of yeast RNA polymerase II holoenzyme. Mol. Cell. Biol. 19: 2967-2976.
18. Longtine, M.S., McKenzie III, A., Demarini, D.J., Shah, N.G., Wach, A., Brachat, A., Philippsen, P., and Pringle, J.R. 1998. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14: 953-961.
19. Malik, S. and Roeder, R.G. 2000. Transcriptional regulation through Mediator-like coactivators in yeast and metazoan cells. Trends Biochem. Sci. 25: 277-283.
20. Naar, A.M., Lemon, B.D., and Tjian, R. 2001. Transcriptional coactivator complexes. Annu. Rev. Biochem. 70: 475-501.
21. Puig, O., Caspary, F., Rigaut, G., Rutz, B., Bouveret, E., Bragado-Nilsson, E., Wilm, M., and Seraphin, B. 2001. The tandem affinity purification (TAP) method: A general procedure of protein complex purification. Methods 24: 218-229.
22. Ranish, J.A. and Hahn, S. 1991. The yeast general transcription factor TFIIA is composed of two polypeptide subunits. J. Biol. Chem. 266: 19320-19327.
23. Ranish, J.A., Yudkovsky, N., and Hahn, S. 1999. Intermediates in formation and activity of the RNA polymerase II preinitiation complex: Holoenzyme recruitment and a postrecruitment role for the TATA box and TFIIB. Genes & Dev. 13: 49-63.
24. Singh, H., Erkine, A.M., Kremer, S.B., Duttweiler, H.M., Davis, D.A., Iqbal, J., Gross, R.R., and Gross, D.S. 2006. A functional module of yeast mediator that governs the dynamic range of heat-shock gene expression. Genetics 172: 2169-2184.
25. Takagi, Y. and Kornberg, R.D. 2006. Mediator as a general transcription factor. J. Biol. Chem. 281: 80-89.
26. Takagi, Y., Calero, G., Komori, H., Brown, J.A., Ehrensberger, A.H., Hudmon, A., Asturias, F., and Kornberg, R.D. 2006. Head module control of mediator interactions. Mol. Cell 23: 355-364.
27. Thompson, C.M., Koleske, A.J., Chao, D.M., and Young, R.A. 1993. A multisubunit complex associated with the RNA polymerase II CTD and TATA-binding protein in yeast. Cell 73: 1361-1375.
28. van de Peppel, J., Kettelarij, N., van Bakel, H., Kockelkorn, T.T.J.P., van Leenen, D., and Holstege, F.C.P. 2005. Mediator expression profiling epistasis reveals a signal transduction pathway with antagonistic submodules and highly specific downstream targets. Mol. Cell 19: 511-522.