A high resolution protein interaction map of the yeast Mediator complex

Nucleic Acids Research

Volumn 32, Issue 18, 2004, Pages 5379-5391

  Guglielmi, Benjamin ^c   van Berkum, Nynke L ^a   Klapholz, Benjamin ^b   Bijma, Theo ^a   Boube, Muriel ^b   Boschiero, Claire ^c   Bourbon, Henri Marc ^b   Holstege, Frank C P ^a   Werner, Michel ^c  

^a UNIVERSITY MEDICAL CENTER UTRECHT   (Netherlands)

^b Centre de Biologie du Developpement Toulouse   (France)

^c CEA SACLAY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE 8; DNA BINDING PROTEIN; MEDIATOR PROTEIN; PROTEIN SUBUNIT; REGULATOR PROTEIN; RNA POLYMERASE II; SOH1 PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; DROSOPHILA PROTEIN; MED31 PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; GEL FILTRATION; GENETIC CONSERVATION; GENETIC SCREENING; IMMUNOPRECIPITATION; METAZOON; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; REGULATORY MECHANISM; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; TWO HYBRID SYSTEM; ANIMAL; CHEMISTRY; DROSOPHILA MELANOGASTER; GENE LIBRARY; GENETICS; MACROMOLECULE; METABOLISM; PROTEIN TERTIARY STRUCTURE;

METAZOA; SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES;

ANIMALS; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; GENOMIC LIBRARY; MACROMOLECULAR SUBSTANCES; PROTEIN STRUCTURE, TERTIARY; PROTEIN SUBUNITS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TWO-HYBRID SYSTEM TECHNIQUES;

EID: 6044249068     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh878     Document Type: Article

References (52)

1. Hampsey,M. (1998) Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol. Mol. Biol. Rev., 62, 465-503.
2. Kim,Y.-J., Börklund,S., Li,Y., Sayre,M.H. and Kornberg,R.D. (1994) A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell, 77, 599-608.
3. 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.
4. Holstege,F.C.P., 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 eakaryotic genome. Cell, 95, 717-728.
5. Ito,M., Yuan,C.X., Malik,S., Gu,W., Fondell,J.D., Yamamura,S., Fu,Z.Y., Zhang,X., Qin,J. and Roeder,R.G. (1999) Identity between TRAP and SMCC complexes indicates novel pathways for the function of nuclear receptors and diverse mammalian activators. Mol. Cell, 3, 361-370.
6. Näär,A.M., Beaurang,P.A., Zhou,S., Abraham,S., Solomon,W. and Tjian,R. (1999) Composite co-activator ARC mediates chromatin-directed transcriptional activation. Nature, 398, 828-832.
7. Ryu,S., Zhou,S., Ladurner,A.G. and Tjian,R. (1999) The transcriptional cofactor complex CRSP is required for activity of the enhancer-binding protein Sp1. Nature, 397, 446-450.
8. Rachez,C., Lemon,B.D., Suldan,Z., Bromleigh,V., Gamble,M., Näär,A.M., Erdjument-Bromage,H., Tempst,P. and Freedman,L.P. (1999) Ligand-dependent transcription activation by nuclear receptors requires the DRIP complex. Nature, 398, 824-828.
9. Sato,S., Tomomori-Sato,C., Parmely,T.J., Florens,L., Zybailov,B., Swanson,S.K., Banks,C.A., Jin,J., Cai,Y., Washburn,M.P. et al. (2004) A set of consensus Mammalian mediator subunits identified by multidimensional protein identification technology. Mol. Cell, 14, 685-691.
10. 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.
11. Park,J.M., Gim,B.S., Kim,J.M., Yoon,J.H., Kim,H.S., Kang,J.G. and Kim,Y.J. (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.
12. Gu,W., Malik,S., Ito,M., Yuan,C.X., Fondell,J.D., Zhang,X., Martinez,E., Qin,J. and Roeder,R.G. (1999) A novel human SRB/MED-containing cofactor complex, SMCC, involved in transcription regulation. Mol. Cell, 3, 97-108.
13. Liao,S.-M., Zhang,J., Jeffrey,D.A., Koleske,A.J., Thompson,C.M., Chao,D.M., Viljoen,M., van Vuuren,H.J.J. and Young,R.A. (1995) A kinase-cyclin pair in the RNA polymerase II holoenzyme. Nature, 374, 193-196.
14. Hengartner,C.J., Myer,V.E., Liao,S.-M., Wilson,C.J., Koh,S.S. and Young,R.A. (1998) Temporal regulation of RNA polymerase II by Srb10 and Kin28 cyclin-dependent kinases. Mol. Cell, 2, 43-53.
15. Nelson,C., Goto,S., Lund,K., Hung,W. and Sadowski,I. (2003) Srb10/ Cdk8 regulates yeast filamentous growth by phosphorylating the transcription factor Ste12. Nature, 421, 187-190.
16. Chi,Y., Huddleston,M.J., Zhang,X., Young,R.A., Annan,R.S., Carr,S.A. and Deshaies,R.J. (2001) Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase. Genes Der., 15, 1078-1092.
17. Hirst,M., Kobor,M.S., Kuriakose,N., Greenblatt,J. and Sadowski,I. (1999) GAL4 is regulated by the RNA polymerase II holoenzyme-associated cyclin-dependent protein kinase SRB10/CDK8. Mol. Cell, 3, 673-678.
18. 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. USA, 97, 14307-14310.
19. Li,Y., Bjorklund,S., Jiang,Y.W., Kim,Y.-J., Lane,W.S., Stillman,D.J. and Kornberg,R.D. (1995) Yeast global transcriptional regulators Sin4 and Rgr1 are components of mediator complex/RNA polymerase II holoenzyme. Proc. Natl Acad. Sci. USA, 92, 10864-10686.
20. Lee,Y.C. and Kim,Y.J. (1998) Requirement for a functional interaction between mediator components Med6 and Srb4 in RNA polymerase II transcription. Mol. Cell. Biol., 18, 5364-5370.
21. Han,S.J., Lee,Y.C., Gim,B.S., Ryu,G.H., Park,S.J., Lane,W.S. and Kim,Y.J. (1999) Activator-specific requirement of yeast mediator proteins for RNA polymerase II transcriptional activation. Mol. Cell. Biol., 19, 979-988.
22. Park,J.M., Kim,H.S., Han,S.J., Hwang,M.S., Lee,Y.C. and Kim,Y.J. (2000) In vivo requirement of activator-specific binding targets of mediator. Mol. Cell. Biol., 20, 8709-8719.
23. Davis,J., Takagi,Y., Kornberg,R. and Asturias,F. (2002) Structure of the yeast RNA polymerase II holoenzyme. Mediator conformation and polymerase interaction. Mol. Cell, 10, 409.
24. 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.
25. Koh,S.S., Ansari,A.Z., Ptashne,M. and Young,R.A. (1998) An activator target in the RNA polymerase II holoenzyme. Mol. Cell, 1, 895-904.
26. Lee,T.I., Wyrick,J.J., Koh,S.S., Jennings,E.G., Gadbois,E.L. and Young,R.A. (1998) Interplay of positive and negative regulators in transcription initiation by RNA polymerase II holoenzyme. Mol. Cell. Biol., 18, 4455-4462.
27. Uetz,P., Giot,L., Cagney,G., Mansfield,T.A., Judson,R.S., Knight,J.R., Lockshon,D., Narayan,V., Srinivasan,M., Pochart,P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.
28. Ito,T., Chiba,T., Ozawa,R., Yoshida,M., Hattori,M. and Sakaki,Y. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA, 98, 4569-4574.
29. Bartel,P.L., Chien,C.-T., Sternglanz,R. and Fields,S. (1993). Using the two hybrid system to detect protein-protein interactions. In Hartley,D.A. (ed.), Cellular Interactions in Development: A Practical Approach. Oxford University Press, Oxford, pp. 153-179.
30. Harper,J.W., Adami,G.R., Wei,N., Keyomarsi,K. and Elledge,S.J. (1993) The p21 Cdk-interacting protein Cip1 is a potent inhibitor of G1 cyclin-dependent kinases. Cell, 75, 805-816.
31. Werner,M., Chaussivert,N., Willis,I.M. and Sentenac,A. (1993) Interaction between a complex of RNA polymerase III subunits and the 70 kDa component of TFIIIB. J. Biol. Chem., 268.
32. Fromont-Racine,M., Rain,J.-C. and Legrain,P. (1997) Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens. Nature Genet., 16, 277-282.
33. Flores,A., Briand,J.-F., Gadal,O., Andrau,J.-C., Rubbi,L., Van Mullem,V., Boschiero,C., Goussot,M., Marck,C., Carles,C. et al. (1999) A protein-protein interaction map of yeast RNA polymerase III. Proc. Natl Acad. Sci. USA, 96, 7815-7820.
34. Rigaut,G., Shevchenko,A., Rutz,B., Wilm,M., Mann,M. and Seraphin,B. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17, 1030-1032.
35. Longtine,M.S., McKenzie,A.,III, Demarini,D.J., Shah,N.G., Wach,A., Brachat,A., Philipsen,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.
36. Fan,H.-Y., Cheng,K.K. and Klein,H.L. (1996) Mutations in the RNA polyinerase II transcription machinery suppress the hyperrecombination mutant hpr1Δ of Saccharomyces cerevisiae. Genetics, 142, 749-759.
37. Chavez,S., Beilharz,T., Rondon,A.G., Erdjument-Bromage,H., Tempst,P., Svejstrup,J.Q., Lithgow,T. and Aguilera,A. (2000) A protein complex containing Tho2, Hpr1, Mft1 and a novel protein, Thp2, connects transcription elongation with mitotic recombination in Saccharomyces cerevisiae. EMBO J., 19, 5824-5834.
38. Gromoller,A. and Lehming,N. (2000) Srb7p is a physical and physiological target of Tup1p. EMBO J., 19, 6845-6852.
39. Naar,A.M., Taatjes,D.J., Zhai,W., Nogales,E. and Tjian,R. (2002) Human CRSP interacts with RNA polymerase II CTD and adopts a specific CTD-bound conformation. Genes Dev., 16, 1339-1344.
40. Taatjes,D.J., Naar,A.M., Andel,I.F., Nogales,E. and Tjian,R. (2002) Structure, function, and activator-induced conformations of the CRSP coactivator. Science, 295, 1058-1062.
41. Myers,L.C. and Kornberg,R.D. (2000) Mediator of transcriptional regulation. Annu. Rev. Biochem., 69, 729-749.
42. Samuelsen,C.O., Baraznenok,V., Khorosjutina,O., Spahr,H., Kieselbach,T., Holmberg,S. and Gustafsson,C.M. (2003) TRAP230/ ARC240 and TRAP240/ARC250 Mediator subunits are functionally conserved through evolution. Proc. Natl Acad. Sci. USA, 100, 6422-6427.
43. Sato,S., Tomomori-Sato,C., Banks,C.A., Sorokina,I., Parmely,T.J., Kong,S.E., Jin,J., Cai,Y., Lane,W.S., Brower,C.S. et al. (2003) Identification of mammalian Mediator subunits with similarities to yeast Mediator subunits Srb5, Srb6, Med11, and Rox3. J. Biol. Chem. 278, 15123-15127.
44. Li,S., Armstrong,C.M., Bertin,N., Ge,H., Milstein,S., Boxem,M., Vidalain,P.O., Han,J.D., Chesneau,A., Hao,T. et al. (2004) A map of the interactome network of the metazoan C.elegans. Science, 303, 540-543.
45. Giot,L., Bader,J.S., Brouwer,C., Chaudburi,A., Kuang,B., Li,Y., Hao,Y.L., Ooi,C.E., Godwin,B., Vitols,E. et al. (2003) A protein interaction map of Drosophila melanogaster. Science, 302, 1727-1736.
46. Fromont-Racine,M., Mayes,A.E., Brunet-Simon,A., Rain,J.C., Colley,A., Dix,I., Decourty,L., Joly,N., Ricard,F., Beggs,J.D. et al. (2000) Genome-wide protein interaction screens reveal functional networks involving Sm-like proteins. Yeast, 17, 95-110.
47. Cramer,P., Bushnell,D.A. and Kornberg,R.D. (2001) Structural basis of transcription: RNA polymerase II at 2.8 ågstrom resolution. Science, 292, 1863-1876.
48. Cramer,P., Bushnell,D.A., Fu,J., Gnatt,A.L., Maier-Davis,B., Thompson,N.E., Burgess,R.R., Edwards,A.M., David,P.R. and Kornberg,R.D. (2000) Architecture of RNA polymerase II and implications for the transcription mechanism. Science, 288, 640-649.
49. Tomomori-Sato,C., Sato,S., Parmely,T.J., Banks,C.A., Sorokina,I., Florens,L., Zybailov,B., Washburn,M.P., Brower,C.S., Conaway,R.C. et al. (2004) A mammalian Mediator subunit that shares properties with Saccharomyces cerevisiae Mediator subunit Cse2. J. Biol. Chem., 279, 5846-5851.
50. Bourbon,H.M., Aguilera,A., Ansari,A.Z., Asturias,F.J., Berk,A.J., Bjorklund,S., Blackwell,T.K., Borggrefe,T., Carey,M., Carlson,M. et al. (2004) A unified nomenclature for protein subunits of Mediator complexes linking transcriptional regulators to RNA polymerase II. Mol. Cell, 14, 553-557.
51. Novatchkova,M. and Eisenhaber,F. (2004) Linking transcriptional mediators via the GACKIX domain super family. Curr. Biol., 14, R54-R55.
52. Rachez,C. and Freedman,L.P. (2001) Mediator complexes and transcription. Curr. Opin. Cell Biol., 13, 274-280.