Core Mediator structure at 3.4 Å extends model of transcription initiation complex

Nature

Volumn 545, Issue 7653, 2017, Pages 248-251

  Nozawa, Kayo ^a   Schneider, Thomas R ^b   Cramer, Patrick ^a  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

^b DESY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MEDIATOR COMPLEX; PHOSPHOTRANSFERASE; TRANSCRIPTION INITIATION FACTOR KINASE; UNCLASSIFIED DRUG; MED6 PROTEIN, S POMBE; PROTEIN SUBUNIT; RNA POLYMERASE II; SCHIZOSACCHAROMYCES POMBE PROTEIN; SRB4 PROTEIN, S POMBE; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR II; TRANSCRIPTION FACTOR IIH;

ACTIVATION ENERGY; CHEMICAL BINDING; CRYSTAL STRUCTURE; DECARBOXYLATION; EXPERIMENTAL STUDY; MICROSCOPY; MUTATION; PROTEIN; YEAST;

ARTICLE; CRYOELECTRON MICROSCOPY; CRYSTAL STRUCTURE; ENZYME PHOSPHORYLATION; MUTATION; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE; TRANSCRIPTION INITIATION; CHEMISTRY; GENETICS; METABOLISM; MOLECULAR MODEL; PHOSPHORYLATION; PROTEIN SUBUNIT; SCHIZOSACCHAROMYCES; ULTRASTRUCTURE; X RAY CRYSTALLOGRAPHY;

SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE;

CRYOELECTRON MICROSCOPY; CRYSTALLOGRAPHY, X-RAY; MEDIATOR COMPLEX; MODELS, MOLECULAR; MUTATION; PHOSPHORYLATION; PROTEIN SUBUNITS; RNA POLYMERASE II; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES; SCHIZOSACCHAROMYCES POMBE PROTEINS; TRANSCRIPTION FACTOR TFIIH; TRANSCRIPTION FACTORS; TRANSCRIPTION FACTORS, TFII; TRANSCRIPTION INITIATION, GENETIC;

EID: 85019255956     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature22328     Document Type: Article

References (51)

1. Kornberg, R. D. Mediator and the mechanism of transcriptional activation. Trends Biochem. Sci. 30, 235-239 (2005).
2. Malik, S. & Roeder, R. G. The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation. Nature Rev. Genet. 11, 761-772 (2010).
3. Allen, B. L. & Taatjes, D. J. The Mediator complex: a central integrator of transcription. Nature Rev. Mol. Cell Biol. 16, 155-166 (2015).
4. Cevher, M. A. et al. Reconstitution of active human core Mediator complex reveals a critical role of the MED14 subunit. Nature Struct. Mol. Biol. 21, 1028-1034 (2014).
5. Plaschka, C. et al. Architecture of the RNA polymerase II-Mediator core initiation complex. Nature 518, 376-380 (2015).
6. Liu, Y, Ranish, J. A., Aebersold, R. & Hahn, S. Yeast nuclear extract contains two major forms of RNA polymerase II Mediator complexes. J. Biol. Chem. 276, 7169-7175 (2001).
7. Jeronimo, C. et al. Tail and kinase modules diferently regulate core Mediator recruitment and function in vivo. Mol. Cell 64, 455-466 (2016).
8. Tsai, K. L. et al. Subunit architecture and functional modular rearrangements of the transcriptional Mediator complex. Cell 157, 1430-1444 (2014).
9. Wang, X. et al. Redefning the modular organization of the core Mediator complex. Cell Res. 24, 796-808 (2014).
10. Robinson, P. J. et al. Molecular architecture of the yeast Mediator complex. eLife 4, e08719 (2015).
11. Plaschka, C, Nozawa, K. & Cramer, P. Mediator architecture and RNA polymerase II interaction. J. Mol. Biol. 428, 2569-2574 (2016).
12. Larivière, L, Seizl, M. & Cramer, P. A structural perspective on Mediator function. Curr. Opin. Cell Biol. 24, 305-313 (2012).
13. Larivière, L. et al. Structure of the Mediator head module. Nature 492, 448-451 (2012).
14. Imasaki, T et al. Architecture of the Mediator head module. Nature 475, 240-243 (2011).
15. Robinson, P. J., Bushnell, D. A., Trnka, M. J., Burlingame, A. L. & Kornberg, R. D. Structure of the Mediator head module bound to the carboxy-terminal domain of RNA polymerase II. Proc. Natl Acad. Sci. USA 109, 17931-17935 (2012).
16. Lee, Y C. & Kim, Y J. Requirement for a functional interaction between Mediator components Med6 and Srb4 in RNA polymerase II transcription. Mol. Cell. Biol. 18, 5364-5370 (1998).
17. Thompson, C. M. & Young, R. A. General requirement for RNA polymerase II holoenzymes in vivo. Proc. Natl Acad. Sci. USA 92, 4587-4590 (1995).
18. Plaschka, C. et al. Transcription initiation complex structures elucidate DNA opening. Nature 533, 353-358 (2016).
19. Baumli, S., Hoeppner, S. & Cramer, P. A conserved Mediator hinge revealed in the structure of the MED7·MED21 (Med7·Srb7) heterodimer. J. Biol. Chem. 280, 18171-18178 (2005).
20. Robinson, P. J. et al. Structure of a complete Mediator-RNA polymerase II pre-initiation complex. Cell 166, 1411-1422 (2016).
21. Koschubs, T. et al. Preparation and topology of the Mediator middle module. Nucleic Acids Res. 38, 3186-3195 (2010).
22. Larivière, L. et al. Model of the Mediator middle module based on protein cross-linking. Nucleic Acids Res. 41, 9266-9273 (2013).
23. Alontaga, A. Y. et al. RWD domain as an E2 (Ubc9)-interaction module. J. Biol. Chem. 290, 16550-16559 (2015).
24. Sheng, Y. et al. A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen. Mol. Cell. Proteomics 11, 329-341 (2012).
25. Seizl, M., Larivière, L., Pfafeneder, T., Wenzeck, L. & Cramer, P. Mediator head subcomplex Med11/22 contains a common helix bundle building block with a specifc function in transcription initiation complex stabilization. Nucleic Acids Res. 39, 6291-6304 (2011).
26. Sato, S. et al. Role for the MED21-MED7 Hinge in assembly of the Mediator-RNA polymerase II holoenzyme. J. Biol. Chem. 291, 26886-26898 (2016).
27. Koschubs, T. et al. Identifcation, structure, and functional requirement of the Mediator submodule Med7N/31. EMBO J. 28, 69-80 (2009).
28. Linder, T., Zhu, X., Baraznenok, V. & Gustafsson, C. M. The classical srb4-138 mutant allele causes dissociation of yeast Mediator. Biochem. Biophys. Res. Commun. 349, 948-953 (2006).
29. Murakami, K. et al. Structure of an RNA polymerase II preinitiation complex. Proc. Natl Acad. Sci. USA 112, 13543-13548 (2015).
30. He, Y. et al. Near-atomic resolution visualization of human transcription promoter opening. Nature 533, 359-365 (2016).
31. Tsai, K. L. et al. Mediator structure and rearrangements required for holoenzyme formation. Nature (2017).
32. Deng, X., Davidson, W. S. & Thompson, T. B. Improving the difraction of apoA-IV crystals through extreme dehydration. Acta Crystallogr. F 68, 105-110 (2012).
33. Kabsch, W. Xds. Acta Crystallogr. D 66, 125-132 (2010).
34. Foadi, J. et al. Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography. Acta Crystallogr. D 69, 1617-1632 (2013).
35. McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658-674 (2007).
36. Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213-221 (2010).
37. Terwilliger, T. C. et al. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard. Acta Crystallogr. D 65, 582-601 (2009).
38. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126-2132 (2004).
39. Larivière, L. et al. Structure and TBP binding of the Mediator head subcomplex Med8-Med18-Med20. Nature Struct. Mol. Biol. 13, 895-901 (2006).
40. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refnement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240-255 (1997).
41. Afonine, P. V. et al. Towards automated crystallographic structure refnement with phenix.refne. Acta Crystallogr. D 68, 352-367 (2012).
42. Webb, B. & Sali, A. Protein structure modeling with MODELLER. Methods Mol. Biol. 1137, 1-15 (2014).
43. Baejen, C. et al. Genome-wide analysis of RNA polymerase II termination at protein-coding genes. Mol. Cell 66, 38-49.e6 (2017).
44. Singh, H. et al. A functional module of yeast Mediator that governs the dynamic range of heat-shock gene expression. Genetics 172, 2169-2184 (2006).
45. Takagi, Y. & Kornberg, R. D. Mediator as a general transcription factor. J. Biol. Chem. 281, 80-89 (2006).
46. Kaufmann, R. et al. Infantile cerebral and cerebellar atrophy is associated with a mutation in the MED17 subunit of the transcription preinitiation Mediator complex. Am. J. Hum. Genet. 87, 667-670 (2010).
47. Soutourina, J., Wydau, S., Ambroise, Y., Boschiero, C. & Werner, M. Direct interaction of RNA polymerase II and Mediator required for transcription in vivo. Science 331, 1451-1454 (2011).
48. Peiró-Chova, L. & Estruch, F. Specifc defects in diferent transcription complexes compensate for the requirement of the negative cofactor 2 repressor in Saccharomyces cerevisiae. Genetics 176, 125-138 (2007).
49. Han, S. J. et al. Activator-specifc requirement of yeast Mediator proteins for RNA polymerase II transcriptional activation. Mol. Cell. Biol. 19, 979-988 (1999).
50. Eychenne, T. et al. Functional interplay between Mediator and TFIIB in preinitiation complex assembly in relation to promoter architecture. Genes Dev. 30, 2119-2132 (2016).
51. Hallberg, M. et al. Functional and physical interactions within the middle domain of the yeast Mediator. Mol. Genet. Genomics 276, 197-210 (2006).