Biology:Mediator (coactivator)

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Diagram of mediator with cyclin-dependent kinase module

Mediator is a multiprotein complex that functions as a transcriptional coactivator in all eukaryotes. It was discovered in 1990 in the lab of Roger D. Kornberg, recipient of the 2006 Nobel Prize in Chemistry.[1][2] Mediator[lower-alpha 1] complexes interact with transcription factors and RNA polymerase II. The main function of mediator complexes is to transmit signals from the transcription factors to the polymerase.[3]

Mediator complexes are variable at the evolutionary, compositional and conformational levels.[3] The first image shows only one "snapshot" of what a particular mediator complex might be composed of,[lower-alpha 2] but it certainly does not accurately depict the conformation of the complex in vivo. During evolution, mediator has become more complex. The yeast Saccharomyces cerevisiae (a simple eukaryote) is thought to have up to 21 subunits in the core mediator (exclusive of the CDK module), while mammals have up to 26.

Individual subunits can be absent or replaced by other subunits under different conditions. Also, there are many intrinsically disordered regions in mediator proteins, which may contribute to the conformational flexibility seen both with and without other bound proteins or protein complexes. A more realistic model of a mediator complex without the CDK module is shown in the second figure.[4]

The mediator complex is required for the successful transcription by RNA polymerase II. Mediator has been shown to make contacts with the polymerase in the transcription preinitiation complex.[3] A recent model showing the association of the polymerase with mediator in the absence of DNA is shown in the figure to the left.[4] In addition to RNA polymerase II, mediator must also associate with transcription factors and DNA. A model of such interactions is shown in the figure to the right.[5] Note that the different morphologies of mediator do not necessarily mean that one of the models is correct; rather those differences may reflect the flexibility of mediator as it interacts with other molecules.[lower-alpha 3] For example, after binding the enhancer and core promoter, the mediator complex undergoes a compositional change in which the kinase module dissociates from the complex to allow association with RNA polymerase II and transcriptional activation.[6]

The Mediator complex is located within the cell nucleus. It is required for the successful transcription of nearly all class II gene promoters in yeast.[7] It works in the same manner in mammals. The mediator functions as a coactivator and binds to the C-terminal domain of RNA polymerase II holoenzyme, acting as a bridge between this enzyme and transcription factors.[8]

Structure

Mediator complex architecture with focus on the disordered "spline" of Med 14[9]

The yeast mediator complex is approximately as massive as a small subunit of a eukaryotic ribosome. The yeast mediator is composed of 25 subunits, while the mammalian mediator complexes are slightly larger.[3] Mediator can be divided into 4 main parts: The head, middle, tail, and the transiently associated CDK8 kinase module.[10]

Mediator subunits have many intrinsically disordered regions called "splines", which may be important to allow the structural changes of the mediator that change the function of the complex.[3][lower-alpha 4] The figure shows how the splines of the Med 14 subunit connect a large portion of the complex together while still allowing flexibility.[4][lower-alpha 5]

Mediator complexes that lack a subunit have been found or produced. These smaller mediators can still function normally in some activity, but lack other capabilities.[3] This indicates a somewhat independent function of some of the subunits while being part of the larger complex.

Another example of structural variability is seen in vertebrates, in which 3 paralogues of subunits of the cyclin-dependent kinase module have evolved by 3 independent gene duplication events followed by sequence divergence.[3]

Mediator structural model[9]

There is a report that mediator forms stable associations with a particular type of non-coding RNA, ncRNA-a.[11][lower-alpha 6] These stable associations have also been shown to regulate gene expression in vivo, and are prevented by mutations in MED12 that produce the human disease FG syndrome.[11] Thus, the structure of a mediator complex can be augmented by RNA as well as proteinaceous transcription factors.[3]

Function

Structural model of the tail and middle of mediator bound to RNA polymerase II[9]

Mediator was originally discovered because it was important for RNA polymerase II function, but it has many more functions than just interactions at the transcription start site.[3]

RNA polymerase II-Mediator core initiation complex

Mediator is a crucial component for transcription initiation. Mediator interacts with the pre-initiation complex, composed of RNA Polymerase II and general transcription factors TFIIB, TFIID, TFIIE, TFIIF, and TFIIH to stabilize and initiate transcription.[12] Studies of Mediator-RNA Pol II contacts in budding yeast have emphasized the importance of TFIIB-Mediator contacts in the formation of the complex. Interactions of Mediator with TFIID in the initiation complex has been shown.[10]

The Structure of a core Mediator (cMed) that's associated with a core pre-initiation complex was elucidated.[12]

RNA synthesis

The preinitiation complex, which contains a mediator, transcription factors, a nucleosome[13][14][lower-alpha 7] and RNA polymerase II, is important to position the polymerase for the start of transcription. Before RNA synthesis can occur, the polymerase must dissociate from mediator. This appears to be accomplished by phosphorylation of part of the polymerase by a kinase. Importantly, mediator and transcription factors do not dissociate from the DNA at the time polymerase begins transcription. Rather, the complex remains at the promoter to recruit another RNA polymerase to begin another round of transcription.[3][lower-alpha 8]

There is some evidence to suggest that mediator in a yeast is involved in regulating RNA polymerase III (Pol III) transcripts of tRNAs[15] In support of that evidence, an independent report showed specific association of mediator with Pol III in Saccharomyces cerevisiae.[16] Those authors also reported specific associations with RNA polymerase I and proteins involved in transcription elongation and RNA processing, supporting other evidence of mediator's involvement in elongation and processing.[16]

Chromatin organization

Mediator is involved in "looping" of chromatin, which brings distant regions of a chromosome into closer physical proximity.[3] The ncRNA-a mentioned above[11] is involved in such looping.[lower-alpha 9] Enhancer RNAs (eRNAs) can function similarly.[3]

In addition to the looping of euchromatin, mediator appears to be involved in formation or maintenance of heterochromatin at centromeres and telomeres.[3]

Signal transduction

TGFβ signaling at the cell membrane results in 2 different intracellular pathways. One of them depends on MED15,[lower-alpha 10] while the other is independent of MED15.[17] In both human cells and Caenorhabditis elegans MED15 is involved in lipid homeostasis through the pathway involving SREBPs[18] In the model plant Arabidopsis thaliana the ortholog of MED15 is required for signaling by the plant hormone Salicylic acid,[19] while MED25 is required for the transcriptional activation of jasmonate and shade signalling responses.[20][21][22] Two components of the CDK module (MED12 and MED13) are involved in the Wnt signaling pathway[3] MED23 is involved in RAS/MAPK/ERK pathway[3] This abbreviated review shows the versatility of individual mediator subunits, and leads to the idea that mediator is an end-point of signaling pathways.[3]

Human disease

Involvement of mediator in various human diseases has been reviewed.[23][24][25][26][27][28][29][30][31][32][33] Since inhibiting one interaction of a disease-causing signaling pathway with a subunit of mediator may not inhibit general transcription needed for normal function, mediator subunits are attractive candidates for therapeutic drugs.[3]

Interactions

Mediator interactome in Saccharomyces cerevisiae[16]

A method employing very gentle cell lysis in yeast followed by co-immunoprecipitation with an antibody to a mediator subunit (Med 17) has confirmed almost all previously reported or predicted interactions and revealed many previously unsuspected specific interactions of various proteins with mediator.[16]

MED 1

The interaction network of MED1 protein from BioPlex 2.0

A discussion of all mediator subunits is beyond the scope of this article, but details of one of the subunits are illustrative of the types of information that may be gathered for other subunits.

regulation by Micro RNAs

Micro RNAs are involved in regulating the expression of many proteins. Med1 is targeted by miR-1, which is important in gene regulation in cancers.[34] The tumor suppressor miR-137 also regulates MED1.[35]

Mouse embryonic development

Null mutants die at an early gestational age (embryonic day 11.5).[36][37] By investigating hypomorphic mutants (which can survive 2 days longer), it was found that placental defects were primarily lethal and that there were also defects in cardiac and hepatic development, but many other organs were normal[37]

Mouse cells and tissues

A mediator mutation causes hairy teeth in mice

Conditional mutations can be produced in mice which affect only specific cells or tissues at specific times, so that the mouse can develop to adulthood and the adult phenotype can be studied. In one case, MED1 was found to participate in controlling the timing of events of meiosis in male mice.[38] Conditional mutants in keratinocytes show differences in skin wound healing.[39] A conditional mutant in mice was found to change dental epithelium into epidermal epithelium, which caused hair to grow associated with the incisors.[40]

Subunit composition

The Mediator complex is composed at least 31 subunits in all eukaryotes studied: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED28, MED29, MED30, MED31, CCNC, and CDK8. There are three fungal-specific components, referred to as Med2, Med3 and Med5.[41]

The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation.

  • The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22.
  • The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4.
  • The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16.
  • The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP.

In other species

Below is a cross-species comparison of mediator complex subunits.[41][42]

Subunit No. Human gene C. elegans gene D. melanogaster gene S. cerevisiae gene Sch. pombe gene
MED1 MED1 Sop3/mdt-1.1, 1.2 MED1 MED1 med1
Med2 [lower-alpha 11] MED2
Med3 [lower-alpha 11] PGD1
MED4 MED4 MED4 MED4 med4
Med5 [lower-alpha 11] NUT1
MED6 MED6 MDT-6 MED6 MED6 med6
MED7 MED7 MDT-7/let-49 MED7 MED7 med7
MED8 MED8 MDT-8 MED8 MED8 med8
MED9 MED9 MED9 CSE2
MED10 MED10 MDT-10 NUT2 med10
MED11 MED11 MDT-11 MED11 MED11 med11
MED12 MED12 MDT-12/dpy-22 MED12 SRB8 srb8
MED12L MED12L
MED13 MED13 MDT-13/let-19 MED13 SSN2 srb9
MED14 MED14 MDT-14/rgr-1 MED14 RGR1 med14
MED15 MED15 mdt-15 MED15 GAL11 YN91_SCHPO [lower-alpha 12]
MED16 MED16 MED16 SIN4
MED17 MED17 MDT-17 MED17 SRB4 med17
MED18 MED18 MDT-18 MED18 SRB5 med18
MED19 MED19 MDT-19 MED19 ROX3[41] med19
MED20 MED20 MDT-20 MED20 SRB2 med20
MED21 MED21 MDT-21 MED21 SRB7 med21
MED22 MED22 MDT-22 MED22 SRB6 med22
MED23 MED23 MDT-23/sur-2 MED23
MED24 MED24 MED24
MED25 MED25 MED25
MED26 MED26 MED26
MED27 MED27 MED27 med27
MED28 MED28 MED28
MED29 MED29 MDT-19 MED29
MED30 MED30 MED30
MED31 MED31 MDT-31 MED31 SOH1 med31
CCNC CCNC cic-1 CycC SSN8 pch1
CDK8 CDK8 cdk-8 Cdk8 SSN3 srb10

Notes

  1. ↑ Mediator is also referred to in scientific literature as the vitamin D receptor interacting protein (DRIP) coactivator complex and the thyroid hormone receptor-associated proteins (TRAP).
  2. ↑ However note that more recently it has been found that the CDK module and MED26 cannot be present concurrently in a complex.[3]
  3. ↑ The sharp bend in the DNA associated with the transcription bubble is shown in the graphical abstract and first figure of this research paper
  4. ↑ Some of those changes are diagrammed in figure 1 of the review article, which can be viewed in slightly larger form by clicking it at that site.
  5. ↑ Note that Med 17 (shown in blue) also has that sort of spline
  6. ↑ These non-coding activating RNAs have not been mentioned yet in the ncRNA article as of 16 February 2017
  7. ↑ This is the +1 nucleosome, which "covers" the transcription start site during the preinitiation phase.
  8. ↑ This is diagrammed in figure 2 of the review article, which can be viewed in slightly larger form by clicking it at that site.
  9. ↑ This is diagrammed in figure 3 of the review article, which can be viewed in slightly larger form by clicking it at that site. That figure also shows Pol II disengaged from mediator, etc, which remains on the DNA
  10. ↑ Also known as ARC105 in Xenopus laevis, the model species in which the work was done.
  11. ↑ 11.0 11.1 11.2 Fungal-specific
  12. ↑ Protein-name in Sch. pombe

References

  1. ↑ "A novel mediator between activator proteins and the RNA polymerase II transcription apparatus". Cell 61 (7): 1209–15. June 1990. doi:10.1016/0092-8674(90)90685-8. PMID 2163759. 
  2. ↑ "A mediator required for activation of RNA polymerase II transcription in vitro". Nature 350 (6317): 436–8. April 1991. doi:10.1038/350436a0. PMID 2011193. Bibcode: 1991Natur.350..436F. 
  3. ↑ 3.00 3.01 3.02 3.03 3.04 3.05 3.06 3.07 3.08 3.09 3.10 3.11 3.12 3.13 3.14 3.15 3.16 3.17 "The Mediator complex: a central integrator of transcription". Nature Reviews Molecular Cell Biology 16 (3): 155–66. March 2015. doi:10.1038/nrm3951. PMID 25693131. 
  4. ↑ 4.0 4.1 4.2 "Molecular architecture of the yeast Mediator complex". eLife 4: e08719. September 2015. doi:10.7554/eLife.08719. PMID 26402457. 
  5. ↑ "Molecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly". PLOS Biology 9 (3): e1000603. March 2011. doi:10.1371/journal.pbio.1000603. PMID 21468301. 
  6. ↑ Petrenko, N; Jin, Y; Wong, KH; Struhl, K (3 November 2016). "Mediator Undergoes a Compositional Change during Transcriptional Activation.". Molecular Cell 64 (3): 443–454. doi:10.1016/j.molcel.2016.09.015. PMID 27773675. 
  7. ↑ "Yeast mediator and its role in transcriptional regulation". Comptes Rendus Biologies 328 (9): 773–82. September 2005. doi:10.1016/j.crvi.2005.03.004. PMID 16168358. https://comptes-rendus.academie-sciences.fr/biologies/articles/10.1016/j.crvi.2005.03.004/. 
  8. ↑ "The yeast Mediator complex and its regulation". Trends in Biochemical Sciences 30 (5): 240–4. May 2005. doi:10.1016/j.tibs.2005.03.008. PMID 15896741. 
  9. ↑ 9.0 9.1 9.2 Robinson, Philip J.; Trnka, Michael J.; Pellarin, Riccardo; Greenberg, Charles H.; Bushnell, David A.; Davis, Ralph; Burlingame, Alma L.; Sali, Andrej et al. (2015-09-24). "Molecular architecture of the yeast Mediator complex". eLife 4: e08719. doi:10.7554/eLife.08719. ISSN 2050-084X. PMID 26402457. 
  10. ↑ 10.0 10.1 Soutourina, Julie (2017-12-06). "Transcription regulation by the Mediator complex". Nature Reviews Molecular Cell Biology 19 (4): 262–274. doi:10.1038/nrm.2017.115. ISSN 1471-0072. PMID 29209056. 
  11. ↑ 11.0 11.1 11.2 Lai, F (2013). "Activating RNAs associate with mediator to enhance chromatin architecture and transcription". Nature 494 (7438): 497–501. doi:10.1038/nature11884. PMID 23417068. PMC 4109059. Bibcode: 2013Natur.494..497L. http://pubman.mpdl.mpg.de/pubman/item/escidoc:2019856/component/escidoc:2019946/Lai.pdf. 
  12. ↑ 12.0 12.1 Plaschka, C.; Larivière, L.; Wenzeck, L.; Seizl, M.; Hemann, M.; Tegunov, D.; Petrotchenko, E. V.; Borchers, C. H. et al. (February 2015). "Architecture of the RNA polymerase II–Mediator core initiation complex". Nature 518 (7539): 376–380. doi:10.1038/nature14229. ISSN 0028-0836. PMID 25652824. Bibcode: 2015Natur.518..376P. https://resolver.sub.uni-goettingen.de/purl?gro-2/2924. 
  13. ↑ "Chromatin potentiates transcription". Proc Natl Acad Sci U S A 114 (7): 1536–154. 2017. doi:10.1073/pnas.1620312114. PMID 28137832. 
  14. ↑ Kornberg, RD. "The Molecular Basis of Eukaryotic Transcription". Israel Institute for Advanced Studies. https://www.youtube.com/watch?v=QZIj062Pd1E&t=1414s. 
  15. ↑ Carlsten, JO; Zhu X, López MD, Samuelsson T, Gustafsson CM (February 2016). "Loss of the Mediator subunit Med20 affects transcription of tRNA and other non-coding RNA genes in fission yeast". Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1859 (2): 339–347. doi:10.1016/j.bbagrm.2015.11.007. PMID 26608234. 
  16. ↑ 16.0 16.1 16.2 16.3 "Proteomic Analysis of the Mediator Complex Interactome in Saccharomyces cerevisiae". Sci Rep 7: 43584. 2017. doi:10.1038/srep43584. PMID 28240253. Bibcode: 2017NatSR...743584U. 
  17. ↑ "A component of the ARC/Mediator complex required for TGF beta/Nodal signalling". Nature 418 (6898): 641–6. 2002. doi:10.1038/nature00969. PMID 12167862. Bibcode: 2002Natur.418..641K. 
  18. ↑ "An ARC/Mediator subunit required for SREBP control of cholesterol and lipid homeostasis". Nature 442 (7103): 700–4. 2006. doi:10.1038/nature04942. PMID 16799563. Bibcode: 2006Natur.442..700Y. 
  19. ↑ "Non-recognition-of-BTH4, an Arabidopsis mediator subunit homolog, is necessary for development and response to salicylic acid". Plant Cell 24 (10): 4220–35. 2012. doi:10.1105/tpc.112.103028. PMID 23064321. 
  20. ↑ Chen, Rong; Jiang, Hongling; Li, Lin; Zhai, Qingzhe; Qi, Linlin; Zhou, Wenkun; Liu, Xiaoqiang; Li, Hongmei et al. (July 2012). "The Arabidopsis Mediator Subunit MED25 Differentially Regulates Jasmonate and Abscisic Acid Signaling through Interacting with the MYC2 and ABI5 Transcription Factors". The Plant Cell 24 (7): 2898–2916. doi:10.1105/tpc.112.098277. PMID 22822206. 
  21. ↑ Sun, Wenjing; Han, Hongyu; Deng, Lei; Sun, Chuanlong; Xu, Yiran; Lin, Lihao; Ren, Panrong; Zhao, Jiuhai et al. (November 2020). "Mediator Subunit MED25 Physically Interacts with PHYTOCHROME INTERACTING FACTOR4 to Regulate Shade-Induced Hypocotyl Elongation in Tomato". Plant Physiology 184 (3): 1549–1562. doi:10.1104/pp.20.00587. PMID 32938743. 
  22. ↑ Hartman, Sjon (November 2020). "MED25 Mediates Shade-Induced Hypocotyl Elongation in Tomato". Plant Physiology 184 (3): 1217–1218. doi:10.1104/pp.20.01324. PMID 33139486. 
  23. ↑ "Mediator kinase module and human tumorigenesis". Crit Rev Biochem Mol Biol 50 (5): 393–426. 2015. doi:10.3109/10409238.2015.1064854. PMID 26182352. 
  24. ↑ "MED12 and uterine smooth muscle oncogenesis: State of the art and perspectives". Eur J Cancer 51 (12): 1603–10. 2015. doi:10.1016/j.ejca.2015.04.023. PMID 26037152. 
  25. ↑ "Involvement of Mediator complex in malignancy". Biochim Biophys Acta 1845 (1): 66–83. 2014. doi:10.1016/j.bbcan.2013.12.001. PMID 24342527. 
  26. ↑ "The roles of mediator complex in cardiovascular diseases". Biochim Biophys Acta 1839 (6): 444–51. 2014. doi:10.1016/j.bbagrm.2014.04.012. PMID 24751643. 
  27. ↑ "Impaired development of neural-crest cell-derived organs and intellectual disability caused by MED13L haploinsufficiency". Hum Mutat 35 (11): 1311–20. 2014. doi:10.1002/humu.22636. PMID 25137640. 
  28. ↑ Grueter CE (2013). "Mediator complex dependent regulation of cardiac development and disease". Genomics Proteomics Bioinformatics 11 (3): 151–7. doi:10.1016/j.gpb.2013.05.002. PMID 23727265. 
  29. ↑ Yang X and Yang F (2013). "Mediating Lipid Biosynthesis: Implications for Cardiovascular Disease". Trends Cardiovasc Med 23 (7): 269–273. doi:10.1016/j.tcm.2013.03.002. PMID 23562092. 
  30. ↑ "Unraveling framework of the ancestral Mediator complex in human diseases". Biochimie 94 (3): 579–87. 2012. doi:10.1016/j.biochi.2011.09.016. PMID 21983542. 
  31. ↑ "Dysregulation of CDK8 and Cyclin C in tumorigenesis". J Genet Genomics 38 (10): 439–52. 2011. doi:10.1016/j.jgg.2011.09.002. PMID 22035865. 
  32. ↑ "Mediator and human disease". Semin Cell Dev Biol 22 (7): 776–87. 2011. doi:10.1016/j.semcdb.2011.07.024. PMID 21840410. 
  33. ↑ Lyons MJ (2008). MED12-Related Disorders (08/11/2016 ed.). University of Washington, Seattle. https://www.ncbi.nlm.nih.gov/books/NBK1676/. 
  34. ↑ "MicroRNA-1 functions as a potential tumor suppressor in osteosarcoma by targeting Med1 and Med31". Oncol Rep 32 (3): 1249–56. 2014. doi:10.3892/or.2014.3274. PMID 24969180. 
  35. ↑ "MiR137 is an androgen regulated repressor of an extended network of transcriptional coregulators". Oncotarget 6 (34): 35710–25. 2015. doi:10.18632/oncotarget.5958. PMID 26461474. 
  36. ↑ "Involvement of the TRAP220 component of the TRAP/SMCC coactivator complex in embryonic development and thyroid hormone action". Mol Cell 5 (4): 683–93. 2000. doi:10.1016/S1097-2765(00)80247-6. PMID 10882104. 
  37. ↑ 37.0 37.1 Landles C, Chalk S, Steel JH, Rosewell I, Spencer-Dene B, Lalani el-N, Parker MG (2003). "The thyroid hormone receptor-associated protein TRAP220 is required at distinct embryonic stages in placental, cardiac, and hepatic development". Mol Endocrinol 17 (12): 2418–35. doi:10.1210/me.2003-0097. PMID 14500757. 
  38. ↑ "Med1 regulates meiotic progression during spermatogenesis in mice". Reproduction 149 (6): 597–604. 2015. doi:10.1530/REP-14-0483. PMID 25778538. 
  39. ↑ "Alteration of skin wound healing in keratinocyte-specific mediator complex subunit 1 null mice". PLOS ONE 9 (8): e102271. 2014. doi:10.1371/journal.pone.0102271. PMID 25122137. Bibcode: 2014PLoSO...9j2271N. 
  40. ↑ "Ablation of coactivator Med1 switches the cell fate of dental epithelia to that generating hair". PLOS ONE 9 (6): e99991. 2014. doi:10.1371/journal.pone.0099991. PMID 24949995. Bibcode: 2014PLoSO...999991Y. 
  41. ↑ 41.0 41.1 41.2 "A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II". Molecular Cell 14 (5): 553–7. 2004. doi:10.1016/j.molcel.2004.05.011. PMID 15175151. 
  42. ↑ Gene names derived from "UniProtKB". https://www.uniprot.org/uniprot/. 



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