Mediator (coactivator)


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. Mediator interacts with transcription factors and RNA polymerase II. It mainly functions to transmit signals from the transcription factors to the polymerase.
Mediator complexes are variable at the evolutionary, compositional and conformational levels. Figure 1 shows only one "snapshot" of what a particular complex might comprise, but it is an inaccurate depiction of the conformation in vivo. During evolution, Mediator has complexified. The yeast Saccharomyces cerevisiae is thought to have up to 21 subunits in the core Mediator, 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 Mediator without the CDK module is shown in Figure 2.
Mediator is required for successful transcription of genes by RNA polymerase II, and contacts the polymerase in the transcription preinitiation complex. A recent model showing the polymerase associating with Mediator without DNA is shown in Figure 3. In addition to RNA polymerase II, Mediator must also associate with transcription factors and DNA; a model of such interactions is shown in Figure 4. Note that the different morphologies of Mediator do not necessarily mean that a particular model is correct; rather those differences may reflect the flexibility of Mediator as it interacts with other molecules. For example, after binding the enhancer and core promoter, the Mediator complex compositionally changes, dissociating the kinase module and associating with RNA polymerase II for transcriptional activation.
Mediator is located within the cell nucleus. It is required for successfully transcribing nearly all class II gene promoters in yeast. It works similarly in mammals. Mediator functions as a coactivator and binds to the C-terminal domain of RNA polymerase II holoenzyme, bridging this enzyme and transcription factors.

Structure

The yeast Mediator complex is approximately as massive as a small subunit of a eukaryotic ribosome. The yeast Mediator has 25 subunits, while the mammalian Mediator is slightly larger. Mediator comprises 4 main parts: the head, middle, tail, and the transiently associated CDK8 kinase module.
Mediator subunits have many intrinsically disordered regions called "splines", which may be important to allow the structural changes of Mediator that change the function of the complex. Figure 5 shows the splines of the MED14 subunit connecting a large portion of the complex together while still allowing flexibility.
Mediator complexes lacking a subunit have been found or produced. These smaller complexes can still function normally in some activity, but lack other capabilities. This indicates a somewhat independent function of some of the subunits while composing 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. There is a report that Mediator stably associates with a particular type of non-coding RNA, ncRNA-a. These stable associations regulate gene expression in vivo, and are prevented by mutations in MED12 that produce the human disease FG syndrome. Thus, the structure of a Mediator complex can be augmented by RNA as well as proteinaceous transcription factors.

Function

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.

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. Studies of Mediator–RNA Pol II contacts in budding yeast showed the importance of TFIIB-Mediator contacts in the formation of the complex. Interactions of Mediator with TFIID in the initiation complex has been shown.
The structure of a core Mediator while associated with a core pre-initiation complex was elucidated.

RNA synthesis

The preinitiation complex, which contains Mediator, transcription factors, a nucleosome and RNA polymerase II, is important for positioning the polymerase for the start of transcription. Before RNA synthesis starts, the polymerase dissociates from Mediator. This is seemingly via phosphorylation of the polymerase by a kinase. Importantly, Mediator and transcription factors do not dissociate from the DNA when the polymerase begins transcription. Rather, the complex remains at the promoter to recruit another RNA polymerase to begin another round of transcription.
There is some evidence to suggest that Mediator in Schizosaccharomyces pombe helps regulate RNA polymerase III transcripts of tRNAs. An independent report confirmed Mediator specifically associating with Pol III in Saccharomyces cerevisiae. 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.

Chromatin organization

Mediator is involved in chromatin looping, which brings distant regions of a chromosome into closer physical proximity. The ncRNA-a mentioned above is involved in such looping. Enhancer RNAs can function similarly.
In addition to euchromatin looping, Mediator helps form or maintain heterochromatin at centromeres and telomeres.

Signal transduction

TGFβ signaling at the cell membrane involves two different intracellular pathways. Only one depends on MED15. In both human cells and Caenorhabditis elegans, MED15 helps lipid homeostasis through the SREBP-containing pathway. In the model plant Arabidopsis thaliana, the ortholog of MED15 is required for signaling by the plant hormone salicylic acid, while MED25 is required for the transcriptional activation of responses to hypoxia, jasmonate and shade signalling. Two components of the CDK module are involved in the Wnt signaling pathway. MED23 is involved in the RAS/MAPK/ERK pathway. This abbreviated review shows the versatility of individual Mediator subunits, and leads to the idea that Mediator is an end-point of signaling pathways.

Human disease

Involvement of Mediator in various human diseases has been reviewed. 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.

Interactions

Very gentle cell lysis in yeast followed by co-immunoprecipitation with an antibody to a MED17 has confirmed almost all previously reported or predicted interactions and revealed many previously unsuspected specific interactions of various proteins with Mediator.

MED1

Details of the first subunit are illustrative of the types of information that may be gathered for other subunits. See for them.

Regulation by MicroRNAs

MicroRNAs help regulate the expression of many proteins. MED1 is targeted by miR-1, which is important in gene regulation in cancers. The tumor suppressor miR-137 also regulates MED1.

Mouse embryonic development

Null mutants die early. Investigating hypomorphic mutants found that placental defects were primarily lethal and that there were also defects in cardiac and hepatic development, but many other organs were normal.

Mouse cells and tissues

In mice, conditional mutations can be produced to affect only specific cells or tissues at specific times, so that the mouse can develop to adulthood to have its adult phenotype studied. In one case, MED1 was found to participate in controlling the timing of events of meiosis in male mice. Conditional mutants in keratinocytes differ in skin wound healing. A conditional mutation in mice changed dental epithelium into epidermal epithelium, which caused hair to grow beside the incisors.

Subunit composition

The Mediator complex is composed of 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.
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.
Subunit No.Human geneC. elegans geneD. melanogaster geneS. cerevisiae geneSch. pombe gene
MED1MED1Sop3/mdt-1.1, 1.2MED1MED1med1
MED2MED2
MED3PGD1
MED4MED4MED4MED4med4
MED5NUT1
MED6MED6MDT-6MED6MED6med6
MED7MED7MDT-7/let-49MED7MED7med7
MED8MED8MDT-8MED8MED8med8
MED9MED9MED9CSE2
MED10MED10MDT-10NUT2med10
MED11MED11MDT-11MED11MED11med11
MED12MED12MDT-12/dpy-22MED12SRB8srb8
MED12LMED12L
MED13MED13MDT-13/let-19MED13SSN2srb9
MED14MED14MDT-14/rgr-1MED14RGR1med14
MED15MED15mdt-15MED15GAL11YN91_SCHPO
MED16MED16MED16SIN4
MED17MED17MDT-17MED17SRB4med17
MED18MED18MDT-18MED18SRB5med18
MED19MED19MDT-19MED19ROX3med19
MED20MED20MDT-20MED20SRB2med20
MED21MED21MDT-21MED21SRB7med21
MED22MED22MDT-22MED22SRB6med22
MED23MED23MDT-23/sur-2MED23
MED24MED24MED24
MED25MED25MED25
MED26MED26MED26
MED27MED27MED27med27
MED28MED28MED28
MED29MED29MDT-19MED29
MED30MED30MED30
MED31MED31MDT-31MED31SOH1med31
CCNCCCNCcic-1CycCSSN8pch1
CDK8CDK8cdk-8Cdk8SSN3srb10