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 (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 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 (CDK) 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 (cMed) 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 (Pol 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 (eRNAs) can function similarly. In addition to euchromatin looping, Mediator helps form or maintain heterochromatin at centromeres and telomeres.

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