Remarkably, our cells only need about 20,000 different types of proteins to manage all of the tasks we need throughout our lives. The trick, of course, is to control when and where these proteins are built and used, so that, for example, muscle cells have plenty of myosin and nerve cells have the appropriate combination of ion channels, transporters, and receptors. Most of these choices are made at the level of transcription. Cells carefully control when messenger RNA molecules are transcribed by RNA polymerase II from particular genes, and used to build proteins. Over 1600 side-specific DNA binding regulatory proteins, termed transcription factors, work together to make these decisions, monitoring the current state of the cell and deciding if action is needed. Mediator, a large protein complex composed of about 30 different protein chains, integrates these many inputs, and mobilizes RNA polymerase II when and where in the body a particular protein is needed.
The structure shown here, from PDB ID 7enc
, is a “pre-initiation complex” poised to start transcription. This complex includes eukaryotic Mediator and RNA polymerase II
, the major RNA polymerase that builds messenger RNAs based on information encoded in the genome. The pre-initiation complex also includes a collection of general transcription factors (described below) that perform the necessary tasks of recognizing the transcription start site of genes, separating the two strands of the DNA double helix
, and facilitating transcription initiation by RNA polymerase II. However, currently available structures of Mediator don't show an important function of the complex. Mediator also interacts with hundreds of other transcription factors that decide which genes need to be transcribed. The structural details of these interactions are still largely a mystery.
Interaction at a Distance
Most of our transcription factors bind to regulatory regions in DNA that are separate from the initiation site, such as promoter-proximal and distal enhancer
elements. Mediator interacts with these transcription factors and helps decide when a pre-initiation complex needs to be built. Researchers have uncovered many interesting aspects of these interactions. Several of the subunits in Mediator are important for the interactions, particularly subunits in the fork-shaped tail seen at the right in the illustration. Mediator can interact with transcription factors at regulatory sites that are far away in the genome, bridging distal enhancers and the pre-initiation complex. To complicate matters further, it is becoming clear that some of these interactions may involve intrinsically disordered segments of Mediator subunits or transcription factors, perhaps forming phase-separated droplets that bring Mediator together with regulatory proteins.
General Transcription Factors
This structure reveals the arrangement of general transcription factors that cradle RNA polymerase in the pre-initiation complex. TATA-binding protein (TBP, part of TFIID)
is the central player that gets the process started. It binds to a distinctive AT-rich sequence and functions as a molecular saddle that sharply bends the DNA. TFIIA and TFIIB interact with surrounding regions of the DNA and, along with TFIIF, assist with positioning of RNA polymerase II at the transcription start site. TFIIE, TFIIH, and other TFIID subunits bring additional functionality to the complex. In particular, part of TFIIH is a translocase that separates the two strands of DNA in preparation for transcription, and the CAK module of TFIIH adds phosphate groups to the long tail of RNA polymerase II, sending the signal that it is time to get started with mRNA synthesis.
The largest subunit of RNA polymerase II, termed RPB1, has a long tail that does not adopt a folded structure (shown here from PDB ID 5iyd
combined with computed structure model AF-P24928F1
). It includes 52 repeats of a distinctive serine-rich protein sequence (termed the heptad repeat). In each repeat, the fifth serine is phosphorylated by the CAK module of TFIIH. When the tail is highly phosphorylated, the interaction between Mediator and RNA polymerase II is weakened, allowing RNA polymerase II to proceed with mRNA synthesis. The phosphorylated chain also recruits enzymes that build the unusual chemical cap
that protects the front end of the mRNA from degradation.