Malleable Machines in Transcription Regulation: The Mediator Complex

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Abstract
The Mediator complex provides an interface between gene-specific regulatory proteins and the general transcription machinery including RNA polymerase II (RNAP II). The complex has a modular architecture (Head, Middle, and Tail) and cryoelectron microscopy analysis suggested that it undergoes dramatic conformational changes upon interactions with activators and RNAP II. These rearrangements have been proposed to play a role in the assembly of the preinitiation complex and also to contribute to the regulatory mechanism of Mediator. In analogy to many regulatory and transcriptional proteins, we reasoned that Mediator might also utilize intrinsically disordered regions (IDRs) to facilitate structural transitions and transmit transcriptional signals. Indeed, a high prevalence of IDRs was found in various subunits of Mediator from both Saccharomyces cerevisiae and Homo sapiens, especially in the Tail and the Middle modules. The level of disorder increases from yeast to man, although in both organisms it significantly exceeds that of multiprotein complexes of a similar size. IDRs can contribute to Mediator's function in three different ways: they can individually serve as target sites for multiple partners having distinctive structures; they can act as malleable linkers connecting globular domains that impart modular functionality on the complex; and they can also facilitate assembly and disassembly of complexes in response to regulatory signals. Short segments of IDRs, termed molecular recognition features (MoRFs) distinguished by a high protein–protein interaction propensity, were identified in 16 and 19 subunits of the yeast and human Mediator, respectively. In Saccharomyces cerevisiae, the functional roles of 11 MoRFs have been experimentally verified, and those in the Med8/Med18/Med20 and Med7/Med21 complexes were structurally confirmed. Although the Saccharomyces cerevisiae and Homo sapiens Mediator sequences are only weakly conserved, the arrangements of the disordered regions and their embedded interaction sites are quite similar in the two organisms. All of these data suggest an integral role for intrinsic disorder in Mediator's function. Intrinsically disordered proteins/regions do not adopt well-defined three dimensional structures; instead, they function as conformational ensembles. They are distinguished in molecular recognition and involved in various regulatory processes. Several components in the transcription machinery–for example, the transactivator domains of transcription factors–are disordered. Mediator, which is a large complex that transduces regulatory information from activators/repressors to the core apparatus, was found to contain a preponderance of intrinsically disordered regions in its various subunits. Such disordered regions are commonly involved in conformational changes coupled to functional transitions, in protein–protein interactions, or in posttranslational modifications. Several such predicted recognition sites were in good agreement with experimental data. Intrinsically disordered regions illuminate a novel aspect of Mediator's regulation and could explain its versatility and specificity in handling transcriptional signals. Their integral role in Mediator function is further underscored by the conserved arrangements of ordered/disordered segments and of the embedded interaction sites.