Figure 1.
Mediator transmits regulatory signals from gene-specific activator proteins to the general transcription machinery, including RNA polymerase II (RNAP II, yellow), and general transcription factors (IIB, IID, IIE, IIF, IIH, light green).
The Tail interacts with a variety of activators/repressors and the regulatory signals are transferred via the Middle module to the Head that physically contacts RNAP II. The Middle also receives signals from the CDK module that dissociates prior to transcription. The shades of the blue colors correlate to the level of disorder in the different modules in Saccharomyces cerevisiae as computed in the present work.
Figure 2.
Average disorder of the available Mediator subunits in Saccharomyces cerevisiae (grey) and in Homo sapiens (crosshatched) as computed by the IUPred algorithm [26].
0.5 (dashed line) is the threshold for disordered state and 0.4 (dotted line) is the average disorder of all disordered segments in the DisProt database [29]. Subunits belonging to the different modules (Head, Middle, Tail, Cdk) are separated by vertical lines.
Figure 3.
Amino acid compositions, relative to the set of globular proteins, of the Mediator (black), and its modules, Head (orange), Middle (green) and Tail (yellow) CDK (blue) in Saccharomyces cerevisiae (A) and in Homo sapiens (B).
Compositional profiling of intrinsically disordered proteins from the DisProt database is shown for comparison (red). The arrangement of the amino acids is by peak height for the set of disordered proteins from DisProt [29]. Confidence intervals were estimated using per-protein bootstrapping with 1,000 iterations.
Figure 4.
Abundance of IDRs in the Mediator complex and its modules.
The number of disordered segments of given length in Saccharomyces cerevisiae (grey) and in Homo sapiens (crosshatched) as computed by the IUPred algorithm [26] is shown in the Mediator complex (A), in the Head (B), Middle (C) and Tail (D) modules.
Figure 5.
Schematic representation of the Mediator complex: Head (orange), Middle (green), Tail (yellow), CDK (blue).
Subunits with higher than 50% average overall disorder (Med2, Med3 in Tail; Med9, Med19, Med26 in Middle and Med8 in Head) or subunits containing intrinsically disordered regions longer than 100 residues (Med12, Med13 of the CDK, Med1, Med9, Med26 of the Middle and Med15 of the Tail) in either Saccharomyces cerevisiae or in Homo sapiens are displayed by darker colors. Med19 and Med26 was assigned to the Middle module according to reference [80].
Table 1.
α-Helical molecular recognition features (MoRFs) predicted in Saccharomyces cerevisiae.
Figure 6.
Location of α-MoRFs predicted by the PONDR VL-XT algorithm in Med7 and Med8 subunits of Saccharomyces cerevisiae in (A) Med7/Med21 (1yke) [27] and (B) Med8/Med18/Med20 (2hzs) [28] complexes.
The recognition motifs in Med7 (195–212) and Med8 (193–210) that are biased for an α-helical conformation in the bound state are shown by red.
Figure 7.
Amino acid conservation of ordered (crosshatched) and disordered (gray) regions in Saccharomyces cerevisiae and in Homo sapiens.
Total amino acid conservation shown in black.
Figure 8.
Conservation of disordered regions in Saccharomyces cerevisiae and in Homo sapiens.
The arrangement of ordered/disordered segments is compared to each other using positional (A) segmental overlap (B) measures on the actual Mediator protein sequences in MED_ALSEQ dataset (grey) and on the corresponding randomized MED_ALRAN dataset (crosshatched).