Structures and compositional dynamics of Mediator in transcription regulation

Abstract

The eukaryotic Mediator, comprising a large Core (cMED) and a dissociable CDK8 kinase module (CKM), functions as a critical coregulator during RNA polymerase II (RNAPII) transcription. cMED recruits RNAPII and facilitates the assembly of the pre-initiation complex (PIC) at promoters. In contrast, CKM prevents RNAPII binding to cMED while simultaneously exerting positive or negative influence on gene transcription through its kinase function. Recent structural studies on cMED and CKM have revealed their intricate architectures and subunit interactions. Here, we explore these structures, providing a comprehensive insight into Mediator (cMED-CKM) architecture and its potential mechanism in regulating RNAPII transcription. Additionally, we discuss the remaining puzzles that require further investigation to fully understand how cMED coordinates with CKM to regulate transcription in various events.

Figure 1.. Subunit composition of the eukaryotic Mediator complex.

(a) and (b) Schematic representations of the yeast and human Mediator complexes with modular composition[4]. The Mediator complex comprises a CKM and a large cMED, which includes Head, Middle and Tail modules. Yeast Med5, Med3 and Med2 (a) are orthologous to MED24, MED27 and MED29 in Metazoans (b). Metazoan-specific subunits are indicated by asterisks in (b).

Figure 2.. Overall structure of the human cMED.

(a) Schematic subunit organization of the human cMED and CKM. The Head, Middle, and Tail modules of the cMED and the dissociable CKM are indicated with corresponding colors. (b-c) The structure of human cMED (PDB code: 7EMF)[28] is shown in surface and cartoon representations.

Figure 3.. Structure of the yeast CKM.

(a) Overall structure of the CKM (PDB code: 7KPX)[14], color-coded by subunits. Each lobe of CKM is indicated. (b) The Kinase-lobe of CKM, indicating an active conformation of the Cdk8 T-loop (red) bound by the N-terminal region of Med12 (Med12N). The RHYT segment of Cdk8 is colored in magenta. The substrate binding site is indicated by a dashed black oval. (c) Structural organization of Med12. Domains are colored and indicated, respectively. (d) Structural comparison of Med13 and the guide RNA-bound human Ago2 (hAgo2) (PDB code: 4W5N)[42]. Each structure is color-coded according to its functional domains. The IDR missing in the structure of Med13 is indicated by a dashed line. The guide RNA in hAgo2 is colored in red.

Figure 4.. Potential mechanisms by which CKM inhibits the interaction of RNAPII with cMED and the formation of cMED-PIC.

(a) Schematic diagram showing the distinct binding modes of yeast CKM (green) to cMED (gray). The positions of CKM subunits and the Hook domain of cMED are indicated. The CKM shown with dashed lines indicates a proposed binding position based on XL-MS analysis[13,39,44]. (b) Schematic diagram of the formation of cMED-PIC at a promoter. (c) CKM binding may impede RNAPII interaction with cMED via (1) steric hindrance, overlapping with the main body of RNAPII, (2) inducing a conformational change in cMED unfavorable for RNAPII binding, or (3) employing another mechanism.