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The Human CDK8 Subcomplex Is a Molecular Switch That Controls Mediator Coactivator Function

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The Human CDK8 Subcomplex Is a Molecular Switch That Controls Mediator Coactivator Function Downloaded from genesdev.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press The human CDK8 subcomplex is a molecular switch that controls Mediator coactivator function Matthew T. Knuesel,1 Krista D. Meyer,1 Carrie Bernecky, and Dylan J. Taatjes2 Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA The human CDK8 subcomplex (CDK8, cyclin C, Med12, and Med13) negatively regulates transcription in ways not completely defined; past studies suggested CDK8 kinase activity was required for its repressive function. Using a reconstituted transcription system together with recombinant or endogenous CDK8 subcomplexes, we demonstrate that, in fact, Med12 and Med13 are critical for subcomplex-dependent repression, whereas CDK8 kinase activity is not. A hallmark of activated transcription is efficient reinitiation from promoter-bound scaffold complexes that recruit a series of pol II enzymes to the gene. Notably, the CDK8 submodule strongly represses even reinitiation events, suggesting a means to fine tune transcript levels. Structural and biochemical studies confirm the CDK8 submodule binds the Mediator leg/tail domain via the Med13 subunit, and this submodule– Mediator association precludes pol II recruitment. Collectively, these results reveal the CDK8 subcomplex functions as a simple switch that controls the Mediator–pol II interaction to help regulate transcription initiation and reinitiation events. As Mediator is generally required for expression of protein-coding genes, this may reflect a common mechanism by which activated transcription is shut down in human cells. [Keywords: CDK8 subcomplex; Med12; Med13; Mediator; transcription] Supplemental material is available at http://www.genesdev.org. Received November 25, 2008; revised version accepted January 6, 2009. The initiation of transcription is controlled in part by numerous roles in controlling PIC function and is re- a macromolecular protein assembly known as the Pre- quired for expression of virtually all protein-coding genes initiation Complex (PIC) (Hahn 2004). This assembly, (Conaway et al. 2005; Malik and Roeder 2005). Although approaching 4 MDa in size, consists of the general the molecular mechanisms by which Mediator functions transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, within the entire PIC are poorly defined, a number of and TFIIH), RNA polymerase II (pol II), and Mediator. physical and functional interactions have been identified Upon initiation of transcription, pol II escapes the pro- with various PIC components. Among these, Mediator moter and leaves behind a so-called scaffold PIC, which interactions with pol II and TFIIH appear to play funda- retains most PIC components, including Mediator, mental roles in activating gene expression. Mediator TFIIH, and TFIID (Yudkovsky et al. 2000). This scaffold interacts directly with pol II and forms a tight, binary complex can then recruit a second pol II enzyme (and so complex with the enzyme (Davis et al. 2002); moreover, on) to complete multiple rounds of activated transcrip- Mediator stimulates TFIIH-dependent phosphorylation tion. Such an efficient means of reinitiation is likely of the pol II CTD, an event that correlates with pol II critical for rapid induction of a gene, a key feature in promoter escape (Kim et al. 1994; Sun et al. 1998). many diverse physiological responses. However, it is Ablation of key subunits in either Mediator, pol II, or equally important that activated transcription is shut TFIIH inhibits transcription of all protein-coding genes in down to prevent inappropriate overexpression of acti- yeast (Holstege et al. 1998); thus, controlling the activity vated genes. Precisely how this occurs remains unclear. of these PIC components lies at the heart of transcrip- At 1.2 MDa, the Mediator complex represents a major tional regulation. subassembly within the PIC; accordingly, Mediator plays Notably, a ‘‘CDK8 subcomplex’’ (containing CDK8, cyclin C, Med12, and Med13) can directly and indirectly impact the biochemical activity of Mediator, pol II, and TFIIH. For example, CDK8 can phosphorylate the pol II 1These authors contributed equally to this work. CTD, which disrupts Mediator–pol II association (which 2Corresponding author. E-MAIL [email protected]; FAX (303) 492-5894. requires a hypophosphorylated CTD) to negatively regu- Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.1767009. late transcription (Hengartner et al. 1998). Moreover, GENES & DEVELOPMENT 23:439–451 Ó 2009 by Cold Spring Harbor Laboratory Press ISSN 0890-9369/09; www.genesdev.org 439 Downloaded from genesdev.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Knuesel et al. human CDK8 can phosphorylate cyclin H, which inhibits Results TFIIH and prevents transcription initiation (Akoulitchev et al. 2000). Thus, there is a link between transcriptional Reconstitution of regulated transcription on chromatin repression and CDK8 kinase activity. Yet Mediator–CDK8 templates submodule association alone appears sufficient to block Mediator interaction with pol II independent of kinase To address mechanistic questions regarding the human activity (Naar et al. 2002; Elmlund et al. 2006). Thus, CDK8 subcomplex, we sought to recapitulate regulated CDK8 kinase function per se may not be required for transcription in vitro by establishing a defined transcrip- repression. Indeed, the Med12 (240-kDa) and Med13 (250- tion system consisting of highly purified and recombi- kDa) subunits comprise a major portion of the 600-kDa nant transcription factors operating on chromatin CDK8 submodule, yet little is known regarding the bio- templates. The advantage of such a system is that it chemical function of these proteins. allows determination of how the CDK8 subcomplex The human Mediator complex exists in two major might impact transcription simply by titrating the sub- forms: a core Mediator complex (or simply, ‘‘Mediator’’) complex into the reaction; moreover, the activity of and a CDK8–Mediator complex. The core complex dis- various mutants could be tested alongside wild-type plays strong coactivator function, whereas the CDK8– subcomplexes to directly compare their biochemical Mediator complex does not. Each complex is highly activities. Furthermore, a reconstituted in vitro assay similar in subunit composition—25 subunits are com- allows various factors to be added at different stages of mon to each—yet only core Mediator contains the Med26 the transcription reaction (e.g., after PIC assembly) in subunit, whereas CDK8–Mediator contains the addi- order to address the potential importance of temporal tional subunits CDK8, cyclin C, Med12, and Med13 regulation. This level of control is simply not possible (Taatjes et al. 2004). Genetic studies in yeast suggest with cell-based assays and enables one to address very CDK8, cyclin C, Med12, and Med13 negatively regulate specific mechanistic questions. Indeed, work from several transcription (Carlson 1997); moreover, mutation of any laboratories has demonstrated the value of such a recon- one of these subunits results in identical or nearly stituted system in uncovering basic regulatory functions identical phenotypes (Holstege et al. 1998; Loncle et al. of the transcription machinery (Naar et al. 1999; An et al. 2007). For these reasons, it was presumed that CDK8, 2004; Lewis et al. 2005; Santoso and Kadonaga 2006). cyclin C, Med12, and Med13 function as a unit and may To establish an in vitro transcription system, TFIIA, exist as a subcomplex. Indeed, a complex containing TFIIB, TFIIE, and TFIIF were recombinantly expressed and CDK8, cyclin C, Med12, and Med13 was isolated in yeast purified according to the protocols outlined in Supplemen- expressing a tagged version of cyclin C (Borggrefe et al. tal Figure 1. Because TFIIH, TFIID, pol II, and Mediator are 2002). each large, multisubunit complexes, these required purifi- To establish whether the CDK8 subcomplex may exist cation directly from human cells. Therefore, isolation of as a stable entity in human cells, we recently purified an these factors required multiple chromatographic steps, endogenous subcomplex using conventional methods including a final antibody/affinity purification step (Sup- (Knuesel et al. 2009). As expected, the free CDK8 sub- plemental Fig. 1). Each factor was purified to near- complex is scarce in human cells: Most appear to be asso- homogeneity, as shown in Figure 1. Included in Figure 1 ciated with Mediator, which is itself a low-abundance are silver-stained gels of the activators used in this study, complex. The low abundance of the endogenous subcom- Sp1, SREBP-1a, and gal4-p53, which were purified follow- plex precludes a rigorous biochemical analysis; in antic- ing recombinant expression in Escherichia coli or insect ipation of this, we also generated the CDK8 subcomplex cells. Once generated, purified factors (Mediator, activa- from recombinant subunits. Recombinant expression tors, and the general transcription factors) were then tested enabled purification of subcomplexes devoid of specific for activity on naked DNA templates and titrated to subunits or with point mutations that inactivate the determine the optimum concentrations for each factor in kinase. We also established a chromatin-based in vitro the transcription reaction (data not shown). transcription system with purified and recombinant hu- Next, we tested whether these purified components man transcription factors. This
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