51
|
Lynch CJ, Bernad R, Calvo I, Serrano M. Manipulating the Mediator complex to induce naïve pluripotency. Exp Cell Res 2020; 395:112215. [PMID: 32771524 PMCID: PMC7584500 DOI: 10.1016/j.yexcr.2020.112215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/08/2020] [Accepted: 08/01/2020] [Indexed: 12/26/2022]
Abstract
Human naïve pluripotent stem cells (PSCs) represent an optimal homogenous starting point for molecular interventions and differentiation strategies. This is in contrast to the standard primed PSCs which fluctuate in identity and are transcriptionally heterogeneous. However, despite many efforts, the maintenance and expansion of human naïve PSCs remains a challenge. Here, we discuss our recent strategy for the stabilization of human PSC in the naïve state based on the use of a single chemical inhibitor of the related kinases CDK8 and CDK19. These kinases phosphorylate and negatively regulate the multiprotein Mediator complex, which is critical for enhancer-driven recruitment of RNA Pol II. The net effect of CDK8/19 inhibition is a global stimulation of enhancers, which in turn reinforces transcriptional programs including those related to cellular identity. In the case of pluripotent cells, the presence of CDK8/19i efficiently stabilizes the naïve state. Importantly, in contrast to previous chemical methods to induced the naïve state based on the inhibition of the FGF-MEK-ERK pathway, CDK8/19i-naïve human PSCs are chromosomally stable and retain developmental potential after long-term expansion. We suggest this could be related to the fact that CDK8/19 inhibition does not induce DNA demethylation. These principles may apply to other fate decisions.
Collapse
Affiliation(s)
- Cian J Lynch
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
| | - Raquel Bernad
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Isabel Calvo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08010, Spain.
| |
Collapse
|
52
|
Liquid-liquid phase separation in biology: mechanisms, physiological functions and human diseases. SCIENCE CHINA. LIFE SCIENCES 2020; 63:953-985. [PMID: 32548680 DOI: 10.1007/s11427-020-1702-x] [Citation(s) in RCA: 151] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/20/2020] [Indexed: 02/06/2023]
Abstract
Cells are compartmentalized by numerous membrane-enclosed organelles and membraneless compartments to ensure that a wide variety of cellular activities occur in a spatially and temporally controlled manner. The molecular mechanisms underlying the dynamics of membrane-bound organelles, such as their fusion and fission, vesicle-mediated trafficking and membrane contactmediated inter-organelle interactions, have been extensively characterized. However, the molecular details of the assembly and functions of membraneless compartments remain elusive. Mounting evidence has emerged recently that a large number of membraneless compartments, collectively called biomacromolecular condensates, are assembled via liquid-liquid phase separation (LLPS). Phase-separated condensates participate in various biological activities, including higher-order chromatin organization, gene expression, triage of misfolded or unwanted proteins for autophagic degradation, assembly of signaling clusters and actin- and microtubule-based cytoskeletal networks, asymmetric segregations of cell fate determinants and formation of pre- and post-synaptic density signaling assemblies. Biomacromolecular condensates can transition into different material states such as gel-like structures and solid aggregates. The material properties of condensates are crucial for fulfilment of their distinct functions, such as biochemical reaction centers, signaling hubs and supporting architectures. Cells have evolved multiple mechanisms to ensure that biomacromolecular condensates are assembled and disassembled in a tightly controlled manner. Aberrant phase separation and transition are causatively associated with a variety of human diseases such as neurodegenerative diseases and cancers. This review summarizes recent major progress in elucidating the roles of LLPS in various biological pathways and diseases.
Collapse
|
53
|
Selective Mediator dependence of cell-type-specifying transcription. Nat Genet 2020; 52:719-727. [PMID: 32483291 PMCID: PMC7610447 DOI: 10.1038/s41588-020-0635-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/24/2020] [Indexed: 12/15/2022]
Abstract
The Mediator complex directs signals from DNA-binding transcription factors to RNA polymerase (Pol) II. Despite this pivotal position, mechanistic understanding of Mediator in human cells remains incomplete. Here, we quantified Mediator-controlled Pol II kinetics by coupling rapid subunit degradation with orthogonal experimental readouts. Consistent with a model of condensate-driven transcription initiation, large clusters of hypo-phosphorylated Pol II rapidly disassembled upon Mediator degradation. This was accompanied by a selective and pronounced disruption of cell type-specifying transcriptional circuits, whose constituent genes featured exceptionally high rates of Pol II turnover. Notably, transcriptional output of most other genes was largely unaffected by acute Mediator ablation. Maintenance of transcriptional activity at these genes was linked to an unexpected, CDK9-dependent compensatory feedback loop that elevated Pol II pause release rates genome-wide. Collectively, our work positions human Mediator as a globally acting coactivator that selectively safeguards the functionality of cell type-specifying transcriptional networks.
Collapse
|
54
|
Lyons DE, McMahon S, Ott M. A combinatorial view of old and new RNA polymerase II modifications. Transcription 2020; 11:66-82. [PMID: 32401151 DOI: 10.1080/21541264.2020.1762468] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The production of mRNA is a dynamic process that is highly regulated by reversible post-translational modifications of the C-terminal domain (CTD) of RNA polymerase II. The CTD is a highly repetitive domain consisting mostly of the consensus heptad sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Phosphorylation of serine residues within this repeat sequence is well studied, but modifications of all residues have been described. Here, we focus on integrating newly identified and lesser-studied CTD post-translational modifications into the existing framework. We also review the growing body of work demonstrating crosstalk between different CTD modifications and the functional consequences of such crosstalk on the dynamics of transcriptional regulation.
Collapse
Affiliation(s)
- Danielle E Lyons
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA
| | - Sarah McMahon
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco , San Francisco, CA, USA
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco , San Francisco, CA, USA
| |
Collapse
|
55
|
Abstract
In this issue of Cell, Casellas and colleagues provide insights into the structural and functional aspects of the mammalian multi-subunit Mediator complex, a conserved and essential transcriptional coregulator. Combining cryo-EM, genetic, and genomic analyses, the work sheds light on Mediator's mode of action as a functional bridge between enhancers and promoters.
Collapse
Affiliation(s)
- Julie Soutourina
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.
| |
Collapse
|
56
|
The Important Function of Mediator Complex in Controlling the Developmental Transitions in Plants. Int J Mol Sci 2020; 21:ijms21082733. [PMID: 32326439 PMCID: PMC7215822 DOI: 10.3390/ijms21082733] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/09/2020] [Accepted: 04/11/2020] [Indexed: 12/24/2022] Open
Abstract
Developmental transitions in plants are tightly associated with changes in the transcriptional regulation of gene expression. One of the most important regulations is conferred by cofactors of RNA polymerase II including the mediator complex, a large complex with a modular organization. The mediator complex recruits transcription factors to bind to the specific sites of genes including protein-coding genes and non-coding RNA genes to promote or repress the transcription initiation and elongation using a protein-protein interaction module. Mediator complex subunits have been isolated and identified in plants and the function of most mediator subunits in whole life cycle plants have been revealed. Studies have shown that the Mediator complex is indispensable for the regulation of plant developmental transitions by recruiting age-, flowering-, or hormone-related transcription factors. Here, we first overviewed the Mediator subunits in plants, and then we summarized the specific Mediator subunits involved in developmental transitions, including vegetative phase change and floral transition. Finally, we proposed the future directions to further explore their roles in plants. The link between Mediator subunits and developmental transitions implies the necessity to explore targets of this complex as a potential application in developing high quality crop varieties.
Collapse
|
57
|
Abstract
RNA polymerase II (Pol II) transcribes all protein-coding genes and many noncoding RNAs in eukaryotic genomes. Although Pol II is a complex, 12-subunit enzyme, it lacks the ability to initiate transcription and cannot consistently transcribe through long DNA sequences. To execute these essential functions, an array of proteins and protein complexes interact with Pol II to regulate its activity. In this review, we detail the structure and mechanism of over a dozen factors that govern Pol II initiation (e.g., TFIID, TFIIH, and Mediator), pausing, and elongation (e.g., DSIF, NELF, PAF, and P-TEFb). The structural basis for Pol II transcription regulation has advanced rapidly in the past decade, largely due to technological innovations in cryoelectron microscopy. Here, we summarize a wealth of structural and functional data that have enabled a deeper understanding of Pol II transcription mechanisms; we also highlight mechanistic questions that remain unanswered or controversial.
Collapse
Affiliation(s)
- Allison C Schier
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80303, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80303, USA
| |
Collapse
|
58
|
A precisely positioned MED12 activation helix stimulates CDK8 kinase activity. Proc Natl Acad Sci U S A 2020; 117:2894-2905. [PMID: 31988137 DOI: 10.1073/pnas.1917635117] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Mediator kinase module regulates eukaryotic transcription by phosphorylating transcription-related targets and by modulating the association of Mediator and RNA polymerase II. The activity of its catalytic core, cyclin-dependent kinase 8 (CDK8), is controlled by Cyclin C and regulatory subunit MED12, with its deregulation contributing to numerous malignancies. Here, we combine in vitro biochemistry, cross-linking coupled to mass spectrometry, and in vivo studies to describe the binding location of the N-terminal segment of MED12 on the CDK8/Cyclin C complex and to gain mechanistic insights into the activation of CDK8 by MED12. Our data demonstrate that the N-terminal portion of MED12 wraps around CDK8, whereby it positions an "activation helix" close to the T-loop of CDK8 for its activation. Intriguingly, mutations in the activation helix that are frequently found in cancers do not diminish the affinity of MED12 for CDK8, yet likely alter the exact positioning of the activation helix. Furthermore, we find the transcriptome-wide gene-expression changes in human cells that result from a mutation in the MED12 activation helix to correlate with deregulated genes in breast and colon cancer. Finally, functional assays in the presence of kinase inhibitors reveal that binding of MED12 remodels the active site of CDK8 and thereby precludes the inhibition of ternary CDK8 complexes by type II kinase inhibitors. Taken together, our results not only allow us to propose a revised model of how CDK8 activity is regulated by MED12, but also offer a path forward in developing small molecules that target CDK8 in its MED12-bound form.
Collapse
|
59
|
Georges A, Gopaul D, Denby Wilkes C, Giordanengo Aiach N, Novikova E, Barrault MB, Alibert O, Soutourina J. Functional interplay between Mediator and RNA polymerase II in Rad2/XPG loading to the chromatin. Nucleic Acids Res 2019; 47:8988-9004. [PMID: 31299084 PMCID: PMC6753472 DOI: 10.1093/nar/gkz598] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/27/2019] [Accepted: 06/29/2019] [Indexed: 12/30/2022] Open
Abstract
Transcription and maintenance of genome integrity are fundamental cellular functions. Deregulation of transcription and defects in DNA repair lead to serious pathologies. The Mediator complex links RNA polymerase (Pol) II transcription and nucleotide excision repair via Rad2/XPG endonuclease. However, the functional interplay between Rad2/XPG, Mediator and Pol II remains to be determined. In this study, we investigated their functional dynamics using genomic and genetic approaches. In a mutant affected in Pol II phosphorylation leading to Mediator stabilization on core promoters, Rad2 genome-wide occupancy shifts towards core promoters following that of Mediator, but decreases on transcribed regions together with Pol II. Specific Mediator mutations increase UV sensitivity, reduce Rad2 recruitment to transcribed regions, lead to uncoupling of Rad2, Mediator and Pol II and to colethality with deletion of Rpb9 Pol II subunit involved in transcription-coupled repair. We provide new insights into the functional interplay between Rad2, Mediator and Pol II and propose that dynamic interactions with Mediator and Pol II are involved in Rad2 loading to the chromatin. Our work contributes to the understanding of the complex link between transcription and DNA repair machineries, dysfunction of which leads to severe diseases.
Collapse
Affiliation(s)
- Adrien Georges
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Diyavarshini Gopaul
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Cyril Denby Wilkes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Nathalie Giordanengo Aiach
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Elizaveta Novikova
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Marie-Bénédicte Barrault
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | | | - Julie Soutourina
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| |
Collapse
|
60
|
Nogales E, Greber BJ. High-resolution cryo-EM structures of TFIIH and their functional implications. Curr Opin Struct Biol 2019; 59:188-194. [PMID: 31600675 PMCID: PMC6951423 DOI: 10.1016/j.sbi.2019.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/27/2019] [Accepted: 08/25/2019] [Indexed: 01/26/2023]
Abstract
Eukaryotic transcription factor IIH (TFIIH) is a 500 kDa-multiprotein complex that harbors two SF2-family DNA-dependent ATPase/helicase subunits and the kinase activity of Cyclin-dependent kinase 7. TFIIH serves as a general transcription factor for transcription initiation by eukaryotic RNA polymerase II and plays an important role in nucleotide excision DNA repair. Aiming to understand the molecular mechanisms of its function and regulation in two key cellular pathways, the high-resolution structure of TFIIH has been pursued for decades. Recent breakthroughs, largely enabled by methodological advances in cryo-electron microscopy, have finally revealed the structure of TFIIH and its interactions in the context of the Pol II-pre-initiation complex, and provide a first glimpse of a TFIIH-containing assembly in DNA repair. Here, we review and discuss these recent structural insights and their functional implications.
Collapse
Affiliation(s)
- Eva Nogales
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA.
| | - Basil J Greber
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA.
| |
Collapse
|
61
|
Femia MR, Evans RM, Zhang J, Sun X, Lebegue CJ, Roggero VR, Allison LA. Mediator subunit MED1 modulates intranuclear dynamics of the thyroid hormone receptor. J Cell Biochem 2019; 121:2909-2926. [PMID: 31692077 DOI: 10.1002/jcb.29532] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 10/10/2019] [Indexed: 12/26/2022]
Abstract
The thyroid hormone receptors (TRs) mediate thyroid hormone (T3 )-dependent gene expression. The nuclear import and export signals that direct TR shuttling are well characterized, but little is known about factors modulating nuclear retention. We used fluorescence-based nucleocytoplasmic scoring and fluorescence recovery after photobleaching in transfected cells to investigate whether Mediator subunits MED1 and MED13 play a role in nuclear retention of TR. When MED1 was overexpressed, there was a striking shift towards a greater nuclear localization of TRβ1 and the oncoprotein v-ErbA, subtypes with cytosolic populations at steady-state, and TRβ1 intranuclear mobility was reduced. For TRα1, there was no observable change in its predominantly nuclear distribution pattern or mobility. Consistent with a role for MED1 in nuclear retention, the cytosolic TRα1 and TRβ1 population were significantly greater in MED1-/- cells, compared with MED1+/+ cells. Exposure to T3 and epidermal growth factor, which induces MED1 phosphorylation, also altered TR intranuclear dynamics. Overexpression of miR-208a, which downregulates MED13, led to a more cytosolic distribution of nuclear-localized TRα1; however, overexpression of MED13 had no effect on TRβ1 localization. The known binding site of MED1 overlaps with a transactivation domain and nuclear export signal in helix 12 of TR's ligand-binding domain (LBD). Coimmunoprecipitation assays demonstrated that TR's LBD interacts directly with exportins 5 and 7, suggesting that binding of exportins and MED1 to TR may be mutually exclusive. Collectively, our data provide evidence that MED1 promotes nuclear retention of TR, and highlight the dual functionality of helix 12 in TR transactivation and nuclear export.
Collapse
Affiliation(s)
- Matthew R Femia
- Department of Biology, William and Mary, Williamsburg, Viginia
| | | | - Jibo Zhang
- Department of Biology, William and Mary, Williamsburg, Viginia
| | - Xiaopeng Sun
- Department of Biology, William and Mary, Williamsburg, Viginia
| | | | | | | |
Collapse
|
62
|
Tuttle LM, Pacheco D, Warfield L, Luo J, Ranish J, Hahn S, Klevit RE. Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex. Cell Rep 2019; 22:3251-3264. [PMID: 29562181 PMCID: PMC5908246 DOI: 10.1016/j.celrep.2018.02.097] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/17/2018] [Accepted: 02/25/2018] [Indexed: 11/12/2022] Open
Abstract
Transcription activation domains (ADs) are inherently disordered proteins that often target multiple coactivator complexes, but the specificity of these interactions is not understood. Efficient transcription activation by yeast Gcn4 requires its tandem ADs and four activator-binding domains (ABDs) on its target, the Mediator subunit Med15. Multiple ABDs are a common feature of coactivator complexes. We find that the large Gcn4-Med15 complex is heterogeneous and contains nearly all possible AD-ABD interactions. Gcn4-Med15 forms via a dynamic fuzzy protein-protein interface, where ADs bind the ABDs in multiple orientations via hydrophobic regions that gain helicity. This combinatorial mechanism allows individual low-affinity and specificity interactions to generate a biologically functional, specific, and higher affinity complex despite lacking a defined protein-protein interface. This binding strategy is likely representative of many activators that target multiple coactivators, as it allows great flexibility in combinations of activators that can cooperate to regulate genes with variable coactivator requirements.
Collapse
Affiliation(s)
- Lisa M Tuttle
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Derek Pacheco
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Linda Warfield
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jie Luo
- The Institute for Systems Biology, Seattle, WA 98109, USA
| | - Jeff Ranish
- The Institute for Systems Biology, Seattle, WA 98109, USA
| | - Steven Hahn
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
63
|
Organization and regulation of gene transcription. Nature 2019; 573:45-54. [PMID: 31462772 DOI: 10.1038/s41586-019-1517-4] [Citation(s) in RCA: 354] [Impact Index Per Article: 70.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/30/2019] [Indexed: 12/18/2022]
Abstract
The regulated transcription of genes determines cell identity and function. Recent structural studies have elucidated mechanisms that govern the regulation of transcription by RNA polymerases during the initiation and elongation phases. Microscopy studies have revealed that transcription involves the condensation of factors in the cell nucleus. A model is emerging for the transcription of protein-coding genes in which distinct transient condensates form at gene promoters and in gene bodies to concentrate the factors required for transcription initiation and elongation, respectively. The transcribing enzyme RNA polymerase II may shuttle between these condensates in a phosphorylation-dependent manner. Molecular principles are being defined that rationalize transcriptional organization and regulation, and that will guide future investigations.
Collapse
|
64
|
Roeder RG. 50+ years of eukaryotic transcription: an expanding universe of factors and mechanisms. Nat Struct Mol Biol 2019; 26:783-791. [PMID: 31439941 DOI: 10.1038/s41594-019-0287-x] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 07/26/2019] [Indexed: 12/12/2022]
Abstract
The landmark 1969 discovery of nuclear RNA polymerases I, II and III in diverse eukaryotes represented a major turning point in the field that, with subsequent elucidation of the distinct structures and functions of these enzymes, catalyzed an avalanche of further studies. In this Review, written from a personal and historical perspective, I highlight foundational biochemical studies that led to the discovery of an expanding universe of the components of the transcriptional and regulatory machineries, and a parallel complexity in gene-specific mechanisms that continue to be explored to the present day.
Collapse
Affiliation(s)
- Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York, USA.
| |
Collapse
|
65
|
El Khattabi L, Zhao H, Kalchschmidt J, Young N, Jung S, Van Blerkom P, Kieffer-Kwon P, Kieffer-Kwon KR, Park S, Wang X, Krebs J, Tripathi S, Sakabe N, Sobreira DR, Huang SC, Rao SSP, Pruett N, Chauss D, Sadler E, Lopez A, Nóbrega MA, Aiden EL, Asturias FJ, Casellas R. A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers. Cell 2019; 178:1145-1158.e20. [PMID: 31402173 PMCID: PMC7533040 DOI: 10.1016/j.cell.2019.07.011] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 05/24/2019] [Accepted: 07/09/2019] [Indexed: 12/11/2022]
Abstract
While Mediator plays a key role in eukaryotic transcription, little is known about its mechanism of action. This study combines CRISPR-Cas9 genetic screens, degron assays, Hi-C, and cryoelectron microscopy (cryo-EM) to dissect the function and structure of mammalian Mediator (mMED). Deletion analyses in B, T, and embryonic stem cells (ESC) identified a core of essential subunits required for Pol II recruitment genome-wide. Conversely, loss of non-essential subunits mostly affects promoters linked to multiple enhancers. Contrary to current models, however, mMED and Pol II are dispensable to physically tether regulatory DNA, a topological activity requiring architectural proteins. Cryo-EM analysis revealed a conserved core, with non-essential subunits increasing structural complexity of the tail module, a primary transcription factor target. Changes in tail structure markedly increase Pol II and kinase module interactions. We propose that Mediator's structural pliability enables it to integrate and transmit regulatory signals and act as a functional, rather than an architectural bridge, between promoters and enhancers.
Collapse
Affiliation(s)
| | - Haiyan Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora CO 80045, USA
| | | | - Natalie Young
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora CO 80045, USA
| | - Seolkyoung Jung
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Peter Van Blerkom
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora CO 80045, USA
| | | | | | - Solji Park
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Xiang Wang
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Jordan Krebs
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | | | - Noboru Sakabe
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Débora R Sobreira
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Su-Chen Huang
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Suhas S P Rao
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Daniel Chauss
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Erica Sadler
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Andrea Lopez
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Marcelo A Nóbrega
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Francisco J Asturias
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora CO 80045, USA.
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA; Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA.
| |
Collapse
|
66
|
Zhai Q, Li C. The plant Mediator complex and its role in jasmonate signaling. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3415-3424. [PMID: 31089685 PMCID: PMC6609880 DOI: 10.1093/jxb/erz233] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 05/07/2019] [Indexed: 05/20/2023]
Abstract
The Mediator complex is an essential, multisubunit transcriptional coactivator that is highly conserved in eukaryotes. Mediator interacts with gene-specific transcription factors, the RNA polymerase II transcriptional machinery, as well as several other factors involved in transcription, and acts as an integral hub to regulate various aspects of transcription. Recent studies of the plant Mediator complex have established that it functions in diverse aspects of plant development and fitness. Jasmonate (JA) is an oxylipin-derived plant hormone that regulates plant immunity and development. The basic helix-loop-helix transcription factor MYC2, which is a master regulator of JA signaling, orchestrates genome-wide transcriptional reprogramming of plant cells to coordinate defense- and growth-related processes. Here, we review the function of the plant Mediator complex in regulating JA signaling. We focus on the multifunctional Mediator subunit MED25, which emerges as an integrative hub for the transcriptional regulation of jasmonate signaling.
Collapse
Affiliation(s)
- Qingzhe Zhai
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Correspondence:
| |
Collapse
|
67
|
Garg J, Saettone A, Nabeel-Shah S, Cadorin M, Ponce M, Marquez S, Pu S, Greenblatt J, Lambert JP, Pearlman RE, Fillingham J. The Med31 Conserved Component of the Divergent Mediator Complex in Tetrahymena thermophila Participates in Developmental Regulation. Curr Biol 2019; 29:2371-2379.e6. [PMID: 31280994 DOI: 10.1016/j.cub.2019.06.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/18/2019] [Accepted: 06/18/2019] [Indexed: 11/24/2022]
Abstract
Mediator is a large protein complex required for basal and regulated expression of most RNA polymerase II (RNAP II)-transcribed genes, in part due to its interaction with and phosphorylation of the conserved C-terminal domain (CTD) of Rpb1 [1, 2]. Mediator has been implicated in many aspects of gene expression including chromatin looping [3], higher-order chromatin folding [4], mRNA processing [5] and export [6], and transcriptional memory [7]. Mediator is thought to have played a major role during eukaryotic diversification [8, 9], although its function remains unknown in evolutionarily deep branching eukaryotes lacking canonical CTD heptad repeats. We used the ciliate protozoan Tetrahymena thermophila as a model organism whose genome encodes a highly divergent Rpb1 lacking canonical CTD heptad repeats. We endogenously tagged the Med31 subunit of the Mediator complex and performed affinity purification coupled with mass spectrometry (AP-MS) to identify Mediator subunits. We found that Med31 physically interacts with a large number of proteins (>20), several of which share similarities to canonical Mediator subunits in yeast and humans as well as Tetrahymena-specific proteins. Furthermore, Med31 ChIP-seq analysis suggested a global role for Mediator in transcription regulation. We demonstrated that MED31 knockdown in growing Tetrahymena results in the ectopic expression of developmental genes important for programmed DNA rearrangements. In addition, indirect immunofluorescence revealed Med31 localization in meiotic micronuclei, implicating Mediator in RNAPII-dependent ncRNA transcription. Our results reveal structural and functional insights and implicate Mediator as an ancient cellular machinery for transcription regulation with a possible involvement in global transcription of ncRNAs.
Collapse
Affiliation(s)
- Jyoti Garg
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Alejandro Saettone
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
| | - Syed Nabeel-Shah
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Matthew Cadorin
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
| | - Marcelo Ponce
- SciNet HPC Consortium, University of Toronto, 661 University Avenue, Suite 1140, Toronto, ON M5G 1M1, Canada
| | - Susanna Marquez
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Shuye Pu
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jack Greenblatt
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jean-Philippe Lambert
- Department of Molecular Medicine and Cancer Research Centre, Université Laval, Quebec, QC, Canada; CHU de Québec Research Center, CHUL, 2705 Laurier Boulevard, Quebec, QC G1V 4G2, Canada
| | - Ronald E Pearlman
- Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
| | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada.
| |
Collapse
|
68
|
Mao X, Kim JI, Wheeler MT, Heintzelman AK, Weake VM, Chapple C. Mutation of Mediator subunit CDK8 counteracts the stunted growth and salicylic acid hyperaccumulation phenotypes of an Arabidopsis MED5 mutant. THE NEW PHYTOLOGIST 2019; 223:233-245. [PMID: 30756399 DOI: 10.1111/nph.15741] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/08/2019] [Indexed: 05/13/2023]
Abstract
The Mediator complex functions as a hub for transcriptional regulation. MED5, an Arabidopsis Mediator tail subunit, is required for maintaining phenylpropanoid homeostasis. A semidominant mutation (ref4-3) that causes a single amino acid substitution in MED5b functions as a strong suppressor of the pathway, leading to decreased soluble phenylpropanoid accumulation, reduced lignin content and dwarfism. By contrast, loss of MED5 results in increased concentrations of phenylpropanoids. We used a reverse genetic approach to identify suppressors of ref4-3 and found that ref4-3 requires CDK8, a kinase module subunit of Mediator, to repress plant growth. The genetic interaction between MED5 and CDK8 was further characterized using mRNA-sequencing (RNA-seq) and metabolite analysis. Growth inhibition and suppression of phenylpropanoid metabolism can be genetically separated in ref4-3 by elimination of CDK8 kinase activity; however, the stunted growth of ref4-3 is not dependent on the phosphorylation event introduced by the G383S mutation. In addition, rather than perturbation of lignin biosynthesis, misregulation of DJC66, a gene encoding a DNAJ protein, is involved in the dwarfism of the med5 mutants. Together, our study reveals genetic interactions between Mediator tail and kinase module subunits and enhances our understanding of dwarfing in phenylpropanoid pathway mutants.
Collapse
Affiliation(s)
- Xiangying Mao
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Jeong Im Kim
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Mitchell T Wheeler
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Anne K Heintzelman
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Northwest Missouri State University, Maryville, MO, 64468, USA
| | - Vikki M Weake
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| |
Collapse
|
69
|
Gopalan S, Gibbon DM, Banks CA, Zhang Y, Florens LA, Washburn MP, Dabas P, Sharma N, Seidel CW, Conaway RC, Conaway JW. Schizosaccharomyces pombe Pol II transcription elongation factor ELL functions as part of a rudimentary super elongation complex. Nucleic Acids Res 2019; 46:10095-10105. [PMID: 30102332 PMCID: PMC6212713 DOI: 10.1093/nar/gky713] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 07/26/2018] [Indexed: 12/21/2022] Open
Abstract
ELL family transcription factors activate the overall rate of RNA polymerase II (Pol II) transcription elongation by binding directly to Pol II and suppressing its tendency to pause. In metazoa, ELL regulates Pol II transcription elongation as part of a large multisubunit complex referred to as the Super Elongation Complex (SEC), which includes P-TEFb and EAF, AF9 or ENL, and an AFF family protein. Although orthologs of ELL and EAF have been identified in lower eukaryotes including Schizosaccharomyces pombe, it has been unclear whether SEC-like complexes function in lower eukaryotes. In this report, we describe isolation from S. pombe of an ELL-containing complex with features of a rudimentary SEC. This complex includes S. pombe Ell1, Eaf1, and a previously uncharacterized protein we designate Ell1 binding protein 1 (Ebp1), which is distantly related to metazoan AFF family members. Like the metazoan SEC, this S. pombe ELL complex appears to function broadly in Pol II transcription. Interestingly, it appears to have a particularly important role in regulating genes involved in cell separation.
Collapse
Affiliation(s)
- Sneha Gopalan
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,The Open University, Milton Keynes, UK
| | - Dana M Gibbon
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Charles As Banks
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Ying Zhang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | | | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Department of Pathology and Laboratory Med icine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Preeti Dabas
- University School of Biotechnology, G.G.S.Indraprastha University, New Delhi 110078, India
| | - Nimisha Sharma
- University School of Biotechnology, G.G.S.Indraprastha University, New Delhi 110078, India
| | | | - Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| |
Collapse
|
70
|
Abstract
In this review, Core et al. discuss the recent advances in our understanding of the early steps in Pol II transcription, highlighting the events and factors involved in the establishment and release of paused Pol II. They also discuss a number of unanswered questions about the regulation and function of Pol II pausing. Precise spatio–temporal control of gene activity is essential for organismal development, growth, and survival in a changing environment. Decisive steps in gene regulation involve the pausing of RNA polymerase II (Pol II) in early elongation, and the controlled release of paused polymerase into productive RNA synthesis. Here we describe the factors that enable pausing and the events that trigger Pol II release into the gene. We also discuss open questions in the field concerning the stability of paused Pol II, nucleosomes as obstacles to elongation, and potential roles of pausing in defining the precision and dynamics of gene expression.
Collapse
Affiliation(s)
- Leighton Core
- Department of Molecular and Cell Biology, Institute of Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| |
Collapse
|
71
|
Trnka MJ, Pellarin R, Robinson PJ. Role of integrative structural biology in understanding transcriptional initiation. Methods 2019; 159-160:4-22. [PMID: 30890443 PMCID: PMC6617507 DOI: 10.1016/j.ymeth.2019.03.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/14/2019] [Accepted: 03/15/2019] [Indexed: 12/12/2022] Open
Abstract
Integrative structural biology combines data from multiple experimental techniques to generate complete structural models for the biological system of interest. Most commonly cross-linking data sets are employed alongside electron microscopy maps, crystallographic structures, and other data by computational methods that integrate all known information and produce structural models at a level of resolution that is appropriate to the input data. The precision of these modelled solutions is limited by the sparseness of cross-links observed, the length of the cross-linking reagent, the ambiguity arisen from the presence of multiple copies of the same protein, and structural and compositional heterogeneity. In recent years integrative structural biology approaches have been successfully applied to a range of RNA polymerase II complexes. Here we will provide a general background to integrative structural biology, a description of how it should be practically implemented and how it has furthered our understanding of the biology of large transcriptional assemblies. Finally, in the context of recent breakthroughs in microscope and direct electron detector technology, where increasingly EM is capable of resolving structural features directly without the aid of other structural techniques, we will discuss the future role of integrative structural techniques.
Collapse
Affiliation(s)
- Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Riccardo Pellarin
- Institut Pasteur, Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, CNRS UMR 3528, C3BI USR 3756 CNRS & IP, Paris, France
| | - Philip J Robinson
- Department of Biological Sciences, Birkbeck University of London, Institute of Structural and Molecular Biology, London, United Kingdom.
| |
Collapse
|
72
|
Fornero C, Rickerd T, Kirik V. Papillae formation on Arabidopsis leaf trichomes requires the function of Mediator tail subunits 2, 14, 15a, 16, and 25. PLANTA 2019; 249:1063-1071. [PMID: 30535640 DOI: 10.1007/s00425-018-3063-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/05/2018] [Indexed: 06/09/2023]
Abstract
Arabidopsis Mediator subunits 2, 14, 15a, 16, and 25 are required for papillae development on the trichome cell wall surface. Arabidopsis leaf hairs exhibit raised protrusions, termed papillae, on their cell wall surfaces. Here, we show that the glassy hair mutant, glh2, exhibits trichomes with an approximate 11-fold decrease in papillae density on their surfaces in comparison to wild type. This phenotype was found to be the result of mutations in Arabidopsis Mediator subunit 16. MED16 is localized to the nucleus of trichomes, consistent with Mediator's role in transcription. The expression patterns of the trichome development reporters, ETR2pro::GUS and GL2pro::GUS, as well as GL2 transcript levels were not altered in the glh2 mutant. Screening of available T-DNA insertion lines in other subunits of the Mediator tail module revealed glassy trichome phenotypes in med2, med14, and med15a mutants. The data suggest that the Mediator complex is required for expression of genes involved in trichome papillae development.
Collapse
Affiliation(s)
- Christy Fornero
- School of Biological Sciences, Illinois State University, Normal, IL, 61790, USA
| | - Trevor Rickerd
- School of Biological Sciences, Illinois State University, Normal, IL, 61790, USA
| | - Viktor Kirik
- School of Biological Sciences, Illinois State University, Normal, IL, 61790, USA.
| |
Collapse
|
73
|
Wood DJ, Endicott JA. Structural insights into the functional diversity of the CDK-cyclin family. Open Biol 2019; 8:rsob.180112. [PMID: 30185601 PMCID: PMC6170502 DOI: 10.1098/rsob.180112] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/10/2018] [Indexed: 12/17/2022] Open
Abstract
Since their characterization as conserved modules that regulate progression through the eukaryotic cell cycle, cyclin-dependent protein kinases (CDKs) in higher eukaryotic cells are now also emerging as significant regulators of transcription, metabolism and cell differentiation. The cyclins, though originally characterized as CDK partners, also have CDK-independent roles that include the regulation of DNA damage repair and transcriptional programmes that direct cell differentiation, apoptosis and metabolic flux. This review compares the structures of the members of the CDK and cyclin families determined by X-ray crystallography, and considers what mechanistic insights they provide to guide functional studies and distinguish CDK- and cyclin-specific activities. Aberrant CDK activity is a hallmark of a number of diseases, and structural studies can provide important insights to identify novel routes to therapy.
Collapse
Affiliation(s)
- Daniel J Wood
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Jane A Endicott
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| |
Collapse
|
74
|
Drosophila Mediator Subunit Med1 Is Required for GATA-Dependent Developmental Processes: Divergent Binding Interfaces for Conserved Coactivator Functions. Mol Cell Biol 2019; 39:MCB.00477-18. [PMID: 30670567 DOI: 10.1128/mcb.00477-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/13/2019] [Indexed: 01/26/2023] Open
Abstract
DNA-bound transcription factors (TFs) governing developmental gene regulation have been proposed to recruit polymerase II machinery at gene promoters through specific interactions with dedicated subunits of the evolutionarily conserved Mediator (MED) complex. However, whether such MED subunit-specific functions and partnerships have been conserved during evolution has been poorly investigated. To address this issue, we generated the first Drosophila melanogaster loss-of-function mutants for Med1, known as a specific cofactor for GATA TFs and hormone nuclear receptors in mammals. We show that Med1 is required for cell proliferation and hematopoietic differentiation depending on the GATA TF Serpent (Srp). Med1 physically binds Srp in cultured cells and in vitro through its conserved GATA zinc finger DNA-binding domain and the divergent Med1 C terminus. Interestingly, GATA-Srp interaction occurs through the longest Med1 isoform, suggesting a functional diversity of MED complex populations. Furthermore, we show that Med1 acts as a coactivator for the GATA factor Pannier during thoracic development. In conclusion, the Med1 requirement for GATA-dependent regulatory processes is a common feature in insects and mammals, although binding interfaces have diverged. Further work in Drosophila should bring valuable insights to fully understand GATA-MED functional partnerships, which probably involve other MED subunits depending on the cellular context.
Collapse
|
75
|
Greber BJ, Toso DB, Fang J, Nogales E. The complete structure of the human TFIIH core complex. eLife 2019; 8:e44771. [PMID: 30860024 PMCID: PMC6422496 DOI: 10.7554/elife.44771] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 03/03/2019] [Indexed: 01/26/2023] Open
Abstract
Transcription factor IIH (TFIIH) is a heterodecameric protein complex critical for transcription initiation by RNA polymerase II and nucleotide excision DNA repair. The TFIIH core complex is sufficient for its repair functions and harbors the XPB and XPD DNA-dependent ATPase/helicase subunits, which are affected by human disease mutations. Transcription initiation additionally requires the CdK activating kinase subcomplex. Previous structural work has provided only partial insight into the architecture of TFIIH and its interactions within transcription pre-initiation complexes. Here, we present the complete structure of the human TFIIH core complex, determined by phase-plate cryo-electron microscopy at 3.7 Å resolution. The structure uncovers the molecular basis of TFIIH assembly, revealing how the recruitment of XPB by p52 depends on a pseudo-symmetric dimer of homologous domains in these two proteins. The structure also suggests a function for p62 in the regulation of XPD, and allows the mapping of previously unresolved human disease mutations.
Collapse
Affiliation(s)
- Basil J Greber
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyUnited States
- Molecular Biophysics and Integrative Bio-Imaging DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Daniel B Toso
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyUnited States
| | - Jie Fang
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
| | - Eva Nogales
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyUnited States
- Molecular Biophysics and Integrative Bio-Imaging DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
- Department of Molecular and Cell BiologyUniversity of CaliforniaBerkeleyUnited States
| |
Collapse
|
76
|
Twenty years of Mediator complex structural studies. Biochem Soc Trans 2019; 47:399-410. [PMID: 30733343 PMCID: PMC6393861 DOI: 10.1042/bst20180608] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/14/2019] [Accepted: 01/16/2019] [Indexed: 11/18/2022]
Abstract
Mediator is a large multiprotein complex conserved in all eukaryotes that plays an essential role in transcriptional regulation. Mediator comprises 25 subunits in yeast and 30 subunits in humans that form three main modules and a separable four-subunit kinase module. For nearly 20 years, because of its size and complexity, Mediator has posed a formidable challenge to structural biologists. The first two-dimensional electron microscopy (EM) projection map of Mediator leading to the canonical view of its division in three topological modules named Head, Middle and Tail, was published in 1999. Within the last few years, optimization of Mediator purification combined with technical and methodological advances in cryo-electron microscopy (cryo-EM) have revealed unprecedented details of Mediator subunit organization, interactions with RNA polymerase II and parts of its core structure at high resolution. To celebrate the twentieth anniversary of the first Mediator EM reconstruction, we look back on the structural studies of Mediator complex from a historical perspective and discuss them in the light of our current understanding of its role in transcriptional regulation.
Collapse
|
77
|
Ježek J, Smethurst DGJ, Stieg DC, Kiss ZAC, Hanley SE, Ganesan V, Chang KT, Cooper KF, Strich R. Cyclin C: The Story of a Non-Cycling Cyclin. BIOLOGY 2019; 8:biology8010003. [PMID: 30621145 PMCID: PMC6466611 DOI: 10.3390/biology8010003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/21/2018] [Accepted: 12/28/2018] [Indexed: 12/14/2022]
Abstract
The class I cyclin family is a well-studied group of structurally conserved proteins that interact with their associated cyclin-dependent kinases (Cdks) to regulate different stages of cell cycle progression depending on their oscillating expression levels. However, the role of class II cyclins, which primarily act as transcription factors and whose expression remains constant throughout the cell cycle, is less well understood. As a classic example of a transcriptional cyclin, cyclin C forms a regulatory sub-complex with its partner kinase Cdk8 and two accessory subunits Med12 and Med13 called the Cdk8-dependent kinase module (CKM). The CKM reversibly associates with the multi-subunit transcriptional coactivator complex, the Mediator, to modulate RNA polymerase II-dependent transcription. Apart from its transcriptional regulatory function, recent research has revealed a novel signaling role for cyclin C at the mitochondria. Upon oxidative stress, cyclin C leaves the nucleus and directly activates the guanosine 5’-triphosphatase (GTPase) Drp1, or Dnm1 in yeast, to induce mitochondrial fragmentation. Importantly, cyclin C-induced mitochondrial fission was found to increase sensitivity of both mammalian and yeast cells to apoptosis. Here, we review and discuss the biology of cyclin C, focusing mainly on its transcriptional and non-transcriptional roles in tumor promotion or suppression.
Collapse
Affiliation(s)
- Jan Ježek
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Daniel G J Smethurst
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - David C Stieg
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Z A C Kiss
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Sara E Hanley
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Vidyaramanan Ganesan
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Kai-Ti Chang
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Katrina F Cooper
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| | - Randy Strich
- Department of Molecular Biology, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084, USA.
| |
Collapse
|
78
|
Greber BJ, Nogales E. The Structures of Eukaryotic Transcription Pre-initiation Complexes and Their Functional Implications. Subcell Biochem 2019; 93:143-192. [PMID: 31939151 DOI: 10.1007/978-3-030-28151-9_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transcription is a highly regulated process that supplies living cells with coding and non-coding RNA molecules. Failure to properly regulate transcription is associated with human pathologies, including cancers. RNA polymerase II is the enzyme complex that synthesizes messenger RNAs that are then translated into proteins. In spite of its complexity, RNA polymerase requires a plethora of general transcription factors to be recruited to the transcription start site as part of a large transcription pre-initiation complex, and to help it gain access to the transcribed strand of the DNA. This chapter reviews the structure and function of these eukaryotic transcription pre-initiation complexes, with a particular emphasis on two of its constituents, the multisubunit complexes TFIID and TFIIH. We also compare the overall architecture of the RNA polymerase II pre-initiation complex with those of RNA polymerases I and III, involved in transcription of ribosomal RNA and non-coding RNAs such as tRNAs and snRNAs, and discuss the general, conserved features that are applicable to all eukaryotic RNA polymerase systems.
Collapse
Affiliation(s)
- Basil J Greber
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| |
Collapse
|
79
|
Knoll ER, Zhu ZI, Sarkar D, Landsman D, Morse RH. Role of the pre-initiation complex in Mediator recruitment and dynamics. eLife 2018; 7:39633. [PMID: 30540252 PMCID: PMC6322861 DOI: 10.7554/elife.39633] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/12/2018] [Indexed: 12/19/2022] Open
Abstract
The Mediator complex stimulates the cooperative assembly of a pre-initiation complex (PIC) and recruitment of RNA Polymerase II (Pol II) for gene activation. The core Mediator complex is organized into head, middle, and tail modules, and in budding yeast (Saccharomyces cerevisiae), Mediator recruitment has generally been ascribed to sequence-specific activators engaging the tail module triad of Med2-Med3-Med15 at upstream activating sequences (UASs). We show that yeast lacking Med2-Med3-Med15 are viable and that Mediator and PolII are recruited to promoters genome-wide in these cells, albeit at reduced levels. To test whether Mediator might alternatively be recruited via interactions with the PIC, we examined Mediator association genome-wide after depleting PIC components. We found that depletion of Taf1, Rpb3, and TBP profoundly affected Mediator association at active gene promoters, with TBP being critical for transit of Mediator from UAS to promoter, while Pol II and Taf1 stabilize Mediator association at proximal promoters.
Collapse
Affiliation(s)
- Elisabeth R Knoll
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, United States
| | - Z Iris Zhu
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, United States
| | - Debasish Sarkar
- Wadsworth Center, New York State Department of Health, Albany, United States
| | - David Landsman
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, Bethesda, United States
| | - Randall H Morse
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, United States.,Wadsworth Center, New York State Department of Health, Albany, United States
| |
Collapse
|
80
|
Bourguet P, de Bossoreille S, López-González L, Pouch-Pélissier MN, Gómez-Zambrano Á, Devert A, Pélissier T, Pogorelcnik R, Vaillant I, Mathieu O. A role for MED14 and UVH6 in heterochromatin transcription upon destabilization of silencing. Life Sci Alliance 2018; 1:e201800197. [PMID: 30574575 PMCID: PMC6291795 DOI: 10.26508/lsa.201800197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/05/2018] [Accepted: 12/05/2018] [Indexed: 01/11/2023] Open
Abstract
The TFIIH component UVH6 and the mediator subunit MED14 are differentially required for the release of heterochromatin silencing, and MED14 regulates non-CG DNA methylation in Arabidopsis. Constitutive heterochromatin is associated with repressive epigenetic modifications of histones and DNA which silence transcription. Yet, particular mutations or environmental changes can destabilize heterochromatin-associated silencing without noticeable changes in repressive epigenetic marks. Factors allowing transcription in this nonpermissive chromatin context remain poorly known. Here, we show that the transcription factor IIH component UVH6 and the mediator subunit MED14 are both required for heat stress–induced transcriptional changes and release of heterochromatin transcriptional silencing in Arabidopsis thaliana. We find that MED14, but not UVH6, is required for transcription when heterochromatin silencing is destabilized in the absence of stress through mutating the MOM1 silencing factor. In this case, our results raise the possibility that transcription dependency over MED14 might require intact patterns of repressive epigenetic marks. We also uncover that MED14 regulates DNA methylation in non-CG contexts at a subset of RNA-directed DNA methylation target loci. These findings provide insight into the control of heterochromatin transcription upon silencing destabilization and identify MED14 as a regulator of DNA methylation.
Collapse
Affiliation(s)
- Pierre Bourguet
- Génétique Reproduction et Développement, Centre National de la Recherche Scientifique (CNRS), Inserm, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Stève de Bossoreille
- Génétique Reproduction et Développement, Centre National de la Recherche Scientifique (CNRS), Inserm, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Leticia López-González
- Génétique Reproduction et Développement, Centre National de la Recherche Scientifique (CNRS), Inserm, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Marie-Noëlle Pouch-Pélissier
- Génétique Reproduction et Développement, Centre National de la Recherche Scientifique (CNRS), Inserm, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ángeles Gómez-Zambrano
- Génétique Reproduction et Développement, Centre National de la Recherche Scientifique (CNRS), Inserm, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Anthony Devert
- Génétique Reproduction et Développement, Centre National de la Recherche Scientifique (CNRS), Inserm, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Thierry Pélissier
- Génétique Reproduction et Développement, Centre National de la Recherche Scientifique (CNRS), Inserm, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Romain Pogorelcnik
- Génétique Reproduction et Développement, Centre National de la Recherche Scientifique (CNRS), Inserm, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Isabelle Vaillant
- Génétique Reproduction et Développement, Centre National de la Recherche Scientifique (CNRS), Inserm, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Olivier Mathieu
- Génétique Reproduction et Développement, Centre National de la Recherche Scientifique (CNRS), Inserm, Université Clermont Auvergne, Clermont-Ferrand, France
| |
Collapse
|
81
|
Herzik MA, Fraser JS, Lander GC. A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality. Structure 2018; 27:344-358.e3. [PMID: 30449687 DOI: 10.1016/j.str.2018.10.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/17/2018] [Accepted: 10/10/2018] [Indexed: 02/06/2023]
Abstract
There does not currently exist a standardized indicator of how well cryo-EM-derived models represent the density from which they were generated. We present a straightforward methodology that utilizes freely available tools to generate a suite of independent models and to evaluate their convergence in an EM density. These analyses provide both a quantitative and qualitative assessment of the precision of the models and their representation of the density, respectively, while concurrently providing a platform for assessing both global and local EM map quality. We further use standardized datasets to provide an expected deviation within a suite of models refined against EM maps reported to be at 5 Å resolution or better. Associating multiple atomic models with a deposited EM map provides a rapid and accessible reporter of convergence, a strong indicator of highly resolved molecular detail, and is an important step toward an FSC-independent assessment of map and model quality.
Collapse
Affiliation(s)
- Mark A Herzik
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James S Fraser
- Department of Bioengineering and Therapeutic Science and California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
82
|
Sierecki E. The Mediator complex and the role of protein-protein interactions in the gene regulation machinery. Semin Cell Dev Biol 2018; 99:20-30. [PMID: 30278226 DOI: 10.1016/j.semcdb.2018.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/13/2018] [Accepted: 08/13/2018] [Indexed: 12/11/2022]
Abstract
At the core of gene regulation, a complex network of dynamic interactions between proteins, DNA and RNA has to be integrated in order to generate a binary biological output. Large protein complexes, called adaptors, transfer information from the transcription factors to the transcription machinery [1,2]. Here we focus on Mediator, one of the largest adaptor proteins in humans [3]. Assembled from 30 different subunits, this system provides extraordinary illustrations for the various roles played by protein-protein interactions. Recruitment of new subunits during evolution is an adaptive mechanism to the growing complexity of the organism. Integration of information happens at multiple scales, with allosteric effects at the level of individual subunits resulting in large conformational changes. Mediator is also rich in disordered regions that increase the potential for interactions by presenting a malleable surface to its environment. Potentially, 3000 transcription factors can interact with Mediator and so understanding the molecular mechanisms that support the processing of this overload of information is one of the great challenges in molecular biology.
Collapse
Affiliation(s)
- Emma Sierecki
- EMBL Australia Node in Single Molecule Science, and School of Medical Sciences, Faculty of Medecine, The University of New South Wales, Sydney, Australia.
| |
Collapse
|
83
|
Hanske J, Sadian Y, Müller CW. The cryo-EM resolution revolution and transcription complexes. Curr Opin Struct Biol 2018; 52:8-15. [PMID: 30015202 PMCID: PMC6302067 DOI: 10.1016/j.sbi.2018.07.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 06/25/2018] [Accepted: 07/02/2018] [Indexed: 01/22/2023]
Abstract
Direct electron detector technology combined with improved imaging processing procedures has dramatically increased the resolution that can be obtained by single-particle cryo-electron microscopy and cryo-electron tomography. These developments-often referred to as the `resolution revolution' in cryo-EM-have had a profound impact on the structural biology of transcription as they allow the determination of atomic or near-atomic resolution structures of very large, flexible and often transient transcription complexes that in many cases had resisted crystal structure determination for decades. In this review, we will discuss recent advances and breakthroughs in the structural biology of transcription complexes enabled by the revolution in cryo-electron microscopy with particular focus on eukaryotic RNA polymerases and their pre-initiation complexes, but also chromatin remodelers and epigenetic regulators.
Collapse
Affiliation(s)
- Jonas Hanske
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Yashar Sadian
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Christoph W Müller
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
| |
Collapse
|
84
|
Transcriptome Analysis of Four Arabidopsis thaliana Mediator Tail Mutants Reveals Overlapping and Unique Functions in Gene Regulation. G3-GENES GENOMES GENETICS 2018; 8:3093-3108. [PMID: 30049745 PMCID: PMC6118316 DOI: 10.1534/g3.118.200573] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The Mediator complex is a central component of transcriptional regulation in Eukaryotes. The complex is structurally divided into four modules known as the head, middle, tail and kinase modules, and in Arabidopsis thaliana, comprises 28-34 subunits. Here, we explore the functions of four Arabidopsis Mediator tail subunits, MED2, MED5a/b, MED16, and MED23, by comparing the impact of mutations in each on the Arabidopsis transcriptome. We find that these subunits affect both unique and overlapping sets of genes, providing insight into the functional and structural relationships between them. The mutants primarily exhibit changes in the expression of genes related to biotic and abiotic stress. We find evidence for a tissue specific role for MED23, as well as in the production of alternative transcripts. Together, our data help disentangle the individual contributions of these MED subunits to global gene expression and suggest new avenues for future research into their functions.
Collapse
|
85
|
Monté D, Clantin B, Dewitte F, Lens Z, Rucktooa P, Pardon E, Steyaert J, Verger A, Villeret V. Crystal structure of human Mediator subunit MED23. Nat Commun 2018; 9:3389. [PMID: 30140054 PMCID: PMC6107663 DOI: 10.1038/s41467-018-05967-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/01/2018] [Indexed: 11/18/2022] Open
Abstract
The Mediator complex transduces regulatory information from enhancers to promoters and performs essential roles in the initiation of transcription in eukaryotes. Human Mediator comprises 26 subunits forming three modules termed Head, Middle and Tail. Here we present the 2.8 Å crystal structure of MED23, the largest subunit from the human Tail module. The structure identifies 25 HEAT repeats-like motifs organized into 5 α-solenoids. MED23 adopts an arch-shaped conformation, with an N-terminal domain (Nter) protruding from a large core region. In the core four solenoids, motifs wrap on themselves, creating triangular-shaped structural motifs on both faces of the arch, with extended grooves propagating through the interfaces between the solenoid motifs. MED23 is known to interact with several specific transcription activators and is involved in splicing, elongation, and post-transcriptional events. The structure rationalizes previous biochemical observations and paves the way for improved understanding of the cross-talk between Mediator and transcriptional activators. Mediator is a large multi-subunits complex essential to the regulation of transcription by RNA pol II. Here the authors report the crystal structure of MED23—one of the largest subunits of the complex together with MED1 and MED14—revealing a complex architecture and filling an important gap in the structural characterization of Mediator.
Collapse
Affiliation(s)
- Didier Monté
- CNRS, UMR 8576-UGSF- Unité de Glycobiologie Structurale et Fonctionnelle, Univ. Lille, 59000, Lille, France.
| | - Bernard Clantin
- CNRS, UMR 8576-UGSF- Unité de Glycobiologie Structurale et Fonctionnelle, Univ. Lille, 59000, Lille, France
| | - Frédérique Dewitte
- CNRS, UMR 8576-UGSF- Unité de Glycobiologie Structurale et Fonctionnelle, Univ. Lille, 59000, Lille, France
| | - Zoé Lens
- CNRS, UMR 8576-UGSF- Unité de Glycobiologie Structurale et Fonctionnelle, Univ. Lille, 59000, Lille, France
| | - Prakash Rucktooa
- CNRS, UMR 8576-UGSF- Unité de Glycobiologie Structurale et Fonctionnelle, Univ. Lille, 59000, Lille, France.,Heptares Therapeutics Ltd., Broadwater Road, Hertfordshire, AL7 3AX, UK
| | - Els Pardon
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Alexis Verger
- CNRS, UMR 8576-UGSF- Unité de Glycobiologie Structurale et Fonctionnelle, Univ. Lille, 59000, Lille, France
| | - Vincent Villeret
- CNRS, UMR 8576-UGSF- Unité de Glycobiologie Structurale et Fonctionnelle, Univ. Lille, 59000, Lille, France.
| |
Collapse
|
86
|
Mediator, known as a coactivator, can act in transcription initiation in an activator-independent manner in vivo. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:687-696. [DOI: 10.1016/j.bbagrm.2018.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/28/2018] [Accepted: 07/04/2018] [Indexed: 01/20/2023]
|
87
|
Postrecruitment Function of Yeast Med6 Protein during the Transcriptional Activation by Mediator Complex. Biochem Res Int 2018; 2018:6406372. [PMID: 29992056 PMCID: PMC5818915 DOI: 10.1155/2018/6406372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 10/29/2017] [Indexed: 11/17/2022] Open
Abstract
Med6 protein (Med6p) is a hallmark component of evolutionarily conserved Mediator complexes, and the genuine role of Med6p in Mediator functions remains elusive. For the functional analysis of Saccharomyces cerevisiae Med6p (scMed6p), we generated a series of scMed6p mutants harboring a small internal deletion. Genetic analysis of these mutants revealed that three regions (amino acids 33-42 (Δ2), 125-134 (Δ5), and 157-166 (Δ6)) of scMed6p are required for cell viability and are located at highly conserved regions of Med6 homologs. Notably, the Med6p-Δ2 mutant was barely detectable in whole-cell extracts and purified Mediator, suggesting a loss of Mediator association and concurrent rapid degradation. Consistent with this, the recombinant forms of Med6p having these mutations partially (Δ2) restore or fail (Δ5 and Δ6) to restore in vitro transcriptional defects caused by temperature-sensitive med6 mutation. In an artificial recruitment assay, Mediator containing a LexA-fused wild-type Med6p or Med6p-Δ5 was recruited to the lexA operator region with TBP and activated reporter gene expression. However, the recruitment of Mediator containing LexA-Med6p-Δ6 to lexA operator region resulted in neither TBP recruitment nor reporter gene expression. This result demonstrates a pivotal role of Med6p in the postrecruitment function of Mediator, which is essential for transcriptional activation by Mediator.
Collapse
|
88
|
Putlyaev EV, Ibragimov AN, Lebedeva LA, Georgiev PG, Shidlovskii YV. Structure and Functions of the Mediator Complex. BIOCHEMISTRY (MOSCOW) 2018; 83:423-436. [PMID: 29626929 DOI: 10.1134/s0006297918040132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mediator is a key factor in the regulation of expression of RNA polymerase II-transcribed genes. Recent studies have shown that Mediator acts as a coordinator of transcription activation and participates in maintaining chromatin architecture in the cell nucleus. In this review, we present current concepts on the structure and functions of Mediator.
Collapse
Affiliation(s)
- E V Putlyaev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
| | | | | | | | | |
Collapse
|
89
|
|
90
|
Pan J, Meyers RM, Michel BC, Mashtalir N, Sizemore AE, Wells JN, Cassel SH, Vazquez F, Weir BA, Hahn WC, Marsh JA, Tsherniak A, Kadoch C. Interrogation of Mammalian Protein Complex Structure, Function, and Membership Using Genome-Scale Fitness Screens. Cell Syst 2018; 6:555-568.e7. [PMID: 29778836 DOI: 10.1016/j.cels.2018.04.011] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/03/2018] [Accepted: 04/24/2018] [Indexed: 11/15/2022]
Abstract
Protein complexes are assemblies of subunits that have co-evolved to execute one or many coordinated functions in the cellular environment. Functional annotation of mammalian protein complexes is critical to understanding biological processes, as well as disease mechanisms. Here, we used genetic co-essentiality derived from genome-scale RNAi- and CRISPR-Cas9-based fitness screens performed across hundreds of human cancer cell lines to assign measures of functional similarity. From these measures, we systematically built and characterized functional similarity networks that recapitulate known structural and functional features of well-studied protein complexes and resolve novel functional modules within complexes lacking structural resolution, such as the mammalian SWI/SNF complex. Finally, by integrating functional networks with large protein-protein interaction networks, we discovered novel protein complexes involving recently evolved genes of unknown function. Taken together, these findings demonstrate the utility of genetic perturbation screens alone, and in combination with large-scale biophysical data, to enhance our understanding of mammalian protein complexes in normal and disease states.
Collapse
Affiliation(s)
- Joshua Pan
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Biomedical and Biological Sciences Program, Harvard Medical School, Boston, MA 02115, USA
| | - Robin M Meyers
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Brittany C Michel
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Biomedical and Biological Sciences Program, Harvard Medical School, Boston, MA 02115, USA
| | - Nazar Mashtalir
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Ann E Sizemore
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Jonathan N Wells
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Seth H Cassel
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Biomedical and Biological Sciences Program, Harvard Medical School, Boston, MA 02115, USA; Medical Scientist Training Program, Harvard Medical School, Boston, MA 02115, USA
| | - Francisca Vazquez
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Barbara A Weir
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - William C Hahn
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Aviad Tsherniak
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Cigall Kadoch
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
91
|
Weber H, Garabedian MJ. The mediator complex in genomic and non-genomic signaling in cancer. Steroids 2018; 133:8-14. [PMID: 29157917 PMCID: PMC5864542 DOI: 10.1016/j.steroids.2017.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/04/2017] [Accepted: 11/14/2017] [Indexed: 12/12/2022]
Abstract
Mediator is a conserved, multi-subunit macromolecular machine divided structurally into head, middle, and tail modules, along with a transiently associating kinase module. Mediator functions as an integrator of transcriptional regulatory activity by interacting with DNA-bound transcription factors and with RNA polymerase II (Pol II) to both activate and repress gene expression. Mediator has been shown to affect multiple steps in transcription, including chromatin looping between enhancers and promoters, pre-initiation complex formation, transcriptional elongation, and mRNA splicing. Individual Mediator subunits participate in regulation of gene expression by the estrogen and androgen receptors and are altered in a number of endocrine cancers, including breast and prostate cancer. In addition to its role in genomic signaling, MED12 has been implicated in non-genomic signaling by interacting with and activating TGF-beta receptor 2 in the cytoplasm. Recent structural studies have revealed extensive inter-domain interactions and complex architecture of the Mediator-Pol II complex, suggesting that Mediator is capable of reorganizing its conformation and composition to fit cellular needs. We propose that alterations in Mediator subunit expression that occur in various cancers could impact the organization and function of Mediator, resulting in changes in gene expression that promote malignancy. A better understanding of the role of Mediator in cancer could reveal new approaches to the diagnosis and treatment of Mediator-dependent endocrine cancers, especially in settings of therapy resistance.
Collapse
Affiliation(s)
- Hannah Weber
- Departments of Microbiology and Urology, NYU School of Medicine, 550 First Ave, New York, NY 10012, United States
| | - Michael J Garabedian
- Departments of Microbiology and Urology, NYU School of Medicine, 550 First Ave, New York, NY 10012, United States.
| |
Collapse
|
92
|
Liu X, Salokas K, Tamene F, Jiu Y, Weldatsadik RG, Öhman T, Varjosalo M. An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations. Nat Commun 2018; 9:1188. [PMID: 29568061 PMCID: PMC5864832 DOI: 10.1038/s41467-018-03523-2] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 02/21/2018] [Indexed: 11/09/2022] Open
Abstract
Protein-protein interactions govern almost all cellular functions. These complex networks of stable and transient associations can be mapped by affinity purification mass spectrometry (AP-MS) and complementary proximity-based labeling methods such as BioID. To exploit the advantages of both strategies, we here design and optimize an integrated approach combining AP-MS and BioID in a single construct, which we term MAC-tag. We systematically apply the MAC-tag approach to 18 subcellular and 3 sub-organelle localization markers, generating a molecular context database, which can be used to define a protein’s molecular location. In addition, we show that combining the AP-MS and BioID results makes it possible to obtain interaction distances within a protein complex. Taken together, our integrated strategy enables the comprehensive mapping of the physical and functional interactions of proteins, defining their molecular context and improving our understanding of the cellular interactome. AP-MS and BioID provide complementary insights into cellular protein interaction networks. To facilitate their combined use, the authors here present an AP-MS- and BioID-compatible affinity tag, enabling efficient determination of cellular protein locations and interaction distances.
Collapse
Affiliation(s)
- Xiaonan Liu
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland
| | - Kari Salokas
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland
| | - Fitsum Tamene
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland.,Proteomics Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Yaming Jiu
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland
| | - Rigbe G Weldatsadik
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland.,Proteomics Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Tiina Öhman
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland.,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland.,Proteomics Unit, University of Helsinki, Helsinki, 00014, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, 00014, Finland. .,Helsinki Institute of Life Science, University of Helsinki, Helsinki, 00014, Finland. .,Proteomics Unit, University of Helsinki, Helsinki, 00014, Finland.
| |
Collapse
|
93
|
Park MJ, Shen H, Spaeth JM, Tolvanen JH, Failor C, Knudtson JF, McLaughlin J, Halder SK, Yang Q, Bulun SE, Al-Hendy A, Schenken RS, Aaltonen LA, Boyer TG. Oncogenic exon 2 mutations in Mediator subunit MED12 disrupt allosteric activation of cyclin C-CDK8/19. J Biol Chem 2018; 293:4870-4882. [PMID: 29440396 DOI: 10.1074/jbc.ra118.001725] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 01/28/2018] [Indexed: 01/26/2023] Open
Abstract
Somatic mutations in exon 2 of the RNA polymerase II transcriptional Mediator subunit MED12 occur at high frequency in uterine fibroids (UFs) and breast fibroepithelial tumors as well as recurrently, albeit less frequently, in malignant uterine leimyosarcomas, chronic lymphocytic leukemias, and colorectal cancers. Previously, we reported that UF-linked mutations in MED12 disrupt its ability to activate cyclin C (CycC)-dependent kinase 8 (CDK8) in Mediator, implicating impaired Mediator-associated CDK8 activity in the molecular pathogenesis of these clinically significant lesions. Notably, the CDK8 paralog CDK19 is also expressed in myometrium, and both CDK8 and CDK19 assemble into Mediator in a mutually exclusive manner, suggesting that CDK19 activity may also be germane to the pathogenesis of MED12 mutation-induced UFs. However, whether and how UF-linked mutations in MED12 affect CDK19 activation is unknown. Herein, we show that MED12 allosterically activates CDK19 and that UF-linked exon 2 mutations in MED12 disrupt its CDK19 stimulatory activity. Furthermore, we find that within the Mediator kinase module, MED13 directly binds to the MED12 C terminus, thereby suppressing an apparent UF mutation-induced conformational change in MED12 that otherwise disrupts its association with CycC-CDK8/19. Thus, in the presence of MED13, mutant MED12 can bind, but cannot activate, CycC-CDK8/19. These findings indicate that MED12 binding is necessary but not sufficient for CycC-CDK8/19 activation and reveal an additional step in the MED12-dependent activation process, one critically dependent on MED12 residues altered by UF-linked exon 2 mutations. These findings confirm that UF-linked mutations in MED12 disrupt composite Mediator-associated kinase activity and identify CDK8/19 as prospective therapeutic targets in UFs.
Collapse
Affiliation(s)
- Min Ju Park
- Departments of Molecular Medicine, San Antonio, Texas 78229
| | - Hailian Shen
- Departments of Molecular Medicine, San Antonio, Texas 78229
| | - Jason M Spaeth
- Departments of Molecular Medicine, San Antonio, Texas 78229
| | - Jaana H Tolvanen
- Genome-Scale Biology Program and Department of Medical Genetics, Haartman Institute, University of Helsinki, Biomedicum, P.O. Box 63 (Haartmaninkatu 8), Helsinki FIN-00014, Finland
| | - Courtney Failor
- Obstetrics and Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229
| | - Jennifer F Knudtson
- Obstetrics and Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229
| | - Jessica McLaughlin
- Obstetrics and Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229
| | - Sunil K Halder
- Department of Obstetrics and Gynecology, Augusta University, Augusta, Georgia 30912
| | - Qiwei Yang
- Department of Obstetrics and Gynecology, Augusta University, Augusta, Georgia 30912
| | - Serdar E Bulun
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611
| | - Ayman Al-Hendy
- Department of Obstetrics and Gynecology, Augusta University, Augusta, Georgia 30912
| | - Robert S Schenken
- Obstetrics and Gynecology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229
| | - Lauri A Aaltonen
- Genome-Scale Biology Program and Department of Medical Genetics, Haartman Institute, University of Helsinki, Biomedicum, P.O. Box 63 (Haartmaninkatu 8), Helsinki FIN-00014, Finland
| | - Thomas G Boyer
- Departments of Molecular Medicine, San Antonio, Texas 78229.
| |
Collapse
|
94
|
Abstract
Experimental methods for the characterization of protein complexes have been instrumental in achieving our current understanding of the protein universe and continue to progress with each year that passes. In this chapter, we review some of the most important tools and techniques in the field, covering the important points in X-ray crystallography, cryo-electron microscopy, NMR spectroscopy, and mass spectrometry. Novel developments are making it possible to study large protein complexes at near-atomic resolutions, and we also now have the ability to study the dynamics and assembly pathways of protein complexes across a range of sizes.
Collapse
Affiliation(s)
- Jonathan N Wells
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK.
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
95
|
Abstract
Alterations in the regulation of gene expression are frequently associated with developmental diseases or cancer. Transcription activation is a key phenomenon in the regulation of gene expression. In all eukaryotes, mediator of RNA polymerase II transcription (Mediator), a large complex with modular organization, is generally required for transcription by RNA polymerase II, and it regulates various steps of this process. The main function of Mediator is to transduce signals from the transcription activators bound to enhancer regions to the transcription machinery, which is assembled at promoters as the preinitiation complex (PIC) to control transcription initiation. Recent functional studies of Mediator with the use of structural biology approaches and functional genomics have revealed new insights into Mediator activity and its regulation during transcription initiation, including how Mediator is recruited to transcription regulatory regions and how it interacts and cooperates with PIC components to assist in PIC assembly. Novel roles of Mediator in the control of gene expression have also been revealed by showing its connection to the nuclear pore and linking Mediator to the regulation of gene positioning in the nuclear space. Clear links between Mediator subunits and disease have also encouraged studies to explore targeting of this complex as a potential therapeutic approach in cancer and fungal infections.
Collapse
Affiliation(s)
- Julie Soutourina
- Institute for Integrative Biology of the Cell (I2BC), Institute of Life Sciences Frédéric Joliot, Commissariat à l'énergie Atomique et aux énergies alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), University Paris Sud, University Paris Saclay, F-91198 Gif-sur-Yvette, France
| |
Collapse
|
96
|
Def1 interacts with TFIIH and modulates RNA polymerase II transcription. Proc Natl Acad Sci U S A 2017; 114:13230-13235. [PMID: 29180430 DOI: 10.1073/pnas.1707955114] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The DNA damage response is an essential process for the survival of living cells. In a subset of stress-responsive genes in humans, Elongin controls transcription in response to multiple stimuli, such as DNA damage, oxidative stress, and heat shock. Yeast Elongin (Ela1-Elc1), along with Def1, is known to facilitate ubiquitylation and degradation of RNA polymerase II (pol II) in response to multiple stimuli, yet transcription activity has not been examined. We have found that Def1 copurifies from yeast whole-cell extract with TFIIH, the largest general transcription factor required for transcription initiation and nucleotide excision repair. The addition of recombinant Def1 and Ela1-Elc1 enhanced transcription initiation in an in vitro reconstituted system including pol II, the general transcription factors, and TFIIS. Def1 also enhanced transcription restart from TFIIS-induced cleavage in a pol II transcribing complex. In the Δdef1 strain, heat shock genes were misregulated, indicating that Def1 is required for induction of some stress-responsive genes in yeast. Taken together, our results extend the understanding of the molecular mechanism of transcription regulation on cellular stress and reveal functional similarities to the mammalian system.
Collapse
|
97
|
Schilbach S, Hantsche M, Tegunov D, Dienemann C, Wigge C, Urlaub H, Cramer P. Structures of transcription pre-initiation complex with TFIIH and Mediator. Nature 2017; 551:204-209. [PMID: 29088706 PMCID: PMC6078178 DOI: 10.1038/nature24282] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 09/14/2017] [Indexed: 12/18/2022]
Abstract
For the initiation of transcription, RNA polymerase II (Pol II) assembles with general transcription factors on promoter DNA to form the pre-initiation complex (PIC). Here we report cryo-electron microscopy structures of the Saccharomyces cerevisiae PIC and PIC-core Mediator complex at nominal resolutions of 4.7 Å and 5.8 Å, respectively. The structures reveal transcription factor IIH (TFIIH), and suggest how the core and kinase TFIIH modules function in the opening of promoter DNA and the phosphorylation of Pol II, respectively. The TFIIH core subunit Ssl2 (a homologue of human XPB) is positioned on downstream DNA by the 'E-bridge' helix in TFIIE, consistent with TFIIE-stimulated DNA opening. The TFIIH kinase module subunit Tfb3 (MAT1 in human) anchors the kinase Kin28 (CDK7), which is mobile in the PIC but preferentially located between the Mediator hook and shoulder in the PIC-core Mediator complex. Open spaces between the Mediator head and middle modules may allow access of the kinase to its substrate, the C-terminal domain of Pol II.
Collapse
Affiliation(s)
- S Schilbach
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - M Hantsche
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - D Tegunov
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - C Dienemann
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - C Wigge
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - H Urlaub
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
- University Medical Center Göttingen, Institute of Clinical Chemistry, Bioanalytics Group, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - P Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| |
Collapse
|
98
|
Jeronimo C, Robert F. The Mediator Complex: At the Nexus of RNA Polymerase II Transcription. Trends Cell Biol 2017; 27:765-783. [DOI: 10.1016/j.tcb.2017.07.001] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/03/2017] [Accepted: 07/06/2017] [Indexed: 12/15/2022]
|
99
|
Abstract
In eukaryotes, RNA polymerase II (pol II) transcribes all protein-coding genes and many noncoding RNAs. Whereas many factors contribute to the regulation of pol II activity, the Mediator complex is required for expression of most, if not all, pol II transcripts. Structural characterization of Mediator is challenging due to its large size (∼20 subunits in yeast and 26 subunits in humans) and conformational flexibility. However, recent studies have revealed structural details at higher resolution. Here, we summarize recent findings and place in context with previous results, highlighting regions within Mediator that are important for regulating its structure and function.
Collapse
Affiliation(s)
- Thomas M Harper
- From the Department of Biochemistry, University of Colorado, Boulder, Colorado 80303
| | - Dylan J Taatjes
- From the Department of Biochemistry, University of Colorado, Boulder, Colorado 80303
| |
Collapse
|
100
|
The cryo-electron microscopy structure of human transcription factor IIH. Nature 2017; 549:414-417. [PMID: 28902838 DOI: 10.1038/nature23903] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/10/2017] [Indexed: 02/04/2023]
Abstract
Human transcription factor IIH (TFIIH) is part of the general transcriptional machinery required by RNA polymerase II for the initiation of eukaryotic gene transcription. Composed of ten subunits that add up to a molecular mass of about 500 kDa, TFIIH is also essential for nucleotide excision repair. The seven-subunit TFIIH core complex formed by XPB, XPD, p62, p52, p44, p34, and p8 is competent for DNA repair, while the CDK-activating kinase subcomplex, which includes the kinase activity of CDK7 as well as the cyclin H and MAT1 subunits, is additionally required for transcription initiation. Mutations in the TFIIH subunits XPB, XPD, and p8 lead to severe premature ageing and cancer propensity in the genetic diseases xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy, highlighting the importance of TFIIH for cellular physiology. Here we present the cryo-electron microscopy structure of human TFIIH at 4.4 Å resolution. The structure reveals the molecular architecture of the TFIIH core complex, the detailed structures of its constituent XPB and XPD ATPases, and how the core and kinase subcomplexes of TFIIH are connected. Additionally, our structure provides insight into the conformational dynamics of TFIIH and the regulation of its activity.
Collapse
|