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Xiong Y, Zhu J, Hu R, Li Y, Yang Y, Liu M. Chemical shift assignments of the ACID domain of MED25, a subunit of the mediator complex in Arabidopsis thaliana. BIOMOLECULAR NMR ASSIGNMENTS 2024; 18:27-31. [PMID: 38334938 DOI: 10.1007/s12104-024-10164-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/24/2024] [Indexed: 02/10/2024]
Abstract
Mediator complex is a key component that bridges various transcription activators and RNA polymerase during eukaryotic transcription initiation. The Arabidopsis thaliana Med25 (aMed25), a subunit of the Mediator complex, plays important roles in regulating hormone signaling, biotic and abiotic stress responses and plant development by interacting with a variety of transcription factors through its activator-interacting domain (ACID). However, the recognition mechanism of aMed25-ACID for various transcription factors remains unknown. Here, we report the nearly complete 1H, 13C, and 15N backbone and side chain resonance assignments of aMED25-ACID (residues 551-681). TALOS-N analysis revealed that aMED25-ACID structure is comprised of three α-helices and seven β-strands, which lacks the C-terminal α-helix existing in the human MED25-ACID. This study lays a foundation for further research on the structure-function relationship of aMED25-ACID.
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Affiliation(s)
- Yue Xiong
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Optics Valley Laboratory, Hubei, 430074, China.
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Optics Valley Laboratory, Hubei, 430074, China
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Monté D, Lens Z, Dewitte F, Villeret V, Verger A. Assessment of machine-learning predictions for the Mediator complex subunit MED25 ACID domain interactions with transactivation domains. FEBS Lett 2024; 598:758-773. [PMID: 38436147 DOI: 10.1002/1873-3468.14837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/01/2024] [Accepted: 02/10/2024] [Indexed: 03/05/2024]
Abstract
The human Mediator complex subunit MED25 binds transactivation domains (TADs) present in various cellular and viral proteins using two binding interfaces, named H1 and H2, which are found on opposite sides of its ACID domain. Here, we use and compare deep learning methods to characterize human MED25-TAD interfaces and assess the predicted models to published experimental data. For the H1 interface, AlphaFold produces predictions with high-reliability scores that agree well with experimental data, while the H2 interface predictions appear inconsistent, preventing reliable binding modes. Despite these limitations, we experimentally assess the validity of MED25 interface predictions with the viral transcriptional activators Lana-1 and IE62. AlphaFold predictions also suggest the existence of a unique hydrophobic pocket for the Arabidopsis MED25 ACID domain.
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Affiliation(s)
- Didier Monté
- CNRS EMR 9002 Integrative Structural Biology, Inserm U 1167 - RID-AGE, Univ. Lille, CHU Lille, Institut Pasteur de Lille, France
| | - Zoé Lens
- CNRS EMR 9002 Integrative Structural Biology, Inserm U 1167 - RID-AGE, Univ. Lille, CHU Lille, Institut Pasteur de Lille, France
| | - Frédérique Dewitte
- CNRS EMR 9002 Integrative Structural Biology, Inserm U 1167 - RID-AGE, Univ. Lille, CHU Lille, Institut Pasteur de Lille, France
| | - Vincent Villeret
- CNRS EMR 9002 Integrative Structural Biology, Inserm U 1167 - RID-AGE, Univ. Lille, CHU Lille, Institut Pasteur de Lille, France
| | - Alexis Verger
- CNRS EMR 9002 Integrative Structural Biology, Inserm U 1167 - RID-AGE, Univ. Lille, CHU Lille, Institut Pasteur de Lille, France
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3
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Chu YH, Lin JD, Nath S, Schachtrup C. Id proteins: emerging roles in CNS disease and targets for modifying neural stemcell behavior. Cell Tissue Res 2021; 387:433-449. [PMID: 34302526 PMCID: PMC8975794 DOI: 10.1007/s00441-021-03490-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/18/2021] [Indexed: 12/14/2022]
Abstract
Neural stem/progenitor cells (NSPCs) are found in the adult brain and spinal cord, and endogenous or transplanted NSPCs contribute to repair processes and regulate immune responses in the CNS. However, the molecular mechanisms of NSPC survival and integration as well as their fate determination and functionality are still poorly understood. Inhibitor of DNA binding (Id) proteins are increasingly recognized as key determinants of NSPC fate specification. Id proteins act by antagonizing the DNA-binding activity of basic helix-loop-helix (bHLH) transcription factors, and the balance of Id and bHLH proteins determines cell fate decisions in numerous cell types and developmental stages. Id proteins are central in responses to environmental changes, as they occur in CNS injury and disease, and cellular responses in adult NSPCs implicate Id proteins as prime candidates for manipulating stemcell behavior. Here, we outline recent advances in understanding Id protein pleiotropic functions in CNS diseases and propose an integrated view of Id proteins and their promise as potential targets in modifying stemcell behavior to ameliorate CNS disease.
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Affiliation(s)
- Yu-Hsuan Chu
- Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Jia-di Lin
- Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Suvra Nath
- Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Christian Schachtrup
- Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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4
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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.
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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.
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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.
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6
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The role of prostate tumor overexpressed 1 in cancer progression. Oncotarget 2017; 8:12451-12471. [PMID: 28029646 PMCID: PMC5355357 DOI: 10.18632/oncotarget.14104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/14/2016] [Indexed: 12/15/2022] Open
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Currie SL, Doane JJ, Evans KS, Bhachech N, Madison BJ, Lau DKW, McIntosh LP, Skalicky JJ, Clark KA, Graves BJ. ETV4 and AP1 Transcription Factors Form Multivalent Interactions with three Sites on the MED25 Activator-Interacting Domain. J Mol Biol 2017; 429:2975-2995. [PMID: 28728983 DOI: 10.1016/j.jmb.2017.06.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/04/2017] [Accepted: 06/05/2017] [Indexed: 01/05/2023]
Abstract
The recruitment of transcriptional cofactors by sequence-specific transcription factors challenges the basis of high affinity and selective interactions. Extending previous studies that the N-terminal activation domain (AD) of ETV5 interacts with Mediator subunit 25 (MED25), we establish that similar, aromatic-rich motifs located both in the AD and in the DNA-binding domain (DBD) of the related ETS factor ETV4 interact with MED25. These ETV4 regions bind MED25 independently, display distinct kinetics, and combine to contribute to a high-affinity interaction of full-length ETV4 with MED25. High-affinity interactions with MED25 are specific for the ETV1/4/5 subfamily as other ETS factors display weaker binding. The AD binds to a single site on MED25 and the DBD interacts with three MED25 sites, allowing for simultaneous binding of both domains in full-length ETV4. MED25 also stimulates the in vitro DNA binding activity of ETV4 by relieving autoinhibition. ETV1/4/5 factors are often overexpressed in prostate cancer and genome-wide studies in a prostate cancer cell line indicate that ETV4 and MED25 occupy enhancers that are enriched for ETS-binding sequences and are both functionally important for the transcription of genes regulated by these enhancers. AP1-motifs, which bind JUN and FOS transcription factor families, were observed in MED25-occupied regions and JUN/FOS also contact MED25; FOS strongly binds to the same MED25 site as ETV4 AD and JUN interacts with the other two MED25 sites. In summary, we describe features of the multivalent ETV4- and AP1-MED25 interactions, thereby implicating these factors in the recruitment of MED25 to transcriptional control elements.
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Affiliation(s)
- Simon L Currie
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84112-5500, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112-5500, USA
| | - Jedediah J Doane
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84112-5500, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112-5500, USA
| | - Kathryn S Evans
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84112-5500, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112-5500, USA
| | - Niraja Bhachech
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84112-5500, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112-5500, USA
| | - Bethany J Madison
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84112-5500, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112-5500, USA
| | - Desmond K W Lau
- Departments of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Lawrence P McIntosh
- Departments of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Jack J Skalicky
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112-5650, USA
| | - Kathleen A Clark
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84112-5500, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112-5500, USA
| | - Barbara J Graves
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT, 84112-5500, USA; Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, 84112-5500, USA; Howard Hughes Medical Institute, Chevy Chase, MD, 20815-6789, USA.
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8
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Zhang Y, Rataj K, Simpson GG, Tong L. Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA. PLoS One 2016; 11:e0160694. [PMID: 27513867 PMCID: PMC4981400 DOI: 10.1371/journal.pone.0160694] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/23/2016] [Indexed: 11/18/2022] Open
Abstract
The Arabidopsis protein FPA controls flowering time by regulating the alternative 3′-end processing of the FLOWERING LOCUS (FLC) antisense RNA. FPA belongs to the split ends (SPEN) family of proteins, which contain N-terminal RNA recognition motifs (RRMs) and a SPEN paralog and ortholog C-terminal (SPOC) domain. The SPOC domain is highly conserved among FPA homologs in plants, but the conservation with the domain in other SPEN proteins is much lower. We have determined the crystal structure of Arabidopsis thaliana FPA SPOC domain at 2.7 Å resolution. The overall structure is similar to that of the SPOC domain in human SMRT/HDAC1 Associated Repressor Protein (SHARP), although there are also substantial conformational differences between them. Structural and sequence analyses identify a surface patch that is conserved among plant FPA homologs. Mutations of two residues in this surface patch did not disrupt FPA functions, suggesting that either the SPOC domain is not required for the role of FPA in regulating RNA 3′-end formation or the functions of the FPA SPOC domain cannot be disrupted by the combination of mutations, in contrast to observations with the SHARP SPOC domain.
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Affiliation(s)
- Yinglu Zhang
- Department of Biological Sciences, Columbia University, New York, NY, 10027, United States of America
| | - Katarzyna Rataj
- Division Plant Sciences & Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, United Kingdom
| | - Gordon G. Simpson
- Division Plant Sciences & Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, United Kingdom
- Cell & Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland, United Kingdom
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY, 10027, United States of America
- * E-mail:
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Functional Characterization of the Serine-Rich Tract of Varicella-Zoster Virus IE62. J Virol 2015; 90:959-71. [PMID: 26537679 DOI: 10.1128/jvi.02096-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/27/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The immediate early 62 protein (IE62) of varicella-zoster virus (VZV), a major viral trans-activator, initiates the virus life cycle and is a key component of pathogenesis. The IE62 possesses several domains essential for trans-activation, including an acidic trans-activation domain (TAD), a serine-rich tract (SRT), and binding domains for USF, TFIIB, and TATA box binding protein (TBP). Transient-transfection assays showed that the VZV IE62 lacking the SRT trans-activated the early VZV ORF61 promoter at only 16% of the level of the full-length IE62. When the SRT of IE62 was replaced with the SRT of equine herpesvirus 1 (EHV-1) IEP, its trans-activation activity was completely restored. Herpes simplex virus 1 (HSV-1) ICP4 that lacks a TAD very weakly (1.5-fold) trans-activated the ORF61 promoter. An IE62 TAD-ICP4 chimeric protein exhibited trans-activation ability (10.2-fold), indicating that the IE62 TAD functions with the SRT of HSV-1 ICP4 to trans-activate viral promoters. When the serine and acidic residues of the SRT were replaced with Ala, Leu, and Gly, trans-activation activities of the modified IE62 proteins IE62-SRTΔSe and IE62-SRTΔAc were reduced to 46% and 29% of wild-type activity, respectively. Bimolecular complementation assays showed that the TAD of IE62, EHV-1 IEP, and HSV-1 VP16 interacted with Mediator 25 in human melanoma MeWo cells. The SRT of IE62 interacted with the nucleolar-ribosomal protein EAP, which resulted in the formation of globular structures within the nucleus. These results suggest that the SRT plays an important role in VZV viral gene expression and replication. IMPORTANCE The immediate early 62 protein (IE62) of varicella-zoster virus (VZV) is a major viral trans-activator and is essential for viral growth. Our data show that the serine-rich tract (SRT) of VZV IE62, which is well conserved within the alphaherpesviruses, is needed for trans-activation mediated by the acidic trans-activation domain (TAD). The TADs of IE62, EHV-1 IEP, and HSV-1 VP16 interacted with cellular Mediator 25 in bimolecular complementation assays. The interaction of the IE62 SRT with nucleolar-ribosomal protein EAP resulted in the formation of globular structures within the nucleus. Understanding the mechanisms by which the TAD and SRT of IE62 contribute to the function of this essential regulatory protein is important in understanding the gene program of this human pathogen.
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Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD. Molecular architecture of the yeast Mediator complex. eLife 2015; 4. [PMID: 26402457 PMCID: PMC4631838 DOI: 10.7554/elife.08719] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/23/2015] [Indexed: 12/18/2022] Open
Abstract
The 21-subunit Mediator complex transduces regulatory information from enhancers to promoters, and performs an essential role in the initiation of transcription in all eukaryotes. Structural information on two-thirds of the complex has been limited to coarse subunit mapping onto 2-D images from electron micrographs. We have performed chemical cross-linking and mass spectrometry, and combined the results with information from X-ray crystallography, homology modeling, and cryo-electron microscopy by an integrative modeling approach to determine a 3-D model of the entire Mediator complex. The approach is validated by the use of X-ray crystal structures as internal controls and by consistency with previous results from electron microscopy and yeast two-hybrid screens. The model shows the locations and orientations of all Mediator subunits, as well as subunit interfaces and some secondary structural elements. Segments of 20–40 amino acid residues are placed with an average precision of 20 Å. The model reveals roles of individual subunits in the organization of the complex. DOI:http://dx.doi.org/10.7554/eLife.08719.001 Inside a cell, proteins are made from instructions encoded by DNA. To produce a particular protein, a section of DNA within a gene is copied into a molecule of messenger ribonucleic acid (or mRNA). This process is called transcription and is carried out by an enzyme known as RNA polymerase. Transcription begins in a region of DNA called a promoter, which is found at the start of the gene. RNA polymerase is brought to the DNA by many proteins, including the so-called Mediator complex. Mediator receives signals from within the cell and from the environment, processes the information, and instructs RNA polymerase whether to transcribe the gene or not. Mediator performs this important role in all organisms from yeast to humans, but it is not clear how it works. A crucial step towards the solution of this problem is to understand the three-dimensional structure of the complex. Previous research using a technique called ‘electron microscopy’ showed that Mediator is composed of three modules, referred to as Head, Middle and Tail. The images from electron microscopy were not sufficiently detailed to reveal the organization of the proteins within these modules. An open-source Integrative Modeling Platform (IMP for short) was recently developed to arrive at structural models of large protein complexes from a combination of experimental data and computer models. Now, Robinson, Trnka, Pellarin et al. have used this platform to study the Mediator complex. First, Robinson, Trnka, Pellarin et al. collected experimental data on the structure of the Mediator complex using two approaches called ‘chemical cross-linking’ and ‘mass spectrometry’. This data was combined with biochemical and structural information from previous studies to generate a three-dimensional model of the structure of the entire Mediator using IMP. The model is detailed enough to show the location and orientation of all the proteins in the complex. For example, a protein called Med17 connects the Head and Middle modules, while another subunit—known as Med14—spans the entire complex and makes extensive contacts with other proteins in all three modules. DOI:http://dx.doi.org/10.7554/eLife.08719.002
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Affiliation(s)
- Philip J Robinson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Riccardo Pellarin
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United States.,Structural Bioinformatics Unit, Paris, France
| | - Charles H Greenberg
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United States
| | - David A Bushnell
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Ralph Davis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, United States
| | - Roger D Kornberg
- Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
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Aguilar X, Blomberg J, Brännström K, Olofsson A, Schleucher J, Björklund S. Interaction studies of the human and Arabidopsis thaliana Med25-ACID proteins with the herpes simplex virus VP16- and plant-specific Dreb2a transcription factors. PLoS One 2014; 9:e98575. [PMID: 24874105 PMCID: PMC4038590 DOI: 10.1371/journal.pone.0098575] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 05/05/2014] [Indexed: 12/17/2022] Open
Abstract
Mediator is an evolutionary conserved multi-protein complex present in all eukaryotes. It functions as a transcriptional co-regulator by conveying signals from activators and repressors to the RNA polymerase II transcription machinery. The Arabidopsis thaliana Med25 (aMed25) ACtivation Interaction Domain (ACID) interacts with the Dreb2a activator which is involved in plant stress response pathways, while Human Med25-ACID (hMed25) interacts with the herpes simplex virus VP16 activator. Despite low sequence similarity, hMed25-ACID also interacts with the plant-specific Dreb2a transcriptional activator protein. We have used GST pull-down-, surface plasmon resonance-, isothermal titration calorimetry and NMR chemical shift experiments to characterize interactions between Dreb2a and VP16, with the hMed25 and aMed25-ACIDs. We found that VP16 interacts with aMed25-ACID with similar affinity as with hMed25-ACID and that the binding surface on aMed25-ACID overlaps with the binding site for Dreb2a. We also show that the Dreb2a interaction region in hMed25-ACID overlaps with the earlier reported VP16 binding site. In addition, we show that hMed25-ACID/Dreb2a and aMed25-ACID/Dreb2a display similar binding affinities but different binding energetics. Our results therefore indicate that interaction between transcriptional regulators and their target proteins in Mediator are less dependent on the primary sequences in the interaction domains but that these domains fold into similar structures upon interaction.
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Affiliation(s)
| | - Jeanette Blomberg
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | | | - Anders Olofsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Jürgen Schleucher
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Stefan Björklund
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
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12
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Sela D, Conkright JJ, Chen L, Gilmore J, Washburn MP, Florens L, Conaway RC, Conaway JW. Role for human mediator subunit MED25 in recruitment of mediator to promoters by endoplasmic reticulum stress-responsive transcription factor ATF6α. J Biol Chem 2013; 288:26179-26187. [PMID: 23864652 DOI: 10.1074/jbc.m113.496968] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transcription factor ATF6α functions as a master regulator of endoplasmic reticulum (ER) stress response genes. In response to ER stress, ATF6α translocates from its site of latency in the ER membrane to the nucleus, where it activates RNA polymerase II transcription of ER stress response genes upon binding sequence-specifically to ER stress response enhancer elements (ERSEs) in their promoter-regulatory regions. In a recent study, we demonstrated that ATF6α activates transcription of ER stress response genes by a mechanism involving recruitment to ERSEs of the multisubunit Mediator and several histone acetyltransferase (HAT) complexes, including Spt-Ada-Gcn5 (SAGA) and Ada-Two-A-containing (ATAC) (Sela, D., Chen, L., Martin-Brown, S., Washburn, M.P., Florens, L., Conaway, J.W., and Conaway, R.C. (2012) J. Biol. Chem. 287, 23035-23045). In this study, we extend our investigation of the mechanism by which ATF6α supports recruitment of Mediator to ER stress response genes. We present findings arguing that Mediator subunit MED25 plays a critical role in this process and identify a MED25 domain that serves as a docking site on Mediator for the ATF6α transcription activation domain.
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Affiliation(s)
- Dotan Sela
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Juliana J Conkright
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Lu Chen
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110,; Department of Biochemistry & Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160, and
| | - Joshua Gilmore
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Michael P Washburn
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110,; Departments of Pathology & Laboratory Medicine, Kansas University Medical Center, Kansas City, Kansas 66160
| | - Laurence Florens
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110
| | - Ronald C Conaway
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110,; Department of Biochemistry & Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160, and
| | - Joan Weliky Conaway
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110,; Department of Biochemistry & Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160, and.
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Çevik V, Kidd BN, Zhang P, Hill C, Kiddle S, Denby KJ, Holub EB, Cahill DM, Manners JM, Schenk PM, Beynon J, Kazan K. MEDIATOR25 acts as an integrative hub for the regulation of jasmonate-responsive gene expression in Arabidopsis. PLANT PHYSIOLOGY 2012; 160:541-55. [PMID: 22822211 PMCID: PMC3440227 DOI: 10.1104/pp.112.202697] [Citation(s) in RCA: 173] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 07/20/2012] [Indexed: 05/18/2023]
Abstract
The PHYTOCHROME AND FLOWERING TIME1 gene encoding the MEDIATOR25 (MED25) subunit of the eukaryotic Mediator complex is a positive regulator of jasmonate (JA)-responsive gene expression in Arabidopsis (Arabidopsis thaliana). Based on the function of the Mediator complex as a bridge between DNA-bound transcriptional activators and the RNA polymerase II complex, MED25 has been hypothesized to function in association with transcriptional regulators of the JA pathway. However, it is currently not known mechanistically how MED25 functions to regulate JA-responsive gene expression. In this study, we show that MED25 physically interacts with several key transcriptional regulators of the JA signaling pathway, including the APETALA2 (AP2)/ETHYLENE RESPONSE FACTOR (ERF) transcription factors OCTADECANOID-RESPONSIVE ARABIDOPSIS AP2/ERF59 and ERF1 as well as the master regulator MYC2. Physical interaction detected between MED25 and four group IX AP2/ERF transcription factors was shown to require the activator interaction domain of MED25 as well as the recently discovered Conserved Motif IX-1/EDLL transcription activation motif of MED25-interacting AP2/ERFs. Using transcriptional activation experiments, we also show that OCTADECANOID-RESPONSIVE ARABIDOPSIS AP2/ERF59- and ERF1-dependent activation of PLANT DEFENSIN1.2 as well as MYC2-dependent activation of VEGETATIVE STORAGE PROTEIN1 requires a functional MED25. In addition, MED25 is required for MYC2-dependent repression of pathogen defense genes. These results suggest an important role for MED25 as an integrative hub within the Mediator complex during the regulation of JA-associated gene expression.
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Affiliation(s)
- Volkan Çevik
- School of Life Sciences, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom.
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Sela D, Chen L, Martin-Brown S, Washburn MP, Florens L, Conaway JW, Conaway RC. Endoplasmic reticulum stress-responsive transcription factor ATF6α directs recruitment of the Mediator of RNA polymerase II transcription and multiple histone acetyltransferase complexes. J Biol Chem 2012; 287:23035-45. [PMID: 22577136 DOI: 10.1074/jbc.m112.369504] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The basic leucine zipper transcription factor ATF6α functions as a master regulator of endoplasmic reticulum (ER) stress response genes. Previous studies have established that, in response to ER stress, ATF6α translocates to the nucleus and activates transcription of ER stress response genes upon binding sequence specifically to ER stress response enhancer elements in their promoters. In this study, we investigate the biochemical mechanism by which ATF6α activates transcription. By exploiting a combination of biochemical and multidimensional protein identification technology-based mass spectrometry approaches, we have obtained evidence that ATF6α functions at least in part by recruiting to the ER stress response enhancer elements of ER stress response genes a collection of RNA polymerase II coregulatory complexes, including the Mediator and multiple histone acetyltransferase complexes, among which are the Spt-Ada-Gcn5 acetyltransferase (SAGA) and Ada-Two-A-containing (ATAC) complexes. Our findings shed new light on the mechanism of action of ATF6α, and they outline a straightforward strategy for applying multidimensional protein identification technology mass spectrometry to determine which RNA polymerase II transcription factors and coregulators are recruited to promoters and other regulatory elements to control transcription.
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Affiliation(s)
- Dotan Sela
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
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15
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Larivière L, Seizl M, Cramer P. A structural perspective on Mediator function. Curr Opin Cell Biol 2012; 24:305-13. [PMID: 22341791 DOI: 10.1016/j.ceb.2012.01.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 01/18/2012] [Accepted: 01/22/2012] [Indexed: 11/16/2022]
Abstract
Gene transcription by RNA polymerase II requires the multiprotein coactivator complex Mediator. Mediator was identified two decades ago, but its molecular mechanisms remain poorly understood, because structural studies are hampered by its large size, modularity, and flexibility. Here we collect all available structural data on Mediator and discuss their functional implications. Progress was made in understanding the interactions of Mediator with gene-specific transcriptional regulators and the general transcription machinery. However, around 80% of the Mediator structure remains unknown and details on the Mediator-Pol II interface are lacking. In the future, an integrated structural biology approach may unravel the functional architecture of Mediator-regulated promoter assemblies and holds the promise of understanding a key mechanism of gene regulation.
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Affiliation(s)
- Laurent Larivière
- Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany
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