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Malik N, Agarwal P, Tyagi A. Emerging functions of multi-protein complex Mediator with special emphasis on plants. Crit Rev Biochem Mol Biol 2017; 52:475-502. [DOI: 10.1080/10409238.2017.1325830] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Naveen Malik
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Akhilesh Tyagi
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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2
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Information Integration and Energy Expenditure in Gene Regulation. Cell 2017; 166:234-44. [PMID: 27368104 DOI: 10.1016/j.cell.2016.06.012] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 03/08/2016] [Accepted: 06/01/2016] [Indexed: 11/22/2022]
Abstract
The quantitative concepts used to reason about gene regulation largely derive from bacterial studies. We show that this bacterial paradigm cannot explain the sharp expression of a canonical developmental gene in response to a regulating transcription factor (TF). In the absence of energy expenditure, with regulatory DNA at thermodynamic equilibrium, information integration across multiple TF binding sites can generate the required sharpness, but with strong constraints on the resultant "higher-order cooperativities." Even with such integration, there is a "Hopfield barrier" to sharpness; for n TF binding sites, this barrier is represented by the Hill function with the Hill coefficient n. If, however, energy is expended to maintain regulatory DNA away from thermodynamic equilibrium, as in kinetic proofreading, this barrier can be breached and greater sharpness achieved. Our approach is grounded in fundamental physics, leads to testable experimental predictions, and suggests how a quantitative paradigm for eukaryotic gene regulation can be formulated.
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Yang Y, Li L, Qu LJ. Plant Mediator complex and its critical functions in transcription regulation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:106-18. [PMID: 26172375 DOI: 10.1111/jipb.12377] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 07/07/2015] [Indexed: 05/08/2023]
Abstract
The Mediator complex is an important component of the eukaryotic transcriptional machinery. As an essential link between transcription factors and RNA polymerase II, the Mediator complex transduces diverse signals to genes involved in different pathways. The plant Mediator complex was recently purified and comprises conserved and specific subunits. It functions in concert with transcription factors to modulate various responses. In this review, we summarize the recent advances in understanding the plant Mediator complex and its diverse roles in plant growth, development, defense, non-coding RNA production, response to abiotic stresses, flowering, genomic stability and metabolic homeostasis. In addition, the transcription factors interacting with the Mediator complex are also highlighted.
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Affiliation(s)
- Yan Yang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Ling Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Li-Jia Qu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
- The National Plant Gene Research Center (Beijing), Beijing 100101, China
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4
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Miozzo F, Sabéran-Djoneidi D, Mezger V. HSFs, Stress Sensors and Sculptors of Transcription Compartments and Epigenetic Landscapes. J Mol Biol 2015; 427:3793-816. [DOI: 10.1016/j.jmb.2015.10.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 10/02/2015] [Accepted: 10/09/2015] [Indexed: 01/06/2023]
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Nagulapalli M, Maji S, Dwivedi N, Dahiya P, Thakur JK. Evolution of disorder in Mediator complex and its functional relevance. Nucleic Acids Res 2015; 44:1591-612. [PMID: 26590257 PMCID: PMC4770211 DOI: 10.1093/nar/gkv1135] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 10/18/2015] [Indexed: 12/27/2022] Open
Abstract
Mediator, an important component of eukaryotic transcriptional machinery, is a huge multisubunit complex. Though the complex is known to be conserved across all the eukaryotic kingdoms, the evolutionary topology of its subunits has never been studied. In this study, we profiled disorder in the Mediator subunits of 146 eukaryotes belonging to three kingdoms viz., metazoans, plants and fungi, and attempted to find correlation between the evolution of Mediator complex and its disorder. Our analysis suggests that disorder in Mediator complex have played a crucial role in the evolutionary diversification of complexity of eukaryotic organisms. Conserved intrinsic disordered regions (IDRs) were identified in only six subunits in the three kingdoms whereas unique patterns of IDRs were identified in other Mediator subunits. Acquisition of novel molecular recognition features (MoRFs) through evolution of new subunits or through elongation of the existing subunits was evident in metazoans and plants. A new concept of ‘junction-MoRF’ has been introduced. Evolutionary link between CBP and Med15 has been provided which explain the evolution of extended-IDR in CBP from Med15 KIX-IDR junction-MoRF suggesting role of junction-MoRF in evolution and modulation of protein–protein interaction repertoire. This study can be informative and helpful in understanding the conserved and flexible nature of Mediator complex across eukaryotic kingdoms.
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Affiliation(s)
- Malini Nagulapalli
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sourobh Maji
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Nidhi Dwivedi
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pradeep Dahiya
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Jitendra K Thakur
- Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
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Fuxreiter M, Tóth-Petróczy Á, Kraut DA, Matouschek AT, Lim RYH, Xue B, Kurgan L, Uversky VN. Disordered proteinaceous machines. Chem Rev 2014; 114:6806-43. [PMID: 24702702 PMCID: PMC4350607 DOI: 10.1021/cr4007329] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Monika Fuxreiter
- MTA-DE
Momentum Laboratory of Protein Dynamics, Department of Biochemistry
and Molecular Biology, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary
| | - Ágnes Tóth-Petróczy
- Department
of Biological Chemistry, Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Daniel A. Kraut
- Department
of Chemistry, Villanova University, 800 East Lancaster Avenue, Villanova, Pennsylvania 19085, United States
| | - Andreas T. Matouschek
- Section
of Molecular Genetics and Microbiology, Institute for Cellular &
Molecular Biology, The University of Texas
at Austin, 2506 Speedway, Austin, Texas 78712, United States
| | - Roderick Y. H. Lim
- Biozentrum
and the Swiss Nanoscience Institute, University
of Basel, Klingelbergstrasse
70, CH-4056 Basel, Switzerland
| | - Bin Xue
- Department of Cell Biology,
Microbiology and Molecular Biology, College
of Fine Arts and Sciences, and Department of Molecular Medicine and USF Health
Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Lukasz Kurgan
- Department
of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Vladimir N. Uversky
- Department of Cell Biology,
Microbiology and Molecular Biology, College
of Fine Arts and Sciences, and Department of Molecular Medicine and USF Health
Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Institute
for Biological Instrumentation, Russian
Academy of Sciences, 142290 Pushchino, Moscow Region 119991, Russia
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Abstract
The Mediator complex is a multi-subunit assembly that appears to be required for regulating expression of most RNA polymerase II (pol II) transcripts, which include protein-coding and most non-coding RNA genes. Mediator and pol II function within the pre-initiation complex (PIC), which consists of Mediator, pol II, TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH and is approximately 4.0 MDa in size. Mediator serves as a central scaffold within the PIC and helps regulate pol II activity in ways that remain poorly understood. Mediator is also generally targeted by sequence-specific, DNA-binding transcription factors (TFs) that work to control gene expression programs in response to developmental or environmental cues. At a basic level, Mediator functions by relaying signals from TFs directly to the pol II enzyme, thereby facilitating TF-dependent regulation of gene expression. Thus, Mediator is essential for converting biological inputs (communicated by TFs) to physiological responses (via changes in gene expression). In this review, we summarize an expansive body of research on the Mediator complex, with an emphasis on yeast and mammalian complexes. We focus on the basics that underlie Mediator function, such as its structure and subunit composition, and describe its broad regulatory influence on gene expression, ranging from chromatin architecture to transcription initiation and elongation, to mRNA processing. We also describe factors that influence Mediator structure and activity, including TFs, non-coding RNAs and the CDK8 module.
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Affiliation(s)
- Zachary C Poss
- Department of Chemistry and Biochemistry, University of Colorado , Boulder, CO , USA
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Larsson M, Uvell H, Sandström J, Rydén P, Selth LA, Björklund S. Functional studies of the yeast med5, med15 and med16 mediator tail subunits. PLoS One 2013; 8:e73137. [PMID: 23991176 PMCID: PMC3750046 DOI: 10.1371/journal.pone.0073137] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Accepted: 07/23/2013] [Indexed: 11/19/2022] Open
Abstract
The yeast Mediator complex can be divided into three modules, designated Head, Middle and Tail. Tail comprises the Med2, Med3, Med5, Med15 and Med16 protein subunits, which are all encoded by genes that are individually non-essential for viability. In cells lacking Med16, Tail is displaced from Head and Middle. However, inactivation of MED5/MED15 and MED15/MED16 are synthetically lethal, indicating that Tail performs essential functions as a separate complex even when it is not bound to Middle and Head. We have used the N-Degron method to create temperature-sensitive (ts) mutants in the Mediator tail subunits Med5, Med15 and Med16 to study the immediate effects on global gene expression when each subunit is individually inactivated, and when Med5/15 or Med15/16 are inactivated together. We identify 25 genes in each double mutant that show a significant change in expression when compared to the corresponding single mutants and to the wild type strain. Importantly, 13 of the 25 identified genes are common for both double mutants. We also find that all strains in which MED15 is inactivated show down-regulation of genes that have been identified as targets for the Ace2 transcriptional activator protein, which is important for progression through the G1 phase of the cell cycle. Supporting this observation, we demonstrate that loss of Med15 leads to a G1 arrest phenotype. Collectively, these findings provide insight into the function of the Mediator Tail module.
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Affiliation(s)
- Miriam Larsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Hanna Uvell
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Jenny Sandström
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Patrik Rydén
- Department of Statistics, Umeå University, Umeå, Sweden
| | - Luke A. Selth
- Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, South Mimms, United Kingdom
| | - Stefan Björklund
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- * E-mail:
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9
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Steimel A, Suh J, Hussainkhel A, Deheshi S, Grants JM, Zapf R, Moerman DG, Taubert S, Hutter H. The C. elegans CDK8 Mediator module regulates axon guidance decisions in the ventral nerve cord and during dorsal axon navigation. Dev Biol 2013; 377:385-98. [PMID: 23458898 DOI: 10.1016/j.ydbio.2013.02.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 01/21/2013] [Accepted: 02/14/2013] [Indexed: 11/30/2022]
Abstract
Receptors expressed on the growth cone of outgrowing axons detect cues required for proper navigation. The pathway choices available to an axon are in part defined by the set of guidance receptors present on the growth cone. Regulated expression of receptors and genes controlling the localization and activity of receptors ensures that axons respond only to guidance cues relevant for reaching their targets. In genetic screens for axon guidance mutants, we isolated an allele of let-19/mdt-13, a component of the Mediator, a large ~30 subunit protein complex essential for gene transcription by RNA polymerase II. LET-19/MDT-13 is part of the CDK8 module of the Mediator. By testing other Mediator components, we found that all subunits of the CDK8 module as well as some other Mediator components are required for specific axon navigation decisions in a subset of neurons. Expression profiling demonstrated that let-19/mdt-13 regulates the expression of a large number of genes in interneurons. A mutation in the sax-3 gene, encoding a receptor for the repulsive guidance cue SLT-1, suppresses the commissure navigation defects found in cdk-8 mutants. This suggests that the CDK8 module specifically represses the SAX-3/ROBO pathway to ensure proper commissure navigation.
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Affiliation(s)
- Andreas Steimel
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
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Kim AR, Martinez C, Ionides J, Ramos AF, Ludwig MZ, Ogawa N, Sharp DH, Reinitz J. Rearrangements of 2.5 kilobases of noncoding DNA from the Drosophila even-skipped locus define predictive rules of genomic cis-regulatory logic. PLoS Genet 2013; 9:e1003243. [PMID: 23468638 PMCID: PMC3585115 DOI: 10.1371/journal.pgen.1003243] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 11/30/2012] [Indexed: 01/19/2023] Open
Abstract
Rearrangements of about 2.5 kilobases of regulatory DNA located 5′ of the transcription start site of the Drosophila even-skipped locus generate large-scale changes in the expression of even-skipped stripes 2, 3, and 7. The most radical effects are generated by juxtaposing the minimal stripe enhancers MSE2 and MSE3 for stripes 2 and 3 with and without small “spacer” segments less than 360 bp in length. We placed these fusion constructs in a targeted transformation site and obtained quantitative expression data for these transformants together with their controlling transcription factors at cellular resolution. These data demonstrated that the rearrangements can alter expression levels in stripe 2 and the 2–3 interstripe by a factor of more than 10. We reasoned that this behavior would place tight constraints on possible rules of genomic cis-regulatory logic. To find these constraints, we confronted our new expression data together with previously obtained data on other constructs with a computational model. The model contained representations of thermodynamic protein–DNA interactions including steric interference and cooperative binding, short-range repression, direct repression, activation, and coactivation. The model was highly constrained by the training data, which it described within the limits of experimental error. The model, so constrained, was able to correctly predict expression patterns driven by enhancers for other Drosophila genes; even-skipped enhancers not included in the training set; stripe 2, 3, and 7 enhancers from various Drosophilid and Sepsid species; and long segments of even-skipped regulatory DNA that contain multiple enhancers. The model further demonstrated that elevated expression driven by a fusion of MSE2 and MSE3 was a consequence of the recruitment of a portion of MSE3 to become a functional component of MSE2, demonstrating that cis-regulatory “elements” are not elementary objects. Metazoan genes, including those of humans, contain large noncoding regions that are required for viability. Sequence variations in these regions are statistically associated with human disease, but the mechanisms underlying these associations are not well understood. These regions regulate transcription and are frequently larger than the gene's transcript by an order of magnitude. In this paper we attempt to elucidate the regulatory code of these noncoding segments of DNA by means of quantitative spatially resolved gene expression data and a computational model. The expression data comes from the early embryo of the fruit fly Drosophila melanogaster. We chose a family of DNA constructs to analyze that drive very different patterns of expression when very small changes in DNA sequence are made, reasoning that this sensitivity would reveal important properties of the regulatory code. The model reproduced the training data with precision greater than the expected accuracy of the training data itself. It was able to correctly predict from DNA sequence the expression of 44 segments of DNA from many genes and species.
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Affiliation(s)
- Ah-Ram Kim
- Department of Ecology and Evolution, Chicago Center for Systems Biology, University of Chicago, Chicago, Illinois, United States of America
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, United States of America
| | - Carlos Martinez
- Department of Ecology and Evolution, Chicago Center for Systems Biology, University of Chicago, Chicago, Illinois, United States of America
| | - John Ionides
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alexandre F. Ramos
- Escola de Artes, Ciências e Humanidades, Universidade de São Paulo, São Paulo, Brazil
| | - Michael Z. Ludwig
- Department of Ecology and Evolution, Chicago Center for Systems Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Nobuo Ogawa
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - David H. Sharp
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - John Reinitz
- Department of Ecology and Evolution, Chicago Center for Systems Biology, University of Chicago, Chicago, Illinois, United States of America
- Department of Statistics, Department of Molecular Genetics and Cell Biology, and Institute of Genomics and Systems Biology, University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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Xu M, Sharma P, Pan S, Malik S, Roeder RG, Martinez E. Core promoter-selective function of HMGA1 and Mediator in Initiator-dependent transcription. Genes Dev 2012; 25:2513-24. [PMID: 22156211 DOI: 10.1101/gad.177360.111] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The factors and mechanisms underlying the differential activity and regulation of eukaryotic RNA polymerase II on different types of core promoters have remained elusive. Here we show that the architectural factor HMGA1 and the Mediator coregulator complex cooperate to enhance basal transcription from core promoters containing both a TATA box and an Initiator (INR) element but not from "TATA-only" core promoters. INR-dependent activation by HMGA1 and Mediator requires the TATA-binding protein (TBP)-associated factors (TAFs) within the TFIID complex and counteracts negative regulators of TBP/TATA-dependent transcription such as NC2 and Topoisomerase I. HMGA1 interacts with TFIID and Mediator and is required for the synergy of TATA and INR elements in mammalian cells. Accordingly, natural HMGA1-activated genes in embryonic stem cells tend to have both TATA and INR elements in a synergistic configuration. Our results suggest a core promoter-specific regulation of Mediator and the basal transcription machinery by HMGA1.
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Affiliation(s)
- Muyu Xu
- Department of Biochemistry, University of California at Riverside, Riverside, California 92521, USA
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12
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Mathur S, Vyas S, Kapoor S, Tyagi AK. The Mediator complex in plants: structure, phylogeny, and expression profiling of representative genes in a dicot (Arabidopsis) and a monocot (rice) during reproduction and abiotic stress. PLANT PHYSIOLOGY 2011; 157:1609-27. [PMID: 22021418 PMCID: PMC3327187 DOI: 10.1104/pp.111.188300] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Accepted: 10/20/2011] [Indexed: 05/20/2023]
Abstract
The Mediator (Med) complex relays regulatory information from DNA-bound transcription factors to the RNA polymerase II in eukaryotes. This macromolecular unit is composed of three core subcomplexes in addition to a separable kinase module. In this study, conservation of Meds has been investigated in 16 plant species representing seven diverse groups across the plant kingdom. Using Hidden Markov Model-based conserved motif searches, we have identified all the known yeast/metazoan Med components in one or more plant groups, including the Med26 subunits, which have not been reported so far for any plant species. We also detected orthologs for the Arabidopsis (Arabidopsis thaliana) Med32, -33, -34, -35, -36, and -37 in all the plant groups, and in silico analysis identified the Med32 and Med33 subunits as apparent orthologs of yeast/metazoan Med2/29 and Med5/24, respectively. Consequently, the plant Med complex appears to be composed of one or more members of 34 subunits, as opposed to 25 and 30 members in yeast and metazoans, respectively. Despite low similarity in primary Med sequences between the plants and their fungal/metazoan partners, secondary structure modeling of these proteins revealed a remarkable similarity between them, supporting the conservation of Med organization across kingdoms. Phylogenetic analysis between plant, human, and yeast revealed single clade relatedness for 29 Med genes families in plants, plant Meds being closer to human than to yeast counterparts. Expression profiling of rice (Oryza sativa) and Arabidopsis Med genes reveals that Meds not only act as a basal regulator of gene expression but may also have specific roles in plant development and under abiotic stress conditions.
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Demakov SA, Vatolina TY, Babenko VN, Semeshin VF, Belyaeva ES, Zhimulev IF. Protein composition of interband regions in polytene and cell line chromosomes of Drosophila melanogaster. BMC Genomics 2011; 12:566. [PMID: 22093916 PMCID: PMC3240664 DOI: 10.1186/1471-2164-12-566] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 11/18/2011] [Indexed: 12/20/2022] Open
Abstract
Background Despite many efforts, little is known about distribution and interactions of chromatin proteins which contribute to the specificity of chromomeric organization of interphase chromosomes. To address this issue, we used publicly available datasets from several recent Drosophila genome-wide mapping and annotation projects, in particular, those from modENCODE project, and compared molecular organization of 13 interband regions which were accurately mapped previously. Results Here we demonstrate that in interphase chromosomes of Drosophila cell lines, the interband regions are enriched for a specific set of proteins generally characteristic of the "open" chromatin (RNA polymerase II, CHRIZ (CHRO), BEAF-32, BRE1, dMI-2, GAF, NURF301, WDS and TRX). These regions also display reduced nucleosome density, histone H1 depletion and pronounced enrichment for ORC2, a pre-replication complex component. Within the 13 interband regions analyzed, most were around 3-4 kb long, particularly those where many of said protein features were present. We estimate there are about 3500 regions with similar properties in chromosomes of D. melanogaster cell lines, which fits quite well the number of cytologically observed interbands in salivary gland polytene chromosomes. Conclusions Our observations suggest strikingly similar organization of interband chromatin in polytene chromosomes and in chromosomes from cell lines thereby reflecting the existence of a universal principle of interphase chromosome organization.
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Affiliation(s)
- Sergey A Demakov
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia
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14
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Vatolina TY, Boldyreva LV, Demakova OV, Demakov SA, Kokoza EB, Semeshin VF, Babenko VN, Goncharov FP, Belyaeva ES, Zhimulev IF. Identical functional organization of nonpolytene and polytene chromosomes in Drosophila melanogaster. PLoS One 2011; 6:e25960. [PMID: 22022482 PMCID: PMC3191165 DOI: 10.1371/journal.pone.0025960] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2011] [Accepted: 09/14/2011] [Indexed: 12/29/2022] Open
Abstract
Salivary gland polytene chromosomes demonstrate banding pattern, genetic meaning of which is an enigma for decades. Till now it is not known how to mark the band/interband borders on physical map of DNA and structures of polytene chromosomes are not characterized in molecular and genetic terms. It is not known either similar banding pattern exists in chromosomes of regular diploid mitotically dividing nonpolytene cells. Using the newly developed approach permitting to identify the interband material and localization data of interband-specific proteins from modENCODE and other genome-wide projects, we identify physical limits of bands and interbands in small cytological region 9F13-10B3 of the X chromosome in D. melanogaster, as well as characterize their general molecular features. Our results suggests that the polytene and interphase cell line chromosomes have practically the same patterns of bands and interbands reflecting, probably, the basic principle of interphase chromosome organization. Two types of bands have been described in chromosomes, early and late-replicating, which differ in many aspects of their protein and genetic content. As appeared, origin recognition complexes are located almost totally in the interbands of chromosomes.
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Affiliation(s)
- Tatyana Yu. Vatolina
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Lidiya V. Boldyreva
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Olga V. Demakova
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Sergey A. Demakov
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena B. Kokoza
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Valeriy F. Semeshin
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Vladimir N. Babenko
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Fedor P. Goncharov
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena S. Belyaeva
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Igor F. Zhimulev
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- * E-mail:
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15
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Interactions between subunits of the Mediator complex with gene-specific transcription factors. Semin Cell Dev Biol 2011; 22:759-68. [PMID: 21839847 DOI: 10.1016/j.semcdb.2011.07.022] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 07/26/2011] [Accepted: 07/28/2011] [Indexed: 11/24/2022]
Abstract
The Mediator complex forms the bridge between gene-specific transcription factors and the RNA polymerase II (RNAP II) machinery. Mediator is a large polypetide complex consisting of about thirty polypeptides that are mostly conserved from yeast to human. Mediator coordinates RNAP II recruitment, phosphorylation of the C-terminal domain of RNAP II, enhancer-loop formation and post-initiation events. The focus of the review is to summarize the current knowledge of transcription factor/Mediator interactions in higher eukaryotes and illuminate the physiological and gene-selective roles of Mediator.
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16
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Conaway RC, Conaway JW. Origins and activity of the Mediator complex. Semin Cell Dev Biol 2011; 22:729-34. [PMID: 21821140 DOI: 10.1016/j.semcdb.2011.07.021] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/19/2011] [Accepted: 07/20/2011] [Indexed: 11/16/2022]
Abstract
The Mediator is a large, multisubunit RNA polymerase II transcriptional regulator that was first identified in Saccharomyces cerevisiae as a factor required for responsiveness of Pol II and the general initiation factors to DNA binding transactivators. Since its discovery in yeast, Mediator has been shown to be an integral and highly evolutionarily conserved component of the Pol II transcriptional machinery with critical roles in multiple stages of transcription, from regulation of assembly of the Pol II initiation complex to regulation of Pol II elongation. Here we provide a brief overview of the evolutionary origins of Mediator, its subunit composition, and its remarkably diverse collection of activities in Pol II transcription.
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Affiliation(s)
- Ronald C Conaway
- Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, MO 64110, USA.
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17
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Fedorova EV, Pindyurin AV, Baricheva EM. Maintenance of the patterns of expression of homeotic genes in the development of Drosophila melanogaster by proteins of the polycomb, trithorax, and ETP groups. RUSS J GENET+ 2009. [DOI: 10.1134/s1022795409100019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Tóth-Petróczy Á, Oldfield CJ, Simon I, Takagi Y, Dunker AK, Uversky VN, Fuxreiter M. Malleable machines in transcription regulation: the mediator complex. PLoS Comput Biol 2008; 4:e1000243. [PMID: 19096501 PMCID: PMC2588115 DOI: 10.1371/journal.pcbi.1000243] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Accepted: 11/06/2008] [Indexed: 11/19/2022] Open
Abstract
The Mediator complex provides an interface between gene-specific regulatory proteins and the general transcription machinery including RNA polymerase II (RNAP II). The complex has a modular architecture (Head, Middle, and Tail) and cryoelectron microscopy analysis suggested that it undergoes dramatic conformational changes upon interactions with activators and RNAP II. These rearrangements have been proposed to play a role in the assembly of the preinitiation complex and also to contribute to the regulatory mechanism of Mediator. In analogy to many regulatory and transcriptional proteins, we reasoned that Mediator might also utilize intrinsically disordered regions (IDRs) to facilitate structural transitions and transmit transcriptional signals. Indeed, a high prevalence of IDRs was found in various subunits of Mediator from both Saccharomyces cerevisiae and Homo sapiens, especially in the Tail and the Middle modules. The level of disorder increases from yeast to man, although in both organisms it significantly exceeds that of multiprotein complexes of a similar size. IDRs can contribute to Mediator's function in three different ways: they can individually serve as target sites for multiple partners having distinctive structures; they can act as malleable linkers connecting globular domains that impart modular functionality on the complex; and they can also facilitate assembly and disassembly of complexes in response to regulatory signals. Short segments of IDRs, termed molecular recognition features (MoRFs) distinguished by a high protein-protein interaction propensity, were identified in 16 and 19 subunits of the yeast and human Mediator, respectively. In Saccharomyces cerevisiae, the functional roles of 11 MoRFs have been experimentally verified, and those in the Med8/Med18/Med20 and Med7/Med21 complexes were structurally confirmed. Although the Saccharomyces cerevisiae and Homo sapiens Mediator sequences are only weakly conserved, the arrangements of the disordered regions and their embedded interaction sites are quite similar in the two organisms. All of these data suggest an integral role for intrinsic disorder in Mediator's function.
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Affiliation(s)
- Ágnes Tóth-Petróczy
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary
| | - Christopher J. Oldfield
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - István Simon
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary
| | - Yuichiro Takagi
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Vladimir N. Uversky
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Institute for Intrinsically Disordered Protein Research, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Monika Fuxreiter
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest, Hungary
- * E-mail:
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19
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Identification, structure, and functional requirement of the Mediator submodule Med7N/31. EMBO J 2008; 28:69-80. [PMID: 19057509 DOI: 10.1038/emboj.2008.254] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Accepted: 11/07/2008] [Indexed: 12/24/2022] Open
Abstract
Mediator is a modular multiprotein complex required for regulated transcription by RNA polymerase (Pol) II. Here, we show that the middle module of the Mediator core contains a submodule of unique structure and function that comprises the N-terminal part of subunit Med7 (Med7N) and the highly conserved subunit Med31 (Soh1). The Med7N/31 submodule shows a conserved novel fold, with two proline-rich stretches in Med7N wrapping around the right-handed four-helix bundle of Med31. In vitro, Med7N/31 is required for activated transcription and can act in trans when added exogenously. In vivo, Med7N/31 has a predominantly positive function on the expression of a specific subset of genes, including genes involved in methionine metabolism and iron transport. Comparative phenotyping and transcriptome profiling identify specific and overlapping functions of different Mediator submodules.
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20
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Bourbon HM. Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex. Nucleic Acids Res 2008; 36:3993-4008. [PMID: 18515835 PMCID: PMC2475620 DOI: 10.1093/nar/gkn349] [Citation(s) in RCA: 254] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The multisubunit Mediator (MED) complex bridges DNA-bound transcriptional regulators to the RNA polymerase II (PolII) initiation machinery. In yeast, the 25 MED subunits are distributed within three core subcomplexes and a separable kinase module composed of Med12, Med13 and the Cdk8-CycC pair thought to control the reversible interaction between MED and PolII by phosphorylating repeated heptapeptides within the Rpb1 carboxyl-terminal domain (CTD). Here, MED conservation has been investigated across the eukaryotic kingdom. Saccharomyces cerevisiae Med2, Med3/Pgd1 and Med5/Nut1 subunits are apparent homologs of metazoan Med29/Intersex, Med27/Crsp34 and Med24/Trap100, respectively, and these and other 30 identified human MED subunits have detectable counterparts in the amoeba Dictyostelium discoideum, indicating that none is specific to metazoans. Indeed, animal/fungal subunits are also conserved in plants, green and red algae, entamoebids, oomycetes, diatoms, apicomplexans, ciliates and the 'deep-branching' protists Trichomonas vaginalis and Giardia lamblia. Surprisingly, although lacking CTD heptads, T. vaginalis displays 44 MED subunit homologs, including several CycC, Med12 and Med13 paralogs. Such observations have allowed the identification of a conserved 17-subunit framework around which peripheral subunits may be assembled, and support a very ancient eukaryotic origin for a large, four-module MED. The implications of this comprehensive work for MED structure-function relationships are discussed.
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Affiliation(s)
- Henri-Marc Bourbon
- Centre de Biologie du Développement, UMR5547 CNRS/Toulouse III, IFR109, Université Paul Sabatier, 31062 Toulouse, France.
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21
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Establishment of cell fate during early Drosophila embryogenesis requires transcriptional Mediator subunit dMED31. Dev Biol 2008; 313:802-13. [DOI: 10.1016/j.ydbio.2007.11.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Revised: 10/25/2007] [Accepted: 11/17/2007] [Indexed: 01/26/2023]
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22
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Wang X, Yang N, Uno E, Roeder RG, Guo S. A subunit of the mediator complex regulates vertebrate neuronal development. Proc Natl Acad Sci U S A 2006; 103:17284-9. [PMID: 17088561 PMCID: PMC1859923 DOI: 10.1073/pnas.0605414103] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The unique profiles of gene expression dictate distinct cellular identity. How these profiles are established during development is not clear. Here we report that the mutant motionless (mot), identified in a genetic screen for mutations that affect neuronal development in zebrafish, displays deficits of monoaminergic neurons and cranial sensory ganglia, whereas expression of the pan-neuronal marker Hu is largely unperturbed; GABAergic and subsets of cranial motor neurons do not appear to be deficient. Positional cloning reveals that mot encodes Med12, a component of the evolutionarily conserved Mediator complex, whose in vivo function is not well understood in vertebrates. mot/med12 transcripts are enriched in the embryonic brain and appear distinct from two other Mediator components Med17 and Med21. Delivery of human med12 RNA into zebrafish restores normality to the mot mutant and, strikingly, leads to premature neuronal differentiation and an increased production of monoaminergic neuronal subtypes in WT. Further investigation reveals that mot/med12 is necessary to regulate, and when overexpressed is capable of increasing, the expression of distinct neuronal determination genes, including zash1a and lim1, and serves as an in vivo cofactor for Sox9 in this process. Together, our analyses reveal a regulatory role of Mot/Med12 in vertebrate neuronal development.
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Affiliation(s)
- Xiaoqun Wang
- *Programs in Genetics, Neuroscience, and Developmental Biology, Department of Biopharmaceutical Sciences, and Center for Human Genetics, University of California, San Francisco, CA 94143; and
| | - Nan Yang
- *Programs in Genetics, Neuroscience, and Developmental Biology, Department of Biopharmaceutical Sciences, and Center for Human Genetics, University of California, San Francisco, CA 94143; and
| | - Etsuko Uno
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021
| | - Robert G. Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021
| | - Su Guo
- *Programs in Genetics, Neuroscience, and Developmental Biology, Department of Biopharmaceutical Sciences, and Center for Human Genetics, University of California, San Francisco, CA 94143; and
- To whom correspondence should be addressed. E-mail:
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23
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Rau MJ, Fischer S, Neumann CJ. Zebrafish Trap230/Med12 is required as a coactivator for Sox9-dependent neural crest, cartilage and ear development. Dev Biol 2006; 296:83-93. [PMID: 16712834 DOI: 10.1016/j.ydbio.2006.04.437] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2005] [Revised: 04/05/2006] [Accepted: 04/05/2006] [Indexed: 11/26/2022]
Abstract
The vertebrate Sox9 transcription factor directs the development of neural crest, otic placodes, cartilage and bone. In zebrafish, there are two Sox9 orthologs, Sox9a and Sox9b, which together perform the functions of the single-copy tetrapod Sox9. In a large-scale genetic screen, we have identified a novel zebrafish mutant that strongly resembles the Sox9a/Sox9b double mutant phenotype. We show that this mutation disrupts the zebrafish Trap230/Med12 ortholog, a member of the Mediator complex. Mediator is a coactivator complex transducing the interaction of DNA-binding transcription factors with RNA polymerase II, and our results reveal a critical function of the Trap230 subunit as a coactivator for Sox9.
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Affiliation(s)
- Marlene J Rau
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
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24
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Meinhart A, Kamenski T, Hoeppner S, Baumli S, Cramer P. A structural perspective of CTD function. Genes Dev 2005; 19:1401-15. [PMID: 15964991 DOI: 10.1101/gad.1318105] [Citation(s) in RCA: 255] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The C-terminal domain (CTD) of RNA polymerase II (Pol II) integrates nuclear events by binding proteins involved in mRNA biogenesis. CTD-binding proteins recognize a specific CTD phosphorylation pattern, which changes during the transcription cycle, due to the action of CTD-modifying enzymes. Structural and functional studies of CTD-binding and -modifying proteins now reveal some of the mechanisms underlying CTD function. Proteins recognize CTD phosphorylation patterns either directly, by contacting phosphorylated residues, or indirectly, without contact to the phosphate. The catalytic mechanisms of CTD kinases and phosphatases are known, but the basis for CTD specificity of these enzymes remains to be understood.
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Affiliation(s)
- Anton Meinhart
- Department of Chemistry and Biochemistry, Gene Center, University of Munich (LMU), 81377 Munich, Germany
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25
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Abstract
Mediator was first identified because of its activity in activator-stimulated transcription in vivo and in vitro. Later, biochemical fractionation led to the co-purification of the multi-subunit Mediator complex and RNA polymerase II (pol II). Results of these studies suggested a model whereby transcription-activator proteins, which bind to specific gene regulatory sequences, recruit both Mediator and pol II as a holoenzyme in a one-step mechanism. More recent studies of Drosophila Mediator and additional studies in yeast have demonstrated that different transcription activators can bind and recruit Mediator to promoters in vivo in a step that is independent of pol II recruitment. Moreover, the different activators in Drosophila bind and recruit Mediator via physical interactions with specific subsets of proteins. These features of Mediator function seem to be broadly conserved.
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Affiliation(s)
- Young-Joon Kim
- Department of Biochemistry, Yonsei University, 134 Sinchon-dong, Seodaemoon-gu, Seoul 120-749, Republic of Korea
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26
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Takeyama KI, Ito S, Sawatsubashi S, Shirode Y, Yamamoto A, Suzuki E, Maki A, Yamagata K, Zhao Y, Kouzmenko A, Tabata T, Kato S. A novel genetic system for analysis of co-activators for the N-terminal transactivation function domain of the human androgen receptor. Biosci Biotechnol Biochem 2005; 68:1209-15. [PMID: 15215582 DOI: 10.1271/bbb.68.1209] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Androgen receptor (hAR) regulates transcription of target genes in a ligand-dependent manner and recruits a number of co-activators for the ligand-induced transactivation via the N-terminal, activation function-1 (AF-1), and C-terminal, AF-2, transactivation domains. But the co-regulator functions on each of AR domains have not yet been fully understood. We have established a Drosophila transgenic system in which hAR and its deletion mutants are ectopically expressed in fly tissues together with an AR response element (ARE)-GFP reporter gene, and have confirmed that hAR was functional in ARE transactivation without affecting the expression of endogenous genes. We found that transcriptional activity of the hAR AF-1 domain was markedly reduced in Drosophila deficiency mutants of homologs for known mammalian co-activators of the AR ligand-dependent AF-2 domain. This suggests that hAR AF-1 recruits co-activators previously known only to interact with the AF-2 domain. Therefore, Drosophila with the hAR AF-1 transgene provides a relevant genetic system in which to uncover novel functions of vertebrate steroid hormone receptors and to screen for novel AF-1 co-regulators.
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Affiliation(s)
- Ken-Ichi Takeyama
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo, Japan
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27
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Blazek E, Mittler G, Meisterernst M. The Mediator of RNA polymerase II. Chromosoma 2005; 113:399-408. [PMID: 15690163 DOI: 10.1007/s00412-005-0329-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2004] [Revised: 12/21/2004] [Accepted: 12/22/2004] [Indexed: 11/28/2022]
Abstract
Mediator (TRAP/ARC/PC2) is a large (22-28 subunit) protein complex that binds RNA polymerase II and controls transcription from class II genes. The evolutionarily conserved core of Mediator is found in all eukaryotes. It binds RNA polymerase II and is probably critical for basal transcription but it also mediates activation and repression of transcription. During evolution the complex has acquired additional species-specific subunits. These serve as an interface for regulatory factors and support specific signalling pathways. Recent mechanistic studies are consistent with the hypothesis that Mediator marks genes for binding by RNA polymerase II whereupon it subsequently activates the preinitiation complex. It is further likely that Mediator coordinates the recruitment of chromatin-modifying cofactor activities.
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Affiliation(s)
- Erik Blazek
- National Research Center for Environment and Health-GSF, Gene Expression, Institute of Molecular Immunology, Marchioninistrasse 25, 81377, Munich, Germany
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28
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Linder T, Gustafsson CM. The Soh1/MED31 Protein Is an Ancient Component of Schizosaccharomyces pombe and Saccharomyces cerevisiae Mediator. J Biol Chem 2004; 279:49455-9. [PMID: 15356001 DOI: 10.1074/jbc.m409046200] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We here demonstrated that the Soh1/MED31 protein is a stable component of Mediator complex isolated from Schizosaccharomyces pombe and Saccharomyces cerevisiae. Bioinformatic analysis traces the Soh1/MED31 family of Mediator subunits to the point of major eukaryotic divergence, before the appearance of the canonical heptapeptide repeat structure of the RNA polymerase II C-terminal domain.
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Affiliation(s)
- Tomas Linder
- Department of Medical Nutrition, Karolinska Institute, Novum, Karolinska University Hospital, SE-141 86 Stockholm, Sweden
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29
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Guglielmi B, van Berkum NL, Klapholz B, Bijma T, Boube M, Boschiero C, Bourbon HM, Holstege FCP, Werner M. A high resolution protein interaction map of the yeast Mediator complex. Nucleic Acids Res 2004; 32:5379-91. [PMID: 15477388 PMCID: PMC524289 DOI: 10.1093/nar/gkh878] [Citation(s) in RCA: 181] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2004] [Revised: 09/20/2004] [Accepted: 09/20/2004] [Indexed: 11/13/2022] Open
Abstract
Mediator is a large, modular protein complex remotely conserved from yeast to man that conveys regulatory signals from DNA-binding transcription factors to RNA polymerase II. In Saccharomyces cerevisiae, Mediator is thought to be composed of 24 subunits organized in four sub-complexes, termed the head, middle, tail and Cdk8 (Srb8-11) modules. In this work, we have used screening and pair-wise two-hybrid approaches to investigate protein-protein contacts between budding yeast Mediator subunits. The derived interaction map includes the delineation of numerous interaction domains between Mediator subunits, frequently corresponding to segments that have been conserved in evolution, as well as novel connections between the Cdk8 (Srb8-11) and head modules, the head and middle modules, and the middle and tail modules. The two-hybrid analysis, together with co-immunoprecipitation studies and gel filtration experiments revealed that Med31 (Soh1) is associated with the yeast Mediator that therefore comprises 25 subunits. Finally, analysis of the protein interaction network within the Drosophila Mediator middle module indicated that the structural organization of the Mediator complex is conserved from yeast to metazoans. The resulting interaction map provides a framework for delineating Mediator structure-function and investigating how Mediator function is regulated.
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Affiliation(s)
- Benjamin Guglielmi
- Service de Biochimie et Génétique Moléculaire, Bâtiment 144, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France
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30
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Malik S, Guermah M, Yuan CX, Wu W, Yamamura S, Roeder RG. Structural and functional organization of TRAP220, the TRAP/mediator subunit that is targeted by nuclear receptors. Mol Cell Biol 2004; 24:8244-54. [PMID: 15340084 PMCID: PMC515042 DOI: 10.1128/mcb.24.18.8244-8254.2004] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2004] [Revised: 04/07/2004] [Accepted: 06/17/2004] [Indexed: 01/21/2023] Open
Abstract
The TRAP/Mediator complex serves as a coactivator for many transcriptional activators, including nuclear receptors such as the thyroid hormone receptor (TR) that targets the TRAP220 subunit. The critical but selective function of TRAP220 is evidenced by the embryonic lethal phenotype of Trap220(-)(/)(-) mice and by the observation that Trap220(-)(/)(-) fibroblasts (isolated before embryonic death) are impaired in specific nuclear receptor-dependent pathways. Here we have used a biochemical and genetic approach to understand the basis of specificity in TRAP220 function. We show that Trap220(-)(/)(-) cells possess a TRAP/Mediator complex that is relatively intact and compromised in its ability to support TR-dependent, but not VP16-dependent, transcription in vitro. Transfection studies using TRAP220 mutants revealed that the N terminus of TRAP220 is necessary and sufficient for stable association with the TRAP/Mediator complex and, further, that TRAP220-dependent TR function in transfected cells requires both of the NR boxes that contain the LXXLL motif implicated in nuclear receptor binding. Similarly, an analysis of isolated TRAP/Mediator complexes with mutations in either or both of the two NR boxes confirmed a critical role for them in in vitro coactivator function. The implications of these observations are discussed in terms of our present understanding of coactivator function.
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Affiliation(s)
- Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, Rockefeller University, 1230 York Ave., New York, NY 10021, USA
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31
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Kim TW, Kwon YJ, Kim JM, Song YH, Kim SN, Kim YJ. MED16 and MED23 of Mediator are coactivators of lipopolysaccharide- and heat-shock-induced transcriptional activators. Proc Natl Acad Sci U S A 2004; 101:12153-8. [PMID: 15297616 PMCID: PMC514449 DOI: 10.1073/pnas.0401985101] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2004] [Accepted: 06/21/2004] [Indexed: 11/18/2022] Open
Abstract
Transcriptional activators interact with diverse proteins and recruit transcriptional machinery to the activated promoter. Recruitment of the Mediator complex by transcriptional activators is usually the key step in transcriptional activation. However, it is unclear how Mediator recognizes different types of activator proteins. To systematically identify the subunits responsible for the signal- and activator-specific functions of Mediator in Drosophila melanogaster, each Mediator subunit was depleted by RNA interference, and its effect on transcriptional activation of endogenous as well as synthetic promoters was examined. The depletion of some Mediator gene products caused general transcriptional defects, whereas depletion of others caused defects specifically related to activation. In particular, MED16 and MED23 were required for lipopolysaccharide- and heat-shock-specific gene expression, respectively, and their activator-specific functions appeared to result from interaction with specific activators. The corequirement of MED16 for other forms of differentiation-inducing factor-induced transcription was confirmed by microarray analysis of differentiation-inducing factor (DIF)- and MED16-depleted cells individually. These results suggest that distinct Mediator subunits interact with specific activators to coordinate and transfer activator-specific signals to the transcriptional machinery.
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Affiliation(s)
- Tae Whan Kim
- Department of Biochemistry, Yonsei University, Seoul 120-749, South Korea
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32
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Bourbon HM, Aguilera A, Ansari AZ, Asturias FJ, Berk AJ, Bjorklund S, Blackwell TK, Borggrefe T, Carey M, Carlson M, Conaway JW, Conaway RC, Emmons SW, Fondell JD, Freedman LP, Fukasawa T, Gustafsson CM, Han M, He X, Herman PK, Hinnebusch AG, Holmberg S, Holstege FC, Jaehning JA, Kim YJ, Kuras L, Leutz A, Lis JT, Meisterernest M, Naar AM, Nasmyth K, Parvin JD, Ptashne M, Reinberg D, Ronne H, Sadowski I, Sakurai H, Sipiczki M, Sternberg PW, Stillman DJ, Strich R, Struhl K, Svejstrup JQ, Tuck S, Winston F, Roeder RG, Kornberg RD. A Unified Nomenclature for Protein Subunits of Mediator Complexes Linking Transcriptional Regulators to RNA Polymerase II. Mol Cell 2004; 14:553-7. [PMID: 15175151 DOI: 10.1016/j.molcel.2004.05.011] [Citation(s) in RCA: 218] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Noor MAF, Michalak P, Donze D. Characterization of a male-predominant antisense transcript underexpressed in hybrids of Drosophila pseudoobscura and D. persimilis. Genetics 2004; 165:1823-30. [PMID: 14704168 PMCID: PMC1462881 DOI: 10.1093/genetics/165.4.1823] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Characterizing genes that are misregulated in hybrids may elucidate the genetic basis of hybrid sterility or other hybrid dysfunctions that contribute to speciation. Previously, a small segment of a male-predominant transcript that is underexpressed in adult male hybrids of Drosophila pseudoobscura and D. persimilis relative to pure species was identified in a differential display screen. Here, we obtained the full sequence of this 1330-bp transcript and determined that it is an antisense message with high sequence similarity to the D. melanogaster TRAP100 gene, part of the Mediator protein complex that regulates transcriptional initiation during development. Both the sense and the antisense messages are transcribed in D. pseudoobscura, but only the sense message (TRAP100) is transcribed in D. melanogaster complex species. Unlike the antisense message, the sense message is transcribed similarly in D. pseudoobscura males and females and in hybrids of D. pseudoobscura and D. persimilis. The high sequence similarity between distantly related species suggests that the sense message is functionally constrained within the genus. We speculate that the antisense transcript may have evolved a role in male-specific post-transcriptional regulation of TRAP100 in the D. pseudoobscura lineage and that its underexpression in sterile hybrid males may cause an overproduction of TRAP100 protein, possibly yielding deleterious effects.
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Affiliation(s)
- Mohamed A F Noor
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
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34
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Zhimulev IF, Belyaeva ES, Semeshin VF, Koryakov DE, Demakov SA, Demakova OV, Pokholkova GV, Andreyeva EN. Polytene Chromosomes: 70 Years of Genetic Research. INTERNATIONAL REVIEW OF CYTOLOGY 2004; 241:203-75. [PMID: 15548421 DOI: 10.1016/s0074-7696(04)41004-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Polytene chromosomes were described in 1881 and since 1934 they have served as an outstanding model for a variety of genetic experiments. Using the polytene chromosomes, numerous biological phenomena were discovered. First the polytene chromosomes served as a model of the interphase chromosomes in general. In polytene chromosomes, condensed (bands), decondensed (interbands), genetically active (puffs), and silent (pericentric and intercalary heterochromatin as well as regions subject to position effect variegation) regions were found and their features were described in detail. Analysis of the general organization of replication and transcription at the cytological level has become possible using polytene chromosomes. In studies of sequential puff formation it was found for the first time that the steroid hormone (ecdysone) exerts its action through gene activation, and that the process of gene activation upon ecdysone proceeds as a cascade. Namely on the polytene chromosomes a new phenomenon of cellular stress response (heat shock) was discovered. Subsequently chromatin boundaries (insulators) were discovered to flank the heat shock puffs. Major progress in solving the problems of dosage compensation and position effect variegation phenomena was mainly related to studies on polytene chromosomes. This review summarizes the current status of studies of polytene chromosomes and of various phenomena described using this successful model.
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Affiliation(s)
- I F Zhimulev
- Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk, 630090, Russia
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35
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Voellmy R. Transcriptional Regulation of the Metazoan Stress Protein Response. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2004; 78:143-85. [PMID: 15210330 DOI: 10.1016/s0079-6603(04)78004-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
This review provides an updated account of the regulation of the metazoan stress protein response. Where indicated, observations made with yeasts are also included. However, a discussion of the plant stress protein response is intentionally omitted (for a review, see 1). The stress protein response, as discussed hereafter, is understood to relate to the response by virtually all cells to heat and other stressors that results in the induced expression of so-called heat shock or stress genes. The protein products of these genes localize largely to the cytoplasm, nucleus, or organelles. An analogous response controls the expression of related genes, whose products reside in the endoplasmic reticulum. The response, termed ER stress response or unfolded protein response, is mediated by a separate regulation system that is not discussed in this review. Note, however, that recent work suggests the existence of commonalities between the regulatory systems controlling the stress protein and ER stress responses (2).
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Affiliation(s)
- Richard Voellmy
- Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL 33136, USA
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Lewis BA, Reinberg D. The mediator coactivator complex: functional and physical roles in transcriptional regulation. J Cell Sci 2003; 116:3667-75. [PMID: 12917354 DOI: 10.1242/jcs.00734] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In vivo, the DNA is packed into chromatin and transcription is dependent upon activators that recruit other factors to reverse the repressive effects of chromatin. The response to activators requires additional factors referred to as coactivators. One such coactivator, mediator, is a multi-subunit complex capable of responding to different activators. It plays an key role in activation, bridging DNA-bound activators, the general transcriptional machinery, especially RNA polymerase II, and the core promoter. Its subunits are necessary for a variety of positive and negative regulatory processes and serve as the direct targets of activators themselves. In vivo and in vitro studies support various roles for mediator in transcription initiation, while structural studies demonstrate that it engages in multiple interactions with RNA polymerase II, and adopts conformations that are activator specific.
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Affiliation(s)
- Brian A Lewis
- Howard Hughes Medical Institute, Division of Nucleic Acids Enzymology, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
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Wu SY, Zhou T, Chiang CM. Human mediator enhances activator-facilitated recruitment of RNA polymerase II and promoter recognition by TATA-binding protein (TBP) independently of TBP-associated factors. Mol Cell Biol 2003; 23:6229-42. [PMID: 12917344 PMCID: PMC180944 DOI: 10.1128/mcb.23.17.6229-6242.2003] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2003] [Accepted: 05/29/2003] [Indexed: 12/30/2022] Open
Abstract
Mediator is a general cofactor implicated in the functions of many transcriptional activators. Although Mediator with different protein compositions has been isolated, it remains unclear how Mediator facilitates activator-dependent transcription, independent of its general stimulation of basal transcription. To define the mechanisms of Mediator function, we isolated two forms of human Mediator complexes (Mediator-P.5 and Mediator-P.85) and demonstrated that Mediator-P.5 clearly functions by enhancing activator-mediated recruitment of RNA polymerase II (pol II), whereas Mediator-P.85 works mainly by stimulating overall basal transcription. The coactivator function of Mediator-P.5 was not impaired when TATA-binding protein (TBP) was used in place of TFIID, but it was abolished when another general cofactor, PC4, was omitted from the reaction or when Mediator-P.5 was added after pol II entry into the preinitiation complex. Moreover, Mediator- P.5 is able to enhance TBP binding to the TATA box in an activator-dependent manner. Our data provides biochemical evidence that Mediator functions by facilitating activator-mediated recruitment of pol II and also promoter recognition by TBP, both of which can occur in the absence of TBP-associated factors in TFIID.
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Affiliation(s)
- Shwu-Yuan Wu
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
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Janody F, Martirosyan Z, Benlali A, Treisman JE. Two subunits of the Drosophila mediator complex act together to control cell affinity. Development 2003; 130:3691-701. [PMID: 12835386 DOI: 10.1242/dev.00607] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The organizing centers for Drosophila imaginal disc development are created at straight boundaries between compartments; these are maintained by differences in cell affinity controlled by selector genes and intercellular signals. skuld and kohtalo encode homologs of TRAP240 and TRAP230, the two largest subunits of the Drosophila mediator complex; mutations in either gene cause identical phenotypes. We show here that both genes are required to establish normal cell affinity differences at the anterior-posterior and dorsal-ventral compartment boundaries of the wing disc. Mutant cells cross from the anterior to the posterior compartment, and can distort the dorsal-ventral boundary in either the dorsal or ventral direction. The Skuld and Kohtalo proteins physically interact in vivo and have synergistic effects when overexpressed, consistent with a skuld kohtalo double-mutant phenotype that is indistinguishable from either single mutant. We suggest that these two subunits do not participate in all of the activities of the mediator complex, but form a submodule that is required to regulate specific target genes, including those that control cell affinity.
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Affiliation(s)
- Florence Janody
- Skirball Institute of Biomolecular Medicine and Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
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Kim M, Park CH, Lee MS, Carlson BA, Hatfield DL, Lee BJ. A novel TBP-interacting zinc finger protein represses transcription by inhibiting the recruitment of TFIIA and TFIIB. Biochem Biophys Res Commun 2003; 306:231-8. [PMID: 12788093 DOI: 10.1016/s0006-291x(03)00939-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We isolated a novel gene encoding a zinc finger protein from Xenopus laevis, designated NZFP that interacts with the TATA-binding protein (TBP). NZFP contains a highly conserved sequence designated finger associated box (FAX) and SUMO-1 consensus-binding motifs at the N-terminal half and 10 C2H2 type zinc finger motifs at the C-terminal half, respectively. Deletion mutants of NZFP fused with the Gal4 DNA binding domain were used to determine the function of NZFP during gene transcription by transfecting them into a Xenopus kidney cell line. Both full-length NZFP and the FAX domain repressed transcription activity by 3-5-fold. Moreover, an in vitro pull-down assay showed that the C-terminal core domain of TBP makes direct contact with the N-terminal portion of NZFP. We also found through chromatin immunoprecipitation experiments that the interaction between NZFP and TBP inhibits binding of TFIIA and TFIIB. These data strongly suggest that the repression by NZFP occurs through its binding to both DNA and TBP and the resulting NZFP-TBP-promoter complex inhibits preinitiation complex assembly by preventing binding of TFIIA and TFIIB.
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Affiliation(s)
- Mijin Kim
- Laboratory of Molecular Genetics, School of Biological Sciences, Seoul National University, 151-742, Seoul, South Korea
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Wu CH, Yamaguchi Y, Benjamin LR, Horvat-Gordon M, Washinsky J, Enerly E, Larsson J, Lambertsson A, Handa H, Gilmour D. NELF and DSIF cause promoter proximal pausing on the hsp70 promoter in Drosophila. Genes Dev 2003; 17:1402-14. [PMID: 12782658 PMCID: PMC196072 DOI: 10.1101/gad.1091403] [Citation(s) in RCA: 236] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2003] [Accepted: 04/02/2003] [Indexed: 11/24/2022]
Abstract
NELF and DSIF collaborate to inhibit elongation by RNA polymerase IIa in extracts from human cells. A multifaceted approach was taken to investigate the potential role of these factors in promoter proximal pausing on the hsp70 gene in Drosophila. Immunodepletion of DSIF from a Drosophila nuclear extract reduced the level of polymerase that paused in the promoter proximal region of hsp70. Depletion of one NELF subunit in salivary glands using RNA interference also reduced the level of paused polymerase. In vivo protein-DNA cross-linking showed that NELF and DSIF associate with the promoter region before heat shock. Immunofluorescence analysis of polytene chromosomes corroborated the cross-linking result and showed that NELF, DSIF, and RNA polymerase IIa colocalize at the hsp70 genes, small heat shock genes, and many other chromosomal locations. Finally, following heat shock induction, DSIF and polymerase but not NELF were strongly recruited to chromosomal puffs harboring the hsp70 genes. We propose that NELF and DSIF cause polymerase to pause in the promoter proximal region of hsp70. The transcriptional activator, HSF, might cause NELF to dissociate from the elongation complex. DSIF continues to associate with the elongation complex and could serve a positive role in elongation.
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Affiliation(s)
- Chwen-Huey Wu
- Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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41
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Park JM, Kim JM, Kim LK, Kim SN, Kim-Ha J, Kim JH, Kim YJ. Signal-induced transcriptional activation by Dif requires the dTRAP80 mediator module. Mol Cell Biol 2003; 23:1358-67. [PMID: 12556495 PMCID: PMC141132 DOI: 10.1128/mcb.23.4.1358-1367.2003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Mediator complex is the major multiprotein transcriptional coactivator complex in Drosophila melanogaster. Mediator components interact with diverse sets of transcriptional activator proteins to elicit the sophisticated regulation of gene expression. The distinct phenotypes associated with certain mutations in some of the Mediator genes and the specific in vitro interactions of Mediator gene products with transcriptional activator proteins suggest the presence of activator-specific binding subunits within the Mediator complex. However, the physiological relevance of these selective in vitro interactions has not been addressed. Therefore, we analyzed dTRAP80, one of the putative activator-binding subunits of the Mediator, for specificity of binding to a number of natural transcriptional activators from Drosophila. Among the group of activator proteins that requires the Mediator complex for transcriptional activation, only a subset of these proteins interacted with dTRAP80 in vitro and only these dTRAP80-interacting activators were defective for activation under dTRAP80-deficient in vivo conditions. In particular, activation of Drosophila antimicrobial peptide drosomycin gene expression by the NF-kappa B-like transcription factor Dif during induction of the Toll signaling pathway was dependent on the dTRAP80 module. These results, and the indirect support from the dTRAP80 artificial recruitment assay, indicate that dTRAP80 serves as a genuine activator-binding target responsible for a distinct group of activators.
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Affiliation(s)
- Jin Mo Park
- Department of Biochemistry, National Creative Research Initiative Center for Genome Regulation, Yonsei University. Digital Genomics, Inc., Seoul 120-749, Korea
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42
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Acevedo ML, Kraus WL. Mediator and p300/CBP-steroid receptor coactivator complexes have distinct roles, but function synergistically, during estrogen receptor alpha-dependent transcription with chromatin templates. Mol Cell Biol 2003; 23:335-48. [PMID: 12482985 PMCID: PMC140681 DOI: 10.1128/mcb.23.1.335-348.2003] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ligand-dependent transcriptional activation by nuclear receptors involves the recruitment of various coactivators to the promoters of hormone-regulated genes assembled into chromatin. Nuclear receptor coactivators include histone acetyltransferase complexes, such as p300/CBP-steroid receptor coactivator (SRC), as well as the multisubunit mediator complexes ("Mediator"), which may help recruit RNA polymerase II to the promoter. We have used a biochemical approach, including an in vitro chromatin assembly and transcription system, to examine the functional role for Mediator in the transcriptional activity of estrogen receptor alpha (ERalpha) with chromatin templates, as well as functional interplay between Mediator and p300/CBP during ERalpha-dependent transcription. Using three different approaches to functionally inactivate Mediator (immunoneutralization, immunodepletion, and inhibitory polypeptides), we find that Mediator is required for maximal transcriptional activation by ligand-activated ERalpha. In addition, we demonstrate synergism between Mediator and p300/CBP-SRC during ERalpha-dependent transcription with chromatin templates, but not with naked DNA. This synergism is important for promoting the formation of a stable transcription preinitiation complex leading to the initiation of transcription. Interestingly, we find that Mediator has an additional distinct role during ERalpha-dependent transcription not shared by p300/CBP-SRC: namely, to promote preinitiation complex formation for subsequent rounds of transcription reinitiation. These results suggest that one functional consequence of Mediator-ERalpha interactions is the stimulation of multiple cycles of transcription reinitiation. Collectively, our results indicate an important role for Mediator, as well as its functional interplay with p300/CBP-SRC, in the enhancement of ERalpha-dependent transcription with chromatin templates.
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Affiliation(s)
- Mari Luz Acevedo
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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43
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Gutiérrez L, Zurita M, Kennison JA, Vázquez M. The Drosophila trithorax group gene tonalli (tna) interacts genetically with the Brahma remodeling complex and encodes an SP-RING finger protein. Development 2003; 130:343-54. [PMID: 12466201 DOI: 10.1242/dev.00222] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The trithorax group genes are required for positive regulation of homeotic gene function. The trithorax group gene brahma encodes a SWI2/SNF2 family ATPase that is a catalytic subunit of the Brm chromatin-remodeling complex. We identified the tonalli (tna) gene in Drosophila by genetic interactions with brahma. tna mutations suppress Polycomb phenotypes and tna is required for the proper expressions of the Antennapedia, Ultrabithorax and Sex combs reduced homeotic genes. The tna gene encodes at least two proteins, a large isoform (TnaA) and a short isoform (TnaB). The TnaA protein has an SP-RING Zn finger, conserved in proteins from organisms ranging from yeast to human and thought to be involved in the sumoylation of protein substrates. Besides the SP-RING finger, the TnaA protein also has extended homology with other eukaryotic proteins, including human proteins. We show that tna mutations also interact with mutations in additional subunits of the Brm complex, with mutations in subunits of the Mediator complex, and with mutations of the SWI2/SNF2 family ATPase gene kismet. We propose that Tna is involved in postranslational modification of transcription complexes.
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Affiliation(s)
- Luis Gutiérrez
- Departamento de Fisiología Molecular y Genética del Desarrollo, Instituto de Biotecnología, UNAM, Cuernavaca, Morelos 62250, México
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44
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Martinez E. Multi-protein complexes in eukaryotic gene transcription. PLANT MOLECULAR BIOLOGY 2002; 50:925-47. [PMID: 12516863 DOI: 10.1023/a:1021258713850] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Specific transcription initiation by RNA polymerase II at eukaryotic protein-coding genes involves the cooperative assembly at the core promoter of more than 40 distinct proteins--with a total mass of over 2 MDa--including RNA polymerase II itself and general/basal transcription initiation factors, to form a stable pre-initiation complex (PIC). In vivo, PIC assembly is a major point of regulation by sequence-specific transcription regulators (activators and repressors) and is hindered by the packaging of promoter DNA into nucleosomes and higher order chromatin structures. Genetic and biochemical studies have recently identified a variety of transcription cofactors/co-regulators (coactivators and corepressors) that interact with sequence-specific regulators and/or various components of the general/basal transcription machinery and are essential for regulated transcription. An emerging view from these studies is that regulators must target two types of transcription cofactors: chromatin-modifying/remodeling cofactors and general cofactors that associate with and/or influence the activities of components of the general/basal transcription machinery. The recent biochemical identification and characterization of many different chromatin-modifying and general transcription cofactors has revealed their often complex multi-subunit nature and a previously unsuspected level of structural and functional redundancy. Another emerging theme is the multi-functional nature of chromatin-modifying cofactor complexes that appear to couple gene-specific transcription to other cellular processes.
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Affiliation(s)
- Ernest Martinez
- Department of Biochemistry, University of California, Riverside, CA 92521, USA.
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45
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Boube M, Joulia L, Cribbs DL, Bourbon HM. Evidence for a mediator of RNA polymerase II transcriptional regulation conserved from yeast to man. Cell 2002; 110:143-51. [PMID: 12150923 DOI: 10.1016/s0092-8674(02)00830-9] [Citation(s) in RCA: 215] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mediator complexes (MED) link transcriptional regulators to RNA polymerase II. Here, we summarize the latest advances on the functional organization of yeast Mediator. We argue for the existence of a "universal" Mediator structurally conserved from yeast to man, based on an extensive analysis of sequence databases. Finally, we examine the implications of these observations for the physiological roles of metazoan MED subunits.
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Affiliation(s)
- Muriel Boube
- Centre de Biologie du Développement, Université Paul Sabatier, 31062, Toulouse Cedex, France
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46
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Gu JY, Park JM, Song EJ, Mizuguchi G, Yoon JH, Kim-Ha J, Lee KJ, Kim YJ. Novel Mediator proteins of the small Mediator complex in Drosophila SL2 cells. J Biol Chem 2002; 277:27154-61. [PMID: 12021283 DOI: 10.1074/jbc.m204144200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Mediator complex is generally required for transcriptional regulation in species ranging from yeast to human. Throughout evolution, the functional diversity of the Mediator complex has been enhanced to meet the increasing requirements for sophisticated gene regulation. It is likely that greater structural complexity is thus required to accomplish these new, complex regulatory functions. In this study, we took systematic steps to examine various types of Mediator complexes in Drosophila melanogaster. Such efforts led to the identification of three distinct forms of Mediator complexes. In exploring their compositional and functional heterogeneity, we found that the smallest complex (C1) is highly enriched in a certain type of Drosophila cells and possesses novel Mediator proteins. The subunits shared among the three Mediator complexes (C1, C2, and C3) appear to form a stable modular structure that serves as a binding surface for transcriptional activator proteins. However, only C2 and C3 were able to support activated transcription in vitro. These findings suggest that different cell types may require distinct Mediator complexes, some of which may participate in nuclear processes other than the previously identified functions.
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Affiliation(s)
- Ji-Young Gu
- National Creative Research Initiative Center for Genome Regulation, Department of Biochemistry, Yonsei University, Seoul 120-749, Korea
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47
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Baek HJ, Malik S, Qin J, Roeder RG. Requirement of TRAP/mediator for both activator-independent and activator-dependent transcription in conjunction with TFIID-associated TAF(II)s. Mol Cell Biol 2002; 22:2842-52. [PMID: 11909976 PMCID: PMC133729 DOI: 10.1128/mcb.22.8.2842-2852.2002] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The multiprotein human TRAP/Mediator complex, which is phylogenetically related to the yeast SRB/Mediator coactivator, facilitates activation through a wide variety of transcriptional activators. However, it remains unclear how TRAP/Mediator functions in the context of other coactivators. Here we have identified a previously uncharacterized integral subunit (TRAP25) of the complex that is apparently metazoan specific. An antibody that is specific for TRAP25 allowed quantitative immunodepletion of essentially all TRAP/Mediator components from HeLa nuclear extract, without detectably affecting levels of RNA polymerase II and corresponding general transcription factors. Surprisingly, the TRAP/Mediator-depleted nuclear extract displayed severely reduced levels of both basal and activator-dependent transcription from DNA templates. Both activities were efficiently restored upon readdition of purified TRAP/Mediator. Moreover, restoration of basal and activator-dependent transcription to extracts that were simultaneously depleted of TRAP/Mediator and TFIID (TBP plus the major TAF(II)s) required addition of both TBP and associated TAF(II)s, as well as TRAP/Mediator. These observations indicate that TAF(II)s and Mediator are jointly required for both basal and activated transcription in the context of a more physiological complement of nuclear proteins. We propose a close mechanistic linkage between these components that most likely operates at the level of combined effects on the general transcription machinery and, in addition, a direct role for Mediator in relaying activation signals to this machinery.
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Affiliation(s)
- Hwa Jin Baek
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York 10021, USA
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48
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Gim BS, Park JM, Yoon JH, Kang C, Kim YJ. Drosophila Med6 is required for elevated expression of a large but distinct set of developmentally regulated genes. Mol Cell Biol 2001; 21:5242-55. [PMID: 11438678 PMCID: PMC87248 DOI: 10.1128/mcb.21.15.5242-5255.2001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mediator is the evolutionarily conserved coactivator required for the integration and recruitment of diverse regulatory signals to basal transcription machinery. To elucidate the functions of metazoan Mediator, we isolated Drosophila melanogaster Med6 mutants. dMed6 is essential for viability and/or proliferation of most cells. dMed6 mutants failed to pupate and died in the third larval instar with severe proliferation defects in imaginal discs and other larval mitotic cells. cDNA microarray, quantitative reverse transcription-PCR, and in situ expression analyses of developmentally regulated genes in dMed6 mutants showed that transcriptional activation of many, but not all, genes was affected. Among the genes found to be affected were some that play a role in cell proliferation and metabolism. Therefore, dMed6 is required in most cells for transcriptional regulation of many genes important for diverse aspects of Drosophila development.
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Affiliation(s)
- B S Gim
- Department of Biochemistry, National Creative Research Initiative Center for Genome Regulation, Yonsei University, Seoul 120-749, Korea
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49
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Park JM, Werner J, Kim JM, Lis JT, Kim YJ. Mediator, not holoenzyme, is directly recruited to the heat shock promoter by HSF upon heat shock. Mol Cell 2001; 8:9-19. [PMID: 11511356 DOI: 10.1016/s1097-2765(01)00296-9] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Activators of RNA polymerase II (Pol II) transcription have been shown to bind several coactivators and basal factors in vitro. Whether such interactions play a primary regulatory role in recruiting these factors to activator-associated chromosomal target sites in living cells remains unclear. Here, we show that upon heat shock the Pol II-free form of Mediator is rapidly recruited to HSF binding sites. Unlike the TAFs and Pol II, the interaction between Mediator and HSF on chromosomal loci is direct and mechanistically separable from the preinitiation complex assembly step. Therefore, the activator-Mediator interaction likely underlies the initiation of signal transfer from enhancer-bound activators to the basal transcription machinery.
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Affiliation(s)
- J M Park
- National Creative Research Initiative Center for Genome Regulation, Department of Biochemistry, Yonsei University, 120-749, Seoul, South Korea
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