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Tetter S, Arseni D, Murzin AG, Buhidma Y, Peak-Chew SY, Garringer HJ, Newell KL, Vidal R, Apostolova LG, Lashley T, Ghetti B, Ryskeldi-Falcon B. TAF15 amyloid filaments in frontotemporal lobar degeneration. Nature 2024; 625:345-351. [PMID: 38057661 PMCID: PMC10781619 DOI: 10.1038/s41586-023-06801-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/30/2023] [Indexed: 12/08/2023]
Abstract
Frontotemporal lobar degeneration (FTLD) causes frontotemporal dementia (FTD), the most common form of dementia after Alzheimer's disease, and is often also associated with motor disorders1. The pathological hallmarks of FTLD are neuronal inclusions of specific, abnormally assembled proteins2. In the majority of cases the inclusions contain amyloid filament assemblies of TAR DNA-binding protein 43 (TDP-43) or tau, with distinct filament structures characterizing different FTLD subtypes3,4. The presence of amyloid filaments and their identities and structures in the remaining approximately 10% of FTLD cases are unknown but are widely believed to be composed of the protein fused in sarcoma (FUS, also known as translocated in liposarcoma). As such, these cases are commonly referred to as FTLD-FUS. Here we used cryogenic electron microscopy (cryo-EM) to determine the structures of amyloid filaments extracted from the prefrontal and temporal cortices of four individuals with FTLD-FUS. Surprisingly, we found abundant amyloid filaments of the FUS homologue TATA-binding protein-associated factor 15 (TAF15, also known as TATA-binding protein-associated factor 2N) rather than of FUS itself. The filament fold is formed from residues 7-99 in the low-complexity domain (LCD) of TAF15 and was identical between individuals. Furthermore, we found TAF15 filaments with the same fold in the motor cortex and brainstem of two of the individuals, both showing upper and lower motor neuron pathology. The formation of TAF15 amyloid filaments with a characteristic fold in FTLD establishes TAF15 proteinopathy in neurodegenerative disease. The structure of TAF15 amyloid filaments provides a basis for the development of model systems of neurodegenerative disease, as well as for the design of diagnostic and therapeutic tools targeting TAF15 proteinopathy.
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Affiliation(s)
| | - Diana Arseni
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Yazead Buhidma
- Department of Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, London, UK
| | | | - Holly J Garringer
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kathy L Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Ruben Vidal
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Liana G Apostolova
- Department of Neurology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Tammaryn Lashley
- Department of Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, London, UK
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, London, UK
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
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2
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Bernardini A, Mukherjee P, Scheer E, Kamenova I, Antonova S, Mendoza Sanchez PK, Yayli G, Morlet B, Timmers HTM, Tora L. Hierarchical TAF1-dependent co-translational assembly of the basal transcription factor TFIID. Nat Struct Mol Biol 2023; 30:1141-1152. [PMID: 37386215 PMCID: PMC10442232 DOI: 10.1038/s41594-023-01026-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 05/31/2023] [Indexed: 07/01/2023]
Abstract
Large heteromeric multiprotein complexes play pivotal roles at every step of gene expression in eukaryotic cells. Among them, the 20-subunit basal transcription factor TFIID nucleates the RNA polymerase II preinitiation complex at gene promoters. Here, by combining systematic RNA-immunoprecipitation (RIP) experiments, single-molecule imaging, proteomics and structure-function analyses, we show that human TFIID biogenesis occurs co-translationally. We discovered that all protein heterodimerization steps happen during protein synthesis. We identify TAF1-the largest protein in the complex-as a critical factor for TFIID assembly. TAF1 acts as a flexible scaffold that drives the co-translational recruitment of TFIID submodules preassembled in the cytoplasm. Altogether, our data suggest a multistep hierarchical model for TFIID biogenesis that culminates with the co-translational assembly of the complex onto the nascent TAF1 polypeptide. We envision that this assembly strategy could be shared with other large heteromeric protein complexes.
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Affiliation(s)
- Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Pooja Mukherjee
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Ivanka Kamenova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Nature Protocols, London, UK
| | - Simona Antonova
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
- The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Paulina Karen Mendoza Sanchez
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Gizem Yayli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - H T Marc Timmers
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.
- Centre National de la Recherche Scientifique, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France.
- Université de Strasbourg, Illkirch, France.
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3
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Woike S, Eustermann S, Jung J, Wenzl SJ, Hagemann G, Bartho J, Lammens K, Butryn A, Herzog F, Hopfner KP. Structural basis for TBP displacement from TATA box DNA by the Swi2/Snf2 ATPase Mot1. Nat Struct Mol Biol 2023; 30:640-649. [PMID: 37106137 PMCID: PMC7615866 DOI: 10.1038/s41594-023-00966-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 03/13/2023] [Indexed: 04/29/2023]
Abstract
The Swi2/Snf2 family transcription regulator Modifier of Transcription 1 (Mot1) uses adenosine triphosphate (ATP) to dissociate and reallocate the TATA box-binding protein (TBP) from and between promoters. To reveal how Mot1 removes TBP from TATA box DNA, we determined cryogenic electron microscopy structures that capture different states of the remodeling reaction. The resulting molecular video reveals how Mot1 dissociates TBP in a process that, intriguingly, does not require DNA groove tracking. Instead, the motor grips DNA in the presence of ATP and swings back after ATP hydrolysis, moving TBP to a thermodynamically less stable position on DNA. Dislodged TBP is trapped by a chaperone element that blocks TBP's DNA binding site. Our results show how Swi2/Snf2 proteins can remodel protein-DNA complexes through DNA bending without processive DNA tracking and reveal mechanistic similarities to RNA gripping DEAD box helicases and RIG-I-like immune sensors.
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Affiliation(s)
- Stephan Woike
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany
| | - Sebastian Eustermann
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - James Jung
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Simon Josef Wenzl
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany
| | - Götz Hagemann
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany
| | - Joseph Bartho
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany
| | - Katja Lammens
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany
| | - Agata Butryn
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany
- Macromolecular Machines Laboratory, Francis Crick Institute, London, UK
| | - Franz Herzog
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany
- Institute Krems Bioanalytics, IMC University of Applied Sciences, Krems, Austria
| | - Karl-Peter Hopfner
- Department of Biochemistry, Ludwig-Maximilians-Universität, Munich, Germany.
- Gene Center, Ludwig-Maximilians-Universität, Munich, Germany.
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Friis Theisen F, Salladini E, Davidsen R, Jo Rasmussen C, Staby L, Kragelund BB, Skriver K. αα-hub coregulator structure and flexibility determine transcription factor binding and selection in regulatory interactomes. J Biol Chem 2022; 298:101963. [PMID: 35452682 PMCID: PMC9127584 DOI: 10.1016/j.jbc.2022.101963] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 11/23/2022] Open
Abstract
Formation of transcription factor (TF)-coregulator complexes is a key step in transcriptional regulation, with coregulators having essential functions as hub nodes in molecular networks. How specificity and selectivity are maintained in these nodes remain open questions. In this work, we addressed specificity in transcriptional networks using complexes formed between TFs and αα-hubs, which are defined by a common αα-hairpin secondary structure motif, as a model. Using NMR spectroscopy and binding thermodynamics, we analyzed the structure, dynamics, stability, and ligand-binding properties of the Arabidopsis thaliana RST domains from TAF4 and known binding partner RCD1, and the TAFH domain from human TAF4, allowing comparison across species, functions, and architectural contexts. While these αα-hubs shared the αα-hairpin motif, they differed in length and orientation of accessory helices as well as in their thermodynamic profiles of ligand binding. Whereas biologically relevant RCD1-ligand pairs displayed high affinity driven by enthalpy, TAF4-ligand interactions were entropy driven and exhibited less binding-induced structuring. We in addition identified a thermal unfolding state with a structured core for all three domains, although the temperature sensitivity differed. Thermal stability studies suggested that initial unfolding of the RCD1-RST domain localized around helix 1, lending this region structural malleability, while effects in TAF4-RST were more stochastic, suggesting variability in structural adaptability upon binding. Collectively, our results support a model in which hub structure, flexibility, and binding thermodynamics contribute to αα-hub-TF binding specificity, a finding of general relevance to the understanding of coregulator-ligand interactions and interactome sizes.
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Affiliation(s)
- Frederik Friis Theisen
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Edoardo Salladini
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rikke Davidsen
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Christina Jo Rasmussen
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Staby
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Birthe B Kragelund
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Karen Skriver
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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5
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Bugge K, Staby L, Salladini E, Falbe-Hansen RG, Kragelund BB, Skriver K. αα-Hub domains and intrinsically disordered proteins: A decisive combo. J Biol Chem 2021; 296:100226. [PMID: 33361159 PMCID: PMC7948954 DOI: 10.1074/jbc.rev120.012928] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/22/2020] [Accepted: 12/22/2020] [Indexed: 01/02/2023] Open
Abstract
Hub proteins are central nodes in protein-protein interaction networks with critical importance to all living organisms. Recently, a new group of folded hub domains, the αα-hubs, was defined based on a shared αα-hairpin supersecondary structural foundation. The members PAH, RST, TAFH, NCBD, and HHD are found in large proteins such as Sin3, RCD1, TAF4, CBP, and harmonin, which organize disordered transcriptional regulators and membrane scaffolds in interactomes of importance to human diseases and plant quality. In this review, studies of structures, functions, and complexes across the αα-hubs are described and compared to provide a unified description of the group. This analysis expands the associated molecular concepts of "one domain-one binding site", motif-based ligand binding, and coupled folding and binding of intrinsically disordered ligands to additional concepts of importance to signal fidelity. These include context, motif reversibility, multivalency, complex heterogeneity, synergistic αα-hub:ligand folding, accessory binding sites, and supramodules. We propose that these multifaceted protein-protein interaction properties are made possible by the characteristics of the αα-hub fold, including supersite properties, dynamics, variable topologies, accessory helices, and malleability and abetted by adaptability of the disordered ligands. Critically, these features provide additional filters for specificity. With the presentations of new concepts, this review opens for new research questions addressing properties across the group, which are driven from concepts discovered in studies of the individual members. Combined, the members of the αα-hubs are ideal models for deconvoluting signal fidelity maintained by folded hubs and their interactions with intrinsically disordered ligands.
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Affiliation(s)
- Katrine Bugge
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Staby
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Edoardo Salladini
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus G Falbe-Hansen
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Birthe B Kragelund
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Karen Skriver
- REPIN and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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Louka A, Zacco E, Temussi PA, Tartaglia GG, Pastore A. RNA as the stone guest of protein aggregation. Nucleic Acids Res 2020; 48:11880-11889. [PMID: 33068411 PMCID: PMC7708036 DOI: 10.1093/nar/gkaa822] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/12/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022] Open
Abstract
The study of prions as infectious aggregates dates several decades. From its original formulation, the definition of a prion has progressively changed to the point that many aggregation-prone proteins are now considered bona fide prions. RNA molecules, not included in the original 'protein-only hypothesis', are also being recognized as important factors contributing to the 'prion behaviour', that implies the transmissibility of an aberrant fold. In particular, an association has recently emerged between aggregation and the assembly of prion-like proteins in RNA-rich complexes, associated with both physiological and pathological events. Here, we discuss the historical rising of the concept of prion-like domains, their relation to RNA and their role in protein aggregation. As a paradigmatic example, we present the case study of TDP-43, an RNA-binding prion-like protein associated with amyotrophic lateral sclerosis. Through this example, we demonstrate how the current definition of prions has incorporated quite different concepts making the meaning of the term richer and more stimulating. An important message that emerges from our analysis is the dual role of RNA in protein aggregation, making RNA, that has been considered for many years a 'silent presence' or the 'stone guest' of protein aggregation, an important component of the process.
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Affiliation(s)
- Alexandra Louka
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London SE5 9RT, UK
| | - Elsa Zacco
- Center for Human Technologies, Central RNA laboratory, Istituto Italiano di Tecnologia, Genova 16152, Italy
| | - Piero Andrea Temussi
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London SE5 9RT, UK
- University “Federico II’’ Napoli, via Cynthia, Napoli 80100, Italy
| | - Gian Gaetano Tartaglia
- Center for Human Technologies, Central RNA laboratory, Istituto Italiano di Tecnologia, Genova 16152, Italy
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain and ICREA, 23 Passeig Lluıs Companys, Barcelona 08010, Spain
- Charles Darwin department of Biology and Biotechnology, Sapienza University of Rome, Piazzale A. Moro 5, Rome 00185, Italy
| | - Annalisa Pastore
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London SE5 9RT, UK
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7
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Gupta K, Watson AA, Baptista T, Scheer E, Chambers AL, Koehler C, Zou J, Obong-Ebong I, Kandiah E, Temblador A, Round A, Forest E, Man P, Bieniossek C, Laue ED, Lemke EA, Rappsilber J, Robinson CV, Devys D, Tora L, Berger I. Architecture of TAF11/TAF13/TBP complex suggests novel regulation properties of general transcription factor TFIID. eLife 2017; 6:e30395. [PMID: 29111974 PMCID: PMC5690282 DOI: 10.7554/elife.30395] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/03/2017] [Indexed: 11/13/2022] Open
Abstract
General transcription factor TFIID is a key component of RNA polymerase II transcription initiation. Human TFIID is a megadalton-sized complex comprising TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). TBP binds to core promoter DNA, recognizing the TATA-box. We identified a ternary complex formed by TBP and the histone fold (HF) domain-containing TFIID subunits TAF11 and TAF13. We demonstrate that TAF11/TAF13 competes for TBP binding with TATA-box DNA, and also with the N-terminal domain of TAF1 previously implicated in TATA-box mimicry. In an integrative approach combining crystal coordinates, biochemical analyses and data from cross-linking mass-spectrometry (CLMS), we determine the architecture of the TAF11/TAF13/TBP complex, revealing TAF11/TAF13 interaction with the DNA binding surface of TBP. We identify a highly conserved C-terminal TBP-interaction domain (CTID) in TAF13, which is essential for supporting cell growth. Our results thus have implications for cellular TFIID assembly and suggest a novel regulatory state for TFIID function.
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Affiliation(s)
- Kapil Gupta
- BrisSynBio Centre, The School of Biochemistry, Faculty of Biomedical SciencesUniversity of BristolBristolUnited Kingdom
- European Molecular Biology LaboratoryGrenobleFrance
| | | | - Tiago Baptista
- Institut de Génétique et de Biologie Moléculaire et Cellulaire IGBMCIllkirchFrance
- Centre National de la Recherche ScientifiqueIllkirchFrance
- Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire IGBMCIllkirchFrance
- Centre National de la Recherche ScientifiqueIllkirchFrance
- Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Anna L Chambers
- BrisSynBio Centre, The School of Biochemistry, Faculty of Biomedical SciencesUniversity of BristolBristolUnited Kingdom
| | | | - Juan Zou
- Wellcome Trust Centre for Cell BiologyUniversity of EdinburghEdinburghUnited Kingdom
- Chair of BioanalyticsInstitute of Biotechnology, Technische Universität BerlinBerlinGermany
| | - Ima Obong-Ebong
- Physical and Theoretical Chemistry LaboratoryOxfordUnited Kingdom
| | - Eaazhisai Kandiah
- European Molecular Biology LaboratoryGrenobleFrance
- Institut de Biologie Structurale IBSGrenobleFrance
| | | | - Adam Round
- European Molecular Biology LaboratoryGrenobleFrance
| | - Eric Forest
- Institut de Biologie Structurale IBSGrenobleFrance
| | - Petr Man
- Institute of MicrobiologyThe Czech Academy of SciencesVestecCzech Republic
- BioCeV - Faculty of ScienceCharles UniversityPragueCzech Republic
| | | | - Ernest D Laue
- Department of BiochemistryUniversity of CambridgeCambridgeUnited Kingdom
| | | | - Juri Rappsilber
- Wellcome Trust Centre for Cell BiologyUniversity of EdinburghEdinburghUnited Kingdom
- Chair of BioanalyticsInstitute of Biotechnology, Technische Universität BerlinBerlinGermany
| | - Carol V Robinson
- Physical and Theoretical Chemistry LaboratoryOxfordUnited Kingdom
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire IGBMCIllkirchFrance
- Centre National de la Recherche ScientifiqueIllkirchFrance
- Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Làszlò Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire IGBMCIllkirchFrance
- Centre National de la Recherche ScientifiqueIllkirchFrance
- Institut National de la Santé et de la Recherche MédicaleIllkirchFrance
- Université de StrasbourgIllkirchFrance
| | - Imre Berger
- BrisSynBio Centre, The School of Biochemistry, Faculty of Biomedical SciencesUniversity of BristolBristolUnited Kingdom
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8
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Hibino E, Inoue R, Sugiyama M, Kuwahara J, Matsuzaki K, Hoshino M. Identification of heteromolecular binding sites in transcription factors Sp1 and TAF4 using high-resolution nuclear magnetic resonance spectroscopy. Protein Sci 2017; 26:2280-2290. [PMID: 28857320 PMCID: PMC5654864 DOI: 10.1002/pro.3287] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/26/2017] [Accepted: 08/28/2017] [Indexed: 01/17/2023]
Abstract
The expression of eukaryotic genes is precisely controlled by interactions between general transcriptional factors and promoter-specific transcriptional activators. The fourth element of TATA-box binding protein-associated factor (TAF4), an essential subunit of the general transcription factor TFIID, serves as a coactivator for various promoter-specific transcriptional regulators. Interactions between TAF4 and site-specific transcriptional activators, such as Sp1, are important for regulating the expression levels of genes of interest. However, only limited information is available on the molecular mechanisms underlying the interactions between these transcriptional regulatory proteins. We herein analyzed the interaction between the transcriptional factors Sp1 and TAF4 using high-resolution solution nuclear magnetic resonance spectroscopy. We found that four glutamine-rich (Q-rich) regions in TAF4 were largely disordered under nearly physiological conditions. Among them, the first Q-rich region in TAF4 was essential for the interaction with another Q-rich region in the Sp1 molecule, most of which was largely disordered. The residues responsible for this interaction were specific and highly localized in a defined region within a range of 20-30 residues. Nevertheless, a detailed analysis of 13 C-chemical shift values suggested that no significant conformational change occurred upon binding. These results indicate a prominent and exceptional binding mode for intrinsically disordered proteins other than the well-accepted concept of "coupled folding and binding."
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Affiliation(s)
- Emi Hibino
- Graduate School of Pharmaceutical SciencesKyoto UniversityKyotoSakyo‐ku606‐8501Japan
| | - Rintaro Inoue
- Research Reactor Institute, Kyoto UniversitySennan‐gunOsaka590‐0494Japan
| | - Masaaki Sugiyama
- Research Reactor Institute, Kyoto UniversitySennan‐gunOsaka590‐0494Japan
| | - Jun Kuwahara
- Faculty of Pharmaceutical SciencesDoshisha Women's UniversityKyotanabe cityKyoto610‐0395Japan
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical SciencesKyoto UniversityKyotoSakyo‐ku606‐8501Japan
| | - Masaru Hoshino
- Graduate School of Pharmaceutical SciencesKyoto UniversityKyotoSakyo‐ku606‐8501Japan
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Hibino E, Inoue R, Sugiyama M, Kuwahara J, Matsuzaki K, Hoshino M. Interaction between intrinsically disordered regions in transcription factors Sp1 and TAF4. Protein Sci 2016; 25:2006-2017. [PMID: 27515574 PMCID: PMC5079245 DOI: 10.1002/pro.3013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 08/08/2016] [Indexed: 11/09/2022]
Abstract
The expression of eukaryotic genes is precisely controlled by specific interactions between general transcription initiation factors and gene-specific transcriptional activators. The general transcription factor TFIID, which plays an essential role in mediating transcriptional activation, is a multisubunit complex comprising the TATA box-binding protein (TBP) and multiple TBP-associated factors (TAFs). On the other hand, biochemical and genetic approaches have shown that the promoter-specific transcriptional activator Sp1 has the ability to interact with one of the components of TFIID, the TBP-associated factor TAF4. We herein report the structural details of the glutamine-rich domains (Q-domains) of Sp1 and TAF4 using circular dichroism (CD) and heteronuclear magnetic resonance (NMR) spectroscopy. We found that the two Q-domains of Sp1 and four Q-domains of TAF4 were disordered under physiological conditions. We also quantitatively analyzed the interaction between the Q-domains of Sp1 and TAF4 by NMR and surface plasmon resonance, and detected a weak but specific association between them. Nevertheless, a detailed analysis of CD spectra suggested that any significant conformational change did not occur concomitantly with this association, at least at the level of the overall secondary structure. These results may represent a prominent and exceptional binding mode for the IDPs, which are not categorized in a well-accepted concept of "coupled folding and binding."
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Affiliation(s)
- Emi Hibino
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Rintaro Inoue
- Research Reactor Institute, Kyoto University, Kumatori, Sennan-Gun, Osaka, 590-0494, Japan
| | - Masaaki Sugiyama
- Research Reactor Institute, Kyoto University, Kumatori, Sennan-Gun, Osaka, 590-0494, Japan
| | - Jun Kuwahara
- Faculty of Pharmaceutical Sciences, Doshisha Women's University, Kodo, Kyotanabe City, 610-0395, Japan
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Masaru Hoshino
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi, Sakyo-Ku, Kyoto, 606-8501, Japan.
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10
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Chau BL, Ng KP, Li KKC, Lee KA. RGG boxes within the TET/FET family of RNA-binding proteins are functionally distinct. Transcription 2016; 7:141-51. [PMID: 27159574 PMCID: PMC4984686 DOI: 10.1080/21541264.2016.1183071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 01/08/2023] Open
Abstract
The multi-functional TET (TAF15/EWS/TLS) or FET (FUS/EWS/TLS) protein family of higher organisms harbor a transcriptional-activation domain (EAD) and an RNA-binding domain (RBD). The transcriptional activation function is, however, only revealed in oncogenic TET-fusion proteins because in native TET proteins it is auto-repressed by RGG-boxes within the TET RBD. Auto-repression is suggested to involve direct cation-pi interactions between multiple Arg residues within RGG boxes and EAD aromatics. Via analysis of TET transcriptional activity in different organisms, we report herein that repression is not autonomous but instead requires additional trans-acting factors. This finding is not supportive of a proposed model whereby repression occurs via a simple intramolecular EAD/RGG-box interaction. We also show that RGG-boxes present within reiterated YGGDRGG repeats that are unique to TAF15, are defective for repression due to the conserved Asp residue. Thus, RGG boxes within TET proteins can be functionally distinguished. While our results show that YGGDRGG repeats are not involved in TAF15 auto-repression, their remarkable number and conservation strongly suggest that they may confer specialized properties to TAF15 and thus contribute to functional differentiation within the TET/FET protein family.
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Affiliation(s)
- Bess Ling Chau
- Division of Life Science, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
| | - King Pan Ng
- Division of Life Science, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
| | - Kim K C Li
- Division of Life Science, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
| | - Kevin A.W. Lee
- Division of Life Science, The Hong Kong University of Science & Technology, Clear Water Bay, Kowloon, Hong Kong S.A.R., China
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11
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Kashyap M, Ganguly AK, Bhavesh NS. Sequence-specific resonance assignments of human TAF15-RRM and TAF15-RRM-RanBP2. Biomol NMR Assign 2015; 9:103-106. [PMID: 24659459 DOI: 10.1007/s12104-014-9553-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 03/15/2014] [Indexed: 06/03/2023]
Abstract
Human TATA binding protein associated factor 2 N (TAF15) is a RNA/DNA binding protein involved in many aspects of RNA and DNA metabolism. TAF15 contains an N-terminal transcriptional activation domain and C-terminal region comprising the RNA recognition motif (RRM) and RanBP2 type zinc finger domains with interspersed RGG motifs. In this study we report the complete backbone and side chain resonance assignments of human TAF15-RRM and backbone assignments of TAF15-RRM-RanBP2.
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12
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Borck G, Hög F, Dentici ML, Tan PL, Sowada N, Medeira A, Gueneau L, Thiele H, Kousi M, Lepri F, Wenzeck L, Blumenthal I, Radicioni A, Schwarzenberg TL, Mandriani B, Fischetto R, Morris-Rosendahl DJ, Altmüller J, Reymond A, Nürnberg P, Merla G, Dallapiccola B, Katsanis N, Cramer P, Kubisch C. BRF1 mutations alter RNA polymerase III-dependent transcription and cause neurodevelopmental anomalies. Genome Res 2015; 25:155-66. [PMID: 25561519 PMCID: PMC4315290 DOI: 10.1101/gr.176925.114] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 11/26/2014] [Indexed: 01/11/2023]
Abstract
RNA polymerase III (Pol III) synthesizes tRNAs and other small noncoding RNAs to regulate protein synthesis. Dysregulation of Pol III transcription has been linked to cancer, and germline mutations in genes encoding Pol III subunits or tRNA processing factors cause neurogenetic disorders in humans, such as hypomyelinating leukodystrophies and pontocerebellar hypoplasia. Here we describe an autosomal recessive disorder characterized by cerebellar hypoplasia and intellectual disability, as well as facial dysmorphic features, short stature, microcephaly, and dental anomalies. Whole-exome sequencing revealed biallelic missense alterations of BRF1 in three families. In support of the pathogenic potential of the discovered alleles, suppression or CRISPR-mediated deletion of brf1 in zebrafish embryos recapitulated key neurodevelopmental phenotypes; in vivo complementation showed all four candidate mutations to be pathogenic in an apparent isoform-specific context. BRF1 associates with BDP1 and TBP to form the transcription factor IIIB (TFIIIB), which recruits Pol III to target genes. We show that disease-causing mutations reduce Brf1 occupancy at tRNA target genes in Saccharomyces cerevisiae and impair cell growth. Moreover, BRF1 mutations reduce Pol III-related transcription activity in vitro. Taken together, our data show that BRF1 mutations that reduce protein activity cause neurodevelopmental anomalies, suggesting that BRF1-mediated Pol III transcription is required for normal cerebellar and cognitive development.
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Affiliation(s)
- Guntram Borck
- Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany;
| | - Friederike Hög
- Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | | | - Perciliz L Tan
- Center for Human Disease Modeling, Duke University, Durham, North Carolina 27710, USA
| | - Nadine Sowada
- Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany
| | - Ana Medeira
- Serviço de Genética, Departamento de Pediatria, Hospital S. Maria, CHLN, 1649-035 Lisboa, Portugal
| | - Lucie Gueneau
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
| | - Maria Kousi
- Center for Human Disease Modeling, Duke University, Durham, North Carolina 27710, USA
| | | | - Larissa Wenzeck
- Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Ian Blumenthal
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Antonio Radicioni
- Department of Experimental Medicine, Sapienza University, 00161 Rome, Italy
| | | | - Barbara Mandriani
- IRCCS Casa Sollievo Della Sofferenza, Medical Genetics Unit, 71013 San Giovanni Rotondo, Italy; PhD Program, Molecular Genetics applied to Medical Sciences, University of Brescia, 25121 Brescia, Italy
| | - Rita Fischetto
- U.O. Malattie Metaboliche PO Giovanni XXIII, AOU Policlinico Consorziale, 70120 Bari, Italy
| | | | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany; Institute for Human Genetics, University of Cologne, 50931 Cologne, Germany
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Giuseppe Merla
- IRCCS Casa Sollievo Della Sofferenza, Medical Genetics Unit, 71013 San Giovanni Rotondo, Italy
| | | | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina 27710, USA
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, 37077 Göttingen, Germany
| | - Christian Kubisch
- Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany; Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
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13
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Bhattacharya S, Lou X, Hwang P, Rajashankar KR, Wang X, Gustafsson JÅ, Fletterick RJ, Jacobson RH, Webb P. Structural and functional insight into TAF1-TAF7, a subcomplex of transcription factor II D. Proc Natl Acad Sci U S A 2014; 111:9103-8. [PMID: 24927529 PMCID: PMC4078864 DOI: 10.1073/pnas.1408293111] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transcription factor II D (TFIID) is a multiprotein complex that nucleates formation of the basal transcription machinery. TATA binding protein-associated factors 1 and 7 (TAF1 and TAF7), two subunits of TFIID, are integral to the regulation of eukaryotic transcription initiation and play key roles in preinitiation complex (PIC) assembly. Current models suggest that TAF7 acts as a dissociable inhibitor of TAF1 histone acetyltransferase activity and that this event ensures appropriate assembly of the RNA polymerase II-mediated PIC before transcriptional initiation. Here, we report the 3D structure of a complex of yeast TAF1 with TAF7 at 2.9 Å resolution. The structure displays novel architecture and is characterized by a large predominantly hydrophobic heterodimer interface and extensive cofolding of TAF subunits. There are no obvious similarities between TAF1 and known histone acetyltransferases. Instead, the surface of the TAF1-TAF7 complex contains two prominent conserved surface pockets, one of which binds selectively to an inhibitory trimethylated histone H3 mark on Lys27 in a manner that is also regulated by phosphorylation at the neighboring H3 serine. Our findings could point toward novel roles for the TAF1-TAF7 complex in regulation of PIC assembly via reading epigenetic histone marks.
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Affiliation(s)
- Suparna Bhattacharya
- Genomic Medicine Program, Houston Methodist Research Institute, Houston, TX 77030
| | - Xiaohua Lou
- Genomic Medicine Program, Houston Methodist Research Institute, Houston, TX 77030;Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX 77204
| | - Peter Hwang
- University of California Medical Center, San Francisco, CA 94158
| | - Kanagalaghatta R Rajashankar
- The Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL 60439; and
| | - Xiaoping Wang
- Department of Molecular Biology and Biochemistry, MD Anderson Cancer Center, Houston, TX 77030
| | - Jan-Åke Gustafsson
- Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX 77204;
| | | | - Raymond H Jacobson
- Department of Molecular Biology and Biochemistry, MD Anderson Cancer Center, Houston, TX 77030
| | - Paul Webb
- Genomic Medicine Program, Houston Methodist Research Institute, Houston, TX 77030;
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14
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Marko M, Leichter M, Patrinou-Georgoula M, Guialis A. Selective interactions of hnRNP M isoforms with the TET proteins TAF15 and TLS/FUS. Mol Biol Rep 2014; 41:2687-95. [PMID: 24474660 DOI: 10.1007/s11033-014-3128-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 01/11/2014] [Indexed: 11/26/2022]
Abstract
The molecular composition of macromolecular assemblies engaged in transcription and splicing influences biogenesis of mRNA transcripts. Preference for one over the other interactive protein partner within those complexes is expected to change the gene expression pattern and to affect subsequent cellular events. We report here the novel and selective associations between RNA-binding proteins, namely the hnRNP M1-4 isoforms-involved in early spliceosome assembly and alternative splicing-and the transcription factors TAF15 and TLS/FUS. In immunoprecipitation studies on HeLa nuclear extracts, TAF15 co-immunoprecipitates preferably with the higher molecular weight hnRNP M3/4 isoforms, opposite to TLS/FUS that associates with the lower molecular weight hnRNP M1/2 species. We demonstrate that these associations can be mediated through direct protein-protein interactions via the amino-termini of the TET proteins, independently of RNA. Finally, we show partial co-localization of TAF15 and TLS/FUS with hnRNP M proteins in HeLa nuclei, supporting the biochemically obtained data. The participation of hnRNP M in an expanding network of protein-protein interactions suggests its important functioning in the coordination of transcriptional and post-transcriptional events.
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Affiliation(s)
- Marija Marko
- Medical Faculty, Institute for Biochemistry I, University of Cologne, Joseph-Stelzmann-Str. 52, 50931, Cologne, Germany,
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15
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Poorey K, Viswanathan R, Carver MN, Karpova TS, Cirimotich SM, McNally JG, Bekiranov S, Auble DT. Measuring chromatin interaction dynamics on the second time scale at single-copy genes. Science 2013; 342:369-72. [PMID: 24091704 PMCID: PMC3997053 DOI: 10.1126/science.1242369] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The chromatin immunoprecipitation (ChIP) assay is widely used to capture interactions between chromatin and regulatory proteins, but it is unknown how stable most native interactions are. Although live-cell imaging suggests short-lived interactions at tandem gene arrays, current methods cannot measure rapid binding dynamics at single-copy genes. We show, by using a modified ChIP assay with subsecond temporal resolution, that the time dependence of formaldehyde cross-linking can be used to extract in vivo on and off rates for site-specific chromatin interactions varying over a ~100-fold dynamic range. By using the method, we show that a regulatory process can shift weakly bound TATA-binding protein to stable promoter interactions, thereby facilitating transcription complex formation. This assay provides an approach for systematic, quantitative analyses of chromatin binding dynamics in vivo.
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Affiliation(s)
- Kunal Poorey
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Ramya Viswanathan
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Melissa N. Carver
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Tatiana S. Karpova
- Center for Cancer Research Core Fluorescence Imaging Facility, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Shana M. Cirimotich
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - James G. McNally
- Center for Cancer Research Core Fluorescence Imaging Facility, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - David T. Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
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16
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Kazantseva J, Kivil A, Tints K, Kazantseva A, Neuman T, Palm K. Alternative splicing targeting the hTAF4-TAFH domain of TAF4 represses proliferation and accelerates chondrogenic differentiation of human mesenchymal stem cells. PLoS One 2013; 8:e74799. [PMID: 24098348 PMCID: PMC3788782 DOI: 10.1371/journal.pone.0074799] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 08/06/2013] [Indexed: 01/07/2023] Open
Abstract
Transcription factor IID (TFIID) activity can be regulated by cellular signals to specifically alter transcription of particular subsets of genes. Alternative splicing of TFIID subunits is often the result of external stimulation of upstream signaling pathways. We studied tissue distribution and cellular expression of different splice variants of TFIID subunit TAF4 mRNA and biochemical properties of its isoforms in human mesenchymal stem cells (hMSCs) to reveal the role of different isoforms of TAF4 in the regulation of proliferation and differentiation. Expression of TAF4 transcripts with exons VI or VII deleted, which results in a structurally modified hTAF4-TAFH domain, increases during early differentiation of hMSCs into osteoblasts, adipocytes and chondrocytes. Functional analysis data reveals that TAF4 isoforms with the deleted hTAF4-TAFH domain repress proliferation of hMSCs and preferentially promote chondrogenic differentiation at the expense of other developmental pathways. This study also provides initial data showing possible cross-talks between TAF4 and TP53 activity and switching between canonical and non-canonical WNT signaling in the processes of proliferation and differentiation of hMSCs. We propose that TAF4 isoforms generated by the alternative splicing participate in the conversion of the cellular transcriptional programs from the maintenance of stem cell state to differentiation, particularly differentiation along the chondrogenic pathway.
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Affiliation(s)
| | - Anri Kivil
- Protobios LLC, Tallinn, Estonia
- The Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | | | - Anna Kazantseva
- Protobios LLC, Tallinn, Estonia
- The Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
| | | | - Kaia Palm
- Protobios LLC, Tallinn, Estonia
- The Department of Gene Technology, Tallinn University of Technology, Tallinn, Estonia
- * E-mail:
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17
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Steiner S, Magno A, Huang D, Caflisch A. Does bromodomain flexibility influence histone recognition? FEBS Lett 2013; 587:2158-63. [PMID: 23711371 DOI: 10.1016/j.febslet.2013.05.032] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 05/10/2013] [Accepted: 05/13/2013] [Indexed: 12/27/2022]
Abstract
Bromodomains are protein modules that selectively recognize histones by binding to acetylated lysines. Here, we have carried out multiple molecular dynamics simulations of 20 human bromodomains to investigate the flexibility of their binding site. Some bromodomains show alternative side chain orientations of three evolutionarily conserved residues: the Asn involved in acetyl-lysine binding and two conserved aromatic residues. Furthermore, for the BAZ2B and CREBBP bromodomains we observe occlusion of the binding site which is coupled to the displacement of the two aromatic residues. In contrast to available structures, the simulations reveal large variability of the binding site accessibility. The simulations suggest that the flexibility of the bromodomain binding site and presence of self-occluded metastable states influence the recognition of acetyl-lysine on histone tails.
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Affiliation(s)
- Sandra Steiner
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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18
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Abstract
Background Life and death decisions of metazoan cells hinge on the balance between the expression of pro- versus anti-apoptotic gene products. The general RNA polymerase II transcription factor, TFIID, plays a central role in the regulation of gene expression through its core promoter recognition and co-activator functions. The core TFIID subunit TAF6 acts in vitro as an essential co-activator of transcription for the p53 tumor suppressor protein. We previously identified a splice variant of TAF6, termed TAF6δ that can be induced during apoptosis. Methodology/Principal Findings To elucidate the impact of TAF6δ on cell death and gene expression, we have employed modified antisense oligonucleotides to enforce expression of endogenous TAF6δ. The induction of endogenous TAF6δ triggered apoptosis in tumor cell lines, including cells devoid of p53. Microarray experiments revealed that TAF6δ activates gene expression independently of cellular p53 status. Conclusions Our data define TAF6δ as a pivotal node in a signaling pathway that controls gene expression programs and apoptosis in the absence of p53.
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Affiliation(s)
- Emmanuelle Wilhelm
- RNA Group, Département de microbiologie et d'infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - François-Xavier Pellay
- Institut des Hautes Études Scientifiques and Institut de Recherche Interdisciplinaire – CNRS USR3078 - Université de Lille, Bures sur Yvette, France
| | - Arndt Benecke
- Institut des Hautes Études Scientifiques and Institut de Recherche Interdisciplinaire – CNRS USR3078 - Université de Lille, Bures sur Yvette, France
| | - Brendan Bell
- RNA Group, Département de microbiologie et d'infectiologie, Faculté de médecine et sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
- * E-mail:
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19
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Maitra S, Chou CF, Luber CA, Lee KY, Mann M, Chen CY. The AU-rich element mRNA decay-promoting activity of BRF1 is regulated by mitogen-activated protein kinase-activated protein kinase 2. RNA 2008; 14:950-959. [PMID: 18326031 PMCID: PMC2327367 DOI: 10.1261/rna.983708] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2008] [Accepted: 01/24/2008] [Indexed: 05/26/2023]
Abstract
Regulated mRNA decay is a highly important process for the tight control of gene expression. Inherently unstable mRNAs contain AU-rich elements (AREs) in the 3' untranslated regions that direct rapid mRNA decay by interaction with decay-promoting ARE-binding proteins (ARE-BPs). The decay of ARE-containing mRNAs is regulated by signaling pathways that are believed to directly target ARE-BPs. Here, we show that BRF1 involved in ARE-mediated mRNA decay (AMD) is phosphorylated by MAPK-activated protein kinase 2 (MK2). In vitro kinase assays using different BRF1 fragments suggest that MK2 phosphorylates BRF1 at four distinct sites, S54, S92, S203, and an unidentified site at the C terminus. Coexpression of an active form of MK2 inhibits ARE mRNA decay activity of BRF1. MK2-mediated inhibition of BRF1 requires phosphorylation at S54, S92, and S203. Phosphorylation of BRF1 by MK2 does not appear to alter its ability to interact with AREs or to associate with mRNA decay enzymes. Thus, MK2 inhibits BRF1-dependent AMD through direct phosphorylation. Although the mechanism underlying this inhibition is still unclear, it appears to target BRF1-dependent AMD at a level downstream from RNA binding and the recruitment of mRNA decay enzymes.
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Affiliation(s)
- Sushmit Maitra
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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20
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Jia L, Tian Y, Tan H. SanT, a bidomain protein, is essential for nikkomycin biosynthesis of Streptomyces ansochromogenes. Biochem Biophys Res Commun 2007; 362:1031-6. [PMID: 17825260 DOI: 10.1016/j.bbrc.2007.08.114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Accepted: 08/17/2007] [Indexed: 10/22/2022]
Abstract
Nikkomycins act as a competitive inhibitor of chitin synthetase and display potent activities against phytopathogenic and human pathogenic fungi. sanT is located in the gene cluster of nikkomycin biosynthesis in Streptomyces ansochromogenes. Sequence analysis revealed that the deduced product of sanT has an unusual domain structure, which consists of an N-terminal acyl carrier protein (ACP) domain and a C-terminal aminotransferase (AMT) domain. Gene disruption and complementation indicated that sanT is essential for nikkomycin biosynthesis. Each domain of SanT was overexpressed in Escherichia coli and then purified. ACP domain is posttranslationally modified with phosphopantetheine (Ppant) prosthetic group at Ser-33. AMT domain catalyzes the transamination of 4-pyridyl-2-oxo-4-hydroxyisovalerate (POHIV), a precursor of peptidyl moiety of nikkomycins, to pyridylhomothreonine (PHT) in vitro. The two domains function independently but both are essential for nikkomycin biosynthesis. The biochemical and genetic evidences suggested that SanT is possibly a bifunctional protein, participating in the biosynthesis of peptidyl moiety and the assembly of nikkomycins.
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Affiliation(s)
- Lianghui Jia
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Graduate School of Chinese Academy of Sciences, Beijing 100039, China
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21
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Mal TK, Takahata S, Ki S, Zheng L, Kokubo T, Ikura M. Functional silencing of TATA-binding protein (TBP) by a covalent linkage of the N-terminal domain of TBP-associated factor 1. J Biol Chem 2007; 282:22228-38. [PMID: 17553784 DOI: 10.1074/jbc.m702988200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
General transcription factor TFIID is comprised of TATA-binding protein (TBP) and TBP-associated factors (TAFs), together playing critical roles in regulation of transcription initiation. The TAF N-terminal domain (TAND) of yeast TAF1 containing two subdomains, TAND1 (residues 10-37) and TAND2 (residues 46-71), is sufficient to interact with TBP and suppress the TATA binding activity of TBP. However, the detailed structural analysis of the complex between yeast TBP and TAND12 (residues 6-71) was hindered by its poor solubility and stability in solution. Here we report a molecular engineering approach where the N terminus of TBP is fused to the C terminus of TAND12 via linkers of various lengths containing (GGGS)(n) sequence, (n = 1, 2, 3). The length of the linker within the TAND12-TBP fusion has a significant effect on solubility and stability (SAS). The construct with (GGGS)(3) linker produces the best quality single-quantum-coherence (HSQC) NMR spectrum with markedly improved SAS. In parallel to these observations, the TAND12-TBP fusion exhibits marked reduction of TBP function in binding to TAF1 as well as temperature sensitivity in in vivo yeast cell growth. Remarkably, the temperature sensitivity was proportional to the length of the linker in the fusions: the construct with (GGGS)(3) linker did not grow at 20 degrees C, while those with (GGGS)(1) and (GGGS)(2) linkers did. These results together indicate that the native interaction between TBP and TAND12 is well maintained in the TAND12-(GGGS)(3)-TBP fusion and that this fusion approach provides an excellent model system to investigate the structural detail of the TBP-TAF1 interaction.
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Affiliation(s)
- Tapas K Mal
- Division of Signaling Biology, Ontario Cancer Institute, Department of Medical Biophysics, University of Toronto, Toronto Medical Discovery Towers, Toronto, Ontario, Canada
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22
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Rong H, Li Y, Shi X, Zhang X, Gao Y, Dai H, Teng M, Niu L, Liu Q, Hao Q. Structure of human upstream binding factor HMG box 5 and site for binding of the cell-cycle regulatory factor TAF1. Acta Crystallogr D Biol Crystallogr 2007; 63:730-7. [PMID: 17505112 DOI: 10.1107/s0907444907017027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2006] [Accepted: 04/05/2007] [Indexed: 11/10/2022]
Abstract
The fifth HMG-box domain in human upstream binding factor (hUBF) contributes to the synthesis of rRNA by RNA polymerase I (Pol I). The 2.0 A resolution crystal structure of this protein has been solved using the single-wavelength anomalous dispersion method (SAD). The crystal structure and the reported NMR structure have r.m.s. deviations of 2.18-3.03 A for the C(alpha) atoms. However, there are significant differences between the two structures, with displacements of up to 9.0 A. Compared with other HMG-box structures, the r.m.s. deviations for C(alpha) atoms between hUBF HMG box 5 and HMG domains from Drosophila melanogaster protein D and Rattus norvegicus HMG1 are 1.5 and 1.6 A, respectively. This indicates that the differences between the crystal and NMR structures of hUBF HMG box 5 are larger than those with its homologous structures. The differences between the two structures potentially reflect two states with different structures. The specific interactions between the hUBF HMG box 5 and the first bromodomain of TBP-associated factor 1 (TAF1) were studied by ultrasensitive differential scanning calorimetry and chemical shift perturbation. Based on these experimental data, possible sites in hUBF HMG box 5 that may interact with the first bromodomain of TAF1 were proposed.
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Affiliation(s)
- Hui Rong
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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23
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Wang X, Truckses DM, Takada S, Matsumura T, Tanese N, Jacobson RH. Conserved region I of human coactivator TAF4 binds to a short hydrophobic motif present in transcriptional regulators. Proc Natl Acad Sci U S A 2007; 104:7839-44. [PMID: 17483474 PMCID: PMC1876534 DOI: 10.1073/pnas.0608570104] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2006] [Indexed: 11/18/2022] Open
Abstract
TBP-associated factor 4 (TAF4), an essential subunit of the TFIID complex acts as a coactivator for multiple transcriptional regulators, including Sp1 and CREB. However, little is known regarding the structural properties of the TAF4 subunit that lead to the coactivator function. Here, we report the crystal structure at 2.0-A resolution of the human TAF4-TAFH domain, a conserved domain among all metazoan TAF4, TAF4b, and ETO family members. The hTAF4-TAFH structure adopts a completely helical fold with a large hydrophobic groove that forms a binding surface for TAF4 interacting factors. Using peptide phage display, we have characterized the binding preference of the hTAF4-TAFH domain for a hydrophobic motif, DPsiPsizetazetaPsiPhi, that is present in a number of nuclear factors, including several important transcriptional regulators with roles in activating, repressing, and modulating posttranslational modifications. A comparison of the hTAF4-TAFH structure with the homologous ETO-TAFH domain reveals several critical residues important for hTAF4-TAFH target specificity and suggests that TAF4 has evolved in response to the increased transcriptional complexity of metazoans.
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Affiliation(s)
- Xiaoping Wang
- Department of Biochemistry and Molecular Biology, Graduate School in Biomedical Sciences Program in Genes and Development, University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030; and
| | - Dagmar M. Truckses
- Department of Biochemistry and Molecular Biology, Graduate School in Biomedical Sciences Program in Genes and Development, University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030; and
| | - Shinako Takada
- Department of Biochemistry and Molecular Biology, Graduate School in Biomedical Sciences Program in Genes and Development, University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030; and
| | - Tatsushi Matsumura
- Department of Microbiology, New York University School of Medicine, 550 First Avenue, New York, NY 10016
| | - Naoko Tanese
- Department of Microbiology, New York University School of Medicine, 550 First Avenue, New York, NY 10016
| | - Raymond H. Jacobson
- Department of Biochemistry and Molecular Biology, Graduate School in Biomedical Sciences Program in Genes and Development, University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030; and
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Lawit SJ, O'Grady K, Gurley WB, Czarnecka-Verner E. Yeast two-hybrid map of Arabidopsis TFIID. Plant Mol Biol 2007; 64:73-87. [PMID: 17340043 DOI: 10.1007/s11103-007-9135-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Accepted: 01/05/2007] [Indexed: 05/11/2023]
Abstract
General transcription factor IID (TFIID) is a multisubunit protein complex involved in promoter recognition and is fundamental to the nucleation of the RNA polymerase II transcriptional preinitiation complex. TFIID is comprised of the TATA binding protein (TBP) and 12-15 TBP-associated factors (TAFs). While general transcription factors have been extensively studied in metazoans and yeast, little is known about the details of their structure and function in the plant kingdom. This work represents the first attempt to compare the structure of a plant TFIID complex with that determined for other organisms. While no TAF3 homolog has been observed in plants, at least one homolog has been identified for each of the remaining 14 TFIID subunits, including both TAF14 and TAF15 which have previously been shown to be unique to either yeast or humans. The presence of both TAFs 14 and 15 in plants suggests ancient roles for these proteins that were lost in metazoans and fungi, respectively. Yeast two-hybrid interaction assays resulted in a total of 65 binary interactions between putative subunits of Arabidopsis TFIID, including 26 contacts unique to plants. The interaction matrix of Arabidopsis TAFs is largely consistent with the three-lobed topological map for yeast TFIID, which suggests that the structure and composition of TFIID have been highly conserved among eukaryotes.
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Affiliation(s)
- Shai J Lawit
- Pioneer Hi-Bred International, Inc., a DuPont Company, 7300 N.W. 62nd Ave, PO Box 1004, Johnston, IA 50131-1004, USA
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25
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Demény MA, Soutoglou E, Nagy Z, Scheer E, Jànoshàzi À, Richardot M, Argentini M, Kessler P, Tora L. Identification of a small TAF complex and its role in the assembly of TAF-containing complexes. PLoS One 2007; 2:e316. [PMID: 17375202 PMCID: PMC1820849 DOI: 10.1371/journal.pone.0000316] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Accepted: 02/27/2007] [Indexed: 12/03/2022] Open
Abstract
TFIID plays a role in nucleating RNA polymerase II preinitiation complex assembly on protein-coding genes. TFIID is a multisubunit complex comprised of the TATA box binding protein (TBP) and 14 TBP-associated factors (TAFs). Another class of multiprotein transcriptional regulatory complexes having histone acetyl transferase (HAT) activity, and containing TAFs, includes TFTC, STAGA and the PCAF/GCN5 complex. Looking for as yet undiscovered subunits by a proteomic approach, we had identified TAF8 and SPT7L in human TFTC preparations. Subsequently, however, we demonstrated that TAF8 was not a stable component of TFTC, but that it is present in a small TAF complex (SMAT), containing TAF8, TAF10 and SPT7L, that co-purified with TFTC. Thus, TAF8 is a subunit of both TFIID and SMAT. The latter has to be involved in a pathway of complex formation distinct from the other known TAF complexes, since these three histone fold (HF)-containing proteins (TAF8, TAF10 and SPT7L) can never be found together either in TFIID or in STAGA/TFTC HAT complexes. Here we show that TAF8 is absolutely necessary for the integration of TAF10 in a higher order TFIID core complex containing seven TAFs. TAF8 forms a heterodimer with TAF10 through its HF and proline rich domains, and also interacts with SPT7L through its C-terminal region, and the three proteins form a complex in vitro and in vivo. Thus, the TAF8-TAF10 and TAF10-SPT7L HF pairs, and also the SMAT complex, seem to be important regulators of the composition of different TFIID and/or STAGA/TFTC complexes in the nucleus and consequently may play a role in gene regulation.
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Affiliation(s)
- Màté A. Demény
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS) UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM)U 596, Université Louis Pasteur de Strasbourg, Illkirch, Strasbourg, France
| | - Evi Soutoglou
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS) UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM)U 596, Université Louis Pasteur de Strasbourg, Illkirch, Strasbourg, France
| | - Zita Nagy
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS) UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM)U 596, Université Louis Pasteur de Strasbourg, Illkirch, Strasbourg, France
| | - Elisabeth Scheer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS) UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM)U 596, Université Louis Pasteur de Strasbourg, Illkirch, Strasbourg, France
| | - Àgnes Jànoshàzi
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS) UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM)U 596, Université Louis Pasteur de Strasbourg, Illkirch, Strasbourg, France
| | - Magalie Richardot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS) UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM)U 596, Université Louis Pasteur de Strasbourg, Illkirch, Strasbourg, France
| | - Manuela Argentini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS) UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM)U 596, Université Louis Pasteur de Strasbourg, Illkirch, Strasbourg, France
| | - Pascal Kessler
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS) UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM)U 596, Université Louis Pasteur de Strasbourg, Illkirch, Strasbourg, France
| | - Laszlo Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS) UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM)U 596, Université Louis Pasteur de Strasbourg, Illkirch, Strasbourg, France
- * To whom correspondence should be addressed. E-mail:
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Romier C, James N, Birck C, Cavarelli J, Vivarès C, Collart MA, Moras D. Crystal structure, biochemical and genetic characterization of yeast and E. cuniculi TAF(II)5 N-terminal domain: implications for TFIID assembly. J Mol Biol 2007; 368:1292-306. [PMID: 17397863 DOI: 10.1016/j.jmb.2007.02.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Revised: 02/09/2007] [Accepted: 02/13/2007] [Indexed: 11/16/2022]
Abstract
General transcription factor TFIID plays an essential role in transcription initiation by RNA polymerase II at numerous promoters. However, understanding of the assembly and a full structural characterization of this large 15 subunit complex is lacking. TFIID subunit TAF(II)5 has been shown to be present twice in this complex and to be critical for the function and assembly of TFIID. Especially, the TAF(II)5 N-terminal domain is required for its incorporation within TFIID and immuno-labelling experiments carried out by electron microscopy at low resolution have suggested that this domain might homodimerize, possibly explaining the three-lobed architecture of TFIID. However, the resolution at which the electron microscopy (EM) analyses were conducted is not sufficient to determine whether homodimerization occurs or whether a more intricate assembly implying other subunits is required. Here we report the X-ray structures of the fully evolutionary conserved C-terminal sub-domain of the TAF(II)5 N terminus, from yeast and the mammalian parasite Encephalitozoon cuniculi. This sub-domain displays a novel fold with specific surfaces having conserved physico-chemical properties that can form protein-protein interactions. Although a crystallographic dimer implying one of these surfaces is present in one of the crystal forms, several biochemical analyses show that this sub-domain is monomeric in solution, even at various salt conditions and in presence of different divalent cations. Consequently, the N-terminal sub-domain of the TAF(II)5 N terminus, which is homologous to a dimerization motif but has not been fully conserved during evolution, was studied by analytical ultracentrifugation and yeast genetics. Our results show that this sub-domain dimerizes at very high concentration but is neither required for yeast viability, nor for incorporation of two TAF(II)5 molecules within TFIID and for the assembly of this complex. Altogether, although our results do not argue in favour of a homodimerization of the TAF(II)5 N-terminal domain, our structural analyses suggest a role for this domain in assembly of TFIID and its related complexes SAGA, STAGA, TFTC and PCAF.
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Affiliation(s)
- Christophe Romier
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Département de Biologie et Génomique Structurales, 1 rue Laurent Fries, B.P. 10142, 67404 Illkirch Cedex, France
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27
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Bhattacharya S, Takada S, Jacobson RH. Structural analysis and dimerization potential of the human TAF5 subunit of TFIID. Proc Natl Acad Sci U S A 2007; 104:1189-94. [PMID: 17227857 PMCID: PMC1783120 DOI: 10.1073/pnas.0610297104] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2006] [Indexed: 11/18/2022] Open
Abstract
TFIID is an essential factor required for RNA polymerase II transcription but remains poorly understood because of its intrinsic complexity. Human TAF5, a 100-kDa subunit of general transcription factor TFIID, is an essential gene and plays a critical role in assembling the 1.2 MDa TFIID complex. We report here a structural analysis of the TAF5 protein. Our structure at 2.2-A resolution of the TAF5-NTD2 domain reveals an alpha-helical domain with distant structural similarity to RNA polymerase II CTD interacting factors. The TAF5-NTD2 domain contains several conserved clefts likely to be critical for TFIID complex assembly. Our biochemical analysis of the human TAF5 protein demonstrates the ability of the N-terminal half of the TAF5 gene to form a flexible, extended dimer, a key property required for the assembly of the TFIID complex.
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Affiliation(s)
- Suparna Bhattacharya
- Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center and the Program in Genes and Development at the University of Texas, Graduate School in Biochemical Sciences, 1515 Holcombe Boulevard, Unit 1000, Houston, TX 77030
| | - Shinako Takada
- Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center and the Program in Genes and Development at the University of Texas, Graduate School in Biochemical Sciences, 1515 Holcombe Boulevard, Unit 1000, Houston, TX 77030
| | - Raymond H. Jacobson
- Department of Biochemistry and Molecular Biology, University of Texas M. D. Anderson Cancer Center and the Program in Genes and Development at the University of Texas, Graduate School in Biochemical Sciences, 1515 Holcombe Boulevard, Unit 1000, Houston, TX 77030
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28
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Zondlo SC, Lee AE, Zondlo NJ. Determinants of specificity of MDM2 for the activation domains of p53 and p65: proline27 disrupts the MDM2-binding motif of p53. Biochemistry 2006; 45:11945-57. [PMID: 17002294 DOI: 10.1021/bi060309g] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Transcriptional activation and repression via the transcription factors p53 and p65 are mediated by hydrophobic short linear motifs (FXX phi phi) in their activation domains (ADs). To understand the molecular basis for specificity in binding to disparate biological targets, a series of chimeric peptides was synthesized, with sequences derived from the ADs of p53, which binds both the general transcriptional machinery and the repressor protein MDM2, and p65, which is reported to bind the general transcriptional machinery but not MDM2. The FXX phi phi motifs of p53 and p65 differ by only two residues, whereas the flanking sequences have no sequence identity. The affinities of the chimeric peptides to MDM2(25-117) and hTAF(II)31(1-140) were determined. Specificity for binding MDM2 via FXX phi phi motifs derives almost entirely from Trp23 of p53, with a 3.0 kcal mol(-1) loss of binding energy when Trp23 is changed to p65-derived Leu. The identity of the N-terminal flanking sequence did not significantly affect binding to MDM2. In contrast, replacement of the C-terminal sequence of p53 with that of p65 increased the affinity of the chimera for MDM2 by 1.1 kcal mol(-1), contrary to expectations. Replacement of the highly conserved residue Pro27 of p53 with Ser from p65 resulted in a 2.3 kcal mol(-1) improvement in binding to MDM2, generating a ligand (p53-P27S) (Kd = 4.7 nM) that exhibits the highest MDM2 affinity observed for a genetically encodable ligand. The basis for the increased affinity of p53-P27S over p53 was examined by circular dichroism and nuclear magnetic resonance. Pro27 disrupts the recognition alpha-helix of p53, with p53-P27S significantly more alpha-helical than p53.
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Affiliation(s)
- Susan Carr Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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29
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Plevin MJ, Zhang J, Guo C, Roeder RG, Ikura M. The acute myeloid leukemia fusion protein AML1-ETO targets E proteins via a paired amphipathic helix-like TBP-associated factor homology domain. Proc Natl Acad Sci U S A 2006; 103:10242-10247. [PMID: 16803958 PMCID: PMC1502442 DOI: 10.1073/pnas.0603463103] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Up to 15% of acute myeloid leukemias (AMLs) are characterized by the abnormal expression of the eight-twenty-one (ETO) transcriptional corepressor within an AML1-ETO fusion protein. The t(8;21) chromosomal translocation serves not only to disrupt WT AML1 function but also to introduce ETO activity during hematopoiesis. AML1-ETO was recently shown to inhibit E protein transactivation by physically displacing WT coactivator proteins in an interaction mediated by ETO. Here, we present the 3D solution structure of the human ETO TAFH (eTAFH) domain implicated in AML1-ETO:E protein interactions and report an unexpected fold similarity to paired amphipathic helix domains from the transcriptional corepressor Sin3. We identify and characterize a conserved surface on eTAFH that is essential for ETO:E protein recognition and show that the mutation of key conserved residues at this site alleviates ETO-based silencing of E protein transactivation. Our results address uncharacterized aspects of the corepression mechanism of ETO and suggest that eTAFH may serve to recruit ETO (or AML1-ETO) to DNA-bound transcription factors. Together, these findings imply that a cofactor exchange mechanism, analogous to that described for E protein inhibition, may represent a common mode of action for ETO.
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Affiliation(s)
- Michael J Plevin
- *Division of Signaling Biology, Ontario Cancer Institute, University Health Network, and Department of Medical Biophysics, University of Toronto, Toronto Medical Discovery Tower, 101 College Street, Toronto, ON, Canada M5G 1L7
| | - Jinsong Zhang
- Department of Cell Biology, Vontz Center for Molecular Studies, University of Cincinnati College of Medicine, 3125 Eden Avenue, Cincinnati, OH 45267-0521; and
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021
| | - Chun Guo
- Department of Cell Biology, Vontz Center for Molecular Studies, University of Cincinnati College of Medicine, 3125 Eden Avenue, Cincinnati, OH 45267-0521; and
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021
| | - Mitsuhiko Ikura
- *Division of Signaling Biology, Ontario Cancer Institute, University Health Network, and Department of Medical Biophysics, University of Toronto, Toronto Medical Discovery Tower, 101 College Street, Toronto, ON, Canada M5G 1L7;
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30
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Sprouse RO, Brenowitz M, Auble DT. Snf2/Swi2-related ATPase Mot1 drives displacement of TATA-binding protein by gripping DNA. EMBO J 2006; 25:1492-504. [PMID: 16541100 PMCID: PMC1440317 DOI: 10.1038/sj.emboj.7601050] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2005] [Accepted: 02/20/2006] [Indexed: 11/09/2022] Open
Abstract
Mot1 is a conserved Snf2/Swi2-related transcriptional regulator that uses ATP hydrolysis to displace TATA-binding protein (TBP) from DNA. Several models of the enzymatic mechanism have been proposed, including Mot1-catalyzed distortion of TBP structure, competition between Mot1 and DNA for the TBP DNA-binding surface, and ATP-driven translocation of Mot1 along DNA. Here, DNase I footprinting studies provide strong support for a 'DNA-based' mechanism of Mot1, which we propose involves ATP-driven DNA translocation. Mot1 forms an asymmetric complex with the TBP core domain (TBPc)-DNA complex, contacting DNA both upstream and within the major groove of the TATA Box. Contact with upstream DNA is required for Mot1-mediated displacement of TBPc from DNA. Using the SsoRad54-DNA complex as a model, DNA-binding residues in Mot1 were identified that are critical for Mot1-TBPc-DNA complex formation and catalytic activity, thus placing Mot1 mechanistically within the helicase superfamily. We also report a novel ATP-independent TBPc displacement activity for Mot1 and describe conformational heterogeneity in the Mot1 ATPase, which is likely a general feature of other enzymes in this class.
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Affiliation(s)
- Rebekka O Sprouse
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, USA
| | - Michael Brenowitz
- Department of Biochemistry, The Albert Einstein College of Medicine, Bronx, NY, USA
| | - David T Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, 1300 Jefferson Park Avenue, Room 6213, Charlottesville, VA 22908-0733, USA. Tel.: +1 434 243 2629; Fax: +1 434 924 5069; E-mail:
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31
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Abstract
Transcription factor IID (TFIID) plays a central role in regulating the expression of most eukaryotic genes. Of the 14 TBP-associated factor (TAF) subunits that compose TFIID, TAF1 is one of the largest and most functionally diverse. Yeast TAF1 can be divided into four regions including a putative histone acetyltransferase domain and TBP, TAF, and promoter binding domains. Establishing the importance of each region in gene expression through deletion analysis has been hampered by the cellular requirement of TAF1 for viability. To circumvent this limitation we introduced galactose-inducible deletion derivatives of previously defined functional regions of TAF1 into a temperature-sensitive taf1ts2 yeast strain. After galactose induction of the TAF1 mutants and temperature-induced elimination of the resident Taf1ts2 protein, we examined the properties and phenotypes of the mutants, including their impact on genome-wide transcription. Virtually all TAF1-dependent genes, which comprise approximately 90% of the yeast genome, displayed a strong dependence upon all regions of TAF1 that were tested. This finding might reflect the need for each region of TAF1 to stabilize TAF1 against degradation or may indicate that all TAF1-dependent genes require the many activities of TAF1. Paradoxically, deletion of the region of TAF1 that is important for promoter binding interfered with the expression of many genes that are normally TFIID-independent/SAGA (Spt-Ada-Gcn5-acetyltransferase)-dominated, suggesting that this region normally prevents TAF1 (TFIID) from interfering with the expression of SAGA-regulated genes.
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Affiliation(s)
- Jordan D Irvin
- Department of Biochemistry and Molecular Biology, Center for Gene Regulation, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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32
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Abstract
Multifunctional proteins are demonstrating that gene expression is not a series of compartmentalized events beginning with transcription and culminating in delivery of mature mRNA into the cytoplasm, but an integrated pathway of transcription, splicing, RNA metabolism and subcellular targeting of translation. One such multifunctional family is made up of the RNA-binding proteins TLS, EWS and TAF15. These three proteins each contribute a potent transcriptional activation domain to oncogenic fusion proteins, and the formation of these fusion genes are thought to be the primary causes of their associated cancers. Wild-type TLS, EWS and TAF15 can function as classical transcription factors in addition to their better-known functions in splicing and mRNA transport. The interaction between TLS and the stress-response protein YB-1 is an example of how these proteins can induce a multi-faceted change in gene expression, as they can interact to induce changes in both transcription and splicing of target genes. Investigating the multiple functions of TLS, EWS and TAF15 will enhance our understanding of gene expression as a whole, and also allow us to better understand how these proteins may be contributing to the oncogenic pathways the associated fusion proteins initiate.
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Affiliation(s)
- Warren J Law
- Manitoba Institute of Cell Biology and the University of Manitoba, 675 McDermot Avenue, Winnipeg, MB, Canada
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33
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Abstract
In response to gonadotropins, the elevated level of intracellular-cyclic AMP (cAMP) in ovarian granulosa cells triggers an ordered activation of multiple ovarian genes, which in turn promotes various ovarian functions including folliculogenesis and steroidogenesis. Identification and characterization of transcription factors that control ovarian gene expression are pivotal to the understanding of the molecular basis of the tissue-specific gene regulation programs. The recent discovery of the mouse TATA binding protein (TBP)-associated factor 105 (TAF(II)105) as a gonad-selective transcriptional co-activator strongly suggests that general transcription factors such as TFIID may play a key role in regulating tissue-specific gene expression. Here we show that the human TAF(II)105 protein is preferentially expressed in ovarian granulosa cells. We also identified a novel TAF(II)105 mRNA isoform that results from alternative exon inclusion and is predicted to encode a dominant negative mutant of TAF(II)105. Following stimulation by the adenylyl cyclase activator forskolin, TAF(II)105 in granulosa cells undergoes rapid and transient phosphorylation that is dependent upon protein kinase A (PKA). Thus, our work suggests that pre-mRNA processing and post-translational modification represent two important regulatory steps for the gonad-specific functions of human TAF(II)105.
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Affiliation(s)
- Yimin Wu
- Department of Biochemistry and Molecular Genetics, School of Medicine, PO Box 800733, University of Virginia, Charlottesville, Virginia 22908-0733, USA
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Couture JF, Collazo E, Hauk G, Trievel RC. Structural basis for the methylation site specificity of SET7/9. Nat Struct Mol Biol 2006; 13:140-6. [PMID: 16415881 DOI: 10.1038/nsmb1045] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2005] [Accepted: 12/05/2005] [Indexed: 11/09/2022]
Abstract
Human SET7/9 is a protein lysine methyltransferase (PKMT) that methylates histone H3, the tumor suppressor p53 and the TBP-associated factor TAF10. To elucidate the determinants of its substrate specificity, we have solved the enzyme's structure bound to a TAF10 peptide and examined its ability to methylate histone H3, TAF10 and p53 substrates bearing either mutations or covalent modifications within their respective methylation sites. Collectively, our data reveal that SET7/9 recognizes a conserved K/R-S/T/A motif preceding the lysine substrate and has a propensity to bind aspartates and asparagines on the C-terminal side of the lysine target. We then used a sequence-based approach with this motif to identify novel substrates for this PKMT. Among the putative targets is TAF7, which is methylated at Lys5 by the enzyme in vitro. These results demonstrate the predictive value of the consensus motif in identifying novel substrates for SET7/9.
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Affiliation(s)
- Jean-François Couture
- Department of Biological Chemistry, University of Michigan, 1301 Catherine Road, Ann Arbor, Michigan 48109-0606, USA
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35
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Santama N, Ogg SC, Malekkou A, Zographos SE, Weis K, Lamond AI. Characterization of hCINAP, a novel coilin-interacting protein encoded by a transcript from the transcription factor TAFIID32 locus. J Biol Chem 2005; 280:36429-41. [PMID: 16079131 DOI: 10.1074/jbc.m501982200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Coilin is a marker protein for the Cajal body, a subnuclear domain acting as a site for assembly and maturation of nuclear RNA-protein complexes. Using a yeast two-hybrid screen to identify coilin-interacting proteins, we have identified hCINAP (human coilin interacting nuclear ATPase protein), a nuclear factor of 172 amino acids with a P-loop nucleotide binding motif and ATPase activity. The hCINAP protein sequence is highly conserved across its full-length from human to plants and yeast and is ubiquitously expressed in all human tissues and cell lines tested. The yeast orthologue of CINAP is a single copy, essential gene. Tagged hCINAP is present in complexes containing coilin in mammalian cells and recombinant, Escherichia coli expressed hCINAP binds directly to coilin in vitro. The 214 carboxyl-terminal residues of coilin appear essential for the interaction with hCINAP. Both immunofluorescence and fluorescent protein tagging show that hCINAP is specifically nuclear and distributed in a widespread, diffuse nucleoplasmic pattern, excluding nucleoli, with some concentration also in Cajal bodies. Overexpression of hCINAP in HeLa cells results in a decrease in the average number of Cajal bodies per nucleus, consistent with it affecting either the stability of Cajal bodies and/or their rate of assembly. The hCINAP mRNA is an alternatively spliced transcript from the TAF9 locus, which encodes the basal transcription factor subunit TAFIID32. However, hCINAP and TAFIID32 mRNAs are translated from different ATG codons and use distinct reading frames, resulting in them having no identity in their respective protein sequences.
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Affiliation(s)
- Niovi Santama
- Department of Biological Sciences, University of Cyprus and Cyprus Institute of Neurology and Genetics, P.O. Box 20537, 1678 Nicosia, Cyprus.
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36
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Banerjee R, Weidman MK, Navarro S, Comai L, Dasgupta A. Modifications of both selectivity factor and upstream binding factor contribute to poliovirus-mediated inhibition of RNA polymerase I transcription. J Gen Virol 2005; 86:2315-2322. [PMID: 16033979 DOI: 10.1099/vir.0.80817-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Soon after infection, poliovirus (PV) shuts off host-cell transcription, which is catalysed by all three cellular RNA polymerases. rRNA constitutes more than 50 % of all cellular RNA and is transcribed from rDNA by RNA polymerase I (pol I). Here, evidence has been provided suggesting that both pol I transcription factors, SL-1 (selectivity factor) and UBF (upstream binding factor), are modified and inactivated in PV-infected cells. The viral protease 3C(pro) appeared to cleave the TATA-binding protein-associated factor 110 (TAF(110)), a subunit of the SL-1 complex, into four fragments in vitro. In vitro protease-cleavage assays using various mutants of TAF(110) and purified 3C(pro) indicated that the Q(265)G(266) and Q(805)G(806) sites were cleaved by 3C(pro). Both SL-1 and UBF were depleted in PV-infected cells and their disappearance correlated with pol I transcription inhibition. rRNA synthesis from a template containing a human pol I promoter demonstrated that both SL-1 and UBF were necessary to restore pol I transcription fully in PV-infected cell extracts. These results suggested that both SL-1 and UBF are transcriptionally inactivated in PV-infected HeLa cells.
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Affiliation(s)
- Rajeev Banerjee
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, UCLA School of Medicine, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - Mary K Weidman
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, UCLA School of Medicine, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
| | - Sonia Navarro
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Lucio Comai
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Asim Dasgupta
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, UCLA School of Medicine, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA
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37
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Soutoglou E, Demény MA, Scheer E, Fienga G, Sassone-Corsi P, Tora L. The nuclear import of TAF10 is regulated by one of its three histone fold domain-containing interaction partners. Mol Cell Biol 2005; 25:4092-104. [PMID: 15870280 PMCID: PMC1087738 DOI: 10.1128/mcb.25.10.4092-4104.2005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
TFIID, comprising the TATA box binding protein (TBP) and 13 TBP-associated factors (TAFs), plays a role in nucleation in the assembly of the RNA polymerase II preinitiation complexes on protein-encoding genes. TAFs are shared among other transcription regulatory complexes (e.g., SAGA, TBP-free TAF-containing complex [TFTC], STAGA, and PCAF/GCN5). Human TAF10, a subunit of both TFIID and TFTC, has three histone fold-containing interaction partners: TAF3, TAF8, and SPT7Like (SPT7L). In human cells, exogenously expressed TAF10 remains rather cytoplasmic and leptomycin B does not affect this localization. By using fluorescent fusion proteins, we show that TAF10 does not have an intrinsic nuclear localization signal (NLS) and needs one of its three interaction partners to be transported into the nucleus. When the NLS sequences of either TAF8 or SPT7L are mutated, TAF10 remains cytoplasmic, but a heterologous NLS can drive TAF10 into the nucleus. Experiments using fluorescence recovery after photobleaching show that TAF10 does not associate with any cytoplasmic partner but that once transported into the nucleus it binds to nuclear structures. TAF10 binding to importin beta in vitro is dependent on the coexpression of either TAF8 or TAF3, but not SPT7L. The cytoplasmic-nuclear transport of TAF10 is naturally observed during the differentiation of adult male germ cells. Thus, here we describe a novel role of the three mammalian interacting partners in the nuclear localization of TAF10, and our data suggest that a complex network of regulated cytoplasmic associations may exist among these factors and that this network is important for the composition of different TFIID and TFTC-type complexes in the nucleus.
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Affiliation(s)
- Evi Soutoglou
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, UMR 7104, Department of Transcriptional and Post-Transcriptional Control of Gene Regulation, BP 10142, 67404 Illkirch Cedex, CU de Strasbourg, France
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38
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Abstract
A missense mutation within the histone acetyltransferase (HAT) domain of the TATA binding protein-associated factor TAF1 induces ts13 cells to undergo a late G(1) arrest and decreases cyclin D1 transcription. We have found that TAF1 mutants (Delta844-850 and Delta848-850, from which amino acids 844 through 850 and 848 through 850 have been deleted, respectively) deficient in HAT activity are unable to complement the ts13 defect in cell proliferation and cyclin D1 transcription. Chromatin immunoprecipitation assays revealed that histone H3 acetylation was reduced at the cyclin D1 promoter but not the c-fos promoter upon inactivation of TAF1 in ts13 cells. The hypoacetylation of H3 at the cyclin D1 promoter was reversed by treatment with trichostatin A (TSA), a histone deacetylase inhibitor, or by expression of TAF1 proteins that retain HAT activity. Transcription of a chimeric promoter containing the Sp1 sites of cyclin D1 and c-fos core remained TAF1 dependent in ts13 cells. Treatment with TSA restored full activity to the cyclin D1-c-fos chimera at 39.5 degrees C. In vivo genomic footprinting experiments indicate that protein-DNA interactions at the Sp1 sites of the cyclin D1 promoter were compromised at 39.5 degrees C in ts13 cells. These data have led us to hypothesize that TAF1-dependent histone acetylation facilitates transcription factor binding to the Sp1 sites, thereby activating cyclin D1 transcription and ultimately G(1)-to-S-phase progression.
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Affiliation(s)
- Traci L Hilton
- University of Washington, School of Medicine, Department of Pharmacology, 1959 NE Pacific Street, Health Sciences Center, Box 357280, Seattle, WA 98195-7280, USA
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39
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Boyer-Guittaut M, Birsoy K, Potel C, Elliott G, Jaffray E, Desterro JM, Hay RT, Oelgeschläger T. SUMO-1 Modification of Human Transcription Factor (TF) IID Complex Subunits. J Biol Chem 2005; 280:9937-45. [PMID: 15637059 DOI: 10.1074/jbc.m414149200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The TFIID complex is composed of the TATA-binding protein (TBP) and TBP-associated factors (TAFs) and is the only component of the general RNA polymerase II (RNAP II) transcription machinery with intrinsic sequence-specific DNA-binding activity. Binding of transcription factor (TF) IID to the core promoter region of protein-coding genes is a key event in RNAP II transcription activation and is the first and rate-limiting step of transcription initiation complex assembly. Intense research efforts in the past have established that TFIID promoter-binding activity as well as the function of TFIID-promoter complexes is tightly regulated through dynamic TFIID interactions with positive- and negative-acting transcription regulatory proteins. However, very little is known about the role of post-translational modifications in the regulation of TFIID. Here we show that the human TFIID subunits hsTAF5 and hsTAF12 are modified by the small ubiquitin-related modifier SUMO-1 in vitro and in human cells. We identify Lys-14 in hsTAF5 and Lys-19 in hsTAF12 as the primary SUMO-1 acceptor sites and show that SUMO conjugation has no detectable effect on nuclear import or intranuclear distribution of hsTAF5 and hsTAF12. Finally, we demonstrate that purified human TFIID complex can be SUMO-1-modified in vitro at both hsTAF5 and hsTAF12. We find that SUMO-1 conjugation at hsTAF5 interferes with binding of TFIID to promoter DNA, whereas modification of hsTAF12 has no detectable effect on TFIID promoter-binding activity. Our observations suggest that reversible SUMO modification at hsTAF5 contributes to the dynamic regulation of TFIID promoter-binding activity in human cells.
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40
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Abstract
A major function of TFIID is core promoter recognition. TFIID consists of TATA-binding protein (TBP) and 14 TBP-associated factors (TAFs). Most of them contain a histone fold domain (HFD) that lacks the DNA-contacting residues of histones. Whether and how TAF HFDs contribute to core promoter DNA binding are yet unresolved. Here we examined the DNA binding activity of TAF9, TAF6, TAF4b, and TAF12, which are related to histones H3, H4, H2A, and H2B, respectively. Each of these TAFs has intrinsic DNA binding activity adjacent to or within the HFD. The DNA binding domains were mapped to evolutionarily conserved and essential regions. Remarkably, HFD-mediated interaction enhanced the DNA binding activity of each of the TAF6-TAF9 and TAF4b-TAF12 pairs and of a histone-like octamer complex composed of the four TAFs. Furthermore, HFD-mediated interaction stimulated sequence-specific binding by TAF6 and TAF9. These results suggest that TAF HFDs merge with other conserved domains for efficient and specific core promoter binding.
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Affiliation(s)
- Hanshuang Shao
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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41
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Hiller M, Chen X, Pringle MJ, Suchorolski M, Sancak Y, Viswanathan S, Bolival B, Lin TY, Marino S, Fuller MT. Testis-specific TAF homologs collaborate to control a tissue-specific transcription program. Development 2004; 131:5297-308. [PMID: 15456720 DOI: 10.1242/dev.01314] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Alternate forms of the PolII transcription initiation machinery have been proposed to play a role in selective activation of cell-type-specific gene expression programs during cellular differentiation. The cannonball(can) gene of Drosophila encodes a homolog of a TBP-associated factor (dTAF5) protein expressed only in spermatocytes, where it is required for normal transcription of genes required for spermatid differentiation. We show that Drosophila primary spermatocytes also express four additional tissue-specific TAFs: nht (homolog of dTAF4), mia (homolog of dTAF6), sa (homolog of dTAF8) and rye (homolog of dTAF12). Mutations in nht, mia and sa have similar effects in primary spermatocytes on transcription of several target genes involved in spermatid differentiation, and cause the same phenotypes as mutations in can, blocking both meiotic cell cycle progression and spermatid differentiation. The nht, mia, sa and rye proteins contain histone fold domain dimerization motifs. The nht and rye proteins interact structurally when co-expressed in bacteria, similarly to their generally expressed homologs TAF4 and TAF12,which heterodimerize. Strikingly, the structural interaction is tissue specific: nht did not interact with dTAF12 and dTAF4 did not interact with rye in a bacterial co-expression assay. We propose that the products of the five Drosophila genes encoding testis TAF homologs collaborate in an alternative TAF-containing protein complex to regulate a testis-specific gene expression program in primary spermatocytes required for terminal differentiation of male germ cells.
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Affiliation(s)
- Mark Hiller
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329, USA
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42
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Kasahara K, Kawaichi M, Kokubo T. In vivo synthesis of Taf1p lacking the TAF N-terminal domain using alternative transcription or translation initiation sites. Genes Cells 2004; 9:709-21. [PMID: 15298679 DOI: 10.1111/j.1356-9597.2004.00762.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The TAF N-terminal domain (TAND) of TAF1 includes two subdomains, TAND1 and TAND2, which bind to the concave and convex surfaces of TBP, respectively. Previous studies showed that the substitution of yeast TAND1 or TAND2 with the equivalent domain from a Drosophila homologue leads to accumulation of truncated Taf1p in yeast. This study demonstrates that these truncated Taf1p derivatives lack TAND. However, full-length Taf1p and untruncated derivatives are produced in yeast when several Met-to-Ala mutations are introduced in the carboxy-terminus of TAND. In contrast, mutations that reduce expression of full-length TAF1 do not reduce the amount of truncated Taf1p derivatives that are produced. These data suggest that TAND-deficient TAF1 derivatives are produced by initiating translation at alternative initiation sites. In addition, the TAF1 mRNA structure suggests that the TAND-deficient TAF1 derivatives may also be formed in yeast by use of (cryptic) alternative transcription initiation sites. Importantly, TAND-deficient truncated Taf1p appears to be produced at a low level in wild-type yeast as well. Finally, this study also demonstrates that Drosophila TAND2 substitutes functionally for yeast TAND2, but Drosophila TAND1 does not substitute for yeast TAND1.
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Affiliation(s)
- Koji Kasahara
- Division of Molecular and Cellular Biology, Graduate School of Integrated Science, Yokohama City University, 230-0045, Japan
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43
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Wu PYJ, Ruhlmann C, Winston F, Schultz P. Molecular architecture of the S. cerevisiae SAGA complex. Mol Cell 2004; 15:199-208. [PMID: 15260971 DOI: 10.1016/j.molcel.2004.06.005] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2004] [Revised: 05/07/2004] [Accepted: 05/18/2004] [Indexed: 11/21/2022]
Abstract
The Saccharomyces cerevisiae SAGA complex is a multifunctional coactivator that regulates transcription by RNA polymerase II. The 3D structure of SAGA, revealed by electron microscopy, is formed by five modular domains and shows a high degree of structural conservation to human TFTC, reflecting their related subunit composition. The positions of several SAGA subunits were mapped by immunolabeling and by analysis of mutant complexes. The Taf (TBP-associated factor) subunits, shared with TFIID, occupy a central region in SAGA and form a similar structure in both complexes. The locations of two histone fold-containing core subunits, Spt7 and Ada1, are consistent with their role in providing a SAGA-specific interface with the Tafs. Three components that perform distinct regulatory functions, Spt3, Gcn5, and Tra1, are spatially separated, underscoring the modular nature of the complex. Our data provide insights into the molecular architecture of SAGA and imply a functional organization to the complex.
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Affiliation(s)
- Pei-Yun Jenny Wu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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44
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Lively TN, Nguyen TN, Galasinski SK, Goodrich JA. The basic leucine zipper domain of c-Jun functions in transcriptional activation through interaction with the N terminus of human TATA-binding protein-associated factor-1 (human TAF(II)250). J Biol Chem 2004; 279:26257-65. [PMID: 15087451 DOI: 10.1074/jbc.m400892200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We previously reported that c-Jun binds directly to the N-terminal 163 amino acids of Homo sapiens TATA-binding protein-associated factor-1 (hsTAF1), causing a derepression of transcription factor IID (TFIID)-driven transcription (Lively, T. N., Ferguson, H. A., Galasinski, S. K., Seto, A. G., and Goodrich, J. A. (2001) J. Biol. Chem. 276, 25582-25588). This region of hsTAF1 binds TATA-binding protein to repress TFIID DNA binding and transcription. Here we show that the basic leucine zipper domain of c-Jun, which allows for DNA binding and homodimerization, is necessary and sufficient for interaction with hsTAF1. Interestingly, the isolated basic leucine zipper domain of c-Jun was able to derepress TFIID-directed basal transcription in vitro. Moreover, when the N-terminal region of hsTAF1 was added to in vitro transcription reactions and overexpressed in cells, it blocked c-Jun activation. c-Fos, another basic leucine zipper protein, did not interact with hsTAF1, but c-Fos/c-Jun heterodimers did bind the N terminus of hsTAF1. Our studies show that, in addition to dimerization and DNA binding, the well characterized basic leucine zipper domain of c-Jun functions in transcriptional activation by binding to the N terminus of hsTAF1 to derepress transcription.
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Affiliation(s)
- Tricia N Lively
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, USA
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45
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Pereira LA, Klejman MP, Ruhlmann C, Kavelaars F, Oulad-Abdelghani M, Timmers HTM, Schultz P. Molecular architecture of the basal transcription factor B-TFIID. J Biol Chem 2004; 279:21802-7. [PMID: 14988402 DOI: 10.1074/jbc.m313519200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BTAF1 (formerly named TAF(II)170/TAF-172) is an essential, evolutionarily conserved member of the SNF2-like family of ATPase proteins and together with TATA-binding protein (TBP) forms the B-TFIID complex. BTAF1 has been proposed to play a key role in the dynamic regulation of TBP function in RNA polymerase II transcription. We have determined the structure of native B-TFIID purified from human cells by electron microscopy and by image analysis of single particles at a resolution of 28 A. B-TFIID is 15 x 9 nm in size and is organized into a large domain of about 170 kDa, which can be subdivided into two domains. Extending from this domain is a long thumb, which in turn is divided into subdomains of about 25, 15, and 35 kDa, the largest of which is located at the end of the thumb. Immunolabeling experiments localize the extreme carboxyl terminus of BTAF1 within the 170-kDa domain, whereas the amino terminus and TBP co-localize to the end of the protruding thumb. The central portion of BTAF1 localizes to the base of the thumb. Comparison of the native B-TFIID with its recombinant form shows that both share a similar domain organization. Collectively, these data provide the first structural model of the B-TFIID complex and map its key functional domains.
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Affiliation(s)
- Lloyd A Pereira
- Department of Physiological Chemistry, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
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Leurent C, Sanders SL, Demény MA, Garbett KA, Ruhlmann C, Weil PA, Tora L, Schultz P. Mapping key functional sites within yeast TFIID. EMBO J 2004; 23:719-27. [PMID: 14765106 PMCID: PMC381015 DOI: 10.1038/sj.emboj.7600111] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2003] [Accepted: 01/12/2004] [Indexed: 01/14/2023] Open
Abstract
The transcription factor TFIID, composed of the TATA box-binding protein (TBP) and 14 TBP-associated factors (TAFs), plays a key role in the regulation of gene expression by RNA polymerase II. The structure of yeast TFIID, as determined by electron microscopy and digital image analysis, is formed by three lobes, labelled A-C, connected by thin linking domains. Immunomapping revealed that TFIID contains two copies of the WD-40 repeat-containing TAF5 and that TAF5 contributes to the linkers since its C- and N-termini were found in different lobes. This property was confirmed by the finding that a recombinant complex containing TAF5 complexed with six histone fold containing TAFs was able to form a trilobed structure. Moreover, the N-terminal domain of TAF1 was mapped in lobe C, whereas the histone acetyltransferase domain resides in lobe A along with TAF7. TBP was found in the linker domain between lobes A and C in a way that the N-terminal 100 residues of TAF1 are spanned over it. The implications of these data with regard to TFIID function are discussed.
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Affiliation(s)
- Claire Leurent
- Department of transcription, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
| | - Steven L Sanders
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, TN, USA
| | - Màté A Demény
- Department of transcription, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
| | - Krassimira A Garbett
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, TN, USA
| | - Christine Ruhlmann
- Department of Structural Biology and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
- Ecole Supérieure de Biotechnologie de Strasbourg, Pôle API, Illkirch, France
| | - P Anthony Weil
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, TN, USA
| | - Làszlò Tora
- Department of transcription, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
| | - Patrick Schultz
- Department of Structural Biology and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
- Ecole Supérieure de Biotechnologie de Strasbourg, Pôle API, Illkirch, France
- Department of Structural Biology and Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1, rue Laurent Fries, BP10142, F-67404 Illkirch, France. Tel.: +33 3 90 24 4800; Fax: +33 3 88 65 3201; E-mail:
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47
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Abstract
The general transcription initiation factor TFIID and its interactors play critical roles in regulating the transcription from both naked and chromatin DNA. We have isolated a novel TFIID interactor that we denoted as CCG1/TAF(II)250-interacting factor B (CIB). We show here that CIB activates transcription. To further understand the function of this protein, we determined its crystal structure at 2.2-Angstroms resolution. The tertiary structure of CIB reveals an alpha/beta-hydrolase fold that resembles structures in the prokaryotic alpha/beta-hydrolase family proteins. It is not similar in structure or primary sequence to any eukaryotic transcription or chromatin factors that have been reported to date. CIB possesses a conserved catalytic triad that is found in other alpha/beta-hydrolases, and our in vitro studies confirmed that it bears hydrolase activity. However, CIB differs from other alpha/beta-hydrolases in that it lacks a binding site excursion, which facilitates the substrate selectivity of the other alpha/beta-hydrolases. Further functional characterization of CIB based on its tertiary structure and through biochemical studies may provide novel insights into the mechanisms that regulate eukaryotic transcription.
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Affiliation(s)
- Balasundaram Padmanabhan
- Horikoshi Gene Selector Project, Exploratory Research for Advanced Technology, Japan Science and Technology Corporation, 5-9-6 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
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48
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Abstract
Yeast Mot1p, an abundant conserved member of the Snf2p-ATPase family of proteins, both dissociates TBP from DNA in vitro using the energy of ATP and represses gene transcription in vivo, yet paradoxically, loss of Mot1p function also leads to decreased transcription of certain genes. We conducted experiments utilizing fluorescently labeled DNA, TBP, fluorescence anisotropy spectroscopy and native gel electrophoresis to study Mot1p action. We have made a number of observations, the most intriguing being that a stable Mot1p-TBP complex has the ability to bind TATA DNA with high affinity, albeit with dramatically altered specificity. We propose that this altered TBP-DNA recognition is integral to Mot1p's ability to regulate transcription, and further postulate that the Mot1p-TBP complex delivers TBP to TAF-independent mRNA encoding genes.
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Affiliation(s)
- Orlando H Gumbs
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, TN 37232-0615, USA
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Pointud JC, Mengus G, Brancorsini S, Monaco L, Parvinen M, Sassone-Corsi P, Davidson I. The intracellular localisation of TAF7L, a paralogue of transcription factor TFIID subunit TAF7, is developmentally regulated during male germ-cell differentiation. J Cell Sci 2003; 116:1847-58. [PMID: 12665565 DOI: 10.1242/jcs.00391] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcription regulation in male germ cells can involve specialised mechanisms and testis-specific paralogues of the general transcription machinery. Here we describe TAF7L, a germ-cell-specific paralogue of the TFIID subunit TAF7. TAF7L is expressed through most of the male germ-cell differentiation programme, but its intracellular localisation is dynamically regulated from cytoplasmic in spermatogonia and early spermatocytes to nuclear in late pachytene spermatocytes and haploid round spermatids. Import of TAF7L into the nucleus coincides with decreased TAF7 expression and a strong increase in nuclear TBP expression, which suggests that TAF7L replaces TAF7 as a TFIID subunit in late pachytene spermatocytes and in haploid cells. In agreement with this, biochemical experiments indicate that a subpopulation of TAF7L is tightly associated with TBP in both pachytene and haploid cells and TAF7L interacts with the TFIID subunit TAF1. We further show that TAF3, TAF4 and TAF10 are all strongly expressed in early spermatocytes, but that in contrast to TBP and TAF7L, they are downregulated in haploid cells. Hence, different subunits of the TFIID complex are regulated in distinct ways during male germ-cell differentiation. These results show for the first time how the composition of a general transcription factor such as TFIID and other TAF-containing complexes are modulated during a differentiation programme highlighting the unique nature of the transcription regulatory machinery in spermatogenesis.
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Affiliation(s)
- Jean-Christophe Pointud
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch Cédex, France
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50
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Darst RP, Dasgupta A, Zhu C, Hsu JY, Vroom A, Muldrow T, Auble DT. Mot1 regulates the DNA binding activity of free TATA-binding protein in an ATP-dependent manner. J Biol Chem 2003; 278:13216-26. [PMID: 12571241 DOI: 10.1074/jbc.m211445200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mot1 is an essential Snf2/Swi2-related Saccharomyces cerevisiae protein that binds the TATA-binding protein (TBP) and removes TBP from DNA using ATP hydrolysis. Mot1 functions in vivo both as a repressor and as an activator of transcription. Mot1 catalysis of TBP.DNA disruption is consistent with its function as a repressor, but the Mot1 mechanism of activation is unknown. To better understand the physiologic role of Mot1 and its enzymatic mechanism, MOT1 mutants were generated and tested for activity in vitro and in vivo. The results demonstrate a close correlation between the TBP.DNA disruption activity of Mot1 and its essential in vivo function. Previous results demonstrated a large overlap in the gene sets controlled by Mot1 and NC2. Mot1 and NC2 can co-occupy TBP.DNA in vitro, and NC2 binding does not impair Mot1-catalyzed disruption of the complex. Residues on the DNA-binding surface of TBP are important for Mot1 binding and the Mot1.TBP binary complex binds very poorly to DNA and does not dissociate in the presence of ATP. However, the binary complex binds DNA well in the presence of the transition state analog ADP-AlF(4). A model for Mot1 action is proposed in which ATP hydrolysis causes the Mot1 N terminus to displace the TATA box, leading to ejection of Mot1 and TBP from DNA.
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Affiliation(s)
- Russell P Darst
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA
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