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Haijes HA, Koster MJE, Rehmann H, Li D, Hakonarson H, Cappuccio G, Hancarova M, Lehalle D, Reardon W, Schaefer GB, Lehman A, van de Laar IMBH, Tesselaar CD, Turner C, Goldenberg A, Patrier S, Thevenon J, Pinelli M, Brunetti-Pierri N, Prchalová D, Havlovicová M, Vlckova M, Sedláček Z, Lopez E, Ragoussis V, Pagnamenta AT, Kini U, Vos HR, van Es RM, van Schaik RFMA, van Essen TAJ, Kibaek M, Taylor JC, Sullivan J, Shashi V, Petrovski S, Fagerberg C, Martin DM, van Gassen KLI, Pfundt R, Falk MJ, McCormick EM, Timmers HTM, van Hasselt PM. De Novo Heterozygous POLR2A Variants Cause a Neurodevelopmental Syndrome with Profound Infantile-Onset Hypotonia. Am J Hum Genet 2019; 105:283-301. [PMID: 31353023 PMCID: PMC6699192 DOI: 10.1016/j.ajhg.2019.06.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/30/2019] [Indexed: 11/26/2022] Open
Abstract
The RNA polymerase II complex (pol II) is responsible for transcription of all ∼21,000 human protein-encoding genes. Here, we describe sixteen individuals harboring de novo heterozygous variants in POLR2A, encoding RPB1, the largest subunit of pol II. An iterative approach combining structural evaluation and mass spectrometry analyses, the use of S. cerevisiae as a model system, and the assessment of cell viability in HeLa cells allowed us to classify eleven variants as probably disease-causing and four variants as possibly disease-causing. The significance of one variant remains unresolved. By quantification of phenotypic severity, we could distinguish mild and severe phenotypic consequences of the disease-causing variants. Missense variants expected to exert only mild structural effects led to a malfunctioning pol II enzyme, thereby inducing a dominant-negative effect on gene transcription. Intriguingly, individuals carrying these variants presented with a severe phenotype dominated by profound infantile-onset hypotonia and developmental delay. Conversely, individuals carrying variants expected to result in complete loss of function, thus reduced levels of functional pol II from the normal allele, exhibited the mildest phenotypes. We conclude that subtle variants that are central in functionally important domains of POLR2A cause a neurodevelopmental syndrome characterized by profound infantile-onset hypotonia and developmental delay through a dominant-negative effect on pol-II-mediated transcription of DNA.
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Affiliation(s)
- Hanneke A Haijes
- Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands; Department of Biomedical Genetics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands; German Cancer Consortium (DKTK) standort Freiburg and German Cancer Research Center (DKFZ), 79106 Heidelberg, Germany
| | - Maria J E Koster
- Regenerative Medicine Center and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, the Netherlands; German Cancer Consortium (DKTK) standort Freiburg and German Cancer Research Center (DKFZ), 79106 Heidelberg, Germany
| | - Holger Rehmann
- Expertise Center for Structural Biology, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, the Netherlands; Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Oncode Institute, 3584 CT Utrecht, the Netherlands
| | - Dong Li
- Center for Applied Genomics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Human Genetics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University, 80126 Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, 80126 Naples, Italy
| | - Miroslava Hancarova
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Daphne Lehalle
- Department of Genetics, Centre Hospitalier Universitaire de Dijon, 21000 Dijon, France
| | - Willie Reardon
- Department of Clinical and Medical Genetics, Our Lady's Hospital for Sick Children, D12 N512 Dublin, Ireland
| | - G Bradley Schaefer
- Department of Pediatrics, Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas, AR 72223, USA
| | - Anna Lehman
- Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, BC V6H 3N1 Vancouver, Canada
| | - Ingrid M B H van de Laar
- Department of Clinical Genetics, Erasmus Medical University Center Rotterdam, 3000 CA Rotterdam, the Netherlands
| | - Coranne D Tesselaar
- Department of Pediatrics, Amphia Hospital Breda, 4818 CK Breda, the Netherlands
| | - Clesson Turner
- Department of Clinical Genetics and Pediatrics, Walter Reed National Military Medical Center, Bethesda, Maryland, MD 20814, USA
| | - Alice Goldenberg
- Department of Genetics, Rouen University Hospital, Centre de Référence Anomalies du Développement, Normandy Centre for Genomic and Personalized Medicine, 76000 Rouen, France
| | - Sophie Patrier
- Department of Pathology, Rouen University Hospital, Centre de Référence Anomalies du Développement, 76000 Rouen, France
| | - Julien Thevenon
- Department of Genetics and Reproduction, Centre Hospitalier Universitaire de Grenoble, 38700 Grenoble, France
| | - Michele Pinelli
- Department of Translational Medicine, Federico II University, 80126 Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, 80126 Naples, Italy
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University, 80126 Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, 80126 Naples, Italy
| | - Darina Prchalová
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Markéta Havlovicová
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Markéta Vlckova
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Zdeněk Sedláček
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | - Elena Lopez
- Department of Medical Genetics, BC Children's Hospital Research Institute, University of British Columbia, BC V6H 3N1 Vancouver, Canada
| | - Vassilis Ragoussis
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Alistair T Pagnamenta
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Usha Kini
- Department of Genomic Medicine, Oxford Centre for Genomic Medicine, Oxford University Hospitals National Health Service Foundation Trust, OX3 7LE Oxford, UK
| | - Harmjan R Vos
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Oncode Institute, 3584 CT Utrecht, the Netherlands
| | - Robert M van Es
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Oncode Institute, 3584 CT Utrecht, the Netherlands
| | - Richard F M A van Schaik
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Oncode Institute, 3584 CT Utrecht, the Netherlands
| | - Ton A J van Essen
- Department of Clinical Genetics, University Medical Center Groningen, 9713 GZ Groningen, the Netherlands
| | - Maria Kibaek
- H.C. Andersen Children Hospital, Odense University Hospital, 5000 Odense, Denmark
| | - Jenny C Taylor
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Jennifer Sullivan
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, NC 27710, USA
| | - Vandana Shashi
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, NC 27710, USA
| | - Slave Petrovski
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, NC 27710, USA; AstraZeneca Centre for Genomics Research, Precision Medicine and Genomics, IMED Biotech Unit, AstraZeneca, CB4 0WG Cambridge, United Kingdom; Department of Medicine, the University of Melbourne, VIC 3010 Melbourne, Australia
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | - Donna M Martin
- Departments of Pediatrics and Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, MI 48109, USA
| | - Koen L I van Gassen
- Department of Biomedical Genetics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center Nijmegen, 6525 HR Nijmegen, the Netherlands
| | - Marni J Falk
- Division of Human Genetics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Mitochondrial Medicine Frontier Program, Division of Human Genetics, the Children's Hospital of Philadelphia, PA 19104, Philadelphia, USA
| | - Elizabeth M McCormick
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, the Children's Hospital of Philadelphia, PA 19104, Philadelphia, USA
| | - H T Marc Timmers
- Regenerative Medicine Center and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CT Utrecht, the Netherlands; Department of Urology, University Medical Center Freiburg, University of Freiburg, 79110 Freiburg, Germany
| | - Peter M van Hasselt
- Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands.
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Co-translational assembly of mammalian nuclear multisubunit complexes. Nat Commun 2019; 10:1740. [PMID: 30988355 PMCID: PMC6465333 DOI: 10.1038/s41467-019-09749-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/29/2019] [Indexed: 01/07/2023] Open
Abstract
Cells dedicate significant energy to build proteins often organized in multiprotein assemblies with tightly regulated stoichiometries. As genes encoding subunits assembling in a multisubunit complex are dispersed in the genome of eukaryotes, it is unclear how these protein complexes assemble. Here, we show that mammalian nuclear transcription complexes (TFIID, TREX-2 and SAGA) composed of a large number of subunits, but lacking precise architectural details are built co-translationally. We demonstrate that dimerization domains and their positions in the interacting subunits determine the co-translational assembly pathway (simultaneous or sequential). The lack of co-translational interaction can lead to degradation of the partner protein. Thus, protein synthesis and complex assembly are linked in building mammalian multisubunit complexes, suggesting that co-translational assembly is a general principle in mammalian cells to avoid non-specific interactions and protein aggregation. These findings will also advance structural biology by defining endogenous co-translational building blocks in the architecture of multisubunit complexes. Genes encoding protein complex subunits are often dispersed in the genome of eukaryotes, raising the question how these protein complexes assemble. Here, the authors provide evidence that mammalian nuclear transcription complexes are formed co-translationally to ensure specific and functional interactions.
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Baas R, Sijm A, van Teeffelen HAAM, van Es R, Vos HR, Marc Timmers HT. Quantitative Proteomics of the SMAD (Suppressor of Mothers against Decapentaplegic) Transcription Factor Family Identifies Importin 5 as a Bone Morphogenic Protein Receptor SMAD-specific Importin. J Biol Chem 2016; 291:24121-24132. [PMID: 27703004 DOI: 10.1074/jbc.m116.748582] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/03/2016] [Indexed: 01/11/2023] Open
Abstract
Gene-specific transcription factors (GSTFs) control gene transcription by DNA binding and specific protein complex recruitment, which regulates promoter accessibility for transcription initiation by RNA polymerase II. Mutations in the GSTFs Suppressor of Mothers Against Decapentaplegic 2 (SMAD2) and SMAD4 are frequently associated with colon and rectal carcinomas. These proteins play an important role in bone morphogenic protein (BMP) and transforming growth factor β (TGF-β) signaling pathways controlling cell fate and proliferation. To study the protein interactome of the SMAD protein family we generated a quantitative proteomics pipeline that allows for inducible expression of GFP-tagged SMAD proteins followed by affinity purification and quantitative mass spectrometry analysis. Data are available via ProteomeXchange with identifier PXD004529. The nuclear importin IPO5 was identified as a novel interacting protein of SMAD1. Overexpression of IPO5 in various cell lines specifically increases nuclear localization of BMP receptor-activated SMADs (R-SMADs) confirming a functional relationship between IPO5 and BMP but not TGF-β R-SMADs. Finally, we provide evidence that variation in length of the lysine stretch of the nuclear localization sequence is a determinant for importin specificity.
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Affiliation(s)
- Roy Baas
- From the Departments of Molecular Cancer Research and Stem Cells, Regenerative Medicine Center, Center for Molecular Medicine, University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Ayestha Sijm
- From the Departments of Molecular Cancer Research and Stem Cells, Regenerative Medicine Center, Center for Molecular Medicine, University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Hetty A A M van Teeffelen
- From the Departments of Molecular Cancer Research and Stem Cells, Regenerative Medicine Center, Center for Molecular Medicine, University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Robert van Es
- From the Departments of Molecular Cancer Research and Stem Cells, Regenerative Medicine Center, Center for Molecular Medicine, University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Harmjan R Vos
- From the Departments of Molecular Cancer Research and Stem Cells, Regenerative Medicine Center, Center for Molecular Medicine, University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - H Th Marc Timmers
- From the Departments of Molecular Cancer Research and Stem Cells, Regenerative Medicine Center, Center for Molecular Medicine, University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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Viswanathan R, True JD, Auble DT. Molecular Mechanism of Mot1, a TATA-binding Protein (TBP)-DNA Dissociating Enzyme. J Biol Chem 2016; 291:15714-26. [PMID: 27255709 DOI: 10.1074/jbc.m116.730366] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Indexed: 11/06/2022] Open
Abstract
The essential Saccharomyces cerevisiae ATPase Mot1 globally regulates transcription by impacting the genomic distribution and activity of the TATA-binding protein (TBP). In vitro, Mot1 forms a ternary complex with TBP and DNA and can use ATP hydrolysis to dissociate the TBP-DNA complex. Prior work suggested an interaction between the ATPase domain and a functionally important segment of DNA flanking the TATA sequence. However, how ATP hydrolysis facilitates removal of TBP from DNA is not well understood, and several models have been proposed. To gain insight into the Mot1 mechanism, we dissected the role of the flanking DNA segment by biochemical analysis of complexes formed using DNAs with short single-stranded gaps. In parallel, we used a DNA tethered cleavage approach to map regions of Mot1 in proximity to the DNA under different conditions. Our results define non-equivalent roles for bases within a broad segment of flanking DNA required for Mot1 action. Moreover, we present biochemical evidence for two distinct conformations of the Mot1 ATPase, the detection of which can be modulated by ATP analogs as well as DNA sequence flanking the TATA sequence. We also show using purified complexes that Mot1 dissociation of a stable, high affinity TBP-DNA interaction is surprisingly inefficient, suggesting how other transcription factors that bind to TBP may compete with Mot1. Taken together, these results suggest that TBP-DNA affinity as well as other aspects of promoter sequence influence Mot1 function in vivo.
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Affiliation(s)
- Ramya Viswanathan
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
| | - Jason D True
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
| | - David T Auble
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
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5
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Koster M, Snel B, Timmers H. Genesis of Chromatin and Transcription Dynamics in the Origin of Species. Cell 2015; 161:724-36. [DOI: 10.1016/j.cell.2015.04.033] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Indexed: 11/15/2022]
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Funnell APW, Crossley M. Homo- and Heterodimerization in Transcriptional Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 747:105-21. [DOI: 10.1007/978-1-4614-3229-6_7] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Spedale G, Meddens CA, Koster MJE, Ko CW, van Hooff SR, Holstege FCP, Timmers HTM, Pijnappel WWMP. Tight cooperation between Mot1p and NC2β in regulating genome-wide transcription, repression of transcription following heat shock induction and genetic interaction with SAGA. Nucleic Acids Res 2011; 40:996-1008. [PMID: 21976730 PMCID: PMC3273795 DOI: 10.1093/nar/gkr784] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
TATA-binding protein (TBP) is central to the regulation of eukaryotic transcription initiation. Recruitment of TBP to target genes can be positively regulated by one of two basal transcription factor complexes: SAGA or TFIID. Negative regulation of TBP promoter association can be performed by Mot1p or the NC2 complex. Recent evidence suggests that Mot1p, NC2 and TBP form a DNA-dependent protein complex. Here, we compare the functions of Mot1p and NC2βduring basal and activated transcription using the anchor-away technique for conditional nuclear depletion. Genome-wide expression analysis indicates that both proteins regulate a highly similar set of genes. Upregulated genes were enriched for SAGA occupancy, while downregulated genes preferred TFIID binding. Mot1p and NC2β depletion during heat shock resulted in failure to downregulate gene expression after initial activation, which was accompanied by increased TBP and RNA pol II promoter occupancies. Depletion of Mot1p or NC2β displayed preferential synthetic lethality with the TBP-interaction module of SAGA. Our results support the model that Mot1p and NC2β directly cooperate in vivo to regulate TBP function, and that they are involved in maintaining basal expression levels as well as in resetting gene expression after induction by stress.
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Affiliation(s)
- Gianpiero Spedale
- Molecular Cancer Research, Netherlands Proteomics Centre, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
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Structure and mechanism of the Swi2/Snf2 remodeller Mot1 in complex with its substrate TBP. Nature 2011; 475:403-7. [PMID: 21734658 DOI: 10.1038/nature10215] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 05/18/2011] [Indexed: 12/27/2022]
Abstract
Swi2/Snf2-type ATPases regulate genome-associated processes such as transcription, replication and repair by catalysing the disruption, assembly or remodelling of nucleosomes or other protein-DNA complexes. It has been suggested that ATP-driven motor activity along DNA disrupts target protein-DNA interactions in the remodelling reaction. However, the complex and highly specific remodelling reactions are poorly understood, mostly because of a lack of high-resolution structural information about how remodellers bind to their substrate proteins. Mot1 (modifier of transcription 1 in Saccharomyces cerevisiae, denoted BTAF1 in humans) is a Swi2/Snf2 enzyme that specifically displaces the TATA box binding protein (TBP) from the promoter DNA and regulates transcription globally by generating a highly dynamic TBP pool in the cell. As a Swi2/Snf2 enzyme that functions as a single polypeptide and interacts with a relatively simple substrate, Mot1 offers an ideal system from which to gain a better understanding of this important enzyme family. To reveal how Mot1 specifically disrupts TBP-DNA complexes, we combined crystal and electron microscopy structures of Mot1-TBP from Encephalitozoon cuniculi with biochemical studies. Here we show that Mot1 wraps around TBP and seems to act like a bottle opener: a spring-like array of 16 HEAT (huntingtin, elongation factor 3, protein phosphatase 2A and lipid kinase TOR) repeats grips the DNA-distal side of TBP via loop insertions, and the Swi2/Snf2 domain binds to upstream DNA, positioned to weaken the TBP-DNA interaction by DNA translocation. A 'latch' subsequently blocks the DNA-binding groove of TBP, acting as a chaperone to prevent DNA re-association and ensure efficient promoter clearance. This work shows how a remodelling enzyme can combine both motor and chaperone activities to achieve functional specificity using a conserved Swi2/Snf2 translocase.
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Akhtar W, Veenstra GJC. TBP-related factors: a paradigm of diversity in transcription initiation. Cell Biosci 2011; 1:23. [PMID: 21711503 PMCID: PMC3142196 DOI: 10.1186/2045-3701-1-23] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 06/27/2011] [Indexed: 01/24/2023] Open
Abstract
TATA binding protein (TBP) is a key component of the eukaryotic transcription initiation machinery. It functions in several complexes involved in core promoter recognition and assembly of the pre-initiation complex. Through gene duplication eukaryotes have expanded their repertoire of TATA binding proteins, leading to a variable composition of the transcription machinery. In vertebrates this repertoire consists of TBP, TBP-like factor (TLF, also known as TBPL1, TRF2) and TBP2 (also known as TBPL2, TRF3). All three factors are essential, with TLF and TBP2 playing important roles in development and differentiation, in particular gametogenesis and early embryonic development, whereas TBP dominates somatic cell transcription. TBP-related factors may compete for promoters when co-expressed, but also show preferential interactions with subsets of promoters. Initiation factor switching occurs on account of differential expression of these proteins in gametes, embryos and somatic cells. Paralogs of TFIIA and TAF subunits account for additional variation in the transcription initiation complex. This variation in core promoter recognition accommodates the expanded regulatory capacity and specificity required for germ cells and embryonic development in higher eukaryotes.
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Affiliation(s)
- Waseem Akhtar
- Radboud University Nijmegen, Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands.
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Viswanathan R, Auble DT. One small step for Mot1; one giant leap for other Swi2/Snf2 enzymes? BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:488-96. [PMID: 21658482 DOI: 10.1016/j.bbagrm.2011.05.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 05/14/2011] [Accepted: 05/20/2011] [Indexed: 12/13/2022]
Abstract
The TATA-binding protein (TBP) is a major target for transcriptional regulation. Mot1, a Swi2/Snf2-related ATPase, dissociates TBP from DNA in an ATP dependent process. The experimental advantages of this relatively simple reaction have been exploited to learn more about how Swi2/Snf2 ATPases function biochemically. However, many unanswered questions remain and fundamental aspects of the Mot1 mechanism are still under debate. Here, we review the available data and integrate the results with structural and biochemical studies of related enzymes to derive a model for Mot1's catalytic action consistent with the broad literature on enzymes in this family. We propose that the Mot1 ATPase domain is tethered to TBP by a flexible, spring-like linker of alpha helical hairpins. The linker juxtaposes the ATPase domain such that it can engage duplex DNA on one side of the TBP-DNA complex. This allows the ATPase to employ short-range, nonprocessive ATP-driven DNA tracking to pull or push TBP off its DNA site. DNA translocation is a conserved property of ATPases in the broader enzyme family. As such, the model explains how a structurally and functionally conserved ATPase domain has been put to use in a very different context than other enzymes in the Swi2/Snf2 family. This article is part of a Special Issue entitled:Snf2/Swi2 ATPase structure and function.
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Affiliation(s)
- Ramya Viswanathan
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA
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Lim SM, Pereira L, Wong MS, Hirst CE, Van Vranken BE, Pick M, Trounson A, Elefanty AG, Stanley EG. Enforced expression of Mixl1 during mouse ES cell differentiation suppresses hematopoietic mesoderm and promotes endoderm formation. Stem Cells 2009; 27:363-74. [PMID: 19038793 DOI: 10.1634/stemcells.2008-1008] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Mixl1 gene encodes a homeodomain transcription factor that is required for normal mesoderm and endoderm development in the mouse. We have examined the consequences of enforced Mixl1 expression during mouse embryonic stem cell (ESC) differentiation. We show that three independently derived ESC lines constitutively expressing Mixl1 (Mixl1(C) ESCs) differentiate into embryoid bodies (EBs) containing a higher proportion of E-cadherin (E-Cad)(+) cells. Our analysis also shows that this differentiation occurs at the expense of hematopoietic mesoderm differentiation, with Mixl1(C) ESCs expressing only low levels of Flk1 and failing to develop hemoglobinized cells. Immunohistochemistry and immunofluorescence studies revealed that Mixl1(C) EBs have extensive areas containing cells with an epithelial morphology that express E-Cad, FoxA2, and Sox17, consistent with enhanced endoderm formation. Luciferase reporter transfection experiments indicate that Mixl1 can transactivate the Gsc, Sox17, and E-Cad promoters, supporting the hypothesis that Mixl1 has a direct role in definitive endoderm formation. Taken together, these studies suggest that high levels of Mixl1 preferentially allocate cells to the endoderm during ESC differentiation.
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Affiliation(s)
- Sue Mei Lim
- Monash Immunology and Stem Cell Laboratories, Monash University, Clayton, Victoria, Australia
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Sprouse RO, Shcherbakova I, Cheng H, Jamison E, Brenowitz M, Auble DT. Function and structural organization of Mot1 bound to a natural target promoter. J Biol Chem 2008; 283:24935-48. [PMID: 18606810 DOI: 10.1074/jbc.m803749200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mot1 is an essential, conserved TATA-binding protein (TBP)-associated factor in Saccharomyces cerevisiae and a member of the Snf2/Swi2 ATPase family. Mot1 uses ATP hydrolysis to displace TBP from DNA, an activity that can be readily reconciled with its global role in gene repression. Less well understood is how Mot1 directly activates gene expression. It has been suggested that Mot1-mediated activation can occur by displacement of inactive TBP-containing complexes from promoters, thereby permitting assembly of functional transcription complexes. Mot1 may also activate transcription by other mechanisms that have not yet been defined. A gap in our understanding has been the absence of biochemical information related to the activity of Mot1 on natural target genes. Using URA1 as a model Mot1-activated promoter, we show striking differences in the way that both TBP and Mot1 interact with DNA compared with other model DNA substrates analyzed previously. These differences are due at least in part to the propensity of TBP alone to bind to the URA1 promoter in the wrong orientation to direct appropriate assembly of the URA1 preinitiation complex. The results suggest that Mot1-mediated activation of URA1 transcription involves at least two steps, one of which is the removal of TBP bound to the promoter in the opposite orientation required for URA1 transcription.
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Affiliation(s)
- Rebekka O Sprouse
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908, USA
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Arnett DR, Jennings JL, Tabb DL, Link AJ, Weil PA. A proteomics analysis of yeast Mot1p protein-protein associations: insights into mechanism. Mol Cell Proteomics 2008; 7:2090-106. [PMID: 18596064 DOI: 10.1074/mcp.m800221-mcp200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Yeast Mot1p, a member of the Snf2 ATPase family of proteins, is a transcriptional regulator that has the unusual ability to both repress and activate mRNA gene transcription. To identify interactions with other proteins that may assist Mot1p in its regulatory processes, Mot1p was purified from replicate yeast cell extracts, and Mot1p-associated proteins were identified by coupled multidimensional liquid chromatography and tandem mass spectrometry. Using this approach we generated a catalog of Mot1p-interacting proteins. Mot1p interacts with a range of transcriptional co-regulators as well as proteins involved in chromatin remodeling. We propose that interaction with such a wide range of proteins may be one mechanism through which Mot1p subserves its roles as a transcriptional activator and repressor.
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Affiliation(s)
- Diana R Arnett
- Department of Molecular Physiology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0615, USA
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14
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Bendjennat M, Weil PA. The transcriptional repressor activator protein Rap1p is a direct regulator of TATA-binding protein. J Biol Chem 2008; 283:8699-710. [PMID: 18195009 DOI: 10.1074/jbc.m709436200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Essentially all nuclear eukaryotic gene transcription depends upon the function of the transcription factor TATA-binding protein (TBP). Here we show that the abundant, multifunctional DNA binding transcription factor repressor activator protein Rap1p interacts directly with TBP. TBP-Rap1p binding occurs efficiently in vivo at physiological expression levels, and in vitro analyses confirm that this is a direct interaction. The DNA binding domains of the two proteins mediate interaction between TBP and Rap1p. TBP-Rap1p complex formation inhibits TBP binding to TATA promoter DNA. Alterations in either Rap1p or TBP levels modulate mRNA gene transcription in vivo. We propose that Rap1p represents a heretofore unrecognized regulator of TBP.
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Affiliation(s)
- Mourad Bendjennat
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, TN 37232-0615, USA
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15
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Lawit SJ, O'Grady K, Gurley WB, Czarnecka-Verner E. Yeast two-hybrid map of Arabidopsis TFIID. PLANT MOLECULAR BIOLOGY 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] [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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16
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Abstract
In eukaryotes, the core promoter serves as a platform for the assembly of transcription preinitiation complex (PIC) that includes TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, and RNA polymerase II (pol II), which function collectively to specify the transcription start site. PIC formation usually begins with TFIID binding to the TATA box, initiator, and/or downstream promoter element (DPE) found in most core promoters, followed by the entry of other general transcription factors (GTFs) and pol II through either a sequential assembly or a preassembled pol II holoenzyme pathway. Formation of this promoter-bound complex is sufficient for a basal level of transcription. However, for activator-dependent (or regulated) transcription, general cofactors are often required to transmit regulatory signals between gene-specific activators and the general transcription machinery. Three classes of general cofactors, including TBP-associated factors (TAFs), Mediator, and upstream stimulatory activity (USA)-derived positive cofactors (PC1/PARP-1, PC2, PC3/DNA topoisomerase I, and PC4) and negative cofactor 1 (NC1/HMGB1), normally function independently or in combination to fine-tune the promoter activity in a gene-specific or cell-type-specific manner. In addition, other cofactors, such as TAF1, BTAF1, and negative cofactor 2 (NC2), can also modulate TBP or TFIID binding to the core promoter. In general, these cofactors are capable of repressing basal transcription when activators are absent and stimulating transcription in the presence of activators. Here we review the roles of these cofactors and GTFs, as well as TBP-related factors (TRFs), TAF-containing complexes (TFTC, SAGA, SLIK/SALSA, STAGA, and PRC1) and TAF variants, in pol II-mediated transcription, with emphasis on the events occurring after the chromatin has been remodeled but prior to the formation of the first phosphodiester bond.
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Affiliation(s)
- Mary C Thomas
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106-4935, USA
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17
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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] [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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18
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Quadt I, Günther AK, Voss D, Schelhaas M, Knebel-Mörsdorf D. TATA-binding protein and TBP-associated factors during herpes simplex virus type 1 infection: localization at viral DNA replication sites. Virus Res 2005; 115:207-13. [PMID: 16271277 DOI: 10.1016/j.virusres.2005.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2005] [Revised: 09/29/2005] [Accepted: 09/29/2005] [Indexed: 11/18/2022]
Abstract
Host RNA polymerase II (RNAP II) is responsible for viral transcription of the herpes simplex virus type 1 (HSV-1) genome and is relocalized to viral DNA replication compartments. Thus, we investigated whether TATA-binding protein (TBP) and TBP-associated factors (TAFs) are recruited to sites of viral transcription and replication and whether TBP/TAF expressions are influenced upon infection. The protein levels of TBP, hsTAF1/TAF(II)250, hsTAF4/TAF(II)135, and hsTAF5/TAF(II)100 were constant during the early phase of infection and started to decrease late during infection. Only for hsTAF7/TAF(II)55 we sometimes observed a decrease already at 4-8h postinfection (p.i.). Concomitantly with the relocalization of RNAP II, TBP and hsTAFs were redistributed to sites of viral DNA replication and transcription. In the absence of viral DNA replication TBP/hsTAFs were present in distinct nuclear dots, however, enlargement of the nuclear structures did not take place. Our results show that HSV-1 infection has no influence on the protein levels of TFIID components and leads to a redistribution of TBP and hsTAFs to prereplicative sites that enlarge to viral DNA replication compartments.
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Affiliation(s)
- Ilja Quadt
- Max-Planck-Institute for Neurological Research, D-50931 Köln, Germany
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19
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Klejman MP, Zhao X, van Schaik FMA, Herr W, Timmers HTM. Mutational analysis of BTAF1-TBP interaction: BTAF1 can rescue DNA-binding defective TBP mutants. Nucleic Acids Res 2005; 33:5426-36. [PMID: 16179647 PMCID: PMC1236718 DOI: 10.1093/nar/gki850] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The BTAF1 transcription factor interacts with TATA-binding protein (TBP) to form the B–TFIID complex, which is involved in RNA polymerase II transcription. Here, we present an extensive mapping study of TBP residues involved in BTAF1 interaction. This shows that residues in the concave, DNA-binding surface of TBP are important for BTAF1 binding. In addition, BTAF1 interacts with residues in helix 2 on the convex side of TBP as assayed in protein–protein and in DNA-binding assays. BTAF1 drastically changes the TATA-box binding specificity of TBP, as it is able to recruit DNA-binding defective TBP mutants to both TATA-containing and TATA-less DNA. Interestingly, other helix 2 interacting factors, such as TFIIA and NC2, can also stabilize mutant TBP binding to DNA. In contrast, TFIIB which interacts with a distinct surface of TBP does not display this activity. Since many proteins contact helix 2 of TBP, this provides a molecular basis for mutually exclusive TBP interactions and stresses the importance of this structural element for eukaryotic transcription.
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Affiliation(s)
| | - Xuemei Zhao
- Cold Spring Harbor LaboratoryCold Spring Harbor, NY 11724, USA
| | | | - Winship Herr
- Cold Spring Harbor LaboratoryCold Spring Harbor, NY 11724, USA
| | - H. Th. Marc Timmers
- To whom correspondence should be addressed. Tel: +31 30 253 8981; Fax: + 31 30 253 9035;
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20
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Klejman MP, Pereira LA, van Zeeburg HJT, Gilfillan S, Meisterernst M, Timmers HTM. NC2alpha interacts with BTAF1 and stimulates its ATP-dependent association with TATA-binding protein. Mol Cell Biol 2004; 24:10072-82. [PMID: 15509807 PMCID: PMC525489 DOI: 10.1128/mcb.24.22.10072-10082.2004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptional activity of the TATA-binding protein (TBP) is controlled by a variety of proteins. The BTAF1 protein (formerly known as TAF(II)170/TAF-172 and the human ortholog of Saccharomyces cerevisiae Mot1p) and the NC2 complex composed of NC2alpha (DRAP1) and NC2beta (Dr1) are able to bind to TBP directly and regulate RNA polymerase II transcription both positively and negatively. Here, we present evidence that the NC2alpha subunit interacts with BTAF1. In contrast, the NC2beta subunit is not able to associate with BTAF1 and seems to interfere with the BTAF1-TBP interaction. Addition of NC2alpha or the NC2 complex can stimulate the ability of BTAF1 to interact with TBP. This function is dependent on the presence of ATP in cell extracts but does not involve the ATPase activity of BTAF1 nor phosphorylation of NC2alpha. Together, our results constitute the first evidence of the physical cooperation between BTAF1 and NC2alpha in TBP regulation and provide a framework to understand transcription functions of NC2alpha and NC2beta in vivo.
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Affiliation(s)
- Marcin P Klejman
- Department of Physiological Chemistry, Division of Biomedical Genetics, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
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21
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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] [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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22
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Takahata S, Ryu H, Ohtsuki K, Kasahara K, Kawaichi M, Kokubo T. Identification of a novel TATA element-binding protein binding region at the N terminus of the Saccharomyces cerevisiae TAF1 protein. J Biol Chem 2003; 278:45888-902. [PMID: 12939271 DOI: 10.1074/jbc.m306886200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
TFIID, a multiprotein complex composed of TATA element-binding protein (TBP) and 14 TBP-associated factors (TAFs), can directly recognize core promoter elements and mediate transcriptional activation. The TAF N-terminal domain (TAND) of TAF1 may play a significant role in these two principal TFIID functions by regulating the access of TBP to the TATA element. In yeast, TAND consists of two subdomains, TAND1 (10-37 amino acids (aa)) and TAND2 (46-71 aa), which interact with the concave and convex surfaces of TBP, respectively. Here we demonstrate that another region located on the C-terminal side of TAND2 (82-139 aa) can also bind to TBP and induce transcriptional activation when tethered to DNA as a GAL4 fusion protein. As these properties are the same as those of TAND1, we denoted this sequence as TAND3. Detailed mutational analyses revealed that three blocks of hydrophobic amino acid residues located within TAND3 are required not only for TBP binding and transcriptional activation but also for supporting cell growth and the efficient transcription of a subset of genes. We also show that the surface of TBP recognized by TAND3 is broader than that recognized by TAND1, although these regions overlap partially. Supporting these observations is that TAND1 can be at least partly functionally substituted by TAND3.
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Affiliation(s)
- Shinya Takahata
- Division of Molecular and Cellular Biology, Graduate School of Integrated Science, Yokohama City University, Yokohama 230-0045, USA
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23
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Pereira LA, Klejman MP, Timmers HTM. Roles for BTAF1 and Mot1p in dynamics of TATA-binding protein and regulation of RNA polymerase II transcription. Gene 2003; 315:1-13. [PMID: 14557059 DOI: 10.1016/s0378-1119(03)00714-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Regulation of RNA polymerase II (pol II) transcription is a highly dynamic process requiring the coordinated interaction of an array of regulatory proteins. Central to this process is the TATA-binding protein (TBP), the key component of the multiprotein complex TFIID. Interaction of TBP with core promoters nucleates the assembly of the preinitiation complex and subsequent recruitment of pol II. Despite recent advances in our understanding of the dynamic nature of the pol II transcription apparatus, the dynamics of TBP function on pol II promoters has remained largely unexplored. Human BTAF1 (TAF(II)170/TAF-172) and its yeast ortholog, Mot1p, are evolutionarily conserved members of the SNF2-like family of ATPase proteins. Genetic identification of Mot1p as a repressor of pol II transcription was supported by findings that Mot1p and BTAF1 could dissociate TBP from TATA DNA complexes using the energy of ATP hydrolysis. Recent data have revealed new aspects of BTAF1 and Mot1p as positive regulators of TBP function in the pol II system and have described new observations relating to their molecular mechanism of action. We review these data in the context of previous findings with particular attention paid to how human BTAF1 and Mot1p may dynamically regulate TBP function on pol II promoters in cells.
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Affiliation(s)
- Lloyd A Pereira
- Laboratory for Physiological Chemistry, Division of Biomedical Genetics, UMC-U, Universiteitsweg 100, 3584 Utrecht CG, The Netherlands
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24
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Gumbs OH, Campbell AM, Weil PA. High-affinity DNA binding by a Mot1p-TBP complex: implications for TAF-independent transcription. EMBO J 2003; 22:3131-41. [PMID: 12805227 PMCID: PMC162156 DOI: 10.1093/emboj/cdg304] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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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25
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Kou H, Irvin JD, Huisinga KL, Mitra M, Pugh BF. Structural and functional analysis of mutations along the crystallographic dimer interface of the yeast TATA binding protein. Mol Cell Biol 2003; 23:3186-201. [PMID: 12697819 PMCID: PMC153203 DOI: 10.1128/mcb.23.9.3186-3201.2003] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The TATA binding protein (TBP) is a central component of the eukaryotic transcription machinery and is subjected to both positive and negative regulation. As is evident from structural and functional studies, TBP's concave DNA binding surface is inhibited by a number of potential mechanisms, including homodimerization and binding to the TAND domain of the TFIID subunit TAF1 (yTAF(II)145/130). Here we further characterized these interactions by creating mutations at 24 amino acids within the Saccharomyces cerevisiae TBP crystallographic dimer interface. These mutants are impaired for dimerization, TAF1 TAND binding, and TATA binding to an extent that is consistent with the crystal or nuclear magnetic resonance structure of these or related interactions. In vivo, these mutants displayed a variety of phenotypes, the severity of which correlated with relative dimer instability in vitro. The phenotypes included a low steady-state level of the mutant TBP, transcriptional derepression, dominant slow growth (partial toxicity), and synthetic toxicity in combination with a deletion of the TAF1 TAND domain. These phenotypes cannot be accounted for by defective interactions with other known TBP inhibitors and likely reflect defects in TBP dimerization.
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Affiliation(s)
- Haiping Kou
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16803, USA
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26
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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] [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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27
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Spencer JV, Arndt KM. A TATA binding protein mutant with increased affinity for DNA directs transcription from a reversed TATA sequence in vivo. Mol Cell Biol 2002; 22:8744-55. [PMID: 12446791 PMCID: PMC139874 DOI: 10.1128/mcb.22.24.8744-8755.2002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The TATA-binding protein (TBP) nucleates the assembly and determines the position of the preinitiation complex at RNA polymerase II-transcribed genes. We investigated the importance of two conserved residues on the DNA binding surface of Saccharomyces cerevisiae TBP to DNA binding and sequence discrimination. Because they define a significant break in the twofold symmetry of the TBP-TATA interface, Ala100 and Pro191 have been proposed to be key determinants of TBP binding orientation and transcription directionality. In contrast to previous predictions, we found that substitution of an alanine for Pro191 did not allow recognition of a reversed TATA box in vivo; however, the reciprocal change, Ala100 to proline, resulted in efficient utilization of this and other variant TATA sequences. In vitro assays demonstrated that TBP mutants with the A100P and P191A substitutions have increased and decreased affinity for DNA, respectively. The TATA binding defect of TBP with the P191A mutation could be intragenically suppressed by the A100P substitution. Our results suggest that Ala100 and Pro191 are important for DNA binding and sequence recognition by TBP, that the naturally occurring asymmetry of Ala100 and Pro191 is not essential for function, and that a single amino acid change in TBP can lead to elevated DNA binding affinity and recognition of a reversed TATA sequence.
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Affiliation(s)
- J Vaughn Spencer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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28
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Andrau JC, Van Oevelen CJ, Van Teeffelen HA, Weil P, Holstege FC, Timmers H. Mot1p is essential for TBP recruitment to selected promoters during in vivo gene activation. EMBO J 2002; 21:5173-83. [PMID: 12356733 PMCID: PMC129025 DOI: 10.1093/emboj/cdf485] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recruitment of TATA-binding protein (TBP) is central to activation of transcription by RNA polymerase II (pol II). This depends upon co-activator proteins including TBP-associated factors (TAFs). Yeast Mot1p was identified as a general transcriptional repressor in genetic screens and is also found associated with TBP. To obtain insight into Mot1p function in vivo, we determined the mRNA expression profile of the mot1-1 temperature-sensitive (Ts) strain. Unexpectedly, this indicated that Mot1p mostly plays a positive role for transcription. For one potential activation target, HXT2, we analyzed promoter recruitment of Mot1p, TBP, Taf1p (Taf130p) and pol II by chromatin immunoprecipitation assays. Whereas TBP becomes stably associated upon activation of the HXT2 and HXT4 promoters, Mot1p showed only a transient association. TBP recruitment was compromised in two different mot1 mutant strains, but was only moderately affected in a taf1 Ts strain. Together, our data indicate that Mot1p can assist in recruitment of TBP on promoters during gene activation in vivo.
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Affiliation(s)
- Jean-Christophe Andrau
- Laboratory for Physiological Chemistry and Department of Medical Genetics, UMC Utrecht, PO Box 85060, 3508 AB Utrecht, The Netherlands, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232 and Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA Corresponding author e-mail:
| | - Chris J.C. Van Oevelen
- Laboratory for Physiological Chemistry and Department of Medical Genetics, UMC Utrecht, PO Box 85060, 3508 AB Utrecht, The Netherlands, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232 and Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA Corresponding author e-mail:
| | - Hetty A.A.M. Van Teeffelen
- Laboratory for Physiological Chemistry and Department of Medical Genetics, UMC Utrecht, PO Box 85060, 3508 AB Utrecht, The Netherlands, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232 and Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA Corresponding author e-mail:
| | - P.Anthony Weil
- Laboratory for Physiological Chemistry and Department of Medical Genetics, UMC Utrecht, PO Box 85060, 3508 AB Utrecht, The Netherlands, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232 and Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA Corresponding author e-mail:
| | - Frank C.P. Holstege
- Laboratory for Physiological Chemistry and Department of Medical Genetics, UMC Utrecht, PO Box 85060, 3508 AB Utrecht, The Netherlands, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232 and Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA Corresponding author e-mail:
| | - H.Th.Marc Timmers
- Laboratory for Physiological Chemistry and Department of Medical Genetics, UMC Utrecht, PO Box 85060, 3508 AB Utrecht, The Netherlands, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232 and Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA Corresponding author e-mail:
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Martel LS, Brown HJ, Berk AJ. Evidence that TAF-TATA box-binding protein interactions are required for activated transcription in mammalian cells. Mol Cell Biol 2002; 22:2788-98. [PMID: 11909971 PMCID: PMC133715 DOI: 10.1128/mcb.22.8.2788-2798.2002] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Surfaces of human TATA box-binding protein (hsTBP) required for activated transcription in vivo were defined by constructing a library of surface residue substitution mutations and assaying them for their ability to support activated transcription in transient-transfection assays. In earlier work, three regions were identified where mutations inhibited activated transcription without interfering with TATA box DNA binding. One region is on the upstream surface of the N-terminal TBP repeat with respect to the direction of transcription and corresponds to the TBP surface that interacts with TFIIA. A second region on the stirrup of the C-terminal TBP repeat corresponds to the TFIIB-binding surface. Here we report that the third region where mutations inhibit activated transcription in mammalian cells, the convex surface of the N-terminal repeat, corresponds to a surface on TBP that interacts with hsTAF1, the major scaffold subunit of TFIID. Since mutations at the center of the hsTAF1-interacting region inhibit the ability of the protein to support activated transcription in vivo, these results are consistent with the conclusion that an interaction between hsTBP and TAF(II)s is required for activated transcription in mammalian cells.
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Affiliation(s)
- Lisa S Martel
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA
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