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Miyasaka S, Kitada R, Kokubo T. Taf1 N-terminal domain 2 (TAND2) of TFIID promotes formation of stable and mobile unstable TBP-TATA complexes. Gene 2023; 889:147800. [PMID: 37716588 DOI: 10.1016/j.gene.2023.147800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 09/05/2023] [Accepted: 09/12/2023] [Indexed: 09/18/2023]
Abstract
In eukaryotes, TATA-binding protein (TBP) occupancy of the core promoter globally correlates with transcriptional activity of class II genes. Elucidating how TBP is delivered to the TATA box or TATA-like element is crucial to understand the mechanisms of transcriptional regulation. A previous study demonstrated that the inhibitory DNA binding (IDB) surface of human TBP plays an indispensable role during the two-step formation of the TBP-TATA complex, first assuming an unstable and unbent intermediate conformation, and subsequently converting slowly to a stable and bent conformation. The DNA binding property of TBP is altered by physical contact of this surface with TBP regulators. In the present study, we examined whether the interaction between Taf1 N-terminal domain 2 (TAND2) and the IDB surface affected DNA binding property of yeast TBP by exploiting TAND2-fused TBP derivatives. TAND2 promoted formation of two distinct types of TBP-TATA complexes, which we arbitrarily designated as complex I and II. While complex I was stable and similar to the well-characterized original TBP-TATA complex, complex II was unstable and moved along DNA. Removal of TAND2 from TBP after complex formation revealed that continuous contact of TAND2 with the IDB surface was required for formation of complex II but not complex I. Further, TFIIA could be incorporated into the complex of TAND2-fused TBP and the TATA box, which was dependent on the amino-terminal non-conserved region of TBP, implying that this region could facilitate the exchange between TAND2 and TFIIA on the IDB surface. Collectively, these findings provide novel insights into the mechanism by which TBP is relieved from the interaction with TAND to bind the TATA box or TATA-like element within promoter-bound TFIID.
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Affiliation(s)
- Shinji Miyasaka
- Molecular and Cellular Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Ryota Kitada
- Molecular and Cellular Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Tetsuro Kokubo
- Molecular and Cellular Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa, Japan.
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2
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Sneha NP, Dharshini SAP, Taguchi YH, Gromiha MM. Investigating Neuron Degeneration in Huntington's Disease Using RNA-Seq Based Transcriptome Study. Genes (Basel) 2023; 14:1801. [PMID: 37761940 PMCID: PMC10530489 DOI: 10.3390/genes14091801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/02/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Huntington's disease (HD) is a progressive neurodegenerative disorder caused due to a CAG repeat expansion in the huntingtin (HTT) gene. The primary symptoms of HD include motor dysfunction such as chorea, dystonia, and involuntary movements. The primary motor cortex (BA4) is the key brain region responsible for executing motor/movement activities. Investigating patient and control samples from the BA4 region will provide a deeper understanding of the genes responsible for neuron degeneration and help to identify potential markers. Previous studies have focused on overall differential gene expression and associated biological functions. In this study, we illustrate the relationship between variants and differentially expressed genes/transcripts. We identified variants and their associated genes along with the quantification of genes and transcripts. We also predicted the effect of variants on various regulatory activities and found that many variants are regulating gene expression. Variants affecting miRNA and its targets are also highlighted in our study. Co-expression network studies revealed the role of novel genes. Function interaction network analysis unveiled the importance of genes involved in vesicle-mediated transport. From this unified approach, we propose that genes expressed in immune cells are crucial for reducing neuron death in HD.
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Affiliation(s)
- Nela Pragathi Sneha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (N.P.S.); (S.A.P.D.)
| | - S. Akila Parvathy Dharshini
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (N.P.S.); (S.A.P.D.)
| | - Y.-h. Taguchi
- Department of Physics, Chuo University, Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan;
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (N.P.S.); (S.A.P.D.)
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3
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Sun J, Li X, Hou X, Cao S, Cao W, Zhang Y, Song J, Wang M, Wang H, Yan X, Li Z, Roeder RG, Wang W. Structural basis of human SNAPc recognizing proximal sequence element of snRNA promoter. Nat Commun 2022; 13:6871. [PMID: 36369505 PMCID: PMC9652321 DOI: 10.1038/s41467-022-34639-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
In eukaryotes, small nuclear RNAs (snRNAs) function in many fundamental cellular events such as precursor messenger RNA splicing, gene expression regulation, and ribosomal RNA processing. The snRNA activating protein complex (SNAPc) exclusively recognizes the proximal sequence element (PSE) at snRNA promoters and recruits RNA polymerase II or III to initiate transcription. In view that homozygous gene-knockout of SNAPc core subunits causes mouse embryonic lethality, functions of SNAPc are almost housekeeping. But so far, the structural insight into how SNAPc assembles and regulates snRNA transcription initiation remains unclear. Here we present the cryo-electron microscopy structure of the essential part of human SNAPc in complex with human U6-1 PSE at an overall resolution of 3.49 Å. This structure reveals the three-dimensional features of three conserved subunits (N-terminal domain of SNAP190, SNAP50, and SNAP43) and explains how they are assembled into a stable mini-SNAPc in PSE-binding state with a "wrap-around" mode. We identify three important motifs of SNAP50 that are involved in both major groove and minor groove recognition of PSE, in coordination with the Myb domain of SNAP190. Our findings further elaborate human PSE sequence conservation and compatibility for SNAPc recognition, providing a clear framework of snRNA transcription initiation, especially the U6 system.
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Affiliation(s)
- Jianfeng Sun
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China ,grid.27255.370000 0004 1761 1174Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China ,grid.134907.80000 0001 2166 1519Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, 10065 USA
| | - Xue Li
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Xuben Hou
- grid.27255.370000 0004 1761 1174School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Sujian Cao
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Wenjin Cao
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Ye Zhang
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Jinyang Song
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Manfu Wang
- grid.512077.6Wuxi Biortus Biosciences Co. Ltd., Jiangyin, 214437 China
| | - Hao Wang
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Xiaodong Yan
- grid.512077.6Wuxi Biortus Biosciences Co. Ltd., Jiangyin, 214437 China
| | - Zengpeng Li
- grid.453137.70000 0004 0406 0561Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
| | - Robert G. Roeder
- grid.134907.80000 0001 2166 1519Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, 10065 USA
| | - Wei Wang
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China ,grid.27255.370000 0004 1761 1174Interventional Medicine Department, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033 China
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4
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Role of the TATA-box binding protein (TBP) and associated family members in transcription regulation. Gene X 2022; 833:146581. [PMID: 35597524 DOI: 10.1016/j.gene.2022.146581] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/18/2022] [Accepted: 05/16/2022] [Indexed: 11/20/2022] Open
Abstract
The assembly of transcription complexes on eukaryotic promoters involves a series of steps, including chromatin remodeling, recruitment of TATA-binding protein (TBP)-containing complexes, the RNA polymerase II holoenzyme, and additional basal transcription factors. This review describes the transcriptional regulation by TBP and its corresponding homologs that constitute the TBP family and their interactions with promoter DNA. The C-terminal core domain of TBP is highly conserved and contains two structural repeats that fold into a saddle-like structure, essential for the interaction with the TATA-box on DNA. Based on the TBP C-terminal core domain similarity, three TBP-related factors (TRFs) or TBP-like factors (TBPLs) have been discovered in metazoans, TRF1, TBPL1, and TBPL2. TBP is autoregulated, and once bound to DNA, repressors such as Mot1 induce TBP to dissociate, while other factors such as NC2 and the NOT complex convert the active TBP/DNA complex into inactive, negatively regulating TBP. TFIIA antagonizes the TBP repressors but may be effective only in conjunction with the RNA polymerase II holoenzyme recruitment to the promoter by promoter-bound activators. TRF1 has been discovered inDrosophila melanogasterandAnophelesbut found absent in vertebrates and yeast. TBPL1 cannot bind to the TATA-box; instead, TBPL1 prefers binding to TATA-less promoters. However, TBPL1 shows a stronger association with TFIIA than TBP. The TCT core promoter element is present in most ribosomal protein genes inDrosophilaand humans, and TBPL1 is required for the transcription of these genes. TBP directly participates in the DNA repair mechanism, and TBPL1 mediates cell cycle arrest and apoptosis. TBPL2 is closely related to its TBP paralog, showing 95% sequence similarity with the TBP core domain. Like TBP, TBPL2 also binds to the TATA-box and shows interactions with TFIIA, TFIIB, and other basal transcription factors. Despite these advances, much remains to be explored in this family of transcription factors.
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Hardivillé S, Banerjee PS, Selen Alpergin ES, Smith DM, Han G, Ma J, Talbot CC, Hu P, Wolfgang MJ, Hart GW. TATA-Box Binding Protein O-GlcNAcylation at T114 Regulates Formation of the B-TFIID Complex and Is Critical for Metabolic Gene Regulation. Mol Cell 2019; 77:1143-1152.e7. [PMID: 31866147 DOI: 10.1016/j.molcel.2019.11.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/14/2019] [Accepted: 11/26/2019] [Indexed: 12/31/2022]
Abstract
In eukaryotes, gene expression is performed by three RNA polymerases that are targeted to promoters by molecular complexes. A unique common factor, the TATA-box binding protein (TBP), is thought to serve as a platform to assemble pre-initiation complexes competent for transcription. Here, we describe a novel molecular mechanism of nutrient regulation of gene transcription by dynamic O-GlcNAcylation of TBP. We show that O-GlcNAcylation at T114 of TBP blocks its interaction with BTAF1, hence the formation of the B-TFIID complex, and its dynamic cycling on and off of DNA. Transcriptomic and metabolomic analyses of TBPT114A CRISPR/Cas9-edited cells showed that loss of O-GlcNAcylation at T114 increases TBP binding to BTAF1 and directly impacts expression of 408 genes. Lack of O-GlcNAcylation at T114 is associated with a striking reprogramming of cellular metabolism induced by a profound modification of the transcriptome, leading to gross alterations in lipid storage.
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Affiliation(s)
- Stéphan Hardivillé
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Partha S Banerjee
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ebru S Selen Alpergin
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Danielle M Smith
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Guanghui Han
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Junfeng Ma
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - C Conover Talbot
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ping Hu
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michael J Wolfgang
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gerald W Hart
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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6
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Transcription initiation factor TBP: old friend new questions. Biochem Soc Trans 2019; 47:411-423. [DOI: 10.1042/bst20180623] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 01/02/2019] [Accepted: 01/04/2019] [Indexed: 12/14/2022]
Abstract
Abstract
In all domains of life, the regulation of transcription by DNA-dependent RNA polymerases (RNAPs) is achieved at the level of initiation to a large extent. Whereas bacterial promoters are recognized by a σ-factor bound to the RNAP, a complex set of transcription factors that recognize specific promoter elements is employed by archaeal and eukaryotic RNAPs. These initiation factors are of particular interest since the regulation of transcription critically relies on initiation rates and thus formation of pre-initiation complexes. The most conserved initiation factor is the TATA-binding protein (TBP), which is of crucial importance for all archaeal-eukaryotic transcription initiation complexes and the only factor required to achieve full rates of initiation in all three eukaryotic and the archaeal transcription systems. Recent structural, biochemical and genome-wide mapping data that focused on the archaeal and specialized RNAP I and III transcription system showed that the involvement and functional importance of TBP is divergent from the canonical role TBP plays in RNAP II transcription. Here, we review the role of TBP in the different transcription systems including a TBP-centric discussion of archaeal and eukaryotic initiation complexes. We furthermore highlight questions concerning the function of TBP that arise from these findings.
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7
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Li P, Fu X, Li S, Zhang L. Engineering TATA-binding protein Spt15 to improve ethanol tolerance and production in Kluyveromyces marxianus. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:207. [PMID: 30061929 PMCID: PMC6058363 DOI: 10.1186/s13068-018-1206-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 07/16/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Low ethanol tolerance of Kluyveromyces marxianus limits its application in high-temperature ethanol fermentation. As a complex phenotype, ethanol tolerance involves synergistic actions of many genes that are widely distributed throughout the genome, thereby being difficult to engineer. TATA-binding protein is the most common target of global transcription machinery engineering for improvement of complex phenotypes. RESULTS A random mutagenesis library of K. marxianus TATA-binding protein Spt15 was constructed and subjected to screening under ethanol stress. Two mutant strains with improved ethanol tolerance were identified, one of which (denoted as M2) exhibited increased ethanol productivity. The mutant of Spt15 in strain M2 (denoted as Spt15-M2) has a single amino acid substitution at position 31 (Lys → Glu). RNA-Seq-based transcriptomic analysis revealed cellular transcription profile changes resulting from Spt15-M2. Spt15-M2 caused changes in transcriptional level of most of the genes in the central carbon metabolism network. Compared with control strain, 444 differentially expressed genes (DEGs) were identified in strain M2 (fold change > 2, Padj < 0.05), including 48 up-regulated and 396 down-regulated. The up-regulated DEGs are involved in amino acid transport, long-chain fatty acid biosynthesis and MAPK signaling pathway, while the down-regulated DEGs are related to ribosome biogenesis, translation and protein synthesis. Five candidate genes (GAP1, GNP1, FAR1, STE2 and TEC1), which were found to be up-regulated in M2 strain, were overexpressed for a gain-of-function assay. However, the overexpression of no single gene helped improve ethanol tolerance as SPT15-M2 did. CONCLUSIONS This work demonstrates that ethanol tolerance of K. marxianus can be improved by engineering its TATA-binding protein. A single amino acid substitution (K31E) of TATA-binding protein Spt15 is able to bring differential expression of hundreds of genes that acted as an interconnected network for the phenotype of ethanol tolerance. Future perspectives of this technique in K. marxianus were discussed.
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Affiliation(s)
- Pengsong Li
- Institute of New Energy Technology, MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
| | - Xiaofen Fu
- Institute of New Energy Technology, MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
| | - Shizhong Li
- Institute of New Energy Technology, MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
| | - Lei Zhang
- Institute of New Energy Technology, MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
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8
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Verma N, Hurlburt AM, Wolfe A, Kim MK, Kang YS, Kang JJ, Stumph WE. Bdp1 interacts with SNAPc bound to a U6, but not U1, snRNA gene promoter element to establish a stable protein-DNA complex. FEBS Lett 2018; 592:2489-2498. [PMID: 29932462 DOI: 10.1002/1873-3468.13169] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/13/2018] [Accepted: 06/17/2018] [Indexed: 12/15/2022]
Abstract
In metazoans, U6 small nuclear RNA (snRNA) gene promoters utilize a proximal sequence element (PSE) recognized by the small nuclear RNA-activating protein complex (SNAPc). SNAPc interacts with the transcription factor TFIIIB, which consists of the subunits TBP, Brf1 (Brf2 in vertebrates), and Bdp1. Here, we show that, in Drosophila melanogaster, DmSNAPc directly recruits Bdp1 to the U6 promoter, and we identify an 87-residue region of Bdp1 involved in this interaction. Importantly, Bdp1 recruitment requires that DmSNAPc be bound to a U6 PSE rather than a U1 PSE. This is consistent with the concept that DmSNAPc adopts different conformations on U6 and U1 PSEs, which lead to the subsequent recruitment of distinct general transcription factors and RNA polymerases for U6 and U1 gene transcription.
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Affiliation(s)
- Neha Verma
- Department of Biology, Molecular Biology Institute, San Diego State University, CA, USA
| | - Ann Marie Hurlburt
- Department of Biology, Molecular Biology Institute, San Diego State University, CA, USA
| | - Angela Wolfe
- Department of Chemistry and Biochemistry, Molecular Biology Institute, San Diego State University, CA, USA
| | - Mun Kyoung Kim
- Department of Chemistry and Biochemistry, Molecular Biology Institute, San Diego State University, CA, USA
| | - Yoon Soon Kang
- Department of Chemistry and Biochemistry, Molecular Biology Institute, San Diego State University, CA, USA
| | - Jin Joo Kang
- Department of Chemistry and Biochemistry, Molecular Biology Institute, San Diego State University, CA, USA
| | - William E Stumph
- Department of Chemistry and Biochemistry, Molecular Biology Institute, San Diego State University, CA, USA
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9
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Dergai O, Cousin P, Gouge J, Satia K, Praz V, Kuhlman T, Lhôte P, Vannini A, Hernandez N. Mechanism of selective recruitment of RNA polymerases II and III to snRNA gene promoters. Genes Dev 2018; 32:711-722. [PMID: 29785964 PMCID: PMC6004067 DOI: 10.1101/gad.314245.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 04/17/2018] [Indexed: 01/03/2023]
Abstract
RNA polymerase II (Pol II) small nuclear RNA (snRNA) promoters and type 3 Pol III promoters have highly similar structures; both contain an interchangeable enhancer and "proximal sequence element" (PSE), which recruits the SNAP complex (SNAPc). The main distinguishing feature is the presence, in the type 3 promoters only, of a TATA box, which determines Pol III specificity. To understand the mechanism by which the absence or presence of a TATA box results in specific Pol recruitment, we examined how SNAPc and general transcription factors required for Pol II or Pol III transcription of SNAPc-dependent genes (i.e., TATA-box-binding protein [TBP], TFIIB, and TFIIA for Pol II transcription and TBP and BRF2 for Pol III transcription) assemble to ensure specific Pol recruitment. TFIIB and BRF2 could each, in a mutually exclusive fashion, be recruited to SNAPc. In contrast, TBP-TFIIB and TBP-BRF2 complexes were not recruited unless a TATA box was present, which allowed selective and efficient recruitment of the TBP-BRF2 complex. Thus, TBP both prevented BRF2 recruitment to Pol II promoters and enhanced BRF2 recruitment to Pol III promoters. On Pol II promoters, TBP recruitment was separate from TFIIB recruitment and enhanced by TFIIA. Our results provide a model for specific Pol recruitment at SNAPc-dependent promoters.
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Affiliation(s)
- Oleksandr Dergai
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Pascal Cousin
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jerome Gouge
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Karishma Satia
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Viviane Praz
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Tracy Kuhlman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Philippe Lhôte
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
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10
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R. Lambert J, K. Nordeen S. A role for the non-conserved N-terminal domain of the TATA-binding protein in the crosstalk between cell signaling pathways and steroid receptors. AIMS MOLECULAR SCIENCE 2015. [DOI: 10.3934/molsci.2015.2.64] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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11
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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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12
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Abstract
RNA transcription by all the three RNA polymerases (RNAPs) is tightly controlled, and loss of regulation can lead to, for example, cellular transformation and cancer. While most transcription factors act specifically with one polymerase, a small number have been shown to affect more than one polymerase to coordinate overall levels of transcription in cells. Here we show that TLS (translocated in liposarcoma), a protein originally identified as the product of a chromosomal translocation and which associates with both RNAP II and the spliceosome, also represses transcription by RNAP III. TLS was found to repress transcription from all three classes of RNAP III promoters in vitro and to associate with RNAP III genes in vivo, perhaps via a direct interaction with the pan-specific transcription factor TATA-binding protein (TBP). Depletion of TLS by small interfering RNA (siRNA) in HeLa cells resulted in increased steady-state levels of RNAP III transcripts as well as increased RNAP III and TBP occupancy at RNAP III-transcribed genes. Conversely, overexpression of TLS decreased accumulation of RNAP III transcripts. These unexpected findings indicate that TLS regulates both RNAPs II and III and supports the possibility that cross-regulation between RNA polymerases is important in maintaining normal cell growth.
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13
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Jawdekar GW, Henry RW. Transcriptional regulation of human small nuclear RNA genes. BIOCHIMICA ET BIOPHYSICA ACTA 2008; 1779:295-305. [PMID: 18442490 PMCID: PMC2684849 DOI: 10.1016/j.bbagrm.2008.04.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Revised: 04/01/2008] [Accepted: 04/02/2008] [Indexed: 01/06/2023]
Abstract
The products of human snRNA genes have been frequently described as performing housekeeping functions and their synthesis refractory to regulation. However, recent studies have emphasized that snRNA and other related non-coding RNA molecules control multiple facets of the central dogma, and their regulated expression is critical to cellular homeostasis during normal growth and in response to stress. Human snRNA genes contain compact and yet powerful promoters that are recognized by increasingly well-characterized transcription factors, thus providing a premier model system to study gene regulation. This review summarizes many recent advances deciphering the mechanism by which the transcription of human snRNA and related genes are regulated.
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Affiliation(s)
- Gauri W. Jawdekar
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, CA 90095
| | - R. William Henry
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824
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Friedman MJ, Wang CE, Li XJ, Li S. Polyglutamine expansion reduces the association of TATA-binding protein with DNA and induces DNA binding-independent neurotoxicity. J Biol Chem 2008; 283:8283-90. [PMID: 18218637 DOI: 10.1074/jbc.m709674200] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
TATA-binding protein (TBP) is essential for eukaryotic gene transcription. Human TBP contains a polymorphic polyglutamine (polyQ) domain in its N terminus and a DNA-binding domain in its highly conserved C terminus. Expansion of the polyQ domain to >42 glutamines typically results in spinocerebellar ataxia type 17 (SCA17), a neurodegenerative disorder that resembles Huntington disease. Our recent studies have demonstrated that polyQ expansion causes abnormal interaction of TBP with the general transcription factor TFIIB and induces neurodegeneration in transgenic SCA17 mice (Friedman, M. J., Shah, A. G., Fang, Z. H., Ward, E. G., Warren, S. T., Li, S., and Li, X. J. (2007) Nat. Neurosci. 10, 1519-1528). However, it remains unknown how polyQ expansion influences DNA binding by TBP. Here we report that polyQ expansion reduces in vitro binding of TBP to DNA and that mutant TBP fragments lacking an intact C-terminal DNA-binding domain are present in transgenic SCA17 mouse brains. polyQ-expanded TBP with a deletion spanning part of the DNA-binding domain does not bind DNA in vitro but forms nuclear aggregates and inhibits TATA-dependent transcription activity in cultured cells. When this TBP double mutant is expressed in transgenic mice, it forms nuclear inclusions in neurons and causes early death. These findings suggest that the polyQ tract affects the binding of TBP to promoter DNA and that polyQ-expanded TBP can induce neuronal toxicity independent of its interaction with DNA.
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Affiliation(s)
- Meyer J Friedman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
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15
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Polyglutamine domain modulates the TBP-TFIIB interaction: implications for its normal function and neurodegeneration. Nat Neurosci 2007; 10:1519-28. [PMID: 17994014 DOI: 10.1038/nn2011] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Accepted: 10/16/2007] [Indexed: 01/04/2023]
Abstract
Expansion of the polyglutamine (polyQ) tract in human TATA-box binding protein (TBP) causes the neurodegenerative disease spinocerebellar ataxia 17 (SCA17). It remains unclear how the polyQ tract regulates normal protein function and induces selective neuropathology in SCA17. We generated transgenic mice expressing polyQ-expanded TBP. These mice showed weight loss, progressive neurological symptoms and neurodegeneration before early death. Expanded polyQ tracts reduced TBP dimerization but enhanced the interaction of TBP with the general transcription factor IIB (TFIIB). In SCA17 transgenic mice, the small heat shock protein HSPB1, a potent neuroprotective factor, was downregulated, and TFIIB occupancy of the Hspb1 promoter was decreased. Overexpression of HSPB1 or TFIIB alleviated mutant TBP-induced neuritic defects. These findings implicate the polyQ domain of TBP in transcriptional regulation and provide insight into the molecular pathogenesis of SCA17.
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16
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Gu L, Husain-Ponnampalam R, Hoffmann-Benning S, Henry RW. The protein kinase CK2 phosphorylates SNAP190 to negatively regulate SNAPC DNA binding and human U6 transcription by RNA polymerase III. J Biol Chem 2007; 282:27887-96. [PMID: 17670747 DOI: 10.1074/jbc.m702269200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human U6 small nuclear RNA gene transcription by RNA polymerase III requires the general transcription factor SNAP(C), which binds to human small nuclear RNA core promoter elements and nucleates pre-initiation complex assembly with the Brf2-TFIIIB complex. Multiple components in this pathway are phosphorylated by the protein kinase CK2, including the Bdp1 subunit of the Brf2-TFIIIB complex, and RNA polymerase III, with negative and positive outcomes for U6 transcription, respectively. However, a role for CK2 phosphorylation of SNAP(C) in U6 transcription has not been defined. In this report, we investigated the role of CK2 in modulating the transcriptional properties of SNAP(C) and demonstrate that within SNAP(C), CK2 phosphorylates the N-terminal half of the SNAP190 subunit at two regions (amino acids 20-63 and 514-545) that each contain multiple CK2 consensus sites. SNAP190 phosphorylation by CK2 inhibits both SNAP(C) DNA binding and U6 transcription activity. Mutational analyses of SNAP190 support a model wherein CK2 phosphorylation triggers an allosteric inhibition of the SNAP190 Myb DNA binding domain.
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Affiliation(s)
- Liping Gu
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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17
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Abstract
Quantitative characteristics of interaction recombinant TATA-binding protein (TBP) with oligonucleotides identical to natural TATA-containing promoter region genes of mammals are received. In particular, new experimental data about the importance guanine in 8-th position of the TATA-element for affinity to TBP are received. The experimental data, testifying that raised maintenance G and С nucleotides in flanks of TATA-element does the contribution to affinity to TBP are received.
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18
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Rollins J, Veras I, Cabarcas S, Willis I, Schramm L. Human Maf1 negatively regulates RNA polymerase III transcription via the TFIIB family members Brf1 and Brf2. Int J Biol Sci 2007; 3:292-302. [PMID: 17505538 PMCID: PMC1865091 DOI: 10.7150/ijbs.3.292] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Accepted: 04/24/2007] [Indexed: 11/05/2022] Open
Abstract
RNA polymerase III (RNA pol III) transcribes many of the small structural RNA molecules involved in processing and translation, thereby regulating the growth rate of a cell. Initiation of pol III transcription requires the evolutionarily conserved pol III initiation factor TFIIIB. TFIIIB is the molecular target of regulation by tumor suppressors, including p53, RB and the RB-related pocket proteins. However, our understanding of negative regulation of human TFIIIB-mediated transcription by other proteins is limited. In this study we characterize a RNA pol III luciferase assay and further demonstrate in vivo that a human homolog of yeast Maf1 represses RNA pol III transcription. Additionally, we show that Maf1 repression of RNA pol III transcription occurs via TFIIIB, specifically through the TFIIB family members Brf1 and Brf2.
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Affiliation(s)
- Janet Rollins
- 1. Department of Biological Sciences, St. John's University, Queens NY, USA
| | - Ingrid Veras
- 1. Department of Biological Sciences, St. John's University, Queens NY, USA
| | - Stephanie Cabarcas
- 1. Department of Biological Sciences, St. John's University, Queens NY, USA
| | - Ian Willis
- 2. Department of Biochemistry, Albert Einstein College of Medicine, Bronx NY, USA
| | - Laura Schramm
- 1. Department of Biological Sciences, St. John's University, Queens NY, USA
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19
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Tao Z, Goodisman J, Penefsky HS, Souid AK. Caspase activation by anticancer drugs: the caspase storm. Mol Pharm 2007; 4:583-95. [PMID: 17439154 DOI: 10.1021/mp070002r] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This study measures the time-dependence of cellular caspase activation by anticancer drugs and compares it with that of cellular respiration. Intracellular caspase activation and cellular respiration were measured during continuous exposure of Jurkat, HL-60, and HL-60/MX2 (deficient in topoisomerase-II) cells to dactinomycin, doxorubicin, and the platinum (Pt) compounds cisplatin, carboplatin, and oxaliplatin. Caspase activation was measured using the fluorogenic compound N-acetyl-asp-glu-val-asp-7-amino-4-trifluoromethyl coumarin (Ac-DEVD-AFC). We show that this substrate rapidly enters cells where it is efficiently cleaved at the aspartate residue by specific caspases, yielding the fluorescent compound 7-amino-4-trifluoromethyl coumarin (AFC). Following cell disruption, released AFC was separated on HPLC and detected by fluorescence. The appearance of AFC in cells was blocked by the pancaspase inhibitor benzyloxycarbonyl-val-ala-asp-fluoromethylketone, thus establishing that intracellular caspases were responsible for the cleavage. Caspase activity was first noted after about 2 h of incubation with doxorubicin or dactinomycin, the production of AFC being linear with time afterward. Caspase activation by doxorubicin was delayed in HL-60/MX2 cells, reflecting the critical role of topoisomerase-II in doxorubicin cytotoxicity. For both drugs, caspase activity increased rapidly between approximately 2 and approximately 6 h, went through a maximum, and decreased after approximately 8 h ("caspase storm"). Cisplatin treatment induced noticeable caspase activity only after approximately 14 h of incubation, and the fluorescent intensity of AFC became linear with time at approximately 16 h. Exposure of the cells to all of the drugs studied led to impaired cellular respiration and decreased cellular ATP, concomitant with caspase activation. Thus, the mitochondria are rapidly targeted by active caspases.
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Affiliation(s)
- Zhimin Tao
- Department of Chemistry, Syracuse University, 1-014 CST, Syracuse, New York 13244, USA
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20
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Khrapunov S, Brenowitz M. Influence of the N-terminal domain and divalent cations on self-association and DNA binding by the Saccharomyces cerevisiae TATA binding protein. Biochemistry 2007; 46:4876-87. [PMID: 17378582 PMCID: PMC2265637 DOI: 10.1021/bi061651w] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The localization of a single tryptophan to the N-terminal domain and six tyrosines to the C-terminal domain of TBP allows intrinsic fluorescence to separately report on the structures and dynamics of the full-length TATA binding protein (TBP) of Saccharomyces cerevisiae and its C-terminal DNA binding domain (TBPc) as a function of self-association and DNA binding. TBPc is more compact than the C-terminal domain within the full-length protein. Quenching of the intrinsic fluorescence by DNA and external dynamic quenchers shows that the observed tyrosine fluorescence is due to the four residues surrounding the "DNA binding saddle" of the C-terminal domain. TBP's N-terminal domain unfolds and changes its position relative to the C-terminal domain upon DNA binding. It partially shields the DNA binding saddle in octameric TBP, shifting upon dissociation to monomers to expose the saddle to DNA. Structure-energetic correlations were obtained by comparing the contribution that electrostatic interactions make to DNA binding by TBP and TBPc; DNA binding by TBPc is more hydrophobic than that by TBP, suggesting that the N-terminal domain either interacts with bound DNA directly or screens a part of the C-terminal domain, diminishing its electronegativity. The competition between divalent cations, K+, and DNA is not straightforward. Divalent cations strengthen binding of TBP to DNA and do so more strongly for TBPc. We suggest that divalent cations affect the structure of the bound DNA perhaps by stabilizing its distorted conformation in complexes with TBPc and TBP and that the N-terminal domain mimics the effects of divalent cations. These data support an autoinhibitory mechanism in which competition between the N-terminal domain and DNA for the saddle diminishes the DNA binding affinity of the full-length protein.
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Affiliation(s)
- Sergei Khrapunov
- * To whom correspondence should be addressed. S.K.: e-mail, . M.B.: e-mail,
| | - Michael Brenowitz
- * To whom correspondence should be addressed. S.K.: e-mail, . M.B.: e-mail,
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21
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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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22
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Thomas S, Yu MC, Sturm NR, Campbell DA. A non-universal transcription factor? The Leishmania tarentolae TATA box-binding protein LtTBP associates with a subset of promoters. Int J Parasitol 2006; 36:1217-26. [PMID: 16753168 DOI: 10.1016/j.ijpara.2006.04.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Revised: 04/07/2006] [Accepted: 04/12/2006] [Indexed: 11/18/2022]
Abstract
In kinetoplastids a 39-nucleotide spliced leader RNA is trans-spliced to the 5' end of nuclear mRNAs before they can be translated, thus the spliced leader is central to gene expression in kinetoplastid biology. The spliced leader RNA genes in Leishmania tarentolae contain promoters with important sites at approximately -60 and -30. A complex forms specifically on the -60 element as shown by electrophoretic mobility shift. The -60 shift complex has an estimated mass of 159 kDa. An L. tarentolae homologue of TATA-binding protein, LtTBP, co-fractionates with the -60 shift complex. Inclusion of anti-LtTBP antiserum in the shift assay disrupts the shift, indicating that LtTBP is a component of the complex that interacts with the TATA-less -60 element of the spliced leader RNA gene promoter. Both LtTBP and LtSNAP50 are found near the spliced leader RNA gene promoter and the promoters important for tRNAAla and/or U2 snRNA gene transcription, as demonstrated by chromatin immunoprecipitation. The LtTBP appears to interact with a subset of promoters in kinetoplastids with an affinity for short transcription units.
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Affiliation(s)
- Sean Thomas
- Molecular Biology Institute, University of California, Los Angeles, CA 90095-1489, USA
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23
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Emran F, Florens L, Ma B, Swanson SK, Washburn MP, Hernandez N. A role for Yin Yang-1 (YY1) in the assembly of snRNA transcription complexes. Gene 2006; 377:96-108. [PMID: 16769183 DOI: 10.1016/j.gene.2006.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Revised: 03/17/2006] [Accepted: 03/20/2006] [Indexed: 10/24/2022]
Abstract
The RNA polymerase (pol) II and III human small nuclear RNA (snRNA) genes have very similar promoters and recruit a number of common factors. In particular, both types of promoters utilize the small nuclear RNA activating protein complex (SNAP(c)) and the TATA box binding protein (TBP) for basal transcription, and are activated by Oct-1. We find that SNAP(c) purified from cell lines expressing tagged SNAP(c) subunits is associated with Yin Yang-1 (YY1), a factor implicated in both activation and repression of transcription. Recombinant YY1 accelerates the binding of SNAP(c) to the proximal sequence element, its target within snRNA promoters. Moreover, it enhances the formation of a complex on the pol III U6 snRNA promoter containing all the factors (SNAP(c), TBP, TFIIB-related factor 2 (Brf2), and B double prime 1 (Bdp1)) that are sufficient to direct in vitro U6 transcription when complemented with purified pol III, as well as that of a subcomplex containing TBP, Brf2, and Bdp1. YY1 is found on both the RNA polymerase II U1 and the RNA polymerase III U6 promoters as determined by chromatin immunoprecipitations. Thus, YY1 represents a new factor that participates in transcription complexes formed on both pol II and III promoters.
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Affiliation(s)
- Farida Emran
- Stony Brook University, Graduate Program in Molecular and Cellular Pharmacology, Stony Brook, NY 11794, USA
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24
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Hanzlowsky A, Jelencic B, Jawdekar G, Hinkley CS, Geiger JH, Henry RW. Co-expression of multiple subunits enables recombinant SNAPC assembly and function for transcription by human RNA polymerases II and III. Protein Expr Purif 2006; 48:215-23. [PMID: 16603380 PMCID: PMC2714255 DOI: 10.1016/j.pep.2006.02.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Revised: 02/07/2006] [Accepted: 02/19/2006] [Indexed: 11/21/2022]
Abstract
Human small nuclear (sn) RNA genes are transcribed by either RNA polymerase II or III depending upon the arrangement of their core promoter elements. Regardless of polymerase specificity, these genes share a requirement for a general transcription factor called the snRNA activating protein complex or SNAP(C). This multi-subunit complex recognizes the proximal sequence element (PSE) commonly found in the upstream promoters of human snRNA genes. SNAP(C) consists of five subunits: SNAP190, SNAP50, SNAP45, SNAP43, and SNAP19. Previous studies have shown that a partial SNAP(C) composed of SNAP190 (1-514), SNAP50, and SNAP43 expressed in baculovirus is capable of PSE-specific DNA binding and transcription of human snRNA genes by RNA polymerases II and III. Expression in a baculovirus system yields active complex but the concentration of such material is insufficient for many bio-analytical methods. Herein, we describe the co-expression in Escherichia coli of a partial SNAP(C) containing SNAP190 (1-505), SNAP50, SNAP43, and SNAP19. The co-expressed complex binds DNA specifically and recruits TBP to U6 promoter DNA. Importantly, this partial complex functions in reconstituted transcription of both human U1 and U6 snRNA genes by RNA polymerases II and III, respectively. This co-expression system will facilitate the functional characterization of this unusual multi-protein transcription factor that plays an important early role for transcription by two different polymerases.
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Affiliation(s)
- Andrej Hanzlowsky
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Blanka Jelencic
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Gauri Jawdekar
- Department of Microbiology and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Craig S. Hinkley
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - James H. Geiger
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
- Corresponding authors. Fax: +1 517 353 9334. E-mail addresses: (J.H. Geiger), (R.W. Henry)
| | - R. William Henry
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Corresponding authors. Fax: +1 517 353 9334. E-mail addresses: (J.H. Geiger), (R.W. Henry)
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25
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Saxena A, Ma B, Schramm L, Hernandez N. Structure-function analysis of the human TFIIB-related factor II protein reveals an essential role for the C-terminal domain in RNA polymerase III transcription. Mol Cell Biol 2005; 25:9406-18. [PMID: 16227591 PMCID: PMC1265830 DOI: 10.1128/mcb.25.21.9406-9418.2005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The transcription factors TFIIB, Brf1, and Brf2 share related N-terminal zinc ribbon and core domains. TFIIB bridges RNA polymerase II (Pol II) with the promoter-bound preinitiation complex, whereas Brf1 and Brf2 are involved, as part of activities also containing TBP and Bdp1 and referred to here as Brf1-TFIIIB and Brf2-TFIIIB, in the recruitment of Pol III. Brf1-TFIIIB recruits Pol III to type 1 and 2 promoters and Brf2-TFIIIB to type 3 promoters such as the human U6 promoter. Brf1 and Brf2 both have a C-terminal extension absent in TFIIB, but their C-terminal extensions are unrelated. In yeast Brf1, the C-terminal extension interacts with the TBP/TATA box complex and contributes to the recruitment of Bdp1. Here we have tested truncated Brf2, as well as Brf2/TFIIB chimeric proteins for U6 transcription and for assembly of U6 preinitiation complexes. Our results characterize functions of various human Brf2 domains and reveal that the C-terminal domain is required for efficient association of the protein with U6 promoter-bound TBP and SNAP(c), a type 3 promoter-specific transcription factor, and for efficient recruitment of Bdp1. This in turn suggests that the C-terminal extensions in Brf1 and Brf2 are crucial to specific recruitment of Pol III over Pol II.
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Affiliation(s)
- Ashish Saxena
- Genetics Program, Stony Brook University, Stony Brook, NY 11794, USA
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26
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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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27
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Ohtani M, Sugiyama M. Involvement of SRD2-mediated activation of snRNA transcription in the control of cell proliferation competence in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2005; 43:479-90. [PMID: 16098103 DOI: 10.1111/j.1365-313x.2005.02469.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The transcription machinery of small nuclear RNA (snRNA) genes has been investigated extensively in human cell-free systems, but its physiological function in vivo has not been addressed. This paper demonstrates the physiological role of an activator of snRNA transcription using a temperature-sensitive mutant of Arabidopsis thaliana, srd2. Phenotypic characteristics of the srd2 mutant suggest that the SRD2 gene participates in the control of competence in cell proliferation. The SRD2 gene encodes a nuclear protein that shares sequence similarity with the human SNAP50 protein, which is a subunit of SNAPc and is required for snRNA transcription in vitro. Our results, obtained from analysis of snRNA expression in the srd2 mutant, indicate that the SRD2 protein functions in the upregulation of transcription of snRNA genes, the promoters of which contain the upstream sequence element, to elevate cell proliferation competence.
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Affiliation(s)
- Misato Ohtani
- Botanical Gardens, Graduate School of Science, The University of Tokyo, 3-7-1 Hakusan, Bunkyo-ku, Tokyo 112-0001, Japan
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28
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Kundu P, Raychaudhuri S, Tsai W, Dasgupta A. Shutoff of RNA polymerase II transcription by poliovirus involves 3C protease-mediated cleavage of the TATA-binding protein at an alternative site: incomplete shutoff of transcription interferes with efficient viral replication. J Virol 2005; 79:9702-13. [PMID: 16014932 PMCID: PMC1181600 DOI: 10.1128/jvi.79.15.9702-9713.2005] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2004] [Accepted: 04/24/2005] [Indexed: 11/20/2022] Open
Abstract
The TATA-binding protein (TBP) plays a crucial role in cellular transcription catalyzed by all three DNA-dependent RNA polymerases. Previous studies have shown that TBP is targeted by the poliovirus (PV)-encoded protease 3C(pro) to bring about shutoff of cellular RNA polymerase II-mediated transcription in PV-infected cells. The processing of the majority of viral precursor proteins by 3C(pro) involves cleavages at glutamine-glycine (Q-G) sites. We present evidence that suggests that the transcriptional inactivation of TBP by 3C(pro) involves cleavage at the glutamine 104-serine 105 (Q104-S105) site of TBP and not at the Q18-G19 site as previously thought. The TBP Q104-S105 cleavage by 3C(pro) is greatly influenced by the presence of an aliphatic amino acid at the P4 position, a hallmark of 3C(pro)-mediated proteolysis. To examine the importance of host cell transcription shutoff in the PV life cycle, stable HeLa cell lines were created that express recombinant TBP resistant to cleavage by the viral proteases, called GG rTBP. Transcription shutoff was significantly impaired and delayed in GG rTBP cells upon infection with poliovirus compared with the cells that express wild-type recombinant TBP (wt rTBP). Infection of GG rTBP cells with poliovirus resulted in small plaques, significantly reduced viral RNA synthesis, and lower viral yields compared to the wt rTBP cell line. These results suggest that a defect in transcription shutoff can lead to inefficient replication of poliovirus in cultured cells.
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Affiliation(s)
- Pallob Kundu
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA School of Medicine, University of California--Los Angeles, 90095, USA
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29
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Gu L, Esselman WJ, Henry RW. Cooperation between small nuclear RNA-activating protein complex (SNAPC) and TATA-box-binding protein antagonizes protein kinase CK2 inhibition of DNA binding by SNAPC. J Biol Chem 2005; 280:27697-704. [PMID: 15955816 DOI: 10.1074/jbc.m503206200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein kinase CK2 regulates RNA polymerase III transcription of human U6 small nuclear RNA (snRNA) genes both negatively and positively depending upon whether the general transcription machinery or RNA polymerase III is preferentially phosphorylated. Human U1 snRNA genes share similar promoter architectures as that of U6 genes but are transcribed by RNA polymerase II. Herein, we report that CK2 inhibits U1 snRNA gene transcription by RNA polymerase II. Decreased levels of endogenous CK2 correlates with increased U1 expression, whereas CK2 associates with U1 gene promoters, indicating that it plays a direct role in U1 gene regulation. CK2 phosphorylates the general transcription factor small nuclear RNA-activating protein complex (SNAP(C)) that is required for both RNA polymerase II and III transcription, and SNAP(C) phosphorylation inhibits binding to snRNA gene promoters. However, restricted promoter access by phosphorylated SNAP(C) can be overcome by cooperative interactions with TATA-box-binding protein at a U6 promoter but not at a U1 promoter. Thus, CK2 may have the capacity to differentially regulate U1 and U6 transcription even though SNAP(C) is universally utilized for human snRNA gene transcription.
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Affiliation(s)
- Liping Gu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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30
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Jallow Z, Jacobi UG, Weeks DL, Dawid IB, Veenstra GJC. Specialized and redundant roles of TBP and a vertebrate-specific TBP paralog in embryonic gene regulation in Xenopus. Proc Natl Acad Sci U S A 2004; 101:13525-30. [PMID: 15345743 PMCID: PMC518790 DOI: 10.1073/pnas.0405536101] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The general transcription factor TATA-binding protein (TBP) is a key initiation factor involved in transcription by all three eukaryotic RNA polymerases. In addition, the related metazoan-specific TBP-like factor (TLF/TRF2) is essential for transcription of a distinct subset of genes. Here we characterize the vertebrate-specific TBP-like factor TBP2, using in vitro assays, in vivo antisense knockdown, and mRNA rescue experiments, as well as chromatin immunoprecipitation. We show that TBP2 is recruited to promoters in Xenopus oocytes in the absence of detectable TBP recruitment. Furthermore, TBP2 is essential for gastrulation and for the transcription of a subset of genes during Xenopus embryogenesis. In embryos, TBP2 protein is much less abundant than TBP, and moderate overexpression of TBP2 partially rescues an antisense knockdown of TBP levels and restores transcription of many TBP-dependent genes. TBP2 may be a TBP replacement factor in oocytes, whereas in embryos both TBP and TBP2 are required even though they exhibit partial redundancy and gene selectivity.
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Affiliation(s)
- Zainab Jallow
- Department of Molecular Biology, Radboud University Nijmegen Center for Molecular Life Sciences, 6500 HB Nijmegen, The Netherlands
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31
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Abstract
The TATA binding protein (TBP) is a subunit of several macromolecular complexes required for transcription by the three nuclear RNA polymerases. This observation led to the idea that TBP is a "universal" transcription factor. The discovery of three TBP-related factors and a macromolecular complex which lacks TBP but can support RNA polymerase II transcription in vitro has led to a reappraisal of the universal character of TBP. Several in vivo studies have rather shown that TBP plays a specific role in the activation of a subset of cellular genes controlling the cell cycle. In mammals, the aminoterminal region of TBP plays a highly selective role in the maternal immunotolerance of pregnancy.
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Affiliation(s)
- Irwin Davidson
- Institut de génétique et de biologie moléculaire et cellulaire, 1, rue Laurent Fries, 67404 Illkirch, France.
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32
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Zhao X, Herr W. Role of the inhibitory DNA-binding surface of human TATA-binding protein in recruitment of human TFIIB family members. Mol Cell Biol 2003; 23:8152-60. [PMID: 14585974 PMCID: PMC262358 DOI: 10.1128/mcb.23.22.8152-8160.2003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
TATA box recognition by TATA-binding protein (TBP) is a key step in transcriptional initiation complex assembly on TATA-box-containing RNA polymerase (Pol) II and III promoters. This process is inhibited by the inhibitory DNA-binding (IDB) surface on the human TBP core domain (TBP(CORE)) and is stimulated by promoter-specific basal transcription factors, such as two human TFIIB family members, the Pol II factor TFIIB and the Pol III factor Brf2, which is required for transcription from TATA-box-containing Pol III promoters. In contrast, the third TFIIB family member, Brf1, which is required for transcription from TATA-less Pol III promoters, does not stimulate TBP binding to the TATA box. We show here that in addition to its role in regulating TBP binding to a TATA box, the TBP IDB surface is unexpectedly involved in TBP association with all three TFIIB family members. Interestingly, the loss of IDB function has specific and diverse effects on each TFIIB family member. Indeed, the IDB and prototypical TFIIB contact surfaces of TBP, which lie on opposite sides of the TBP(CORE), cooperate to form the wild-type TFIIB-TBP-TATA box complex. These results reveal how, through differential usage of opposite surfaces of the TBP(CORE), TBP can achieve versatility in the assembly of Pol II and Pol III promoter complexes with TFIIB family proteins.
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Affiliation(s)
- Xuemei Zhao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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33
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Adams CA, Kar SR, Hopper JE, Fried MG. Self-association of the amino-terminal domain of the yeast TATA-binding protein. J Biol Chem 2003; 279:1376-82. [PMID: 14534318 DOI: 10.1074/jbc.m307867200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The amino-terminal domain of yeast TATA-binding protein has been proposed to play a crucial role in the self-association mechanism(s) of the full-length protein. Here we tested the ability of this domain to self-associate under a variety of solution conditions. Escherichia coli two-hybrid assays, in vitro pull-down assays, and in vitro cross-linking provided qualitative evidence for a limited and specific self-association. Sedimentation equilibrium analysis using purified protein was consistent with a monomer-dimer equilibrium with an apparent dissociation constant of approximately 8.4 microM. Higher stoichiometry associations remain possible but could not be detected by any of these methods. These results demonstrate that the minimal structure necessary for amino-terminal domain self-association must be present even in the absence of carboxyl-terminal domain structures. On the basis of these results we propose that amino-terminal domain structures contribute to the oligomerization interface of the full-length yeast TATA-binding protein.
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Affiliation(s)
- Claire A Adams
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA
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Affiliation(s)
- Irwin Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 Rue Laurent Fries, 67404 Illkirch Cédex, France.
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35
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Dasgupta A, Scovell WM. TFIIA abrogates the effects of inhibition by HMGB1 but not E1A during the early stages of assembly of the transcriptional preinitiation complex. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1627:101-10. [PMID: 12818428 DOI: 10.1016/s0167-4781(03)00080-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Successful assembly of the transcriptional preinitiation complex (PIC) is prerequisite to transcriptional initiation. At each stage of PIC assembly, regulation may occur as repressors and activators compete with and influence the incorporation of general transcription factors (GTFs). Both TFIIA and HMGB1 bind individually to the TATA-binding protein (TBP) to increase the rate of binding and to stabilize TBP binding to the TATA element. The competitive binding between these two cofactors for TBP/TATA was examined to show that TFIIA binds preferentially to TBP and inhibits HMGB1 binding. TFIIA can also readily dissociate HMGB1 from the preestablished HMGB1/TBP/TATA complex. This suggests that TFIIA and HMGB1 may bind to the same or overlapping sites on TBP and/or compete for similar DNA sites that are 5' to the TATA element. In addition, EMSA studies show that adenovirus E1A(13S) oncoprotein is unable to disrupt either the preestablished TFIIA/TBP/TATA or TFIIA/TFIIB/TBP/TATA complexes, but does inhibit complex formation when all transcription factors were simultaneously added. The inhibitory effect of E1A(13S) on the assembly of the PIC is overcome when excess TBP is added back in the reaction, while addition of either excess TFIIA or TFIIB were ineffective. This shows that the main target for E1A(13S) is free TBP and emphasizes the primary competition between E1A and the TATA-element for unbound TBP. This may be the principal point, if not the only point, at which E1A can target TBP to exert its inhibitory effect. This work, coupled with previous findings in our laboratory, indicates that TFIIA is much more effective than TFIIB in reversing the inhibitory effect of HMGB1 binding in the early stages of PIC assembly, which is consistent with the in vitro transcription results.
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Affiliation(s)
- A Dasgupta
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403-0213, USA
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36
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Abstract
Autoinhibitory domains are regions of proteins that negatively regulate the function of other domains via intramolecular interactions. Autoinhibition is a potent regulatory mechanism that provides tight "on-site" repression. The discovery of autoinhibition generates valuable clues to how a protein is regulated within a biological context. Mechanisms that counteract the autoinhibition, including proteolysis, post-translational modifications, as well as addition of proteins or small molecules in trans, often represent central regulatory pathways. In this review, we document the diversity of instances in which autoinhibition acts in cell regulation. Seven well-characterized examples (e.g., sigma(70), Ets-1, ERM, SNARE and WASP proteins, SREBP, Src) are covered in detail. Over thirty additional examples are listed. We present experimental approaches to characterize autoinhibitory domains and discuss the implications of this widespread phenomenon for biological regulation in both the normal and diseased states.
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Affiliation(s)
- Miles A Pufall
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, 2000 Circle of Hope, Salt Lake City 84112-5550, USA.
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37
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Hinkley CS, Hirsch HA, Gu L, LaMere B, Henry RW. The small nuclear RNA-activating protein 190 Myb DNA binding domain stimulates TATA box-binding protein-TATA box recognition. J Biol Chem 2003; 278:18649-57. [PMID: 12621023 DOI: 10.1074/jbc.m204247200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human U6 small nuclear RNA (snRNA) gene transcription by RNA polymerase III requires cooperative promoter binding involving the snRNA-activating protein complex (SNAP(c)) and the TATA-box binding protein (TBP). To investigate the role of SNAP(c) for TBP function at U6 promoters, TBP recruitment assays were performed using full-length TBP and a mini-SNAP(c) containing SNAP43, SNAP50, and a truncated SNAP190. Mini-SNAP(c) efficiently recruits TBP to the U6 TATA box, and two SNAP(c) subunits, SNAP43 and SNAP190, directly interact with the TBP DNA binding domain. Truncated SNAP190 containing only the Myb DNA binding domain is sufficient for TBP recruitment to the TATA box. Therefore, the SNAP190 Myb domain functions both to specifically recognize the proximal sequence element present in the core promoters of human snRNA genes and to stimulate TBP recognition of the neighboring TATA box present in human U6 snRNA promoters. The SNAP190 Myb domain also stimulates complex assembly with TBP and Brf2, a subunit of a snRNA-specific TFIIIB complex. Thus, interactions between the DNA binding domains of SNAP190 and TBP at juxtaposed promoter elements define the assembly of a RNA polymerase III-specific preinitiation complex.
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Affiliation(s)
- Craig S Hinkley
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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38
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Schmidt EE, Bondareva AA, Radke JR, Capecchi MR. Fundamental cellular processes do not require vertebrate-specific sequences within the TATA-binding protein. J Biol Chem 2003; 278:6168-74. [PMID: 12471023 DOI: 10.1074/jbc.m211205200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 180-amino acid core of the TATA-binding protein (TBPcore) is conserved from Archae bacteria to man. Vertebrate TBPs contain, in addition, a large and highly conserved N-terminal region that is not found in other phyla. We have generated a line of mice in which the tbp allele is replaced with a version, tbp(Delta N), which lacks 111 of 135 N-terminal amino acid residues. Most tbp(Delta N/Delta N) fetuses die in midgestation. To test whether a disruption of general cellular processes contributed to this fetal loss, primary fibroblast cultures were established from +/+, Delta N/+, and Delta N/Delta N fetuses. The cultures exhibited no genotype-dependent differences in proliferation or in expression of the proliferative markers dihydrofolate reductase (DHFR) mRNA (S phase-specific) and cdc25B mRNA (G(2)-specific). The mutation had no effect on transcription initiation site fidelity by either RNA polymerase II (pol II) or pol III. Moreover, the mutation did not cause differences in levels of U6 RNA, a pol III-dependent component of the splicing machinery, in mRNA splicing efficiency, in expression of housekeeping genes from either TATA-containing or TATA-less promoters, or in global gene expression. Our results indicated that general eukaryotic cell functions are unaffected by deletion of these vertebrate-specific sequences from TBP. Thus, all activities of this polypeptide domain must either be compensated for by redundant activities or be restricted to situations that are not represented by primary fibroblasts.
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Affiliation(s)
- Edward E Schmidt
- Department of Veterinary Molecular Biology, Marsh Laboratories, Montana State University, Bozeman, Montana 59717, USA.
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39
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Zhao X, Schramm L, Hernandez N, Herr W. A shared surface of TBP directs RNA polymerase II and III transcription via association with different TFIIB family members. Mol Cell 2003; 11:151-61. [PMID: 12535529 DOI: 10.1016/s1097-2765(02)00797-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The TATA box binding protein TBP is highly conserved and the only known basal factor that is involved in transcription by all three eukaryotic nuclear RNA polymerases from promoters with or without a TATA box. By mutagenesis and analysis on a selected set of four model pol II and pol III TATA box-containing and TATA-less promoters, we demonstrate that human TBP utilizes two modes to achieve its versatile functions. First, it uses a different set of surfaces on the conserved and structured TBP core domain to direct transcription from each of the four model promoters. Second, unlike yeast TBP, human TBP can use a shared surface to interact with two different TFIIB family members--TFIIB and Brf2--to initiate transcription by different RNA polymerases.
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Affiliation(s)
- Xuemei Zhao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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40
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Ma B, Hernandez N. Redundant cooperative interactions for assembly of a human U6 transcription initiation complex. Mol Cell Biol 2002; 22:8067-78. [PMID: 12391172 PMCID: PMC134731 DOI: 10.1128/mcb.22.22.8067-8078.2002] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The core human U6 promoter consists of a proximal sequence element (PSE) located upstream of a TATA box. The PSE is recognized by the snRNA-activating protein complex (SNAP(c)), which consists of five types of subunits, SNAP190, SNAP50, SNAP45, SNAP43, and SNAP19. The TATA box is recognized by TATA box binding protein (TBP). In addition, basal U6 transcription requires the SANT domain protein Bdp1 and the transcription factor IIB-related factor Brf2. SNAP(c) and mini-SNAP(c), which consists of just SNAP43, SNAP50, and the N-terminal third of SNAP190, bind cooperatively with TBP to the core U6 promoter. By generating complexes smaller than mini-SNAP(c), we have identified a 50-amino-acid region within SNAP190 that is (i) required for cooperative binding with TBP in the context of mini-SNAP(c) and (ii) sufficient for cooperative binding with TBP when fused to a heterologous DNA binding domain. We show that derivatives of mini-SNAP(c) lacking this region are active for transcription and that with such complexes, TBP can still be recruited to the U6 promoter through cooperative interactions with Brf2. Our results identify complexes smaller than mini-SNAP(c) that are transcriptionally active and show that there are at least two redundant mechanisms to stably recruit TBP to the U6 transcription initiation complex.
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Affiliation(s)
- Beicong Ma
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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41
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Affiliation(s)
- Laura Schramm
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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42
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Cabart P, Murphy S. Assembly of human small nuclear RNA gene-specific transcription factor IIIB complex de novo on and off promoter. J Biol Chem 2002; 277:26831-8. [PMID: 12016223 DOI: 10.1074/jbc.m203119200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In humans, transcription factor IIIB (TFIIIB)-alpha governs basal transcription from small nuclear RNA genes by RNA polymerase III (pol III). One of the components of this complex, BRFU/TFIIIB50, is specific for these promoters, whereas TATA-binding protein (TBP) and hB" are required for pol III transcription from both gene external and internal promoters. We show that hB" is specifically recruited to a promoter-bound TBP.BRFU complex, which we have previously demonstrated as forming on TATA-containing templates. The N-terminal region of BRFU, containing a zinc ribbon domain, acts as a damper of hB" binding. TBP deactivates this negative mechanism through protein-protein contacts with both BRFU and hB", which may then promote their cooperative binding to form TFIIIB-alpha. In addition, we have identified a GC-rich sequence downstream from the TATA box (the BURE) which, depending on the strength of TATA box, can either enhance BRFU binding to the TBP.DNA complex or hB" association with the BRFU.TBP.DNA complex, and subsequently stimulate pol III transcription. Moreover, mutation of the BURE reduces pol III transcription and induces transcription by RNA polymerase II from the U2 gene promoter carrying a minimal TATA box.
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Affiliation(s)
- Pavel Cabart
- Chemical Pathology Unit, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom.
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43
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Zhao X, Herr W. A regulated two-step mechanism of TBP binding to DNA: a solvent-exposed surface of TBP inhibits TATA box recognition. Cell 2002; 108:615-27. [PMID: 11893333 DOI: 10.1016/s0092-8674(02)00648-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The TATA box binding protein TBP plays a universally important role in eukaryotic nuclear transcription. By mutagenesis, we have discovered a solvent-exposed surface of the structured TBP core domain that is important for inhibition of the DNA binding and DNA-bending activities of full-length wild-type TBP. Full-length wild-type TBP initially binds the TATA box to form an unstable complex containing unbent DNA, and then it slowly forms a stable complex containing bent DNA. TFIIB greatly accelerates formation of a bent TFIIB-TBP-TATA box complex, and the inhibitory DNA binding surface of TBP contributes to the cooperativity of binding to TFIIB. Using TBP and TFIIB, we show that TBP can bind the TATA box through a regulated two-step mechanism, involving a transition from unbent complex to bent complex.
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Affiliation(s)
- Xuemei Zhao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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44
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Cabart P, Murphy S. BRFU, a TFIIB-like factor, is directly recruited to the TATA-box of polymerase III small nuclear RNA gene promoters through its interaction with TATA-binding protein. J Biol Chem 2001; 276:43056-64. [PMID: 11564744 DOI: 10.1074/jbc.m108515200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human snRNA genes transcribed by RNA polymerase II (pol II) and III (pol III) have different core promoter elements. Both gene types contain similar proximal sequence elements (PSEs) but differ in the absence (pol II) or presence (pol III) of a TATA-box, which, together with the PSE, determines the assembly of a pol III-specific pre-initiation complex. BRFU is a factor exclusively required for transcription of the pol III-type snRNA genes. We report that recruitment of BRFU to the TATA-box of these promoters is TATA-binding protein (TBP)-dependent. BRFU in turn stabilizes TBP on TATA-containing template and extends the TBP footprint both upstream and downstream of the TATA element. The core domain of TBP is sufficient for BRFU.TBP.DNA complex formation and for interaction with BRFU off the template. We have mapped amino acid residues within TBP and domains of BRFU that mediate this interaction. BRFU has no specificity for sequences flanking the TATA-box and also forms a stable complex on the TATA-box of the pol II-specific adenovirus major late promoter (AdMLP). Furthermore, pol III-type transcription can initiate from an snRNA gene promoter containing an AdMLP TATA-box and flanking sequences. Therefore, the polymerase recruitment is not simply determined by the sequence of the TATA-box and immediate flanking sequences.
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Affiliation(s)
- P Cabart
- Chemical Pathology Unit, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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45
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Hamada M, Huang Y, Lowe TM, Maraia RJ. Widespread use of TATA elements in the core promoters for RNA polymerases III, II, and I in fission yeast. Mol Cell Biol 2001; 21:6870-81. [PMID: 11564871 PMCID: PMC99864 DOI: 10.1128/mcb.21.20.6870-6881.2001] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In addition to directing transcription initiation, core promoters integrate input from distal regulatory elements. Except for rare exceptions, it has been generally found that eukaryotic tRNA and rRNA genes do not contain TATA promoter elements and instead use protein-protein interactions to bring the TATA-binding protein (TBP), to the core promoter. Genomewide analysis revealed TATA elements in the core promoters of tRNA and 5S rRNA (Pol III), U1 to U5 snRNA (Pol II), and 37S rRNA (Pol I) genes in Schizosaccharomyces pombe. Using tRNA-dependent suppression and other in vivo assays, as well as in vitro transcription, we demonstrated an obligatory requirement for upstream TATA elements for tRNA and 5S rRNA expression in S. pombe. The Pol III initiation factor Brf is found in complexes with TFIIIC and Pol III in S. pombe, while TBP is not, consistent with independent recruitment of TBP by TATA. Template commitment assays are consistent with this and confirm that the mechanisms of transcription complex assembly and initiation by Pol III in S. pombe differ substantially from those in other model organisms. The results were extended to large-rRNA synthesis, as mutation of the TATA element in the Pol I promoter also abolishes rRNA expression in fission yeast. A survey of other organisms' genomes reveals that a substantial number of eukaryotes may use widespread TATAs for transcription. These results indicate the presence of TATA-unified transcription systems in contemporary eukaryotes and provide insight into the residual need for TBP by all three Pols in other eukaryotes despite a lack of TATA elements in their promoters.
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MESH Headings
- Amino Acid Motifs
- Amino Acid Sequence
- Base Sequence
- Conserved Sequence
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Evolution, Molecular
- Genome, Fungal
- Immunoblotting
- Molecular Sequence Data
- Promoter Regions, Genetic
- RNA Polymerase I/genetics
- RNA Polymerase I/metabolism
- RNA Polymerase II/genetics
- RNA Polymerase II/metabolism
- RNA Polymerase III/genetics
- RNA Polymerase III/metabolism
- RNA, Ribosomal/metabolism
- RNA, Ribosomal, 5S/genetics
- RNA, Transfer/metabolism
- Schizosaccharomyces/metabolism
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- TATA-Box Binding Protein
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Transcription, Genetic
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Affiliation(s)
- M Hamada
- Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892-2753, USA
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46
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Das D, Scovell WM. The binding interaction of HMG-1 with the TATA-binding protein/TATA complex. J Biol Chem 2001; 276:32597-605. [PMID: 11390376 DOI: 10.1074/jbc.m011792200] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
High mobility protein-1 (HMG-1) has been shown to regulate transcription by RNA polymerase II. In the context that it acts as a transcriptional repressor, it binds to the TATA-binding protein (TBP) to form the HMG-1/TBP/TATA complex, which is proposed to inhibit the assembly of the preinitiation complex. By using electrophoretic mobility shift assays, we show that the acidic C-terminal domain of HMG-1 and the N terminus of human TBP are the domains that are essential for the formation of a stable HMG-1/TBP/TATA complex. HMG-1 binding increases the affinity of TBP for the TATA element by 20-fold, which is reflected in a significant stimulation of the rate of TBP binding, with little effect on the dissociation rate constant. In support of the binding target of HMG-1 being the N terminus of hTBP, the N-terminal polypeptide of human TBP competes with and inhibits HMG-1/TBP/TATA complex formation. Deletion of segments of the N terminus of human TBP was used to map the region(s) where HMG-1 binds. These findings indicate that interaction of HMG-1 with the Q-tract (amino acids 55-95) in hTBP is primarily responsible for stable complex formation. In addition, HMG-1 and the monoclonal antibody, 1C2, specific to the Q-tract, compete for the same site. Furthermore, calf thymus HMG-1 forms a stable complex with the TBP/TATA complex that contains TBP from either human or Drosophila but not yeast. This is again consistent with the importance of the Q-tract for this stable interaction and shows that the interaction extends over many species but does not include yeast TBP.
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Affiliation(s)
- D Das
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, USA
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47
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Hernandez N. Small nuclear RNA genes: a model system to study fundamental mechanisms of transcription. J Biol Chem 2001; 276:26733-6. [PMID: 11390411 DOI: 10.1074/jbc.r100032200] [Citation(s) in RCA: 181] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- N Hernandez
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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48
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Huang Y, Maraia RJ. Comparison of the RNA polymerase III transcription machinery in Schizosaccharomyces pombe, Saccharomyces cerevisiae and human. Nucleic Acids Res 2001; 29:2675-90. [PMID: 11433012 PMCID: PMC55761 DOI: 10.1093/nar/29.13.2675] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Multi-subunit transcription factors (TF) direct RNA polymerase (pol) III to synthesize a variety of essential small transcripts such as tRNAs, 5S rRNA and U6 snRNA. Use by pol III of both TATA-less and TATA-containing promoters, together with progress in the Saccharomyces cerevisiae and human systems towards elucidating the mechanisms of actions of the pol III TFs, provides a paradigm for eukaryotic gene transcription. Human and S.cerevisiae pol III components reveal good general agreement in the arrangement of orthologous TFs that are distributed along tRNA gene control elements, beginning upstream of the transcription initiation site and extending through the 3' terminator element, although some TF subunits have diverged beyond recognition. For this review we have surveyed the Schizosaccharomyces pombe database and identified 26 subunits of pol III and associated TFs that would appear to represent the complete core set of the pol III machinery. We also compile data that indicate in vivo expression and/or function of 18 of the fission yeast proteins. A high degree of homology occurs in pol III, TFIIIB, TFIIIA and the three initiation-related subunits of TFIIIC that are associated with the proximal promoter element, while markedly less homology is apparent in the downstream TFIIIC subunits. The idea that the divergence in downstream TFIIIC subunits is associated with differences in pol III termination-related mechanisms that have been noted in the yeast and human systems but not reviewed previously is also considered.
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Affiliation(s)
- Y Huang
- Laboratory of Molecular Growth Regulation, National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Drive MSC 2753, Bethesda, MD 20892-2753, USA
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49
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Affiliation(s)
- E P Geiduschek
- Division of Biology and Center for Molecular Genetics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0634, USA.
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Chong SS, Hu P, Hernandez N. Reconstitution of transcription from the human U6 small nuclear RNA promoter with eight recombinant polypeptides and a partially purified RNA polymerase III complex. J Biol Chem 2001; 276:20727-34. [PMID: 11279001 DOI: 10.1074/jbc.m100088200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human U6 small nuclear (sn) RNA core promoter consists of a proximal sequence element, which recruits the multisubunit factor SNAP(c), and a TATA box, which recruits the TATA box-binding protein, TBP. In addition to SNAP(c) and TBP, transcription from the human U6 promoter requires two well defined factors. The first is hB", a human homologue of the B" subunit of yeast TFIIIB generally required for transcription of RNA polymerase III genes, and the second is hBRFU, one of two human homologues of the yeast TFIIIB subunit BRF specifically required for transcription of U6-type RNA polymerase III promoters. Here, we have partially purified and characterized a RNA polymerase III complex that can direct transcription from the human U6 promoter when combined with recombinant SNAP(c), recombinant TBP, recombinant hB", and recombinant hBRFU. These results open the way to reconstitution of U6 transcription from entirely defined components.
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Affiliation(s)
- S S Chong
- Department of Microbiology and Graduate Program of Molecular and Cellular Biology, State University of New York at Stony Brook, Stony Brook, New York 11794, USA
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