1
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Daiß JL, Griesenbeck J, Tschochner H, Engel C. Synthesis of the ribosomal RNA precursor in human cells: mechanisms, factors and regulation. Biol Chem 2023; 404:1003-1023. [PMID: 37454246 DOI: 10.1515/hsz-2023-0214] [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: 05/12/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
The ribosomal RNA precursor (pre-rRNA) comprises three of the four ribosomal RNAs and is synthesized by RNA polymerase (Pol) I. Here, we describe the mechanisms of Pol I transcription in human cells with a focus on recent insights gained from structure-function analyses. The comparison of Pol I-specific structural and functional features with those of other Pols and with the excessively studied yeast system distinguishes organism-specific from general traits. We explain the organization of the genomic rDNA loci in human cells, describe the Pol I transcription cycle regarding structural changes in the enzyme and the roles of human Pol I subunits, and depict human rDNA transcription factors and their function on a mechanistic level. We disentangle information gained by direct investigation from what had apparently been deduced from studies of the yeast enzymes. Finally, we provide information about how Pol I mutations may contribute to developmental diseases, and why Pol I is a target for new cancer treatment strategies, since increased rRNA synthesis was correlated with rapidly expanding cell populations.
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Affiliation(s)
- Julia L Daiß
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Joachim Griesenbeck
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Herbert Tschochner
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Christoph Engel
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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2
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Benc M, Martinkova S, Rychtarova J, Fulka J, Bartkova A, Fulka H, Laurincik J. Assessing the effect of interspecies oocyte nucleolar material dosage on embryonic development. Theriogenology 2020; 155:17-24. [PMID: 32590076 DOI: 10.1016/j.theriogenology.2020.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/26/2020] [Accepted: 06/01/2020] [Indexed: 12/19/2022]
Abstract
Sequence differences are considered to be the basic cause of developmental failure in interspecies embryos when more distant species are combined. However, other phenomena, such as insufficient or excessive quantity of specific cellular factors, might also influence the outcome. These effects are usually not considered. One of the organelles shown to contain different amount of proteins is the oocyte nucleolus-like body. Here we show that upon interspecies transfer, a single porcine nucleolus-like body is unable to support the development of a mouse parthenogenetic embryo derived from an enucleolated oocyte. However, when the amount of the porcine nucleolar material is increased to equalize the amount of mouse nucleolar material by transferring two nucleolus-like bodies, mouse embryos are able to pass the developmental block elicited by enucleolation. These embryos progress to the blastocyst stage at rates comparable to controls. Thus, using the model of an interspecies nucleolus-like body transplantation between mouse and pig oocytes, we show that an inadequate amount of nucleolar factors, rather than the species origin, affects the development. In a wider context of interspecies nuclear transfer schemes, the observed incompatibility between more distant species might not stem simply from sequence differences but also from improper dosage of key cellular factors.
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Affiliation(s)
- Michal Benc
- Institute of Animal Science, Prague, Czech Republic; Constantine the Philosopher University in Nitra, Faculty of Natural Sciences, Nitra, Slovak Republic
| | | | | | - Josef Fulka
- Institute of Animal Science, Prague, Czech Republic
| | - Alexandra Bartkova
- Constantine the Philosopher University in Nitra, Faculty of Natural Sciences, Nitra, Slovak Republic; Institute of Animal Physiology and Genetics AS CR, Libechov, Czech Republic
| | - Helena Fulka
- Institute of Experimental Medicine CAS, Prague, Czech Republic.
| | - Jozef Laurincik
- Constantine the Philosopher University in Nitra, Faculty of Natural Sciences, Nitra, Slovak Republic; Institute of Animal Physiology and Genetics AS CR, Libechov, Czech Republic
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3
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Organization and regulation of gene transcription. Nature 2019; 573:45-54. [PMID: 31462772 DOI: 10.1038/s41586-019-1517-4] [Citation(s) in RCA: 332] [Impact Index Per Article: 66.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/30/2019] [Indexed: 12/18/2022]
Abstract
The regulated transcription of genes determines cell identity and function. Recent structural studies have elucidated mechanisms that govern the regulation of transcription by RNA polymerases during the initiation and elongation phases. Microscopy studies have revealed that transcription involves the condensation of factors in the cell nucleus. A model is emerging for the transcription of protein-coding genes in which distinct transient condensates form at gene promoters and in gene bodies to concentrate the factors required for transcription initiation and elongation, respectively. The transcribing enzyme RNA polymerase II may shuttle between these condensates in a phosphorylation-dependent manner. Molecular principles are being defined that rationalize transcriptional organization and regulation, and that will guide future investigations.
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4
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Gottesfeld JM. Milestones in transcription and chromatin published in the Journal of Biological Chemistry. J Biol Chem 2019; 294:1652-1660. [PMID: 30710013 DOI: 10.1074/jbc.tm118.004162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
During Herbert Tabor's tenure as Editor-in-Chief from 1971 to 2010, JBC has published many seminal papers in the fields of chromatin structure, epigenetics, and regulation of transcription in eukaryotes. As of this writing, more than 21,000 studies on gene transcription at the molecular level have been published in JBC since 1971. This brief review will attempt to highlight some of these ground-breaking discoveries and show how early studies published in JBC have influenced current research. Papers published in the Journal have reported the initial discovery of multiple forms of RNA polymerase in eukaryotes, identification and purification of essential components of the transcription machinery, and identification and mechanistic characterization of various transcriptional activators and repressors and include studies on chromatin structure and post-translational modifications of the histone proteins. The large body of literature published in the Journal has inspired current research on how chromatin organization and epigenetics impact regulation of gene expression.
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Affiliation(s)
- Joel M Gottesfeld
- Departments of Molecular Medicine and Chemistry, The Scripps Research Institute, La Jolla, California 92037.
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5
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Jin R, Zhou W. TIF-IA: An oncogenic target of pre-ribosomal RNA synthesis. Biochim Biophys Acta Rev Cancer 2016; 1866:189-196. [PMID: 27641688 DOI: 10.1016/j.bbcan.2016.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 09/13/2016] [Accepted: 09/14/2016] [Indexed: 12/30/2022]
Abstract
Cancer cells devote the majority of their energy consumption to ribosome biogenesis, and pre-ribosomal RNA transcription accounts for 30-50% of all transcriptional activity. This aberrantly elevated biological activity is an attractive target for cancer therapeutic intervention if approaches can be developed to circumvent the development of side effects in normal cells. TIF-IA is a transcription factor that connects RNA polymerase I with the UBF/SL-1 complex to initiate the transcription of pre-ribosomal RNA. Its function is conserved in eukaryotes from yeast to mammals, and its activity is promoted by the phosphorylation of various oncogenic kinases in cancer cells. The depletion of TIF-IA induces cell death in lung cancer cells and mouse embryonic fibroblasts but not in several other normal tissue types evaluated in knock-out studies. Furthermore, the nuclear accumulation of TIF-IA under UTP down-regulated conditions requires the activity of LKB1 kinase, and LKB1-inactivated cancer cells are susceptible to cell death under such stress conditions. Therefore, TIF-IA may be a unique target to suppress ribosome biogenesis without significantly impacting the survival of normal tissues.
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Affiliation(s)
- Rui Jin
- Department of Hematology and Medical Oncology, The Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Wei Zhou
- Department of Hematology and Medical Oncology, The Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA; Department of Pathology and Laboratory Medicine and Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
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6
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Marstad A, Landsverk OJB, Strømme O, Otterlei M, Collas P, Sundan A, Brede G. A-kinase anchoring protein AKAP95 is a novel regulator of ribosomal RNA synthesis. FEBS J 2016; 283:757-70. [PMID: 26683827 DOI: 10.1111/febs.13630] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 11/23/2015] [Accepted: 12/14/2015] [Indexed: 11/30/2022]
Abstract
The RNA polymerase I transcription apparatus acquires and integrates the combined information from multiple cellular signalling cascades to regulate ribosome production essential for cell growth and proliferation. In the present study, we show that a subpopulation of A-kinase anchoring protein 95 (AKAP95) targets the nucleolus during interphase and is involved in regulating rRNA production. We show that AKAP95 co-localizes with the nucleolar upstream binding factor, an essential rRNA transcription factor. Similar to other members of the C2 H2 -zinc finger family, we show, using systematic selection and evolution of ligands by exponential enrichment and in vitro binding analysis, that AKAP95 has a preference for GC-rich DNA in vitro, whereas fluorescence recovery after photobleaching analysis reveals AKAP95 to be a highly mobile protein that exhibits RNA polymerase I and II dependent nucleolar trafficking. In line with its GC-binding features, chromatin immunoprecipitation analysis revealed AKAP95 to be associated with ribosomal chromatin in vivo. Manipulation of AKAP95-expression in U2OS cells revealed a reciprocal relationship between the expression of AKAP95 and 47S rRNA. Taken together, our data indicate that AKAP95 is a novel nucleolus-associated protein with a regulatory role on rRNA production.
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Affiliation(s)
- Anne Marstad
- Centre of Molecular Inflammation Research (CEMIR), Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Ole Jørgen B Landsverk
- Department of Pathology, Centre for Immune Regulation, Oslo University Hospital Norway, Norway
| | - Olaf Strømme
- Centre of Molecular Inflammation Research (CEMIR), Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Marit Otterlei
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Norway
| | - Anders Sundan
- Centre of Molecular Inflammation Research (CEMIR), Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,KG Jebsen Centre for Myeloma Research, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Gaute Brede
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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7
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Dieci G, Fermi B, Bosio MC. Investigating transcription reinitiation through in vitro approaches. Transcription 2015; 5:e27704. [PMID: 25764113 DOI: 10.4161/trns.27704] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
By influencing the number of RNA molecules repeatedly synthesized from the same gene, the control of transcription reinitiation has the potential to shape the transcriptome. Transcription reinitiation mechanisms have been mainly addressed in vitro, through approaches based on both crude and reconstituted systems. These studies support the notion that transcription reinitiation and its regulation rely on dedicated networks of molecular interactions within transcription machineries. At the same time, comparison with in vivo transcription rates suggests that additional mechanisms, factors and conditions must exist in the nucleus, whose biochemical elucidation is a fascinating challenge for future in vitro transcription studies.
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Affiliation(s)
- Giorgio Dieci
- a Dipartimento di Bioscienze; Università degli Studi di Parma; Parma, Italy
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8
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Voit R, Seiler J, Grummt I. Cooperative Action of Cdk1/cyclin B and SIRT1 Is Required for Mitotic Repression of rRNA Synthesis. PLoS Genet 2015; 11:e1005246. [PMID: 26023773 PMCID: PMC4449194 DOI: 10.1371/journal.pgen.1005246] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 04/27/2015] [Indexed: 12/29/2022] Open
Abstract
Mitotic repression of rRNA synthesis requires inactivation of the RNA polymerase I (Pol I)-specific transcription factor SL1 by Cdk1/cyclin B-dependent phosphorylation of TAFI110 (TBP-associated factor 110) at a single threonine residue (T852). Upon exit from mitosis, T852 is dephosphorylated by Cdc14B, which is sequestered in nucleoli during interphase and is activated upon release from nucleoli at prometaphase. Mitotic repression of Pol I transcription correlates with transient nucleolar enrichment of the NAD+-dependent deacetylase SIRT1, which deacetylates another subunit of SL1, TAFI68. Hypoacetylation of TAFI68 destabilizes SL1 binding to the rDNA promoter, thereby impairing transcription complex assembly. Inhibition of SIRT1 activity alleviates mitotic repression of Pol I transcription if phosphorylation of TAFI110 is prevented. The results demonstrate that reversible phosphorylation of TAFI110 and acetylation of TAFI68 are key modifications that regulate SL1 activity and mediate fluctuations of pre-rRNA synthesis during cell cycle progression. In metazoans, transcription is arrested during mitosis. Previous studies have established that mitotic repression of cellular transcription is mediated by Cdk1/cyclin B-dependent phosphorylation of basal transcription factors that nucleate transcription complex formation. Repression of rDNA transcription at the onset of mitosis is brought about by inactivation of the TBP-containing transcription factor SL1 by Cdk1/cyclin B-dependent phosphorylation of the TAFI110 subunit, which impairs the interaction with UBF and the assembly of pre-initiation complexes. Here we show that hCdc14B, the phosphatase that regulates Cdk1/cyclin B activity and progression through mitosis, promotes reactivation of rDNA transcription by dephosphorylating TAFI110. In addition, the NAD+-dependent deacetylase SIRT1 becomes transiently enriched in nucleoli at the onset of mitosis. SIRT1 deacetylates TAFI68, another subunit of SL1, hypoacetylation of TAFI68 destabilizing SL1 binding to the rDNA promoter and impairing transcription complex assembly. The results reveal that modulation of SL1 activity by reversible acetylation of TAFI68 and phosphorylation of TAFI110 are key modifications that mediate oscillation of rDNA transcription during cell cycle progression.
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Affiliation(s)
- Renate Voit
- Division of Molecular Biology of the Cell II, German Cancer Research Center, DKFZ-ZMBH Alliance, Heidelberg, Germany
- * E-mail:
| | - Jeanette Seiler
- Division of Molecular Biology of the Cell II, German Cancer Research Center, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Ingrid Grummt
- Division of Molecular Biology of the Cell II, German Cancer Research Center, DKFZ-ZMBH Alliance, Heidelberg, Germany
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9
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Shi G, Wu M, Fang L, Yu F, Cheng S, Li J, Du JX, Wong J. PHD finger protein 2 (PHF2) represses ribosomal RNA gene transcription by antagonizing PHF finger protein 8 (PHF8) and recruiting methyltransferase SUV39H1. J Biol Chem 2014; 289:29691-700. [PMID: 25204660 DOI: 10.1074/jbc.m114.571653] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Regulation of rDNA transcription is central to cell growth and proliferation. PHF2 and PHF8 belong to a subfamily of histone demethylases that also possess a PHD domain-dependent di-/trimethylated histone 3 lysine 4 (H3K4me2/3) binding activity and are known to be enriched in the nucleolus. In this study, we show that, unlike PHF8 that activates rDNA transcription, PHF2 inhibits rDNA transcription. Depletion of PHF2 by RNA interference increases and overexpression of PHF2 decreases rDNA transcription, respectively, whereas simultaneous depletion of PHF8 and PHF2 restores the level of rDNA transcription. The inhibition of rDNA transcription by PHF2 depends on its H3K4me2/3 binding activity that is also required for PHF2 association with the promoter of rDNA genes but not its demethylase activity. We provide evidence that PHF2 is likely to repress rDNA transcription by competing with PHF8 for binding of rDNA promoter and by recruiting H3K9me2/3 methyltransferase SUV39H1. We also provide evidence that, whereas PHF8 promotes, PHF2 represses the transcriptional activity of RARα, Oct4, and KLF4 and a few PHF8 target genes tested. Taken together, our study demonstrates a repressive role for PHF2 in transcription by RNA polymerase I and II.
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Affiliation(s)
- Guang Shi
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Meng Wu
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Lan Fang
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Fang Yu
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Shimeng Cheng
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiwen Li
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - James X Du
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiemin Wong
- From the Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
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10
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Blattner C, Jennebach S, Herzog F, Mayer A, Cheung AC, Witte G, Lorenzen K, Hopfner KP, Heck AJ, Aebersold R, Cramer P. Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth. Genes Dev 2011; 25:2093-105. [PMID: 21940764 PMCID: PMC3197207 DOI: 10.1101/gad.17363311] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 08/24/2011] [Indexed: 01/24/2023]
Abstract
Cell growth is regulated during RNA polymerase (Pol) I transcription initiation by the conserved factor Rrn3/TIF-IA in yeast/humans. Here we provide a structure-function analysis of Rrn3 based on a combination of structural biology with in vivo and in vitro functional assays. The Rrn3 crystal structure reveals a unique HEAT repeat fold and a surface serine patch. Phosphorylation of this patch represses human Pol I transcription, and a phospho-mimetic patch mutation prevents Rrn3 binding to Pol I in vitro and reduces cell growth and Pol I gene occupancy in vivo. Cross-linking indicates that Rrn3 binds Pol I between its subcomplexes, AC40/19 and A14/43, which faces the serine patch. The corresponding region of Pol II binds the Mediator head that cooperates with transcription factor (TF) IIB. Consistent with this, the Rrn3-binding factor Rrn7 is predicted to be a TFIIB homolog. This reveals the molecular basis of Rrn3-regulated Pol I initiation and cell growth, and indicates a general architecture of eukaryotic transcription initiation complexes.
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Affiliation(s)
- Claudia Blattner
- Gene Center, Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Stefan Jennebach
- Gene Center, Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Franz Herzog
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössiche Technische Hochschule (ETH) Zurich, 8093 Zurich, Switzerland
| | - Andreas Mayer
- Gene Center, Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Alan C.M. Cheung
- Gene Center, Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Gregor Witte
- Gene Center, Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Kristina Lorenzen
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands
| | - Karl-Peter Hopfner
- Gene Center, Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössiche Technische Hochschule (ETH) Zurich, 8093 Zurich, Switzerland
- Faculty of Science, University of Zurich, 8057 Zurich, Switzerland
| | - Patrick Cramer
- Gene Center, Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
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11
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Lebedev A, Scharffetter-Kochanek K, Iben S. A novel activity enhances promoter escape of RNA polymerase I. Biochem Biophys Res Commun 2009; 380:695-8. [PMID: 19285024 DOI: 10.1016/j.bbrc.2009.01.154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Accepted: 01/26/2009] [Indexed: 11/27/2022]
Abstract
We have characterized a novel transcriptional activity from HeLa cells that is required for ribosomal gene transcription by RNA polymerase I. This activity has a native molecular mass of 16 kDa and does not bind to conventional chromatographic resins. Single-round and immobilized-template experiments revealed that initiation complex formation is independent of the novel activity. Functional studies showed that it stimulates the transition from initiation to elongation, promoter escape. Thus the novel activity does not resemble the mouse initiation/elongation factor TIF-IC but is a true novel entity.
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Affiliation(s)
- Anton Lebedev
- Department of Dermatology and Allergic Diseases, University of Ulm, Meyerhofstrasse N27, 89081 Ulm, Germany
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12
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Lebedev A, Scharffetter-Kochanek K, Iben S. Truncated Cockayne Syndrome B Protein Represses Elongation by RNA Polymerase I. J Mol Biol 2008; 382:266-74. [DOI: 10.1016/j.jmb.2008.07.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 07/02/2008] [Accepted: 07/08/2008] [Indexed: 12/21/2022]
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13
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Lutomska A, Lebedev A, Scharffetter-Kochanek K, Iben S. The transcriptional response to distinct growth factors is impaired in Werner syndrome cells. Exp Gerontol 2008; 43:820-6. [PMID: 18625297 DOI: 10.1016/j.exger.2008.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Revised: 04/16/2008] [Accepted: 06/12/2008] [Indexed: 10/21/2022]
Abstract
The Werner syndrome protein (WRN) is mutated in Werner syndrome (WS) and plays a role in telomere maintenance, DNA repair and transcription. WS represents a premature aging syndrome with severe growth retardation. Here we show that WRN is critically required to mediate the stimulatory effect of vascular endothelial growth factor (VEGF), basic fibroblast growth factor (FGF-b) and epidermal growth factor (EGF) on the activity of RNA polymerase I (Pol I). Recombinant WRN specifically reconstitutes RNA polymerase I transcription in extracts from Werner syndrome fibroblasts in vitro. In addition, we identified a critical role for WRN during promoter clearance of Pol I transcription, but not in elongation. Notably, WRN was isolated in a complex with Pol I and was crosslinked to the unmethylated, active proportion of rDNA genes in quiescent cells suggesting a so far unknown role for WRN in epigenetic regulation. This together with alterations in Pol I transcription provide a novel mechanism possibly underlying at least in part the severe growth retardation and premature aging in Werner syndrome patients.
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Affiliation(s)
- Anna Lutomska
- Department of Dermatology and Allergic Diseases, University of Ulm, Maienweg 12, 89081 Ulm, Germany
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14
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Lin CH, Platt MD, Ficarro SB, Hoofnagle MH, Shabanowitz J, Comai L, Hunt DF, Owens GK. Mass spectrometric identification of phosphorylation sites of rRNA transcription factor upstream binding factor. Am J Physiol Cell Physiol 2007; 292:C1617-24. [PMID: 17182730 DOI: 10.1152/ajpcell.00176.2006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
rRNA transcription is a fundamental requirement for all cellular growth processes and is activated by the phosphorylation of the upstream binding factor (UBF) in response to growth stimulation. Even though it is well known that phosphorylation of UBF is required for its activation and is a key step in activation of rRNA transcription, as yet, there has been no direct mapping of the UBF phosphorylation sites. The results of the present studies employed sophisticated nano-flow HPLC-microelectrospray-ionization tandem mass spectrometry (nHPLC-μESI-MS/MS) coupled with immobilized metal affinity chromatography (IMAC) and computer database searching algorithms to identify 10 phosphorylation sites on UBF at serines 273, 336, 364, 389, 412, 433, 484, 546, 584, and 638. We then carried out functional analysis of two of these sites, serines 389 and 584. Serine-alanine substitution mutations of 389 (S389A) abrogated rRNA transcription in vitro and in vivo, whereas mutation of serine 584 (S584A) reduced transcription in vivo but not in vitro. In contrast, serine-glutamate mutation of 389 (S389E) restored transcriptional activity. Moreover, S389A abolished UBF-SL1 interaction in vitro, while S389E partially restored UBF-SL1 interaction. Taken together, the results of these studies suggest that growth factor stimulation induces an increase in rRNA transcriptional activity via phosphorylation of UBF at serine 389 in part by facilitating a rate-limiting step in the recruitment of RNA polymerase I: i.e., recruitment of SL1. Moreover, studies provide critical new data regarding multiple additional UBF phosphorylation sites that will require further characterization by the field.
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MESH Headings
- Algorithms
- Amino Acid Sequence
- Animals
- Cells, Cultured
- Chromatography, Affinity
- Chromatography, High Pressure Liquid
- Databases, Protein
- Molecular Sequence Data
- Mutation
- Myocytes, Smooth Muscle/metabolism
- Nanotechnology
- Peptide Mapping/methods
- Phosphorylation
- Pol1 Transcription Initiation Complex Proteins/biosynthesis
- Pol1 Transcription Initiation Complex Proteins/genetics
- Pol1 Transcription Initiation Complex Proteins/isolation & purification
- Pol1 Transcription Initiation Complex Proteins/metabolism
- Protein Processing, Post-Translational
- RNA Polymerase I/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Rats
- Recombinant Proteins/metabolism
- Serine/metabolism
- Spectrometry, Mass, Electrospray Ionization
- Tandem Mass Spectrometry
- Transcription, Genetic
- Transfection
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Affiliation(s)
- C Huie Lin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Box 800736, 1300 Jefferson Park Ave., Charlottesville, VA 22908, USA
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15
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Gorski JJ, Pathak S, Panov K, Kasciukovic T, Panova T, Russell J, Zomerdijk JCBM. A novel TBP-associated factor of SL1 functions in RNA polymerase I transcription. EMBO J 2007; 26:1560-8. [PMID: 17318177 PMCID: PMC1829371 DOI: 10.1038/sj.emboj.7601601] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2006] [Accepted: 01/22/2007] [Indexed: 11/09/2022] Open
Abstract
In mammalian RNA polymerase I transcription, SL1, an assembly of TBP and associated factors (TAFs), is essential for preinitiation complex formation at ribosomal RNA gene promoters in vitro. We provide evidence for a novel component of SL1, TAF(I)41 (MGC5306), which functions in Pol I transcription. TAF(I)41 resides at the rDNA promoter in the nucleolus and co-purifies and co-immunoprecipitates with SL1. TAF(I)41 immunodepletion from nuclear extracts dramatically reduces Pol I transcription; addition of SL1 restores the ability of these extracts to support Pol I transcription. In cells, siRNA-mediated decreased expression of TAF(I)41 leads to loss of SL1 from the rDNA promoter in vivo, with concomitant loss of Pol I from the rDNA and reduced synthesis of the pre-rRNA. Extracts from these cells support reduced levels of Pol I transcription; addition of SL1 to the extracts raises the level of Pol I transcription. These data suggest that TAF(I)41 is integral to transcriptionally active SL1 and imply a role for SL1, including the TAF(I)41 subunit, in Pol I recruitment and, therefore, preinitiation complex formation in vivo.
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Affiliation(s)
- Julia J Gorski
- Division of Gene Regulation and Expression, College of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Shalini Pathak
- Division of Gene Regulation and Expression, College of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Kostya Panov
- Division of Gene Regulation and Expression, College of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Taciana Kasciukovic
- Division of Gene Regulation and Expression, College of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Tanya Panova
- Division of Gene Regulation and Expression, College of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Jackie Russell
- Division of Gene Regulation and Expression, College of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Joost C B M Zomerdijk
- Division of Gene Regulation and Expression, College of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
- Division of Gene Regulation and Expression, College of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dow Street, Dundee DD1 5EH, UK. Tel.: +44 1382 384242; Fax: +44 1382 348072; E-mail:
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16
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Panova TB, Panov KI, Russell J, Zomerdijk JCBM. Casein kinase 2 associates with initiation-competent RNA polymerase I and has multiple roles in ribosomal DNA transcription. Mol Cell Biol 2006; 26:5957-68. [PMID: 16880508 PMCID: PMC1592790 DOI: 10.1128/mcb.00673-06] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mammalian RNA polymerase I (Pol I) complexes contain a number of associated factors, some with undefined regulatory roles in transcription. We demonstrate that casein kinase 2 (CK2) in human cells is associated specifically only with the initiation-competent Pol Ibeta isoform and not with Pol Ialpha. Chromatin immunoprecipitation analysis places CK2 at the ribosomal DNA (rDNA) promoter in vivo. Pol Ibeta-associated CK2 can phosphorylate topoisomerase IIalpha in Pol Ibeta, activator upstream binding factor (UBF), and selectivity factor 1 (SL1) subunit TAFI110. A potent and selective CK2 inhibitor, 3,8-dibromo-7-hydroxy-4-methylchromen-2-one, limits in vitro transcription to a single round, suggesting a role for CK2 in reinitiation. Phosphorylation of UBF by CK2 increases SL1-dependent stabilization of UBF at the rDNA promoter, providing a molecular mechanism for the stimulatory effect of CK2 on UBF activation of transcription. These positive effects of CK2 in Pol I transcription contrast to that wrought by CK2 phosphorylation of TAFI110, which prevents SL1 binding to rDNA, thereby abrogating the ability of SL1 to nucleate preinitiation complex (PIC) formation. Thus, CK2 has the potential to regulate Pol I transcription at multiple levels, in PIC formation, activation, and reinitiation of transcription.
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Affiliation(s)
- Tatiana B Panova
- Division of Gene Regulation and Expression, School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee DD1 5EH, United Kingdom
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Panov KI, Friedrich JK, Russell J, Zomerdijk JCBM. UBF activates RNA polymerase I transcription by stimulating promoter escape. EMBO J 2006; 25:3310-22. [PMID: 16858408 PMCID: PMC1523182 DOI: 10.1038/sj.emboj.7601221] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Accepted: 06/09/2006] [Indexed: 01/10/2023] Open
Abstract
Ribosomal RNA gene transcription by RNA polymerase I (Pol I) is the driving force behind ribosome biogenesis, vital to cell growth and proliferation. The key activator of Pol I transcription, UBF, has been proposed to act by facilitating recruitment of Pol I and essential basal factor SL1 to rDNA promoters. However, we found no evidence that UBF could stimulate recruitment or stabilization of the pre-initiation complex (PIC) in reconstituted transcription assays. In this, UBF is fundamentally different from archetypal activators of transcription. Our data imply that UBF exerts its stimulatory effect on RNA synthesis, after PIC formation, promoter opening and first phosphodiester bond formation and before elongation. We provide evidence to suggest that UBF activates transcription in the transition between initiation and elongation, at promoter escape by Pol I. This novel role for UBF in promoter escape would allow control of rRNA synthesis at active rDNA repeats, independent of and complementary to the promoter-specific targeting of SL1 and Pol I during PIC assembly. We posit that stimulation of promoter escape could be a general mechanism of activator function.
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Affiliation(s)
- Kostya I Panov
- Division of Gene Regulation and Expression, School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - J Karsten Friedrich
- Division of Gene Regulation and Expression, School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Jackie Russell
- Division of Gene Regulation and Expression, School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Joost C B M Zomerdijk
- Division of Gene Regulation and Expression, School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
- Division of Gene Regulation and Expression, School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee DD1 5EH, UK. Tel.: +44 1382 384242; Fax: +44 1382 388072; E-mail:
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Nováková Z, Man P, Novák P, Hozák P, Hodný Z. Separation of nuclear protein complexes by blue native polyacrylamide gel electrophoresis. Electrophoresis 2006; 27:1277-87. [PMID: 16502463 DOI: 10.1002/elps.200500504] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The nucleus is a highly structured organelle with distinct compartmentalization of specific functions. To understand the functions of these nuclear compartments, detailed description of protein complexes which form these structures is of crucial importance. We explored therefore the potential of blue native PAGE (BN-PAGE) method for the separation of nuclear protein complexes. We focused on (i) solubility and stability of nuclear complexes under conditions prerequisite for the separation by BN-PAGE, (ii) improved separation of native nuclear protein complexes using 2-D colorless native/blue native PAGE (CN-/BN-PAGE), and (iii) mass spectrometric analysis of protein complexes which were isolated directly from native 1-D or from 2-D CN/BN-PAGE gels. The suitability of BN-PAGE for nuclear proteomic research is demonstrated by the successful separation of polymerase I and polymerase II complexes, and by mass spectrometric determination of U1 small nuclear ribonucleoprotein particle composition. Moreover, practical advice for sample preparation is provided.
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Affiliation(s)
- Zora Nováková
- Department of Cell Ultrastructure and Molecular Biology, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Praque, Czech Republic
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19
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Friedrich JK, Panov KI, Cabart P, Russell J, Zomerdijk JCBM. TBP-TAF complex SL1 directs RNA polymerase I pre-initiation complex formation and stabilizes upstream binding factor at the rDNA promoter. J Biol Chem 2005; 280:29551-8. [PMID: 15970593 PMCID: PMC3858828 DOI: 10.1074/jbc.m501595200] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Knowledge of the role of components of the RNA polymerase I transcription machinery is paramount to understanding regulation of rDNA expression. We describe key findings for the roles of essential transcription factor SL1 and activator upstream binding factor (UBF). We demonstrate that human SL1 can direct accurate Pol I transcription in the absence of UBF and can interact with the rDNA promoter independently and stably, consistent with studies of rodent SL1 but contrary to previous reports of human SL1. UBF itself does not bind stably to rDNA but rapidly associates and dissociates. We show that SL1 significantly reduces the rate of dissociation of UBF from the rDNA promoter. Our findings challenge the idea that UBF activates transcription through recruitment of SL1 at the rDNA promoter and suggest that the rate of pre-initiation complex (PIC) formation is primarily determined by the rate of association of SL1, rather than UBF, with the promoter. Therefore, we propose that SL1 directs PIC formation, functioning in core promoter binding, RNA polymerase I recruitment, and UBF stabilization and that SL1-promoter complex formation is a necessary prerequisite to the assembly of functional and stable PICs that include the UBF activator in mammalian cells.
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Affiliation(s)
| | | | | | | | - Joost C. B. M. Zomerdijk
- A Wellcome Trust Senior Research Fellow in the Basic Biomedical Sciences. To whom correspondence should be addressed. Tel.: 44-1382-344242; Fax: 44-1382-348072;
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Bric A, Radebaugh CA, Paule MR. Photocross-linking of the RNA Polymerase I Preinitiation and Immediate Postinitiation Complexes. J Biol Chem 2004; 279:31259-67. [PMID: 15161919 DOI: 10.1074/jbc.m311828200] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The architecture of eukaryotic rRNA transcription complexes was analyzed, revealing facts significant to the RNA polymerase (pol) I initiation process. Functional initiation and elongation complexes were mapped by site-specific photocross-linking to template DNA. Polymerase I is recruited to the promoter via protein-protein interactions with DNA-bound transcription initiation factor-IB. The latter's TATA-binding protein (TBP) and TAFs photocross-link to the promoter from -78 to +10 relative to the tis (+1). Although TBP does not bind DNA using its TATA-binding saddle, it does photocross-link to a 22-bp sequence that does not resemble a TATA box. Only TAF(I)96 (the mammalian TAF(I) 68, yeast Rrn7p homolog) overlaps significantly with the DNA interaction cleft of pol I based on modeling to the pol II crystal structure. None of the pol I-specific subunits that are localized on the lips of the cleft (A49 and A34.5) or the pol I-specific stalk (A43 and A14) cross-link to DNA. Pol I does not extend significantly upstream of the promoter-proximal border of the factor complex (-11 to -14), and similarly in the promoter proximal elongation complex, the enzyme does not contact DNA upstream of its normal exit from the cleft.
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Affiliation(s)
- Anka Bric
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
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Affiliation(s)
- Lucio Comai
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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22
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Hemleben V, Volkov RA, Zentgraf U, Medina FJ. Molecular Cell Biology: Organization and Molecular Evolution of rDNA, Nucleolar Dominance, and Nucleolus Structure. PROGRESS IN BOTANY 2004. [DOI: 10.1007/978-3-642-18819-0_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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23
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Claypool JA, French SL, Johzuka K, Eliason K, Vu L, Dodd JA, Beyer AL, Nomura M. Tor pathway regulates Rrn3p-dependent recruitment of yeast RNA polymerase I to the promoter but does not participate in alteration of the number of active genes. Mol Biol Cell 2003; 15:946-56. [PMID: 14595104 PMCID: PMC329406 DOI: 10.1091/mbc.e03-08-0594] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Yeast cells entering into stationary phase decrease rRNA synthesis rate by decreasing both the number of active genes and the transcription rate of individual active genes. Using chromatin immunoprecipitation assays, we found that the association of RNA polymerase I with the promoter and the coding region of rDNA is decreased in stationary phase, but association of transcription factor UAF with the promoter is unchanged. Similar changes were also observed when growing cells were treated with rapamycin, which is known to inhibit the Tor signaling system. Rapamycin treatment also caused a decrease in the amount of Rrn3p-polymerase I complex, similar to stationary phase. Because recruitment of Pol I to the rDNA promoter is Rrn3p-dependent as shown in this work, these data suggest that the decrease in the transcription rate of individual active genes in stationary phase is achieved by the Tor signaling system acting at the Rrn3p-dependent polymerase recruitment step. Miller chromatin spreads of cells treated with rapamycin and cells in post-log phase confirm this conclusion and demonstrate that the Tor system does not participate in alteration of the number of active genes observed for cells entering into stationary phase.
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Affiliation(s)
- Jonathan A Claypool
- Department of Biological Chemistry, University of California, Irvine, Irvine, California 92697-1700, USA
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24
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Grummt I. Life on a planet of its own: regulation of RNA polymerase I transcription in the nucleolus. Genes Dev 2003; 17:1691-702. [PMID: 12865296 DOI: 10.1101/gad.1098503r] [Citation(s) in RCA: 412] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ingrid Grummt
- Division of Molecular Biology of the Cell II, German Cancer Research Center, D-69120 Heidelberg, Germany.
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25
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Dundr M, Hoffmann-Rohrer U, Hu Q, Grummt I, Rothblum LI, Phair RD, Misteli T. A kinetic framework for a mammalian RNA polymerase in vivo. Science 2002; 298:1623-6. [PMID: 12446911 DOI: 10.1126/science.1076164] [Citation(s) in RCA: 350] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We have analyzed the kinetics of assembly and elongation of the mammalian RNA polymerase I complex on endogenous ribosomal genes in the nuclei of living cells with the use of in vivo microscopy. We show that components of the RNA polymerase I machinery are brought to ribosomal genes as distinct subunits and that assembly occurs via metastable intermediates. With the use of computational modeling of imaging data, we have determined the in vivo elongation time of the polymerase, and measurements of recruitment and incorporation frequencies show that incorporation of components into the assembling polymerase is inefficient. Our data provide a kinetic and mechanistic framework for the function of a mammalian RNA polymerase in living cells.
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Affiliation(s)
- Miroslav Dundr
- National Cancer Institute (NCI), National Institutes of Health, Bethesda, MD 20892, USA
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26
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Iben S, Tschochner H, Bier M, Hoogstraten D, Hozák P, Egly JM, Grummt I. TFIIH plays an essential role in RNA polymerase I transcription. Cell 2002; 109:297-306. [PMID: 12015980 DOI: 10.1016/s0092-8674(02)00729-8] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
TFIIH is a multisubunit protein complex that plays an essential role in nucleotide excision repair and transcription of protein-coding genes. Here, we report that TFIIH is also required for ribosomal RNA synthesis in vivo and in vitro. In yeast, pre-rRNA synthesis is impaired in TFIIH ts strains. In a mouse, part of cellular TFIIH is localized within the nucleolus and is associated with subpopulations of both RNA polymerase I and the basal factor TIF-IB. Transcription systems lacking TFIIH are inactive and exogenous TFIIH restores transcriptional activity. TFIIH is required for productive but not abortive rDNA transcription, implying a postinitiation role in transcription. The results provide a molecular link between RNA polymerase I transcription and transcription-coupled repair of active ribosomal RNA genes.
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Affiliation(s)
- Sebastian Iben
- Division of Molecular Biology of the Cell II, German Cancer Research Center, D-69120, Heidelberg, Germany
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27
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Al-Khouri AM, Paule MR. A novel RNA polymerase I transcription initiation factor, TIF-IE, commits rRNA genes by interaction with TIF-IB, not by DNA binding. Mol Cell Biol 2002; 22:750-61. [PMID: 11784852 PMCID: PMC133551 DOI: 10.1128/mcb.22.3.750-761.2002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the small, free-living amoeba Acanthamoeba castellanii, rRNA transcription requires, in addition to RNA polymerase I, a single DNA-binding factor, transcription initiation factor IB (TIF-IB). TIF-IB is a multimeric protein that contains TATA-binding protein (TBP) and four TBP-associated factors that are specific for polymerase I transcription. TIF-IB is required for accurate and promoter-specific initiation of rRNA transcription, recruiting and positioning the polymerase on the start site by protein-protein interaction. In A. castellanii, partially purified TIF-IB can form a persistent complex with the ribosomal DNA (rDNA) promoter while homogeneous TIF-IB cannot. An additional factor, TIF-IE, is required along with homogeneous TIF-IB for the formation of a stable complex on the rDNA core promoter. We show that TIF-IE by itself, however, does not bind to the rDNA promoter and thus differs in its mechanism from the upstream binding factor and upstream activating factor, which carry out similar complex-stabilizing functions in vertebrates and yeast, respectively. In addition to its presence in impure TIF-IB, TIF-IE is found in highly purified fractions of polymerase I, with which it associates. Renaturation of polypeptides excised from sodium dodecyl sulfate-polyacrylamide gels showed that a 141-kDa polypeptide possesses all the known activities of TIF-IE.
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Affiliation(s)
- Anna Maria Al-Khouri
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
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28
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Abstract
Using an immobilized template assay, we observed two steps in assembly of the yeast RNA polymerase I (Pol I) preinitiation complex: stable binding of upstream activating factor (UAF) followed by recruitment of Pol I-Rrn3p and core factor (CF). Pol I is required for stable association of CF with the promoter and can be recruited in the absence of Rrn3p. Upon transcription initiation, Pol I-Rrn3p and CF dissociate from the promoter while UAF remains behind. These findings support a novel model in which the Pol I basal machinery cycles on and off the promoter with each round of transcription. This model accounts for previous observations that rRNA synthesis may be controlled by regulating both promoter accessibility and polymerase activity.
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Affiliation(s)
- P Aprikian
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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29
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Panov KI, Friedrich JK, Zomerdijk JC. A step subsequent to preinitiation complex assembly at the ribosomal RNA gene promoter is rate limiting for human RNA polymerase I-dependent transcription. Mol Cell Biol 2001; 21:2641-9. [PMID: 11283244 PMCID: PMC86895 DOI: 10.1128/mcb.21.8.2641-2649.2001] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The assembly, disassembly, and functional properties of transcription preinitiation complexes (PICs) of human RNA polymerase I (Pol I) play a crucial role in the regulation of rRNA gene expression. To study the factors and processes involved, an immobilized-promoter template assay has been developed that allows the isolation from nuclear extracts of functional PICs, which support accurate initiation of transcription. Immunoblotting of template-bound factors showed that these complexes contained the factors required to support initiation of transcription, SL1, upstream binding factor (UBF), and Pol I. We have demonstrated that, throughout a single round of transcription, SL1 and UBF remain promoter bound. Moreover, the promoter-bound SL1 and UBF retain the ability to function in transcription initiation. SL1 has a central role in the stable association of the PIC with the promoter DNA. The polymerase component of the PIC is released from the promoter during transcription yet is efficiently recycled and able to reinitiate from "poised" promoters carrying SL1 and UBF, since the PICs captured on the immobilized templates sustained multiple rounds of transcription. Kinetic analyses of initiation of transcription by Pol I revealed that Pol I-dependent transcription is rate limited in a step subsequent to recruitment and assembly of Pol I PICs. The rate of RNA synthesis is primarily determined by the rates at which the polymerase initiates transcription and escapes the promoter, referred to as promoter clearance. This rate-limiting step in Pol I transcription is likely to be a major target in the regulation of rRNA gene expression.
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Affiliation(s)
- K I Panov
- Division of Gene Regulation and Expression, Wellcome Trust Biocentre, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
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30
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Laurincik J, Zakhartchenko V, Avery B, Stojkovic M, Brem G, Wolf E, Muller M, Hyttel P. Activation of ribosomal RNA genes in pre-implantation In Vitro-produced and nuclear transfer bovine embryos. Reprod Domest Anim 2000. [DOI: 10.1046/j.1439-0531.2000.00275.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Abstract
In plants and animals, RNA polymerase I (pol I) can be purified in a form that is self-sufficient for accurate rRNA gene promoter-dependent transcription and that has biochemical properties suggestive of a single complex, or holoenzyme. In this study, we examined the promoter binding properties of a highly purified Brassica pol I holoenzyme activity. DNase I footprinting revealed protection of the core promoter region from approximately -30 to +20, in good agreement with the boundaries of the minimal promoter defined by deletion analyses (-33 to +6). Using conventional polyacrylamide electrophoretic mobility shift assays (EMSA), protein-DNA complexes were mostly excluded from the gel. However, agarose EMSA revealed promoter-specific binding activity that co-purified with promoter-dependent transcription activity. Titration, time-course, and competition experiments revealed the formation or dissociation of a single protein-DNA complex. This protein-DNA complex could be labeled by incorporation of radioactive ribonucleotides into RNA in the presence of alpha-amanitin, suggesting that the polymerase I enzyme is part of the complex. Collectively, these results suggest that transcriptionally competent pol I holoenzymes can associate with rRNA gene promoters in a single DNA binding event.
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Affiliation(s)
- J Saez-Vasquez
- Biology Department, Washington University, St. Louis, Missouri 63130, USA
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32
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Torres-Montaner A, Bolívar J, Astola A, Gimenez-Mas JA, Brieva JA, Valdivia MM. Immunohistochemical detection of ribosomal transcription factor UBF and AgNOR staining identify apoptotic events in neoplastic cells of Hodgkin's disease and in other lymphoid cells. J Histochem Cytochem 2000; 48:1521-30. [PMID: 11036095 DOI: 10.1177/002215540004801109] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Ribosomal RNA synthesis is a key molecular process for understanding the mechanisms that drive cell proliferation. In this process, the upstream binding factor (UBF) is involved in regulating rDNA transcription at the nucleolus, together with RNA polymerase I. Recently, UBF was demonstrated to be a substrate for selective cleavage by specific proteases during apoptosis. Here we studied the expression of UBF in several cases of Hodgkin's disease (HD) by immunostaining and found it to be absent or clearly diminished in a high proportion of Reed-Sternberg cells and Hodgkin cells compared to small reactive lymphocytes. This result contrasted with labeling of those cells by the AgNOR technique, a marker of cell proliferation dependent on increased amounts of several proteins related to ribosome assembly. Disappearance of UBF and preservation of other NOR proteins is consistent with the pattern of selective proteolysis by caspases described in early stages of apoptosis. This correlates well with our results observed on induction of apoptosis in Jurkat cells treated with anti-FAS/APO-1 serum and with those in aged germinal center B-cells, in which UBF was no longer seen although the staining signal of other NOR proteins was maintained. These results support the concept that the rate of apoptosis is higher in neoplastic cells of HD than in the benign reactive lymphocyte population. Differential proteolysis of NOR proteins, as revealed by double staining of UBF and AgNOR, may prove valuable for identification of early stages of apoptosis in cytological and histopathological samples.
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Affiliation(s)
- A Torres-Montaner
- Servicio de Anatomía Patológica, Hospital Universitario de Puerto Real, Cádiz, Spain
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33
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Chen M, von Mikecz A. Specific inhibition of rRNA transcription and dynamic relocation of fibrillarin induced by mercury. Exp Cell Res 2000; 259:225-38. [PMID: 10942594 DOI: 10.1006/excr.2000.4923] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Current evidence suggests that the nucleolus is composed of different substructures that are dynamic and form in response to the requirement for new ribosome synthesis. Thus, agents that disrupt nucleolar organization may deregulate basic cellular events and eventually contribute to human disease. Here we report that environmentally relevant concentrations (5 microM) of inorganic mercury induce a redistribution of nucleolar protein fibrillarin from the nucleolus to the nucleoplasm in epithelial cell lines. Since treatment with transcription inhibitors led to a similar relocation of fibrillarin, the effects of mercury on transcription were studied by run-on transcription assays: mercuric ions specifically blocked synthesis of ribosomal RNA, whereas activity of RNA polymerase II remained unchanged and occurred throughout the nucleoplasm. Moreover, we show by double-labeling that inhibition of nucleolar transcription and redistribution of fibrillarin occur simultaneously, underlining that fibrillarin relocation is a consequence of the blockade of ribosomal RNA synthesis by mercury. We also detected redistribution of fibrillarin in vivo, e.g., in splenic cells of mice chronically exposed to HgCl(2). Thus, implications of this alteration of nuclear structure and function for mercury-induced autoimmunity are discussed.
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Affiliation(s)
- M Chen
- Junior Research Group of Molecular Cell Biology, Heinrich-Heine-University, Düsseldorf, Germany
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34
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Abstract
Ribosomal RNA transcription initiation requires the melting of DNA to form an open complex, formation of the first few phosphodiester bonds, commencement of RNA polymerase I movement along the DNA, clearance of the promoter, and the formation of a steady-state ternary elongation complex. We examined DNA melting and promoter clearance by using potassium permanganate, diethylpyrocarbonate and methidiumpropylEDTA.Fe(II) footprinting. In combination, these methods demonstrated: (1) TIF-IB and RNA polymerase I are the only proteins required for formation of an initial approximately 9 base-pair open promoter region. This finding contradicts earlier results using diethylpyrocarbonate alone, which suggested an RNA synthesis requirement for stable melting. (2) DNA melting is temperature-dependent, with a tm between 15 and 20 degrees C. (3) Temperature-dependency of melting, as well as stalling the polymerase at sites close to the transcription start site revealed that the melted DNA region initially opens upstream of the transcription initiation site, and enlarges in a downstream direction coordinate with initiation, eventually attaining a steady-state transcription bubble of approximately 19 base-pairs. (4) The RNA-DNA hybrid protects the template DNA from single-strand footprinting reagents. The hybrid is 9 bp in length, consistent with the longer hybrid estimated by some for the Escherichia coli polymerase and with the hybrids estimated for eukaryotic polymerases II and III.
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Affiliation(s)
- B F Kahl
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins 80523-1870, USA
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Moorefield B, Greene EA, Reeder RH. RNA polymerase I transcription factor Rrn3 is functionally conserved between yeast and human. Proc Natl Acad Sci U S A 2000; 97:4724-9. [PMID: 10758157 PMCID: PMC18300 DOI: 10.1073/pnas.080063997] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have cloned a human cDNA that is related to the RNA polymerase I transcription factor Rrn3 of Saccharomyces cerevisiae. The recombinant human protein displays both sequence similarity and immunological crossreactivity to yeast Rrn3 and is capable of rescuing a yeast strain carrying a disruption of the RRN3 gene in vivo. Point mutation of an amino acid that is conserved between the yeast and human proteins compromises the function of each factor, confirming that the observed sequence similarity is functionally significant. Rrn3 is the first RNA polymerase I-specific transcription factor shown to be functionally conserved between yeast and mammals, suggesting that at least one mechanism that regulates ribosomal RNA synthesis is conserved among eukaryotes.
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Affiliation(s)
- B Moorefield
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
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36
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Roeder RG. Role of general and gene-specific cofactors in the regulation of eukaryotic transcription. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 1999; 63:201-18. [PMID: 10384284 DOI: 10.1101/sqb.1998.63.201] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- R G Roeder
- Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, New York 10021, USA
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37
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Grummt I. Regulation of mammalian ribosomal gene transcription by RNA polymerase I. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1999; 62:109-54. [PMID: 9932453 DOI: 10.1016/s0079-6603(08)60506-1] [Citation(s) in RCA: 190] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
All cells, from prokaryotes to vertebrates, synthesize vast amounts of ribosomal RNA to produce the several million new ribosomes per generation that are required to maintain the protein synthetic capacity of the daughter cells. Ribosomal gene (rDNA) transcription is governed by RNA polymerase I (Pol I) assisted by a dedicated set of transcription factors that mediate the specificity of transcription and are the targets of the pleiotrophic pathways the cell uses to adapt rRNA synthesis to cell growth. In the past few years we have begun to understand the specific functions of individual factors involved in rDNA transcription and to elucidate on a molecular level how transcriptional regulation is achieved. This article reviews our present knowledge of the molecular mechanism of rDNA transcriptional regulation.
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Affiliation(s)
- I Grummt
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
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38
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Albert AC, Denton M, Kermekchiev M, Pikaard CS. Histone acetyltransferase and protein kinase activities copurify with a putative Xenopus RNA polymerase I holoenzyme self-sufficient for promoter-dependent transcription. Mol Cell Biol 1999; 19:796-806. [PMID: 9858602 PMCID: PMC83936 DOI: 10.1128/mcb.19.1.796] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mounting evidence suggests that eukaryotic RNA polymerases preassociate with multiple transcription factors in the absence of DNA, forming RNA polymerase holoenzyme complexes. We have purified an apparent RNA polymerase I (Pol I) holoenzyme from Xenopus laevis cells by sequential chromatography on five columns: DEAE-Sepharose, Biorex 70, Sephacryl S300, Mono Q, and DNA-cellulose. Single fractions from every column programmed accurate promoter-dependent transcription. Upon gel filtration chromatography, the Pol I holoenzyme elutes at a position overlapping the peak of Blue Dextran, suggesting a molecular mass in the range of approximately 2 MDa. Consistent with its large mass, Coomassie blue-stained sodium dodecyl sulfate-polyacrylamide gels reveal approximately 55 proteins in fractions purified to near homogeneity. Western blotting shows that TATA-binding protein precisely copurifies with holoenzyme activity, whereas the abundant Pol I transactivator upstream binding factor does not. Also copurifying with the holoenzyme are casein kinase II and a histone acetyltransferase activity with a substrate preference for histone H3. These results extend to Pol I the suggestion that signal transduction and chromatin-modifying activities are associated with eukaryotic RNA polymerases.
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Affiliation(s)
- A C Albert
- Biology Department, Washington University, St. Louis, Missouri 63130, USA
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39
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Keener J, Josaitis CA, Dodd JA, Nomura M. Reconstitution of yeast RNA polymerase I transcription in vitro from purified components. TATA-binding protein is not required for basal transcription. J Biol Chem 1998; 273:33795-802. [PMID: 9837969 DOI: 10.1074/jbc.273.50.33795] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Five purified protein components, RNA polymerase I, Rrn3p, core factor, TBP (TATA-binding protein), and upstream activation factor, are sufficient for high level transcription in vitro from the Saccharomyces cerevisiae rDNA promoter. Rrn3p and pol I form a complex in solution that is active in specific initiation. Three protein components, pol I, Rrn3p, and core factor, and promoter sequence to -38, suffice for basal transcription. Unlike pol II and pol III, yeast pol I basal transcription does not require TBP. Instead, TBP, upstream activation factor, and the upstream element of the promoter together stimulate pol I basal transcription to a fully activated level. The role of TBP in pol I transcription is fundamentally different from its role in pol II or pol III transcription.
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Affiliation(s)
- J Keener
- Department of Biological Chemistry, University of California, Irvine, California 92697-1700, USA
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40
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Kihm AJ, Hershey JC, Haystead TA, Madsen CS, Owens GK. Phosphorylation of the rRNA transcription factor upstream binding factor promotes its association with TATA binding protein. Proc Natl Acad Sci U S A 1998; 95:14816-20. [PMID: 9843972 PMCID: PMC24532 DOI: 10.1073/pnas.95.25.14816] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/1998] [Accepted: 10/16/1998] [Indexed: 11/18/2022] Open
Abstract
rRNA synthesis by RNA polymerase I requires both the promoter selectivity factor 1, which is composed of TATA binding protein (TBP) and three TBP-associated factors, and the activator upstream binding factor (UBF). Whereas there is strong evidence implicating a role for phosphorylation of UBF in the control of growth-induced increases in rRNA transcription, the mechanism of this effect is not known. Results of immunoprecipitation studies with TBP antibodies showed increased recovery of phosphorylated UBF from growth-stimulated smooth muscle cells. Moreover, using an immobilized protein-binding assay, we found that phosphorylation of UBF in vivo in response to stimulation with different growth factors or in vitro with smooth muscle cell nuclear extract increased its binding to TBP. Finally, we demonstrated that UBF-TBP binding depended on the C-terminal 'acidic tail' of UBF that was hyperphosphorylated at multiple serine sites after growth factor stimulation. Results of these studies suggest that phosphorylation of UBF and subsequent binding to TBP represent a key regulatory step in control of growth-induced increases in rRNA synthesis.
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Affiliation(s)
- A J Kihm
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908-0011, USA
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41
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Dundr M, Olson MO. Partially processed pre-rRNA is preserved in association with processing components in nucleolus-derived foci during mitosis. Mol Biol Cell 1998; 9:2407-22. [PMID: 9725903 PMCID: PMC25507 DOI: 10.1091/mbc.9.9.2407] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Previous studies showed that components implicated in pre-rRNA processing, including U3 small nucleolar (sno)RNA, fibrillarin, nucleolin, and proteins B23 and p52, accumulate in perichromosomal regions and in numerous mitotic cytoplasmic particles, termed nucleolus-derived foci (NDF) between early anaphase and late telophase. The latter structures were analyzed for the presence of pre-rRNA by fluorescence in situ hybridization using probes for segments of pre-rRNA with known half-lives. The NDF did not contain the short-lived 5'-external transcribed spacer (ETS) leader segment upstream from the primary processing site in 47S pre-rRNA. However, the NDF contained sequences from the 5'-ETS core, 18S, internal transcribed spacer 1 (ITS1), and 28S segments and also had detectable, but significantly reduced, levels of the 3'-ETS sequence. Northern analyses showed that in mitotic cells, the latter sequences were present predominantly in 45S-46S pre-rRNAs, indicating that high-molecular weight processing intermediates are preserved during mitosis. Two additional essential processing components were also found in the NDF: U8 snoRNA and hPop1 (a protein component of RNase MRP and RNase P). Thus, the NDF appear to be large complexes containing partially processed pre-rRNA associated with processing components in which processing has been significantly suppressed. The NDF may facilitate coordinated assembly of postmitotic nucleoli.
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Affiliation(s)
- M Dundr
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, Mississippi 39216-4505, USA
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42
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Abstract
Cis -diammininedichloroplatinum(II) (cisplatin or cis -DDP) is a DNA-damaging agent that is widely used in cancer chemotherapy. Cisplatin crosslinks DNA and the resulting adducts interact with proteins that contain high-mobility-group (HMG) domains, such as UBF(upstream binding factor). UBF is a transcription factor that binds to the promoter of ribosomal RNA (rRNA) genes thereby supporting initiation of transcription by RNA polymerase I. Here we report that cisplatin causes a redistribution of UBF in the nucleolus of human cells, similar to that observed after inhibition of rRNA synthesis. A similar redistribution was observed for the major components of the rRNA transcription machinery, namely TBP, TAFIs and RNA polymerase I. Furthermore, we provide for the first time direct in vivo evidence that cisplatin blocks synthesis of rRNA, while activity of RNA polymerase II continues to be detected throughout the nucleus. The clinically ineffective trans isomer (trans -DDP) does not alter the localization of either UBF or other components of the RNA polymerase I transcription machinery. These results suggest that disruption of rRNA synthesis, which is stimulated in proliferating cells, plays an important role in the clinical success of cisplatin.
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Affiliation(s)
- P Jordan
- Institute of Histology and Embryology, Faculty of Medicine, University of Lisbon, 1699 Lisboa Codex, Portugal
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43
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Seither P, Iben S, Grummt I. Mammalian RNA polymerase I exists as a holoenzyme with associated basal transcription factors. J Mol Biol 1998; 275:43-53. [PMID: 9451438 DOI: 10.1006/jmbi.1997.1434] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Transcription initiation of ribosomal RNA genes requires RNA polymerase I (Pol I) and auxiliary factors which either bind directly to the rDNA promoter, e.g. TIF-IB/SL1 and UBF, or are assembled into productive transcription initiation complexes via interaction with Pol I, e.g. TIF-IA, and TIF-IC. Here we show that all components required for specific rDNA transcription initiation are capable of physical interaction with Pol I in the absence of DNA and can be co-immunoprecipitated with antibodies against defined subunits of murine Pol I. Sucrose gradient centrifugation and fractionation on gel filtration columns reveals that approximately 10% of cellular Pol I elutes as a defined complex with an apparent molecular mass of > 2000 kDa. The large Pol I complex contains saturating levels of TIF-IA, TIF-IB and UBF, but limiting amounts of TIF-IC. In support of the existence of a functional complex between Pol I and basal factors, the large complex is transcriptionally active after complementation with TIF-IC. The results suggest that, analogous to class II gene transcription, a pre-assembled complex, the "Pol I holoenzyme", exists that appears to be the initiation-competent form of Pol I.
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Affiliation(s)
- P Seither
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg.p6
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44
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Milkereit P, Schultz P, Tschochner H. Resolution of RNA polymerase I into dimers and monomers and their function in transcription. Biol Chem 1997; 378:1433-43. [PMID: 9461342 DOI: 10.1515/bchm.1997.378.12.1433] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We have further analyzed the requirements of yeast RNA polymerase I (pol I) to initiate transcription at the ribosomal gene promoter. Resolution of yeast whole cell extracts through several chromatographic steps yielded three protein fractions required for accurate initiation. One fraction is composed of TBP associated within a 240 kDa protein complex. The fraction contributing the RNA polymerase I (pol I) activity consists of dimeric and monomeric pol I under conditions optimal for in vitro transcription. The capability to utilize the ribosomal gene promoter correlates with monomeric pol I complexes which are possibly associated with further transcription factors. These initiation competent pol I complexes appeared to be resistant to high salt concentrations. Pol I dimers which represent the majority of the isolated pol I, can be reversibly dissociated into monomers and are only active in non-specific RNA synthesis, if single stranded DNA serves as a template. We suggest a model in which dimeric inactive pol I is converted into an active monomeric form that might be associated with other transcription factors to maintain a stable initiation competent complex.
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45
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Geiss GK, Radebaugh CA, Paule MR. The fundamental ribosomal RNA transcription initiation factor-IB (TIF-IB, SL1, factor D) binds to the rRNA core promoter primarily by minor groove contacts. J Biol Chem 1997; 272:29243-54. [PMID: 9361004 DOI: 10.1074/jbc.272.46.29243] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Acanthamoeba castellanii transcription initiation factor-IB (TIF-IB) is the TATA-binding protein-containing transcription factor that binds the rRNA promoter to form the committed complex. Minor groove-specific drugs inhibit TIF-IB binding, with higher concentrations needed to disrupt preformed complexes because of drug exclusion by bound TIF-IB. TIF-IB/DNA interactions were mapped by hydroxyl radical and uranyl nitrate footprinting. TIF-IB contacts four minor grooves in its binding site. TIF-IB and DNA wrap around each other in a right-handed superhelix of high pitch, so the upstream and downstream contacts are on opposite faces of the helix. Dimethyl sulfate protection assays revealed limited contact with a few guanines in the major groove. This detailed analysis suggests significant DNA conformation dependence of the interaction.
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Affiliation(s)
- G K Geiss
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
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46
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Chen L, Guo A, Pape L. An immunoaffinity purified Schizosaccharomyces pombe TBP-containing complex directs correct initiation of the S.pombe rRNA gene promoter. Nucleic Acids Res 1997; 25:1633-40. [PMID: 9092673 PMCID: PMC146630 DOI: 10.1093/nar/25.8.1633] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The multi-protein complex SL1, containing TBP, which is essential for RNA polymerase I catalyzed transcription, has been analyzed in fission yeast. It was immunopurified based on association of component subunits with epitope-tagged TBP. To enable this analysis, a strain of Schizosaccharomyces pombe was created where the only functional TBP coding sequences were those of FLAG-TBP. RNA polymerase I transcription components were fractionated from this strain and the TBP-associated polypeptides were subsequently immunopurified together with the epitope- tagged TBP. An assessment of the activity of this candidate SL1 complex was undertaken cross-species. This fission yeast TBP-containing complex displays two activities in redirecting transcriptional initiation of an S. pombe rDNA gene promoter cross-species in Saccharomyces cerevisiae transcription reactions: it both blocks an incorrect transcriptional start site at +7 and directs initiation at the correct site for S. pombe rRNA synthesis. This complex is essential for accurate initiation of the S.pombe rRNA gene: rRNA synthesis is reconstituted when this S.pombe TBP-containing complex is combined with a S.pombe fraction immunodepleted of TBP.
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MESH Headings
- Base Sequence
- Chromatography, Affinity
- Chromosomes, Fungal
- Cloning, Molecular
- DNA, Ribosomal/metabolism
- DNA-Binding Proteins/isolation & purification
- DNA-Binding Proteins/metabolism
- Escherichia coli
- Molecular Sequence Data
- Oligopeptides
- Peptides
- Pol1 Transcription Initiation Complex Proteins
- Promoter Regions, Genetic
- RNA Polymerase I/metabolism
- RNA, Fungal/biosynthesis
- RNA, Fungal/genetics
- RNA, Ribosomal/biosynthesis
- RNA, Ribosomal/genetics
- Schizosaccharomyces/genetics
- Schizosaccharomyces/metabolism
- TATA-Box Binding Protein
- Transcription Factor TFIID
- Transcription Factors/isolation & purification
- Transcription Factors/metabolism
- Transcription Factors, TFII/metabolism
- Transcription, Genetic
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Affiliation(s)
- L Chen
- Department of Chemistry, New York University, New York, NY 10003, USA
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47
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Heix J, Zomerdijk JC, Ravanpay A, Tjian R, Grummt I. Cloning of murine RNA polymerase I-specific TAF factors: conserved interactions between the subunits of the species-specific transcription initiation factor TIF-IB/SL1. Proc Natl Acad Sci U S A 1997; 94:1733-8. [PMID: 9050847 PMCID: PMC19985 DOI: 10.1073/pnas.94.5.1733] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Promoter selectivity for all three classes of eukaryotic RNA polymerases is brought about by multimeric protein complexes containing TATA box binding protein (TBP) and specific TBP-associated factors (TAFs). Unlike class II- and III-specific TBP-TAF complexes, the corresponding murine and human class I-specific transcription initiation factor TIF-IB/SL1 exhibits a pronounced selectivity for its homologous promoter. As a first step toward understanding the molecular basis of species-specific promoter recognition, we cloned the cDNAs encoding the three mouse pol I-specific TBP-associated factors (TAFIs) and compared the amino acid sequences of the murine TAFIs with their human counterparts. The four subunits from either species can form stable chimeric complexes that contain stoichiometric amounts of TBP and TAFIs, demonstrating that differences in the primary structure of human and mouse TAFIs do not dramatically alter the network of protein-protein contacts responsible for assembly of the multimeric complex. Thus, primate vs. rodent promoter selectivity mediated by the TBP-TAFI complex is likely to be the result of cumulative subtle differences between individual subunits that lead to species-specific properties of RNA polymerase I transcription.
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Affiliation(s)
- J Heix
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg
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48
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Bolívar J, Goenechea LG, Grenett H, Pendón C, Valdivia MM. Cloning and sequencing of the genes encoding the hamster ribosomal transcription factors UBF1 and UBF2. Gene X 1996; 176:257-8. [PMID: 8918262 DOI: 10.1016/0378-1119(96)00207-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The RNA polymerase I transcription factor, UBF, belongs to a family of high-mobility-group DNA-binding proteins. Here, a human autoantibody reactive with the nucleolus organizer regions (NOR) was used to select cDNA clones encoding the hamster transcription factors, UBF1 and UBF2. Comparison at the nucleotide level showed a high degree of homology with other mammalian upstream binding factors (UBF) already identified. The deduced amino acid sequences are identical for both UBF1 and UBF2, except for a 37 amino acid insertion found in UBF1. This insertion is completely conserved among mammalian UBF1 which indicates a putative role of this region on the function of this transcript.
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Affiliation(s)
- J Bolívar
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Cádiz, Spain
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49
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Marks F, Angel P. Signal transduction into the nucleus: fifth colloquium on cellular signal transduction. Heidelberg, Germany, January 1996. J Cancer Res Clin Oncol 1996; 122:638-42. [PMID: 8879263 DOI: 10.1007/bf01221198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- F Marks
- DKFZ, Department 0235, Heidelberg, Germany
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50
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Schnapp G, Graveley BR, Grummt I. TFIIS binds to mouse RNA polymerase I and stimulates transcript elongation and hydrolytic cleavage of nascent rRNA. MOLECULAR & GENERAL GENETICS : MGG 1996; 252:412-9. [PMID: 8879242 DOI: 10.1007/bf02173006] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Efficient transcription elongation by RNA polymerase I (Pol I) requires a specific Pol I-associated factor, termed TIF-IC. Here we show that TFIIS, a factor that has previously been shown to promote read-through past many types of blocks to elongation by RNA polymerase II, also enhances Pol I-directed transcription elongation. In a reconstituted transcription system containing purified proteins, TFIIS stimulates Pol I transcription by increasing the overall rate of RNA chain elongation. As with Pol II, ternary Pol I complexes cleave the 3' end of the nascent transcripts in response to TFIIS. The truncated RNAs remain bound to the template, are subject to pyrophosphorolysis, and can be chased into longer transcripts. Moreover, we show by immunoprecipitation and specific affinity chromatography that TFIIS physically interacts with Pol I. The results suggest that nascent transcript cleavage by TFIIS or a TFIIS-related factor may be a general mechanism by which both Pol I and Pol II can bypass transcriptional impediments.
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Affiliation(s)
- G Schnapp
- Division of Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
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