1
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Jacobs RQ, Schneider DA. Transcription elongation mechanisms of RNA polymerases I, II, and III and their therapeutic implications. J Biol Chem 2024; 300:105737. [PMID: 38336292 PMCID: PMC10907179 DOI: 10.1016/j.jbc.2024.105737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Transcription is a tightly regulated, complex, and essential cellular process in all living organisms. Transcription is comprised of three steps, transcription initiation, elongation, and termination. The distinct transcription initiation and termination mechanisms of eukaryotic RNA polymerases I, II, and III (Pols I, II, and III) have long been appreciated. Recent methodological advances have empowered high-resolution investigations of the Pols' transcription elongation mechanisms. Here, we review the kinetic similarities and differences in the individual steps of Pol I-, II-, and III-catalyzed transcription elongation, including NTP binding, bond formation, pyrophosphate release, and translocation. This review serves as an important summation of Saccharomyces cerevisiae (yeast) Pol I, II, and III kinetic investigations which reveal that transcription elongation by the Pols is governed by distinct mechanisms. Further, these studies illustrate how basic, biochemical investigations of the Pols can empower the development of chemotherapeutic compounds.
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Affiliation(s)
- Ruth Q Jacobs
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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2
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Schwank K, Schmid C, Fremter T, Engel C, Milkereit P, Griesenbeck J, Tschochner H. Features of yeast RNA polymerase I with special consideration of the lobe binding subunits. Biol Chem 2023; 404:979-1002. [PMID: 37823775 DOI: 10.1515/hsz-2023-0184] [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: 04/14/2023] [Accepted: 07/13/2023] [Indexed: 10/13/2023]
Abstract
Ribosomal RNAs (rRNAs) are structural components of ribosomes and represent the most abundant cellular RNA fraction. In the yeast Saccharomyces cerevisiae, they account for more than 60 % of the RNA content in a growing cell. The major amount of rRNA is synthesized by RNA polymerase I (Pol I). This enzyme transcribes exclusively the rRNA gene which is tandemly repeated in about 150 copies on chromosome XII. The high number of transcribed rRNA genes, the efficient recruitment of the transcription machinery and the dense packaging of elongating Pol I molecules on the gene ensure that enough rRNA is generated. Specific features of Pol I and of associated factors confer promoter selectivity and both elongation and termination competence. Many excellent reviews exist about the state of research about function and regulation of Pol I and how Pol I initiation complexes are assembled. In this report we focus on the Pol I specific lobe binding subunits which support efficient, error-free, and correctly terminated rRNA synthesis.
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Affiliation(s)
- Katrin Schwank
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Catharina Schmid
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Tobias Fremter
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Christoph Engel
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Philipp Milkereit
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Joachim Griesenbeck
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Herbert Tschochner
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
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3
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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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4
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Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes. Nat Rev Mol Cell Biol 2023; 24:414-429. [PMID: 36732602 DOI: 10.1038/s41580-022-00573-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2022] [Indexed: 02/04/2023]
Abstract
One of the first biological machineries to be created seems to have been the ribosome. Since then, organisms have dedicated great efforts to optimize this apparatus. The ribosomal RNA (rRNA) contained within ribosomes is crucial for protein synthesis and maintenance of cellular function in all known organisms. In eukaryotic cells, rRNA is produced from ribosomal DNA clusters of tandem rRNA genes, whose organization in the nucleolus, maintenance and transcription are strictly regulated to satisfy the substantial demand for rRNA required for ribosome biogenesis. Recent studies have elucidated mechanisms underlying the integrity of ribosomal DNA and regulation of its transcription, including epigenetic mechanisms and a unique recombination and copy-number control system to stably maintain high rRNA gene copy number. In this Review, we disucss how the crucial maintenance of rRNA gene copy number through control of gene amplification and of rRNA production by RNA polymerase I are orchestrated. We also discuss how liquid-liquid phase separation controls the architecture and function of the nucleolus and the relationship between rRNA production, cell senescence and disease.
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5
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Baudin F, Murciano B, Fung HKH, Fromm SA, Mattei S, Mahamid J, Müller CW. Mechanism of RNA polymerase I selection by transcription factor UAF. SCIENCE ADVANCES 2022; 8:eabn5725. [PMID: 35442737 PMCID: PMC9020658 DOI: 10.1126/sciadv.abn5725] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Preribosomal RNA is selectively transcribed by RNA polymerase (Pol) I in eukaryotes. The yeast transcription factor upstream activating factor (UAF) represses Pol II transcription and mediates Pol I preinitiation complex (PIC) formation at the 35S ribosomal RNA gene. To visualize the molecular intermediates toward PIC formation, we determined the structure of UAF in complex with native promoter DNA and transcription factor TATA-box-binding protein (TBP). We found that UAF recognizes DNA using a hexameric histone-like scaffold with markedly different interactions compared with the nucleosome and the histone-fold-rich transcription factor IID (TFIID). In parallel, UAF positions TBP for Core Factor binding, which leads to Pol I recruitment, while sequestering it from DNA and Pol II/III-specific transcription factors. Our work thus reveals the structural basis of RNA Pol selection by a transcription factor.
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Affiliation(s)
- Florence Baudin
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Brice Murciano
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Herman K. H. Fung
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Simon A. Fromm
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- EMBL Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Simone Mattei
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- EMBL Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christoph W. Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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6
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Pilsl M, Engel C. Structural Studies of Eukaryotic RNA Polymerase I Using Cryo-Electron Microscopy. Methods Mol Biol 2022; 2533:71-80. [PMID: 35796983 PMCID: PMC9761920 DOI: 10.1007/978-1-0716-2501-9_5] [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] [Indexed: 06/15/2023]
Abstract
Technical advances have pushed the resolution limit of single-particle cryo-electron microscopy (cryo-EM) throughout the past decade and made the technique accessible to a wide range of samples. Among them, multisubunit DNA-dependent RNA polymerases (Pols) are a prominent example. This review aims at briefly summarizing the architecture and structural adaptations of Pol I, highlighting the importance of cryo-electron microscopy in determining the structures of transcription complexes.
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Affiliation(s)
- Michael Pilsl
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany
| | - Christoph Engel
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany.
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7
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Merkl PE, Schächner C, Pilsl M, Schwank K, Hergert K, Längst G, Milkereit P, Griesenbeck J, Tschochner H. Analysis of Yeast RNAP I Transcription of Nucleosomal Templates In Vitro. Methods Mol Biol 2022; 2533:39-59. [PMID: 35796981 PMCID: PMC9761914 DOI: 10.1007/978-1-0716-2501-9_3] [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] [Indexed: 06/15/2023]
Abstract
Nuclear eukaryotic RNA polymerases (RNAPs) transcribe a chromatin template in vivo. Since the basic unit of chromatin, the nucleosome, renders the DNA largely inaccessible, RNAPs have to overcome the nucleosomal barrier for efficient RNA synthesis. Gaining mechanistical insights in the transcription of chromatin templates will be essential to understand the complex process of eukaryotic gene expression. In this article we describe the use of defined in vitro transcription systems for comparative analysis of highly purified RNAPs I-III from S. cerevisiae (hereafter called yeast) transcribing in vitro reconstituted nucleosomal templates. We also provide a protocol to study promoter-dependent RNAP I transcription of purified native 35S ribosomal RNA (rRNA) gene chromatin.
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Affiliation(s)
- Philipp E Merkl
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
- TUM ForTe, Technische Universität München, Munich, Germany
| | - Christopher Schächner
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Michael Pilsl
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Katrin Schwank
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Kristin Hergert
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Gernot Längst
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Philipp Milkereit
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany.
| | - Joachim Griesenbeck
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany.
| | - Herbert Tschochner
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
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8
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Sanchez-Martin V, Schneider DA, Ortiz-Gonzalez M, Soriano-Lerma A, Linde-Rodriguez A, Perez-Carrasco V, Gutierrez-Fernandez J, Cuadros M, González C, Soriano M, Garcia-Salcedo JA. Targeting ribosomal G-quadruplexes with naphthalene-diimides as RNA polymerase I inhibitors for colorectal cancer treatment. Cell Chem Biol 2021; 28:1590-1601.e4. [PMID: 34166611 DOI: 10.1016/j.chembiol.2021.05.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/05/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022]
Abstract
Guanine quadruplexes (G4s) are non-canonical nucleic acid structures commonly found in regulatory genomic regions. G4 targeting has emerged as a therapeutic approach in cancer. We have screened naphthalene-diimides (NDIs), a class of G4 ligands, in a cellular model of colorectal cancer (CRC). Here, we identify the leading compound T5 with a potent and selective inhibition of cell growth by high-affinity binding to G4s in ribosomal DNA, impairing RNA polymerase I (Pol I) elongation. Consequently, T5 induces a rapid inhibition of Pol I transcription, nucleolus disruption, proteasome-dependent Pol I catalytic subunit A degradation and autophagy. Moreover, we attribute the higher selectivity of carbohydrate-conjugated T5 for tumoral cells to its preferential uptake through the overexpressed glucose transporter 1. Finally, we succinctly demonstrate that T5 could be explored as a therapeutic agent in a patient cohort with CRC. Therefore, we report a mode of action for these NDIs involving ribosomal G4 targeting.
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Affiliation(s)
- Victoria Sanchez-Martin
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, Granada 18014, Spain; Department of Biochemistry, Molecular Biology III and Immunology, University of Granada, Granada 18016, Spain
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Matilde Ortiz-Gonzalez
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Centre for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, Almeria 04001, Spain
| | - Ana Soriano-Lerma
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Department of Physiology, University of Granada, Granada 18011, Spain
| | - Angel Linde-Rodriguez
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, Granada 18014, Spain
| | - Virginia Perez-Carrasco
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, Granada 18014, Spain
| | - Jose Gutierrez-Fernandez
- Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, Granada 18014, Spain; Department of Microbiology, University of Granada, Granada 18011, Spain
| | - Marta Cuadros
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Department of Biochemistry, Molecular Biology III and Immunology, University of Granada, Granada 18016, Spain
| | - Carlos González
- Instituto de Química Física "Rocasolano", CSIC, Madrid 28006, Spain
| | - Miguel Soriano
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Centre for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, Almeria 04001, Spain
| | - Jose A Garcia-Salcedo
- GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada 18016, Spain; Microbiology Unit, Biosanitary Research Institute IBS.Granada, University Hospital Virgen de las Nieves, Granada 18014, Spain.
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9
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Azouzi C, Jaafar M, Dez C, Abou Merhi R, Lesne A, Henras AK, Gadal O. Coupling Between Production of Ribosomal RNA and Maturation: Just at the Beginning. Front Mol Biosci 2021; 8:778778. [PMID: 34765647 PMCID: PMC8575686 DOI: 10.3389/fmolb.2021.778778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/12/2021] [Indexed: 01/28/2023] Open
Abstract
Ribosomal RNA (rRNA) production represents the most active transcription in the cell. Synthesis of the large rRNA precursors (35S/47S in yeast/human) is achieved by up to hundreds of RNA polymerase I (Pol I) enzymes simultaneously transcribing a single rRNA gene. In this review, we present recent advances in understanding the coupling between rRNA production and nascent rRNA folding. Mapping of the distribution of Pol I along ribosomal DNA at nucleotide resolution, using either native elongating transcript sequencing (NET-Seq) or crosslinking and analysis of cDNAs (CRAC), revealed frequent Pol I pausing, and CRAC results revealed a direct coupling between pausing and nascent RNA folding. High density of Pol I per gene imposes topological constraints that establish a defined pattern of polymerase distribution along the gene, with a persistent spacing between transcribing enzymes. RNA folding during transcription directly acts as an anti-pausing mechanism, implying that proper folding of the nascent rRNA favors elongation in vivo. Defects in co-transcriptional folding of rRNA are likely to induce Pol I pausing. We propose that premature termination of transcription, at defined positions, can control rRNA production in vivo.
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Affiliation(s)
- Chaima Azouzi
- Laboratoire de Biologie Moléculaire, Cellulaire et du Développement (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Mariam Jaafar
- Laboratoire de Biologie Moléculaire, Cellulaire et du Développement (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Christophe Dez
- Laboratoire de Biologie Moléculaire, Cellulaire et du Développement (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Raghida Abou Merhi
- Genomic Stability and Biotherapy (GSBT) Laboratory, Faculty of Sciences, Rafik Hariri Campus, Lebanese University, Beirut, Lebanon
| | - Annick Lesne
- CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, Sorbonne Université, Paris, France.,Institut de Génétique Moléculaire de Montpellier, IGMM, CNRS, Université Montpellier, Montpellier, France
| | - Anthony K Henras
- Laboratoire de Biologie Moléculaire, Cellulaire et du Développement (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Olivier Gadal
- Laboratoire de Biologie Moléculaire, Cellulaire et du Développement (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France
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10
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Wakamori M, Okabe K, Ura K, Funatsu T, Takinoue M, Umehara T. Quantification of the effect of site-specific histone acetylation on chromatin transcription rate. Nucleic Acids Res 2021; 48:12648-12659. [PMID: 33238306 PMCID: PMC7736822 DOI: 10.1093/nar/gkaa1050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 12/13/2022] Open
Abstract
Eukaryotic transcription is epigenetically regulated by chromatin structure and post-translational modifications (PTMs). For example, lysine acetylation in histone H4 is correlated with activation of RNA polymerase I-, II- and III-driven transcription from chromatin templates, which requires prior chromatin remodeling. However, quantitative understanding of the contribution of particular PTM states to the sequential steps of eukaryotic transcription has been hampered partially because reconstitution of a chromatin template with designed PTMs is difficult. In this study, we reconstituted a di-nucleosome with site-specifically acetylated or unmodified histone H4, which contained two copies of the Xenopus somatic 5S rRNA gene with addition of a unique sequence detectable by hybridization-assisted fluorescence correlation spectroscopy. Using a Xenopus oocyte nuclear extract, we analyzed the time course of accumulation of nascent 5S rRNA-derived transcripts generated on chromatin templates in vitro. Our mathematically described kinetic model and fitting analysis revealed that tetra-acetylation of histone H4 at K5/K8/K12/K16 increases the rate of transcriptionally competent chromatin formation ∼3-fold in comparison with the absence of acetylation. We provide a kinetic model for quantitative evaluation of the contribution of epigenetic modifications to chromatin transcription.
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Affiliation(s)
- Masatoshi Wakamori
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
| | - Kohki Okabe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Kiyoe Ura
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan.,Graduate School of Science, Chiba University, Chiba, Chiba 263-8522, Japan
| | - Takashi Funatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masahiro Takinoue
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan.,Department of Computer Science, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8502, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan.,PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
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11
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Molecular Topology of RNA Polymerase I Upstream Activation Factor. Mol Cell Biol 2020; 40:MCB.00056-20. [PMID: 32253346 DOI: 10.1128/mcb.00056-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/27/2020] [Indexed: 11/20/2022] Open
Abstract
Upstream activation factor (UAF) is a multifunctional transcription factor in Saccharomyces cerevisiae that plays dual roles in activating RNA polymerase I (Pol I) transcription and repression of Pol II. For Pol I, UAF binds to a specific upstream element in the ribosomal DNA (rDNA) promoter and interacts with two other Pol I initiation factors, the TATA-binding protein (TBP) and core factor (CF). We used an integrated combination of chemical cross-linking mass spectrometry (CXMS), molecular genetics, protein biochemistry, and structural modeling to understand the topological framework responsible for UAF complex formation. Here, we report the molecular topology of the UAF complex, describe new structural and functional domains that play roles in UAF complex integrity, assembly, and biological function, and provide roles for previously identified UAF domains that include the Rrn5 SANT and histone fold domains. We highlight the role of new domains in Uaf30 that include an N-terminal winged helix domain and a disordered tethering domain as well as a BORCS6-like domain found in Rrn9. Together, our results reveal a unique network of topological features that coalesce around a histone tetramer-like core to form the dual-function UAF complex.
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12
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Kramm K, Schröder T, Gouge J, Vera AM, Gupta K, Heiss FB, Liedl T, Engel C, Berger I, Vannini A, Tinnefeld P, Grohmann D. DNA origami-based single-molecule force spectroscopy elucidates RNA Polymerase III pre-initiation complex stability. Nat Commun 2020; 11:2828. [PMID: 32504003 PMCID: PMC7275037 DOI: 10.1038/s41467-020-16702-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 05/13/2020] [Indexed: 01/03/2023] Open
Abstract
The TATA-binding protein (TBP) and a transcription factor (TF) IIB-like factor are important constituents of all eukaryotic initiation complexes. The reason for the emergence and strict requirement of the additional initiation factor Bdp1 in the RNA polymerase (RNAP) III system, however, remained elusive. A poorly studied aspect in this context is the effect of DNA strain arising from DNA compaction and transcriptional activity on initiation complex formation. We made use of a DNA origami-based force clamp to follow the assembly of human initiation complexes in the RNAP II and RNAP III systems at the single-molecule level under piconewton forces. We demonstrate that TBP-DNA complexes are force-sensitive and TFIIB is sufficient to stabilise TBP on a strained promoter. In contrast, Bdp1 is the pivotal component that ensures stable anchoring of initiation factors, and thus the polymerase itself, in the RNAP III system. Thereby, we offer an explanation for the crucial role of Bdp1 for the high transcriptional output of RNAP III.
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Affiliation(s)
- Kevin Kramm
- Single-Molecule Biochemistry Lab, Institute of Microbiology and Archaea Centre, University of Regensburg, 93053, Regensburg, Germany
| | - Tim Schröder
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 80539, München, Germany
| | - Jerome Gouge
- Division of Structural Biology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Andrés Manuel Vera
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 80539, München, Germany
| | - Kapil Gupta
- Bristol Synthetic Biology Centre BrisSynBio, Biomedical Sciences, University of Bristol, 1 Tankard's Close, Clifton, BS8 1TD, UK
| | - Florian B Heiss
- Regensburg Center of Biochemistry (RCB), University of Regensburg, 93053, Regensburg, Germany
| | - Tim Liedl
- Faculty of Physics and Center for Nanoscience (CeNS), Ludwig-Maximilians-Universität München, 80539, Munich, Germany
| | - Christoph Engel
- Regensburg Center of Biochemistry (RCB), University of Regensburg, 93053, Regensburg, Germany
| | - Imre Berger
- Bristol Synthetic Biology Centre BrisSynBio, Biomedical Sciences, University of Bristol, 1 Tankard's Close, Clifton, BS8 1TD, UK
| | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer Research, London, SW7 3RP, UK
- Human Technopole Foundation, Centre of Structural Biology, 20157, Milan, Italy
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience (CeNS), Ludwig-Maximilians-Universität München, 80539, München, Germany
| | - Dina Grohmann
- Single-Molecule Biochemistry Lab, Institute of Microbiology and Archaea Centre, University of Regensburg, 93053, Regensburg, Germany.
- Regensburg Center of Biochemistry (RCB), University of Regensburg, 93053, Regensburg, Germany.
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13
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Pilsl M, Engel C. Structural basis of RNA polymerase I pre-initiation complex formation and promoter melting. Nat Commun 2020; 11:1206. [PMID: 32139698 PMCID: PMC7057995 DOI: 10.1038/s41467-020-15052-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 02/15/2020] [Indexed: 11/09/2022] Open
Abstract
Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is a prerequisite for the biosynthesis of ribosomes in eukaryotes. Compared to Pols II and III, the mechanisms underlying promoter recognition, initiation complex formation and DNA melting by Pol I substantially diverge. Here, we report the high-resolution cryo-EM reconstruction of a Pol I early initiation intermediate assembled on a double-stranded promoter scaffold that prevents the establishment of downstream DNA contacts. Our analyses demonstrate how efficient promoter-backbone interaction is achieved by combined re-arrangements of flexible regions in the ‘core factor’ subunits Rrn7 and Rrn11. Furthermore, structure-function analysis illustrates how destabilization of the melted DNA region correlates with contraction of the polymerase cleft upon transcription activation, thereby combining promoter recruitment with DNA-melting. This suggests that molecular mechanisms and structural features of Pol I initiation have co-evolved to support the efficient melting, initial transcription and promoter clearance required for high-level rRNA synthesis. RNA polymerase I (Pol I) catalyses the transcription of ribosomal RNA precursors, and its transcription initiation mechanism differs from that of Pol II and Pol III. Here the authors present the cryo-EM structure of a trapped early intermediate stage of promoter-recruited Pol I, which reveals the interactions of the basal rDNA transcription machinery with the native promoter, and discuss the mechanistic implications.
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Affiliation(s)
- Michael Pilsl
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Christoph Engel
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany.
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14
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Gallagher JEG. Proteins and RNA sequences required for the transition of the t-Utp complex into the SSU processome. FEMS Yeast Res 2019; 19:5184469. [PMID: 30445532 DOI: 10.1093/femsyr/foy120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 11/12/2018] [Indexed: 12/20/2022] Open
Abstract
Ribosomes are synthesized by large ribonucleoprotein complexes cleaving and properly assembling highly structured rRNAs with ribosomal proteins. Transcription and processing of pre-rRNAs are linked by the transcription-Utp sub-complex (t-Utps), a sub-complex of the small subunit (SSU) processome and prompted the investigations for the requirements of t-Utp formation and transition into the SSU processome. The rDNA promoter, the first 44 nucleotides of the 5΄ETS, and active transcription by pol I were sufficient to recruit the t-Utps to the rDNA. Pol5, accessory factor, dissociated as t-Utps matured into the UtpA complex which permitted later recruitment of the UtpB, U3 snoRNP and the Mpp10 complex into the SSU processome. The t-Utp complex associated with short RNAs 121 and 138 nucleotides long transcribed from the 5΄ETS. These transcripts were not present when pol II transcribed the rDNA or in nondividing cells. Depletion of a t-Utp, but not of other SSU processome components led to decreased levels of the short transcripts. However, ectopic expression of the short transcripts slowed the growth of yeast with impaired rDNA transcription. These results provide insight into how transcription of the rRNA primes the assemble of t-Utp complex with the pre-rRNA into the UtpA complex and the later association of SSU processome components.
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15
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Abstract
In all living organisms, the flow of genetic information is a two-step process: first DNA is transcribed into RNA, which is subsequently used as template for protein synthesis during translation. In bacteria, archaea and eukaryotes, transcription is carried out by multi-subunit RNA polymerases (RNAPs) sharing a conserved architecture of the RNAP core. RNAPs catalyse the highly accurate polymerisation of RNA from NTP building blocks, utilising DNA as template, being assisted by transcription factors during the initiation, elongation and termination phase of transcription. The complexity of this highly dynamic process is reflected in the intricate network of protein-protein and protein-nucleic acid interactions in transcription complexes and the substantial conformational changes of the RNAP as it progresses through the transcription cycle.In this chapter, we will first briefly describe the early work that led to the discovery of multisubunit RNAPs. We will then discuss the three-dimensional organisation of RNAPs from the bacterial, archaeal and eukaryotic domains of life, highlighting the conserved nature, but also the domain-specific features of the transcriptional apparatus. Another section will focus on transcription factors and their role in regulating the RNA polymerase throughout the different phases of the transcription cycle. This includes a discussion of the molecular mechanisms and dynamic events that govern transcription initiation, elongation and termination.
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16
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Genetic analyses led to the discovery of a super-active mutant of the RNA polymerase I. PLoS Genet 2019; 15:e1008157. [PMID: 31136569 PMCID: PMC6555540 DOI: 10.1371/journal.pgen.1008157] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 06/07/2019] [Accepted: 04/25/2019] [Indexed: 01/08/2023] Open
Abstract
Most transcriptional activity of exponentially growing cells is carried out by the RNA Polymerase I (Pol I), which produces a ribosomal RNA (rRNA) precursor. In budding yeast, Pol I is a multimeric enzyme with 14 subunits. Among them, Rpa49 forms with Rpa34 a Pol I-specific heterodimer (homologous to PAF53/CAST heterodimer in human Pol I), which might be responsible for the specific functions of the Pol I. Previous studies provided insight in the involvement of Rpa49 in initiation, elongation, docking and releasing of Rrn3, an essential Pol I transcription factor. Here, we took advantage of the spontaneous occurrence of extragenic suppressors of the growth defect of the rpa49 null mutant to better understand the activity of Pol I. Combining genetic approaches, biochemical analysis of rRNA synthesis and investigation of the transcription rate at the individual gene scale, we characterized mutated residues of the Pol I as novel extragenic suppressors of the growth defect caused by the absence of Rpa49. When mapped on the Pol I structure, most of these mutations cluster within the jaw-lobe module, at an interface formed by the lobe in Rpa135 and the jaw made up of regions of Rpa190 and Rpa12. In vivo, the suppressor allele RPA135-F301S restores normal rRNA synthesis and increases Pol I density on rDNA genes when Rpa49 is absent. Growth of the Rpa135-F301S mutant is impaired when combined with exosome mutation rrp6Δ and it massively accumulates pre-rRNA. Moreover, Pol I bearing Rpa135-F301S is a hyper-active RNA polymerase in an in vitro tailed-template assay. We conclude that RNA polymerase I can be engineered to produce more rRNA in vivo and in vitro. We propose that the mutated area undergoes a conformational change that supports the DNA insertion into the cleft of the enzyme resulting in a super-active form of Pol I. The nuclear genome of eukaryotic cells is transcribed by three RNA polymerases. RNA polymerase I (Pol I) is a multimeric enzyme specialized in the synthesis of ribosomal RNA. Deregulation of the Pol I function is linked to the etiology of a broad range of human diseases. Understanding the Pol I activity and regulation represents therefore a major challenge. We chose the budding yeast Saccharomyces cerevisiae as a model, because Pol I transcription apparatus is genetically amenable in this organism. Analyses of phenotypic consequences of deletion/truncation of Pol I subunits-coding genes in yeast indeed provided insights into the activity and regulation of the enzyme. Here, we characterized mutations in Pol I that can alleviate the growth defect caused by the absence of Rpa49, one of the subunits composing this multi-protein enzyme. We mapped these mutations on the Pol I structure and found that they all cluster in a well-described structural element, the jaw-lobe module. Combining genetic and biochemical approaches, we showed that Pol I bearing one of these mutations in the Rpa135 subunit is able to produce more ribosomal RNA in vivo and in vitro. We propose that this super-activity is explained by structural rearrangement of the Pol I jaw/lobe interface.
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17
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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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18
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Tafur L, Sadian Y, Hanske J, Wetzel R, Weis F, Müller CW. The cryo-EM structure of a 12-subunit variant of RNA polymerase I reveals dissociation of the A49-A34.5 heterodimer and rearrangement of subunit A12.2. eLife 2019; 8:43204. [PMID: 30913026 PMCID: PMC6435322 DOI: 10.7554/elife.43204] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/09/2019] [Indexed: 11/13/2022] Open
Abstract
RNA polymerase (Pol) I is a 14-subunit enzyme that solely transcribes pre-ribosomal RNA. Cryo-electron microscopy (EM) structures of Pol I initiation and elongation complexes have given first insights into the molecular mechanisms of Pol I transcription. Here, we present cryo-EM structures of yeast Pol I elongation complexes (ECs) bound to the nucleotide analog GMPCPP at 3.2 to 3.4 Å resolution that provide additional insight into the functional interplay between the Pol I-specific transcription-like factors A49-A34.5 and A12.2. Strikingly, most of the nucleotide-bound ECs lack the A49-A34.5 heterodimer and adopt a Pol II-like conformation, in which the A12.2 C-terminal domain is bound in a previously unobserved position at the A135 surface. Our structural and biochemical data suggest a mechanism where reversible binding of the A49-A34.5 heterodimer could contribute to the regulation of Pol I transcription initiation and elongation.
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Affiliation(s)
- Lucas Tafur
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Collaboration for joint PhD degree, European Molecular Biology Laboratory and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Yashar Sadian
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jonas Hanske
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rene Wetzel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Felix Weis
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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19
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Transcription initiation factor TBP: old friend new questions. Biochem Soc Trans 2019; 47:411-423. [DOI: 10.1042/bst20180623] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 01/02/2019] [Accepted: 01/04/2019] [Indexed: 12/14/2022]
Abstract
Abstract
In all domains of life, the regulation of transcription by DNA-dependent RNA polymerases (RNAPs) is achieved at the level of initiation to a large extent. Whereas bacterial promoters are recognized by a σ-factor bound to the RNAP, a complex set of transcription factors that recognize specific promoter elements is employed by archaeal and eukaryotic RNAPs. These initiation factors are of particular interest since the regulation of transcription critically relies on initiation rates and thus formation of pre-initiation complexes. The most conserved initiation factor is the TATA-binding protein (TBP), which is of crucial importance for all archaeal-eukaryotic transcription initiation complexes and the only factor required to achieve full rates of initiation in all three eukaryotic and the archaeal transcription systems. Recent structural, biochemical and genome-wide mapping data that focused on the archaeal and specialized RNAP I and III transcription system showed that the involvement and functional importance of TBP is divergent from the canonical role TBP plays in RNAP II transcription. Here, we review the role of TBP in the different transcription systems including a TBP-centric discussion of archaeal and eukaryotic initiation complexes. We furthermore highlight questions concerning the function of TBP that arise from these findings.
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20
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Greber BJ, Nogales E. The Structures of Eukaryotic Transcription Pre-initiation Complexes and Their Functional Implications. Subcell Biochem 2019; 93:143-192. [PMID: 31939151 DOI: 10.1007/978-3-030-28151-9_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transcription is a highly regulated process that supplies living cells with coding and non-coding RNA molecules. Failure to properly regulate transcription is associated with human pathologies, including cancers. RNA polymerase II is the enzyme complex that synthesizes messenger RNAs that are then translated into proteins. In spite of its complexity, RNA polymerase requires a plethora of general transcription factors to be recruited to the transcription start site as part of a large transcription pre-initiation complex, and to help it gain access to the transcribed strand of the DNA. This chapter reviews the structure and function of these eukaryotic transcription pre-initiation complexes, with a particular emphasis on two of its constituents, the multisubunit complexes TFIID and TFIIH. We also compare the overall architecture of the RNA polymerase II pre-initiation complex with those of RNA polymerases I and III, involved in transcription of ribosomal RNA and non-coding RNAs such as tRNAs and snRNAs, and discuss the general, conserved features that are applicable to all eukaryotic RNA polymerase systems.
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Affiliation(s)
- Basil J Greber
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA.
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
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21
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Engel C, Neyer S, Cramer P. Distinct Mechanisms of Transcription Initiation by RNA Polymerases I and II. Annu Rev Biophys 2018; 47:425-446. [DOI: 10.1146/annurev-biophys-070317-033058] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA polymerases I and II (Pol I and Pol II) are the eukaryotic enzymes that catalyze DNA-dependent synthesis of ribosomal RNA and messenger RNA, respectively. Recent work shows that the transcribing forms of both enzymes are similar and the fundamental mechanisms of RNA chain elongation are conserved. However, the mechanisms of transcription initiation and its regulation differ between Pol I and Pol II. Recent structural studies of Pol I complexes with transcription initiation factors provided insights into how the polymerase recognizes its specific promoter DNA, how it may open DNA, and how initiation may be regulated. Comparison with the well-studied Pol II initiation system reveals a distinct architecture of the initiation complex and visualizes promoter- and gene-class-specific aspects of transcription initiation. On the basis of new structural studies, we derive a model of the Pol I transcription cycle and provide a molecular movie of Pol I transcription that can be used for teaching.
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Affiliation(s)
- Christoph Engel
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
- Current affiliation: Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, 93053 Regensburg, Germany
| | - Simon Neyer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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22
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Molecular mechanism of promoter opening by RNA polymerase III. Nature 2018; 553:295-300. [PMID: 29345638 PMCID: PMC5777638 DOI: 10.1038/nature25440] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/08/2017] [Indexed: 01/03/2023]
Abstract
RNA polymerase III (Pol III) assembles together with transcription factor IIIB (TFIIIB) on different promoter types to initiate the transcription of small, structured RNAs. Here, we present structures of Pol III pre-initiation complexes comprising the 17-subunit Pol III and hetero-trimeric transcription factor TFIIIB with subunits TATA-binding protein (TBP), B-related factor 1 (Brf1) and B double prime 1 (Bdp1) bound to a natural promoter in different functional states. Electron cryo-microscopy (cryo-EM) reconstructions varying from 3.7 Å to 5.5 Å resolution include two early intermediates in which the DNA duplex is closed, an open DNA complex and an initially transcribing complex with RNA in the active site. Our structures reveal an extremely tight and multivalent interaction of TFIIIB with promoter DNA and explain how TFIIIB recruits Pol III. TFIIIB and Pol III subunit C37 together activate the intrinsic transcription factor-like activity of the Pol III-specific heterotrimer to initiate melting of double-stranded DNA in a mechanism similar as used in the Pol II system.
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23
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Smith ML, Cui W, Jackobel AJ, Walker-Kopp N, Knutson BA. Reconstitution of RNA Polymerase I Upstream Activating Factor and the Roles of Histones H3 and H4 in Complex Assembly. J Mol Biol 2018; 430:641-654. [PMID: 29357286 PMCID: PMC9746128 DOI: 10.1016/j.jmb.2018.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/04/2018] [Accepted: 01/04/2018] [Indexed: 12/16/2022]
Abstract
RNA polymerase I (Pol I) transcription in Saccharomyces cerevisiae requires four separate factors that recruit Pol I to the promoter to form a pre-initiation complex. Upstream Activating Factor (UAF) is one of two multi-subunit complexes that regulate pre-initiation complex formation by binding to the ribosomal DNA promoter and by stimulating recruitment of downstream Pol I factors. UAF is composed of Rrn9, Rrn5, Rrn10, Uaf30, and histones H3 and H4. We developed a recombinant Escherichia coli-based system to coexpress and purify transcriptionally active UAF complex and to investigate the importance of each subunit in complex formation. We found that no single subunit is required for UAF assembly, including histones H3 and H4. We also demonstrate that histone H3 is able to interact with each UAF-specific subunit, and show that there are at least two copies of histone H3 and one copy of H4 present in the complex. Together, our results provide a new model suggesting that UAF contains a hybrid H3-H4 tetramer-like subcomplex.
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Affiliation(s)
- Marissa L. Smith
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, United States
| | - Weidong Cui
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, MO 63130, United States
| | - Ashleigh J. Jackobel
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, United States
| | - Nancy Walker-Kopp
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, United States
| | - Bruce A. Knutson
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, 750 East Adams Street, Syracuse, NY 13210, United States
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24
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Abstract
In yeast, transcription of ribosomal DNA (rDNA) by RNA polymerase I (Pol I) is regulated by unique mechanisms acting at the level of the enzyme. Under stress situations such as starvation, Pol I hibernates through dimerization. When growth conditions are restored, dimer disassembly and Rrn3 binding drive enzyme activation and subsequent recruitment to rDNA.
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25
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Sasano Y, Kariya T, Usugi S, Sugiyama M, Harashima S. Molecular breeding of Saccharomyces cerevisiae with high RNA content by harnessing essential ribosomal RNA transcription regulator. AMB Express 2017; 7:32. [PMID: 28155199 PMCID: PMC5289932 DOI: 10.1186/s13568-017-0330-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 01/20/2017] [Indexed: 12/24/2022] Open
Abstract
As yeast is commonly used for RNA production, it is industrially important to breed strains with high RNA contents. The upstream activating factor (UAF) plays an important role in transcription of ribosomal RNA (rRNA), a major constituent of intracellular RNA species. Here, we targeted the essential rRNA transcription regulator Rrn5 of Saccharomyces cerevisiae, a component of the UAF complex, and disrupted the genomic RRN5 gene using a helper plasmid carrying an RRN5 gene. Then we isolated nine suppressor mutants (Sup mutants) of RRN5 gene disruption, causing deficiency in rRNA transcription. The Sup mutants had RNA contents of approximately 40% of the wild type level and expansion of rDNA repeats to ca. 400–700 copies. Reintroduction of a functional RRN5 gene into Sup mutants caused a reduction in the number of rDNA repeats to close to the wild type level but did not change RNA content. However, we found that reintroduction of RRN5 into the Sup16 mutant (in which the FOB1 gene encoding the rDNA replication fork barrier site binding protein was disrupted) resulted in a significant increase (17%) in RNA content compared with wild type, although the rDNA repeat copy number was almost identical to the wild type strain. In this case, upregulated transcription of non-transcribed spacers (NTS) occurred, especially in the NTS2 region; this was likely mediated by RNA polymerase II and accounted for the increased RNA content. Thus, we propose a novel breeding strategy for developing high RNA content yeast by harnessing the essential rRNA transcription regulator.
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26
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Sadian Y, Tafur L, Kosinski J, Jakobi AJ, Wetzel R, Buczak K, Hagen WJ, Beck M, Sachse C, Müller CW. Structural insights into transcription initiation by yeast RNA polymerase I. EMBO J 2017; 36:2698-2709. [PMID: 28739580 PMCID: PMC5599796 DOI: 10.15252/embj.201796958] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/20/2017] [Accepted: 06/26/2017] [Indexed: 01/22/2023] Open
Abstract
In eukaryotic cells, RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA (pre‐rRNA) that is subsequently processed into mature rRNA. To initiate transcription, Pol I requires the assembly of a multi‐subunit pre‐initiation complex (PIC) at the ribosomal RNA promoter. In yeast, the minimal PIC includes Pol I, the transcription factor Rrn3, and Core Factor (CF) composed of subunits Rrn6, Rrn7, and Rrn11. Here, we present the cryo‐EM structure of the 18‐subunit yeast Pol I PIC bound to a transcription scaffold. The cryo‐EM map reveals an unexpected arrangement of the DNA and CF subunits relative to Pol I. The upstream DNA is positioned differently than in any previous structures of the Pol II PIC. Furthermore, the TFIIB‐related subunit Rrn7 also occupies a different location compared to the Pol II PIC although it uses similar interfaces as TFIIB to contact DNA. Our results show that although general features of eukaryotic transcription initiation are conserved, Pol I and Pol II use them differently in their respective transcription initiation complexes.
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Affiliation(s)
- Yashar Sadian
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Lucas Tafur
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Jan Kosinski
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Arjen J Jakobi
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany.,European Molecular Biology Laboratory (EMBL), Hamburg Unit, Hamburg, Germany.,The Hamburg Centre for Ultrafast Imaging (CUI), Hamburg, Germany
| | - Rene Wetzel
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Katarzyna Buczak
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Wim Jh Hagen
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Martin Beck
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Carsten Sachse
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Christoph W Müller
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
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27
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Torreira E, Louro JA, Pazos I, González-Polo N, Gil-Carton D, Duran AG, Tosi S, Gallego O, Calvo O, Fernández-Tornero C. The dynamic assembly of distinct RNA polymerase I complexes modulates rDNA transcription. eLife 2017; 6. [PMID: 28262097 PMCID: PMC5362265 DOI: 10.7554/elife.20832] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 03/06/2017] [Indexed: 12/31/2022] Open
Abstract
Cell growth requires synthesis of ribosomal RNA by RNA polymerase I (Pol I). Binding of initiation factor Rrn3 activates Pol I, fostering recruitment to ribosomal DNA promoters. This fundamental process must be precisely regulated to satisfy cell needs at any time. We present in vivo evidence that, when growth is arrested by nutrient deprivation, cells induce rapid clearance of Pol I–Rrn3 complexes, followed by the assembly of inactive Pol I homodimers. This dual repressive mechanism reverts upon nutrient addition, thus restoring cell growth. Moreover, Pol I dimers also form after inhibition of either ribosome biogenesis or protein synthesis. Our mutational analysis, based on the electron cryomicroscopy structures of monomeric Pol I alone and in complex with Rrn3, underscores the central role of subunits A43 and A14 in the regulation of differential Pol I complexes assembly and subsequent promoter association. DOI:http://dx.doi.org/10.7554/eLife.20832.001
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Affiliation(s)
- Eva Torreira
- IPSBB Unit, Centro de Investigaciones Biológicas, Madrid, Spain
| | | | - Irene Pazos
- Institute for Research in Biomedicine, Barcelona, Spain.,The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Noelia González-Polo
- Instituto de Biología Funcional y Genómica, CSIC-Universidad de Salamanca, Salamanca, Spain
| | - David Gil-Carton
- Structural Biology Unit, Cooperative Center for Research in Biosciences CIC bioGUNE, Derio, Spain
| | - Ana Garcia Duran
- Institute for Research in Biomedicine, Barcelona, Spain.,The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sébastien Tosi
- Institute for Research in Biomedicine, Barcelona, Spain.,The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Oriol Gallego
- Institute for Research in Biomedicine, Barcelona, Spain.,The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Olga Calvo
- Instituto de Biología Funcional y Genómica, CSIC-Universidad de Salamanca, Salamanca, Spain
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28
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Structural Basis of RNA Polymerase I Transcription Initiation. Cell 2017; 169:120-131.e22. [DOI: 10.1016/j.cell.2017.03.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/16/2017] [Accepted: 03/01/2017] [Indexed: 11/19/2022]
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29
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Han Y, Yan C, Nguyen THD, Jackobel AJ, Ivanov I, Knutson BA, He Y. Structural mechanism of ATP-independent transcription initiation by RNA polymerase I. eLife 2017; 6:e27414. [PMID: 28623663 PMCID: PMC5489313 DOI: 10.7554/elife.27414] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/17/2017] [Indexed: 12/02/2022] Open
Abstract
Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Saccharomyces cerevisiae Pol I-CF-DNA to 3.8 Å resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from -27 to -16. Core Factor's intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location. Comparison of the three states in this study with the Pol II system suggests that a ratchet motion of the Core Factor-DNA sub-complex at upstream facilitates promoter melting in an ATP-independent manner, distinct from a DNA translocase actively threading the downstream DNA in the Pol II PIC.
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Affiliation(s)
- Yan Han
- Department of Molecular Biosciences, Northwestern University, Evanston, United States
| | - Chunli Yan
- Department of Chemistry, Georgia State University, Atlanta, United States,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, United States
| | | | - Ashleigh J Jackobel
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, United States
| | - Ivaylo Ivanov
- Department of Chemistry, Georgia State University, Atlanta, United States,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, United States
| | - Bruce A Knutson
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, United States, (BAK)
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, United States, (YHe)
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Pilsl M, Merkl PE, Milkereit P, Griesenbeck J, Tschochner H. Analysis of S. cerevisiae RNA Polymerase I Transcription In Vitro. Methods Mol Biol 2016; 1455:99-108. [PMID: 27576713 DOI: 10.1007/978-1-4939-3792-9_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
RNA polymerase I (Pol I) activity is crucial to provide cells with sufficient amounts of ribosomal RNA (rRNA). Synthesis of rRNA takes place in the nucleolus, is tightly regulated and is coordinated with synthesis and assembly of ribosomal proteins, finally resulting in the formation of mature ribosomes. Many studies on Pol I mechanisms and regulation in the model organism S. cerevisiae were performed using either complex in vitro systems reconstituted from more or less purified fractions or genetic analyses. While providing many valuable insights these strategies did not always discriminate between direct and indirect effects in transcription initiation and termination, when mutated forms of Pol I subunits or transcription factors were investigated. Therefore, a well-defined minimal system was developed which allows to reconstitute highly efficient promoter-dependent Pol I initiation and termination of transcription. Transcription can be initiated at a minimal promoter only in the presence of recombinant core factor and extensively purified initiation competent Pol I. Addition of recombinant termination factors triggers transcriptional pausing and release of the ternary transcription complex. This minimal system represents a valuable tool to investigate the direct impact of (lethal) mutations in components of the initiation and termination complexes on the mechanism and regulation of rRNA synthesis.
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Affiliation(s)
- Michael Pilsl
- Biochemie-Zentrum Regensburg (BZR), Lehrstuhl Biochemie III, Universität Regensburg, 93053, Regensburg, Germany
| | - Philipp E Merkl
- Biochemie-Zentrum Regensburg (BZR), Lehrstuhl Biochemie III, Universität Regensburg, 93053, Regensburg, Germany
- Department of Microbiology and Immunobiology, Harvard Medical School, New Research Building Room 954, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Philipp Milkereit
- Biochemie-Zentrum Regensburg (BZR), Lehrstuhl Biochemie III, Universität Regensburg, 93053, Regensburg, Germany
| | - Joachim Griesenbeck
- Biochemie-Zentrum Regensburg (BZR), Lehrstuhl Biochemie III, Universität Regensburg, 93053, Regensburg, Germany
| | - Herbert Tschochner
- Biochemie-Zentrum Regensburg (BZR), Lehrstuhl Biochemie III, Universität Regensburg, 93053, Regensburg, Germany.
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31
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Spt6 Is Essential for rRNA Synthesis by RNA Polymerase I. Mol Cell Biol 2015; 35:2321-31. [PMID: 25918242 DOI: 10.1128/mcb.01499-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/19/2015] [Indexed: 01/04/2023] Open
Abstract
Spt6 (suppressor of Ty6) has many roles in transcription initiation and elongation by RNA polymerase (Pol) II. These effects are mediated through interactions with histones, transcription factors, and the RNA polymerase. Two lines of evidence suggest that Spt6 also plays a role in rRNA synthesis. First, Spt6 physically associates with a Pol I subunit (Rpa43). Second, Spt6 interacts physically and genetically with Spt4/5, which directly affects Pol I transcription. Utilizing a temperature-sensitive allele, spt6-1004, we show that Spt6 is essential for Pol I occupancy of the ribosomal DNA (rDNA) and rRNA synthesis. Our data demonstrate that protein levels of an essential Pol I initiation factor, Rrn3, are reduced when Spt6 is inactivated, leading to low levels of Pol I-Rrn3 complex. Overexpression of RRN3 rescues Pol I-Rrn3 complex formation; however, rRNA synthesis is not restored. These data suggest that Spt6 is involved in either recruiting the Pol I-Rrn3 complex to the rDNA or stabilizing the preinitiation complex. The findings presented here identify an unexpected, essential role for Spt6 in synthesis of rRNA.
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Abstract
Eukaryotic cells employ at least three nuclear, DNA-dependent RNA polymerase systems for the synthesis of cellular RNA. RNA polymerases I, II, and III primarily produce rRNA, mRNA, and tRNA, respectively. In a rapidly growing cell, most RNA synthesis is devoted to production of the translation machinery, with rRNA synthesis by RNA polymerase I representing more than half of total cellular transcription. The fundamental connection between ribosome biogenesis and cell growth is clear; furthermore, recent studies have identified transcription by RNA polymerase I as a key target for anticancer chemotherapy. Thus, efficient methods for characterizing transcription of the ribosomal DNA and its regulation are needed. In order to describe enzymatic features of an enzyme, in vitro assays are critical. Here we describe a method for purifying RNA polymerase I. This approach yields enzyme of sufficiently high quantity and activity for an array of experiments directed at describing the enzymatic properties of RNA polymerase I in detail.
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Binding of the termination factor Nsi1 to its cognate DNA site is sufficient to terminate RNA polymerase I transcription in vitro and to induce termination in vivo. Mol Cell Biol 2014; 34:3817-27. [PMID: 25092870 DOI: 10.1128/mcb.00395-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Different models have been proposed explaining how eukaryotic gene transcription is terminated. Recently, Nsi1, a factor involved in silencing of ribosomal DNA (rDNA), was shown to be required for efficient termination of rDNA transcription by RNA polymerase I (Pol I) in the yeast Saccharomyces cerevisiae. Nsi1 contains Myb-like DNA binding domains and associates in vivo near the 3' end of rRNA genes to rDNA, but information about which and how DNA sequences might influence Nsi1-dependent termination is lacking. Here, we show that binding of Nsi1 to a stretch of 11 nucleotides in the correct orientation was sufficient to pause elongating Pol I shortly upstream of the Nsi1 binding site and to release the transcripts in vitro. The same minimal DNA element triggered Nsi1-dependent termination of pre-rRNA synthesis using an in vivo reporter assay. Termination efficiency in the in vivo system could be enhanced by inclusion of specific DNA sequences downstream of the Nsi1 binding site. These data and the finding that Nsi1 blocks efficiently only Pol I-dependent RNA synthesis in an in vitro transcription system improve our understanding of a unique mechanism of transcription termination.
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Increased transcription of RPL40A and RPL40B is important for the improvement of RNA production in Saccharomyces cerevisiae. J Biosci Bioeng 2013; 116:423-32. [DOI: 10.1016/j.jbiosc.2013.04.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 03/24/2013] [Accepted: 04/01/2013] [Indexed: 11/21/2022]
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35
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Viktorovskaya OV, Engel KL, French SL, Cui P, Vandeventer PJ, Pavlovic EM, Beyer AL, Kaplan CD, Schneider DA. Divergent contributions of conserved active site residues to transcription by eukaryotic RNA polymerases I and II. Cell Rep 2013; 4:974-84. [PMID: 23994471 DOI: 10.1016/j.celrep.2013.07.044] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 07/10/2013] [Accepted: 07/30/2013] [Indexed: 12/29/2022] Open
Abstract
Multisubunit RNA polymerases (msRNAPs) exhibit high sequence and structural homology, especially within their active sites, which is generally thought to result in msRNAP functional conservation. However, we show that mutations in the trigger loop (TL) in the largest subunit of RNA polymerase I (Pol I) yield phenotypes unexpected from studies of Pol II. For example, a well-characterized gain-of-function mutation in Pol II results in loss of function in Pol I (Pol II: rpb1- E1103G; Pol I: rpa190-E1224G). Studies of chimeric Pol II enzymes hosting Pol I or Pol III TLs suggest that consequences of mutations that alter TL dynamics are dictated by the greater enzymatic context and not solely the TL sequence. Although the rpa190-E1224G mutation diminishes polymerase activity, when combined with mutations that perturb Pol I catalysis, it enhances polymerase function, similar to the analogous Pol II mutation. These results suggest that Pol I and Pol II have different rate-limiting steps.
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Affiliation(s)
- Olga V Viktorovskaya
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
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36
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Knutson BA, Hahn S. TFIIB-related factors in RNA polymerase I transcription. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:265-73. [PMID: 22960599 DOI: 10.1016/j.bbagrm.2012.08.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 08/20/2012] [Accepted: 08/21/2012] [Indexed: 01/24/2023]
Abstract
Eukaryotic RNA polymerases (Pol) I, II, III and archaeal Pol use a related set of general transcription factors to recognize promoter sequences and recruit Pol to promoters and to function at key points in the transcription initiation mechanism. The TFIIB-like general transcription factors (GTFs) function during several important and conserved steps in the initiation pathway for Pols II, III, and archaeal Pol. Until recently, the mechanism of Pol I initiation seemed unique, since it appeared to lack a GTF paralogous to the TFIIB-like proteins. The surprising recent discovery of TFIIB-related Pol I general factors in yeast and humans highlights the evolutionary conservation of transcription initiation mechanisms for all eukaryotic and archaeal Pols. These findings reveal new roles for the function of the Pol I GTFs and insight into the function of TFIIB-related factors. Models for Pol I transcription initiation are reexamined in light of these recent findings. This article is part of a Special Issue entitled: Transcription by Odd Pols.
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Affiliation(s)
- Bruce A Knutson
- Fred Hutchinson Cancer Research Center, Division of Basic Sciences, 1100 Fairview Ave. N, P.O. Box 19024, Mailstop A1-162, Seattle, WA 98109, USA.
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37
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Schneider DA. Quantitative analysis of transcription elongation by RNA polymerase I in vitro. Methods Mol Biol 2012; 809:579-91. [PMID: 22113301 DOI: 10.1007/978-1-61779-376-9_37] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The elongation step in transcription has gained attention for its roles in regulation of eukaryotic gene expression and for its influence on RNA processing. Sophisticated genetic analyses have identified factors and/or conditions that may affect transcription elongation rate or processivity; however, differentiation of direct and indirect effects on transcription is difficult using in vivo strategies. Therefore, effective, reproducible in vitro assays have been developed to test whether a given factor or condition can have a direct effect on the kinetics of transcription elongation. We have adapted a fully reconstituted transcription system for RNA polymerase I (Pol I) for kinetic analysis of transcription elongation rate in vitro. The assay described here has proven to be effective in the characterization of defects or enhancement of wild-type transcription elongation by RNA Pol I. Since transcription elongation by RNA Pol I has only recently gained significant attention, this assay will be a valuable resource for years to come.
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Affiliation(s)
- David Alan Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
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38
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Efficient transcription by RNA polymerase I using recombinant core factor. Gene 2011; 492:94-9. [PMID: 22093875 DOI: 10.1016/j.gene.2011.10.049] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 10/28/2011] [Accepted: 10/30/2011] [Indexed: 11/24/2022]
Abstract
Transcription of ribosomal DNA by RNA polymerase I is a central feature of eukaryotic ribosome biogenesis. Since ribosome synthesis is closely linked to cell proliferation, there is a need to define the molecular mechanisms that control transcription by RNA polymerase I. To fully define the factors that control RNA polymerase I activity, biochemical analyses using purified transcription factors are essential. Although such assays exist, one limitation is the low abundance and difficult purification strategies required for some of the essential transcription factors for RNA polymerase I. Here, we describe a new method for expression and purification of the three subunit core factor complex from Escherichia coli. We demonstrate that the recombinant material is more active than yeast-derived core factor in assays for RNA polymerase I transcription in vitro. Finally, we use recombinant core factor to differentiate between two opposing models for the role of the TATA-binding protein in transcription by RNA polymerase I.
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39
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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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40
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Schneider DA. RNA polymerase I activity is regulated at multiple steps in the transcription cycle: recent insights into factors that influence transcription elongation. Gene 2011; 493:176-84. [PMID: 21893173 DOI: 10.1016/j.gene.2011.08.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Revised: 07/11/2011] [Accepted: 08/08/2011] [Indexed: 01/21/2023]
Abstract
Synthesis of the translation apparatus is a central activity in growing and/or proliferating cells. Because of its fundamental importance and direct connection to cell proliferation, ribosome synthesis has been a focus of ongoing research for several decades. As a consequence, much is known about the essential factors involved in this process. Many studies have shown that transcription of the ribosomal DNA by RNA polymerase I is a major target for cellular regulation of ribosome synthesis rates. The initiation of transcription by RNA polymerase I has been implicated as a regulatory target, however, recent studies suggest that the elongation step in transcription is also influenced and regulated by trans-acting factors. This review describes the factors required for rRNA synthesis and focuses on recent works that have begun to identify and characterize factors that influence transcription elongation by RNA polymerase I and its regulation.
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Affiliation(s)
- David Alan Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 720 20th Street South, Kaul Human Genetics, Room 442, Birmingham, AL 35294, USA.
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41
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Abstract
My journey into a research career began in fermentation biochemistry in an applied science department during the difficult post-World War II time in Japan. Subsequently, my desire to do research in basic science developed. I was fortunate to be a postdoctoral fellow in the United States during the early days of molecular biology. From 1957 to 1960, I worked with three pioneers of molecular biology, Sol Spiegelman, James Watson, and Seymour Benzer. These experiences helped me develop into a basic research scientist. My initial research projects at Osaka University, and subsequently at the University of Wisconsin, Madison, were on the mode of action of colicins as well as on mRNA and ribosomes. Following success in the reconstitution of ribosomal subunits, my efforts focused more on ribosomes, initially on the aspects of structure, function, and in vitro assembly, such as the construction of the 30S subunit assembly map. After this, my laboratory studied the regulation of the synthesis of ribosomes and ribosomal components in Escherichia coli. Our achievements included the discovery of translational feedback regulation of ribosomal protein synthesis and the identification of several repressor ribosomal proteins used in this regulation. In 1984, I moved to the University of California, Irvine, and initiated research on rRNA transcription by RNA polymerase I in the yeast Saccharomyces cerevisiae. The use of yeast genetics combined with biochemistry allowed us to identify genes uniquely involved in rRNA synthesis and to elucidate the mechanism of initiation of transcription. This essay is a reflection on my life as a research scientist.
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Affiliation(s)
- Masayasu Nomura
- Department of Biological Chemistry, University of California, Irvine, California 92697-1700
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42
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Chuwattanakul V, Kim YH, Sugiyama M, Nishiuchi H, Miwa H, Kaneko Y, Harashima S. Construction of a Saccharomyces cerevisiae strain with a high level of RNA. J Biosci Bioeng 2011; 112:1-7. [DOI: 10.1016/j.jbiosc.2011.03.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 02/26/2011] [Accepted: 03/21/2011] [Indexed: 11/30/2022]
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Viktorovskaya OV, Appling FD, Schneider DA. Yeast transcription elongation factor Spt5 associates with RNA polymerase I and RNA polymerase II directly. J Biol Chem 2011; 286:18825-33. [PMID: 21467036 PMCID: PMC3099699 DOI: 10.1074/jbc.m110.202119] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 03/23/2011] [Indexed: 11/06/2022] Open
Abstract
Spt5 is a transcription factor conserved in all three domains of life. Spt5 homologues from bacteria and archaea bind the largest subunit of their respective RNA polymerases. Here we demonstrate that Spt5 directly associates with RNA polymerase (Pol) I and RNA Pol II in yeast through its central region containing conserved NusG N-terminal homology and KOW domains. Deletion analysis of SPT5 supports our biochemical data, demonstrating the importance of the KOW domains in Spt5 function. Far Western blot analysis implicates A190 of Pol I as well as Rpb1 of Pol II in binding Spt5. Three additional subunits of Pol I may also participate in this interaction. One of these subunits, A49, has known roles in transcription elongation by Pol I. Interestingly, spt5 truncation mutations suppress the cold-sensitive phenotype of rpa49Δ strain, which lacks the A49 subunit in the Pol I complex. Finally, we observed that Spt5 directly binds to an essential Pol I transcription initiation factor, Rrn3, and to the ribosomal RNA. Based on these data, we propose a model in which Spt5 is recruited to the rDNA early in transcription and propose that it plays an important role in ribosomal RNA synthesis through direct binding to the Pol I complex.
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MESH Headings
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- Models, Biological
- Pol1 Transcription Initiation Complex Proteins/genetics
- Pol1 Transcription Initiation Complex Proteins/metabolism
- Protein Binding
- Protein Structure, Tertiary
- RNA Polymerase I/genetics
- RNA Polymerase I/metabolism
- RNA Polymerase II/genetics
- RNA Polymerase II/metabolism
- RNA, Fungal/biosynthesis
- RNA, Fungal/genetics
- RNA, Ribosomal/biosynthesis
- RNA, Ribosomal/genetics
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Transcription, Genetic/physiology
- Transcriptional Elongation Factors/genetics
- Transcriptional Elongation Factors/metabolism
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Affiliation(s)
- Olga V. Viktorovskaya
- From the Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294-0024
| | - Francis D. Appling
- From the Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294-0024
| | - David A. Schneider
- From the Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294-0024
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44
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Wittner M, Hamperl S, Stöckl U, Seufert W, Tschochner H, Milkereit P, Griesenbeck J. Establishment and Maintenance of Alternative Chromatin States at a Multicopy Gene Locus. Cell 2011; 145:543-54. [DOI: 10.1016/j.cell.2011.03.051] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 01/17/2011] [Accepted: 03/18/2011] [Indexed: 11/15/2022]
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45
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Lewinska A, Wnuk M, Grzelak A, Bartosz G. Nucleolus as an oxidative stress sensor in the yeast Saccharomyces cerevisiae. Redox Rep 2010; 15:87-96. [PMID: 20500990 DOI: 10.1179/174329210x12650506623366] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
In mammals, the nucleolus is thought to be a stress sensor; upon cellular stress conditions, a release of nucleolar proteins and down-regulation of rDNA transcription occurs. Since yeast Rrn3p is a homolog of the mammalian RNA polymerase I (Pol I)-specific transcription factor TIF-IA, we decided to investigate the role of Rrn3p in oxidant-induced nucleolar stress in yeast. We show that, after oxidant treatment, the level of Rrn3p is unaffected but Rrn3p is translocated from the nucleolus into the cytoplasm and a point mutation in the RRN3 gene leads to hypersensitivity of the yeast to oxidants. This hypersensitivity can be abolished by re-introduction of the active RRN3 gene, antioxidant supplementation and anoxic atmosphere. Additionally, we employed the PRINS technique to monitor oxidant-mediated changes in the nucleolar structure. Taken together, our results suggest the role of the yeast nucleolus in the response to oxidative stress signals.
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Affiliation(s)
- Anna Lewinska
- Department of Biochemistry and Cell Biology, University of Rzeszow, Pigonia 6, PL35-959 Rzeszow, Poland.
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46
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Nomura M. Switching from prokaryotic molecular biology to eukaryotic molecular biology. J Biol Chem 2009; 284:9625-35. [PMID: 19074426 DOI: 10.1074/jbc.x800014200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Masayasu Nomura
- Department of Biological Chemistry, University of California, Irvine, California 92697-1700, USA.
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47
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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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48
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Clemente-Blanco A, Mayán-Santos M, Schneider DA, Machín F, Jarmuz A, Tschochner H, Aragón L. Cdc14 inhibits transcription by RNA polymerase I during anaphase. Nature 2009; 458:219-22. [PMID: 19158678 DOI: 10.1038/nature07652] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Accepted: 11/13/2008] [Indexed: 01/13/2023]
Abstract
Chromosome condensation and the global repression of gene transcription are features of mitosis in most eukaryotes. The logic behind this phenomenon is that chromosome condensation prevents the activity of RNA polymerases. In budding yeast, however, transcription was proposed to be continuous during mitosis. Here we show that Cdc14, a protein phosphatase required for nucleolar segregation and mitotic exit, inhibits transcription of yeast ribosomal genes (rDNA) during anaphase. The phosphatase activity of Cdc14 is required for RNA polymerase I (Pol I) inhibition in vitro and in vivo. Moreover Cdc14-dependent inhibition involves nucleolar exclusion of Pol I subunits. We demonstrate that transcription inhibition is necessary for complete chromosome disjunction, because ribosomal RNA (rRNA) transcripts block condensin binding to rDNA, and show that bypassing the role of Cdc14 in nucleolar segregation requires in vivo degradation of nascent transcripts. Our results show that transcription interferes with chromosome condensation, not the reverse. We conclude that budding yeast, like most eukaryotes, inhibit Pol I transcription before segregation as a prerequisite for chromosome condensation and faithful genome separation.
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Affiliation(s)
- Andrés Clemente-Blanco
- Cell Cycle Group, MRC Clinical Sciences Centre, Imperial College, Du Cane Road, London W12 0NN, UK
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Schneider DA, Michel A, Sikes ML, Vu L, Dodd JA, Salgia S, Osheim YN, Beyer AL, Nomura M. Transcription elongation by RNA polymerase I is linked to efficient rRNA processing and ribosome assembly. Mol Cell 2007; 26:217-29. [PMID: 17466624 PMCID: PMC1927085 DOI: 10.1016/j.molcel.2007.04.007] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Revised: 01/26/2007] [Accepted: 04/09/2007] [Indexed: 02/07/2023]
Abstract
The synthesis of ribosomes in eukaryotic cells is a complex process involving many nonribosomal protein factors and snoRNAs. In general, the processes of rRNA transcription and ribosome assembly are treated as temporally or spatially distinct. Here, we describe the identification of a point mutation in the second largest subunit of RNA polymerase I near the active center of the enzyme that results in an elongation-defective enzyme in the yeast Saccharomyces cerevisiae. In vivo, this mutant shows significant defects in rRNA processing and ribosome assembly. Taken together, these data suggest that transcription of rRNA by RNA polymerase I is linked to rRNA processing and maturation. Thus, RNA polymerase I, elongation factors, and rRNA sequence elements appear to function together to optimize transcription elongation, coordinating cotranscriptional interactions of many factors/snoRNAs with pre-rRNA for correct rRNA processing and ribosome assembly.
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Affiliation(s)
- David A. Schneider
- Department of Biological Chemistry, University of California, Irvine, 240-D Medical Sciences I, Irvine, CA 92697-1700, USA
| | - Antje Michel
- Department of Biological Chemistry, University of California, Irvine, 240-D Medical Sciences I, Irvine, CA 92697-1700, USA
| | - Martha L. Sikes
- Department of Microbiology, University of Virginia Health System, Charlottesville, VA 22908-0734, USA
| | - Loan Vu
- Department of Biological Chemistry, University of California, Irvine, 240-D Medical Sciences I, Irvine, CA 92697-1700, USA
| | - Jonathan A. Dodd
- Department of Biological Chemistry, University of California, Irvine, 240-D Medical Sciences I, Irvine, CA 92697-1700, USA
| | - Shilpa Salgia
- Department of Biological Chemistry, University of California, Irvine, 240-D Medical Sciences I, Irvine, CA 92697-1700, USA
| | - Yvonne N. Osheim
- Department of Microbiology, University of Virginia Health System, Charlottesville, VA 22908-0734, USA
| | - Ann L. Beyer
- Department of Microbiology, University of Virginia Health System, Charlottesville, VA 22908-0734, USA
| | - Masayasu Nomura
- Department of Biological Chemistry, University of California, Irvine, 240-D Medical Sciences I, Irvine, CA 92697-1700, USA
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50
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Dasgupta A, Sprouse RO, French S, Aprikian P, Hontz R, Juedes SA, Smith JS, Beyer AL, Auble DT. Regulation of rRNA synthesis by TATA-binding protein-associated factor Mot1. Mol Cell Biol 2007; 27:2886-96. [PMID: 17296733 PMCID: PMC1899949 DOI: 10.1128/mcb.00054-07] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Mot1 is an essential, conserved, TATA-binding protein (TBP)-associated factor in Saccharomyces cerevisiae with well-established roles in the global control of RNA polymerase II (Pol II) transcription. Previous results have suggested that Mot1 functions exclusively in Pol II transcription, but here we report a novel role for Mot1 in regulating transcription by RNA polymerase I (Pol I). In vivo, Mot1 is associated with the ribosomal DNA, and loss of Mot1 results in decreased rRNA synthesis. Consistent with a direct role for Mot1 in Pol I transcription, Mot1 also associates with the Pol I promoter in vitro in a reaction that depends on components of the Pol I general transcription machinery. Remarkably, in addition to Mot1's role in initiation, rRNA processing is delayed in mot1 cells. Taken together, these results support a model in which Mot1 affects the rate and efficiency of rRNA synthesis by both direct and indirect mechanisms, with resulting effects on transcription activation and the coupling of rRNA synthesis to processing.
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MESH Headings
- Adenosine Triphosphatases/metabolism
- Chromatin/metabolism
- DNA Helicases/metabolism
- DNA, Ribosomal/ultrastructure
- Gene Expression Regulation, Fungal
- Genes, Fungal
- Mutation/genetics
- Promoter Regions, Genetic/genetics
- Protein Transport
- RNA Polymerase I/metabolism
- RNA Processing, Post-Transcriptional/genetics
- RNA, Ribosomal/biosynthesis
- RNA, Ribosomal/genetics
- RNA, Ribosomal/ultrastructure
- Repetitive Sequences, Nucleic Acid/genetics
- Saccharomyces cerevisiae/cytology
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae/ultrastructure
- Saccharomyces cerevisiae Proteins/metabolism
- TATA-Binding Protein Associated Factors/metabolism
- Transcription Factors/metabolism
- Transcription, Genetic
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Affiliation(s)
- Arindam Dasgupta
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, 1300 Jefferson Park Avenue, Charlottesville, Virginia 22908-0733, USA.
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