1
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Lin G, Barnes CO, Weiss S, Dutagaci B, Qiu C, Feig M, Song J, Lyubimov A, Cohen AE, Kaplan CD, Calero G. Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser. Proc Natl Acad Sci U S A 2024; 121:e2318527121. [PMID: 39190355 DOI: 10.1073/pnas.2318527121] [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: 11/06/2023] [Accepted: 07/23/2024] [Indexed: 08/28/2024] Open
Abstract
Catalysis and translocation of multisubunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near-atomic resolution and precise arrangement of key active site components have been elusive. Here, we present the free-electron laser (FEL) structures of a matched ATP-bound Pol II and the hyperactive Rpb1 T834P bridge helix (BH) mutant at the highest resolution to date. The radiation-damage-free FEL structures reveal the full active site interaction network, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg2+, and, more importantly, a putative third (site C) Mg2+ analogous to that described for some DNA polymerases but not observed previously for cellular RNA polymerases. Molecular dynamics (MD) simulations of the structures indicate that the third Mg2+ is coordinated and stabilized at its observed position. TL residues provide half of the substrate binding pocket while multiple TL/BH interactions induce conformational changes that could allow translocation upon substrate hydrolysis. Consistent with TL/BH communication, a FEL structure and MD simulations of the T834P mutant reveal rearrangement of some active site interactions supporting potential plasticity in active site function and long-distance effects on both the width of the central channel and TL conformation, likely underlying its increased elongation rate at the expense of fidelity.
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Affiliation(s)
- Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Simon Weiss
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Bercem Dutagaci
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - Chenxi Qiu
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824
| | - Jihnu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Artem Lyubimov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
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2
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Bao L, Zhu J, Shi T, Jiang Y, Li B, Huang J, Ji X. Increased transcriptional elongation and RNA stability of GPCR ligand binding genes unveiled via RNA polymerase II degradation. Nucleic Acids Res 2024; 52:8165-8183. [PMID: 38842922 DOI: 10.1093/nar/gkae478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/01/2024] [Accepted: 05/31/2024] [Indexed: 06/07/2024] Open
Abstract
RNA polymerase II drives mRNA gene expression, yet our understanding of Pol II degradation is limited. Using auxin-inducible degron, we degraded Pol II's RPB1 subunit, resulting in global repression. Surprisingly, certain genes exhibited increased RNA levels post-degradation. These genes are associated with GPCR ligand binding and are characterized by being less paused and comprising polycomb-bound short genes. RPB1 degradation globally increased KDM6B binding, which was insufficient to explain specific gene activation. In contrast, RPB2 degradation repressed nearly all genes, accompanied by decreased H3K9me3 and SUV39H1 occupancy. We observed a specific increase in serine 2 phosphorylated Pol II and RNA stability for RPB1 degradation-upregulated genes. Additionally, α-amanitin or UV treatment resulted in RPB1 degradation and global gene repression, unveiling subsets of upregulated genes. Our findings highlight the activated transcription elongation and increased RNA stability of signaling genes as potential mechanisms for mammalian cells to counter RPB1 degradation during stress.
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Affiliation(s)
- Lijun Bao
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Junyi Zhu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Tingxin Shi
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yongpeng Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Boyuan Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jie Huang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Beijing Advanced Center of RNA Biology (BEACON), Peking University, Beijing 100871, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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3
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Gillis A, Berry S. Global control of RNA polymerase II. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195024. [PMID: 38552781 DOI: 10.1016/j.bbagrm.2024.195024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
RNA polymerase II (Pol II) is the multi-protein complex responsible for transcribing all protein-coding messenger RNA (mRNA). Most research on gene regulation is focused on the mechanisms controlling which genes are transcribed when, or on the mechanics of transcription. How global Pol II activity is determined receives comparatively less attention. Here, we follow the life of a Pol II molecule from 'assembly of the complex' to nuclear import, enzymatic activity, and degradation. We focus on how Pol II spends its time in the nucleus, and on the two-way relationship between Pol II abundance and activity in the context of homeostasis and global transcriptional changes.
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Affiliation(s)
- Alexander Gillis
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, Australia; UNSW RNA Institute, University of New South Wales, Sydney, Australia; Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Scott Berry
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, Australia; UNSW RNA Institute, University of New South Wales, Sydney, Australia; Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
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4
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Feng Z, Liu S, Su M, Song C, Lin C, Zhao F, Li Y, Zeng X, Zhu Y, Hou Y, Ren C, Zhang H, Yi P, Ji Y, Wang C, Li H, Ma M, Luo L, Li L. TANGO6 regulates cell proliferation via COPI vesicle-mediated RPB2 nuclear entry. Nat Commun 2024; 15:2371. [PMID: 38490996 PMCID: PMC10943085 DOI: 10.1038/s41467-024-46720-y] [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: 11/02/2022] [Accepted: 03/01/2024] [Indexed: 03/18/2024] Open
Abstract
Coat protein complex I (COPI) vesicles mediate the retrograde transfer of cargo between Golgi cisternae and from the Golgi to the endoplasmic reticulum (ER). However, their roles in the cell cycle and proliferation are unclear. This study shows that TANGO6 associates with COPI vesicles via two transmembrane domains. The TANGO6 N- and C-terminal cytoplasmic fragments capture RNA polymerase II subunit B (RPB) 2 in the cis-Golgi during the G1 phase. COPI-docked TANGO6 carries RPB2 to the ER and then to the nucleus. Functional disruption of TANGO6 hinders the nuclear entry of RPB2, which accumulates in the cytoplasm, causing cell cycle arrest in the G1 phase. The conditional depletion or overexpression of TANGO6 in mouse hematopoietic stem cells results in compromised or expanded hematopoiesis. Our study results demonstrate that COPI vesicle-associated TANGO6 plays a role in the regulation of cell cycle progression by directing the nuclear transfer of RPB2, making it a potential target for promoting or arresting cell expansion.
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Affiliation(s)
- Zhi Feng
- Research center of Stem cells and Ageing, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China
| | - Shengnan Liu
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University, Chongqing, 400715, PR China
| | - Ming Su
- Research center of Stem cells and Ageing, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China
| | - Chunyu Song
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University, Chongqing, 400715, PR China
| | - Chenyu Lin
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University, Chongqing, 400715, PR China
| | - Fangying Zhao
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University, Chongqing, 400715, PR China
| | - Yang Li
- Research center of Stem cells and Ageing, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China
| | - Xianyan Zeng
- Institute of Life Sciences, Laboratory of Developmental Biology, Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yong Zhu
- Institute of Life Sciences, Laboratory of Developmental Biology, Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yu Hou
- Institute of Life Sciences, Laboratory of Developmental Biology, Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, 400016, PR China
| | - Chunguang Ren
- Institute of Life Sciences, Laboratory of Developmental Biology, Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, 400016, PR China
| | - Huan Zhang
- Institute of Life Sciences, Laboratory of Developmental Biology, Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, 400016, PR China
| | - Ping Yi
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, PR China
| | - Yong Ji
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine; Key Laboratory of Targeted Intervention of Cardiovascular Disease; Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, 211166, PR China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD), Harbin Medical University, Harbin, 150076, Heilongjiang, PR China
| | - Chao Wang
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, PR China
| | - Hongtao Li
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University, Chongqing, 400715, PR China
| | - Ming Ma
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University, Chongqing, 400715, PR China
| | - Lingfei Luo
- Institute of Developmental Biology and Regenerative Medicine, Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Southwest University, Chongqing, 400715, PR China.
| | - Li Li
- Research center of Stem cells and Ageing, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, PR China.
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5
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Pilotto S, Sýkora M, Cackett G, Dulson C, Werner F. Structure of the recombinant RNA polymerase from African Swine Fever Virus. Nat Commun 2024; 15:1606. [PMID: 38383525 PMCID: PMC10881513 DOI: 10.1038/s41467-024-45842-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 02/06/2024] [Indexed: 02/23/2024] Open
Abstract
African Swine Fever Virus is a Nucleo-Cytoplasmic Large DNA Virus that causes an incurable haemorrhagic fever in pigs with a high impact on global food security. ASFV replicates in the cytoplasm of the infected cell and encodes its own transcription machinery that is independent of cellular factors, however, not much is known about how this system works at a molecular level. Here, we present methods to produce recombinant ASFV RNA polymerase, functional assays to screen for inhibitors, and high-resolution cryo-electron microscopy structures of the ASFV RNAP in different conformational states. The ASFV RNAP bears a striking resemblance to RNAPII with bona fide homologues of nine of its twelve subunits. Key differences include the fusion of the ASFV assembly platform subunits RPB3 and RPB11, and an unusual C-terminal domain of the stalk subunit vRPB7 that is related to the eukaryotic mRNA cap 2´-O-methyltransferase 1. Despite the high degree of structural conservation with cellular RNA polymerases, the ASFV RNAP is resistant to the inhibitors rifampicin and alpha-amanitin. The cryo-EM structures and fully recombinant RNAP system together provide an important tool for the design, development, and screening of antiviral drugs in a low biosafety containment environment.
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Affiliation(s)
- Simona Pilotto
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Michal Sýkora
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Gwenny Cackett
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Christopher Dulson
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - Finn Werner
- Institute for Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, United Kingdom.
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6
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Bernardini A, Tora L. Co-translational Assembly Pathways of Nuclear Multiprotein Complexes Involved in the Regulation of Gene Transcription. J Mol Biol 2024; 436:168382. [PMID: 38061625 DOI: 10.1016/j.jmb.2023.168382] [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: 10/25/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023]
Abstract
Most factors that regulate gene transcription in eukaryotic cells are multimeric, often large, protein complexes. The understanding of the biogenesis pathways of such large and heterogeneous protein assemblies, as well as the dimerization partner choice among transcription factors, is crucial to interpret and control gene expression programs and consequent cell fate decisions. Co-translational assembly (Co-TA) is thought to play key roles in the biogenesis of protein complexes by directing complex formation during protein synthesis. In this review we discuss the principles of Co-TA with a special focus for the assembly of transcription regulatory complexes. We outline the expected molecular advantages of establishing co-translational interactions, pointing at the available, or missing, evidence for each of them. We hypothesize different molecular mechanisms based on Co-TA to explain the allocation "dilemma" of paralog proteins and subunits shared by different transcription complexes. By taking as a paradigm the different assembly pathways employed by three related transcription regulatory complexes (TFIID, SAGA and ATAC), we discuss alternative Co-TA strategies for nuclear multiprotein complexes and the widespread - yet specific - use of Co-TA for the formation of nuclear complexes involved in gene transcription. Ultimately, we outlined a series of open questions which demand well-defined lines of research to investigate the principles of gene regulation that rely on the coordinated assembly of protein complexes.
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Affiliation(s)
- Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964 Illkirch, France; Université de Strasbourg, Illkirch, France.
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964 Illkirch, France; Université de Strasbourg, Illkirch, France.
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7
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Garrido-Godino AI, Gupta I, Pelechano V, Navarro F. RNA Pol II Assembly Affects ncRNA Expression. Int J Mol Sci 2023; 25:507. [PMID: 38203678 PMCID: PMC10778713 DOI: 10.3390/ijms25010507] [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: 11/30/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
RNA pol II assembly occurs in the cytoplasm before translocation of the enzyme to the nucleus. Affecting this assembly influences mRNA transcription in the nucleus and mRNA decay in the cytoplasm. However, very little is known about the consequences on ncRNA synthesis. In this work, we show that impairment of RNA pol II assembly leads to a decrease in cryptic non-coding RNAs (preferentially CUTs and SUTs). This alteration is partially restored upon overcoming the assembly defect. Notably, this drop in ncRNAs is only partially dependent on the nuclear exosome, which suggests a major specific effect of enzyme assembly. Our data also point out a defect in transcription termination, which leads us to propose that CTD phosphatase Rtr1 could be involved in this process.
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Affiliation(s)
- Ana I. Garrido-Godino
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain;
| | - Ishaan Gupta
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany;
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain;
- Instituto Universitario de Investigación en Olivar y Aceites de Oliva (INUO), Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
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8
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Michell-Robinson MA, Watt KEN, Grouza V, Macintosh J, Pinard M, Tuznik M, Chen X, Darbelli L, Wu CL, Perrier S, Chitsaz D, Uccelli NA, Liu H, Cox TC, Müller CW, Kennedy TE, Coulombe B, Rudko DA, Trainor PA, Bernard G. Hypomyelination, hypodontia and craniofacial abnormalities in a Polr3b mouse model of leukodystrophy. Brain 2023; 146:5070-5085. [PMID: 37635302 PMCID: PMC10690025 DOI: 10.1093/brain/awad249] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/23/2023] [Accepted: 07/06/2023] [Indexed: 08/29/2023] Open
Abstract
RNA polymerase III (Pol III)-related hypomyelinating leukodystrophy (POLR3-HLD), also known as 4H leukodystrophy, is a severe neurodegenerative disease characterized by the cardinal features of hypomyelination, hypodontia and hypogonadotropic hypogonadism. POLR3-HLD is caused by biallelic pathogenic variants in genes encoding Pol III subunits. While approximately half of all patients carry mutations in POLR3B encoding the RNA polymerase III subunit B, there is no in vivo model of leukodystrophy based on mutation of this Pol III subunit. Here, we determined the impact of POLR3BΔ10 (Δ10) on Pol III in human cells and developed and characterized an inducible/conditional mouse model of leukodystrophy using the orthologous Δ10 mutation in mice. The molecular mechanism of Pol III dysfunction was determined in human cells by affinity purification-mass spectrometry and western blot. Postnatal induction with tamoxifen induced expression of the orthologous Δ10 hypomorph in triple transgenic Pdgfrα-Cre/ERT; R26-Stopfl-EYFP; Polr3bfl mice. CNS and non-CNS features were characterized using a variety of techniques including microCT, ex vivo MRI, immunofluorescence, immunohistochemistry, spectral confocal reflectance microscopy and western blot. Lineage tracing and time series analysis of oligodendrocyte subpopulation dynamics based on co-labelling with lineage-specific and/or proliferation markers were performed. Proteomics suggested that Δ10 causes a Pol III assembly defect, while western blots demonstrated reduced POLR3BΔ10 expression in the cytoplasm and nucleus in human cells. In mice, postnatal Pdgfrα-dependent expression of the orthologous murine mutant protein resulted in recessive phenotypes including severe hypomyelination leading to ataxia, tremor, seizures and limited survival, as well as hypodontia and craniofacial abnormalities. Hypomyelination was confirmed and characterized using classic methods to quantify myelin components such as myelin basic protein and lipids, results which agreed with those produced using modern methods to quantify myelin based on the physical properties of myelin membranes. Lineage tracing uncovered the underlying mechanism for the hypomyelinating phenotype: defective oligodendrocyte precursor proliferation and differentiation resulted in a failure to produce an adequate number of mature oligodendrocytes during postnatal myelinogenesis. In summary, we characterized the Polr3bΔ10 mutation and developed an animal model that recapitulates features of POLR3-HLD caused by POLR3B mutations, shedding light on disease pathogenesis, and opening the door to the development of therapeutic interventions.
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Affiliation(s)
- Mackenzie A Michell-Robinson
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada
| | - Kristin E N Watt
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Vladimir Grouza
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, Montreal, QC H3A 2B4, Canada
| | - Julia Macintosh
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada
| | - Maxime Pinard
- Translational Proteomics Research Unit, Montreal Clinical Research Institute, Montréal, QC H2W 1R7, Canada
| | - Marius Tuznik
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, Montreal, QC H3A 2B4, Canada
| | - Xiaoru Chen
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada
| | - Lama Darbelli
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada
| | - Chia-Lun Wu
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada
| | - Stefanie Perrier
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada
| | - Daryan Chitsaz
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
| | - Nonthué A Uccelli
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
| | - Hanwen Liu
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, Montreal, QC H3A 2B4, Canada
| | - Timothy C Cox
- Department of Oral and Craniofacial Sciences, School of Dentistry, and Pediatrics, School of Medicine, University of Missouri – Kansas City, Kansas City, MO 64108, USA
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Timothy E Kennedy
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
| | - Benoit Coulombe
- Translational Proteomics Research Unit, Montreal Clinical Research Institute, Montréal, QC H2W 1R7, Canada
- Department of Biochemistry and Molecular Medicine, University of Montréal, Montréal, QC H3C 3J7, Canada
| | - David A Rudko
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, Montreal, QC H3A 2B4, Canada
- Department of Biomedical Engineering, McGill University, Montréal, QC H3A 2B4, Canada
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Anatomy and Cell Biology, The University of Kansas School of Medicine, Kansas City, KS 66160, USA
| | - Geneviève Bernard
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC H3A 1A1, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada
- Department of Pediatrics, McGill University, Montréal, QC H4A 3J1, Canada
- Department of Human Genetics, McGill University, Montréal, QC H4A 0C7, Canada
- Department of Specialized Medicine, Division of Medical Genetics, Montreal Children’s Hospital and McGill University Health Centre, Montréal, QC H4A 3J1, Canada
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9
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Collart MA, Audebert L, Bushell M. Roles of the CCR4-Not complex in translation and dynamics of co-translation events. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1827. [PMID: 38009591 PMCID: PMC10909573 DOI: 10.1002/wrna.1827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/06/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
The Ccr4-Not complex is a global regulator of mRNA metabolism in eukaryotic cells that is most well-known to repress gene expression. Delivery of the complex to mRNAs through a multitude of distinct mechanisms accelerates their decay, yet Ccr4-Not also plays an important role in co-translational processes, such as co-translational association of proteins and delivery of translating mRNAs to organelles. The recent structure of Not5 interacting with the translated ribosome has brought to light that embedded information within the codon sequence can be monitored by recruitment of the Ccr4-Not complex to elongating ribosomes. Thereby, the Ccr4-Not complex is empowered with regulatory decisions determining the fate of proteins being synthesized and their encoding mRNAs. This review will focus on the roles of the complex in translation and dynamics of co-translation events. This article is categorized under: Translation > Mechanisms Translation > Regulation.
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Affiliation(s)
- Martine A. Collart
- Department of Microbiology and Molecular MedicineInstitute of Genetics and Genomics Geneva, University of Geneva, Faculty of MedicineGenèveSwitzerland
| | - Léna Audebert
- Department of Microbiology and Molecular MedicineInstitute of Genetics and Genomics Geneva, University of Geneva, Faculty of MedicineGenèveSwitzerland
| | - Martin Bushell
- Cancer Research UK Beatson InstituteGlasgowUK
- School of Cancer Sciences, University of GlasgowGlasgowUK
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10
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Schindler D, Walker RSK, Jiang S, Brooks AN, Wang Y, Müller CA, Cockram C, Luo Y, García A, Schraivogel D, Mozziconacci J, Pena N, Assari M, Sánchez Olmos MDC, Zhao Y, Ballerini A, Blount BA, Cai J, Ogunlana L, Liu W, Jönsson K, Abramczyk D, Garcia-Ruiz E, Turowski TW, Swidah R, Ellis T, Pan T, Antequera F, Shen Y, Nieduszynski CA, Koszul R, Dai J, Steinmetz LM, Boeke JD, Cai Y. Design, construction, and functional characterization of a tRNA neochromosome in yeast. Cell 2023; 186:5237-5253.e22. [PMID: 37944512 DOI: 10.1016/j.cell.2023.10.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 09/22/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023]
Abstract
Here, we report the design, construction, and characterization of a tRNA neochromosome, a designer chromosome that functions as an additional, de novo counterpart to the native complement of Saccharomyces cerevisiae. Intending to address one of the central design principles of the Sc2.0 project, the ∼190-kb tRNA neochromosome houses all 275 relocated nuclear tRNA genes. To maximize stability, the design incorporates orthogonal genetic elements from non-S. cerevisiae yeast species. Furthermore, the presence of 283 rox recombination sites enables an orthogonal tRNA SCRaMbLE system. Following construction in yeast, we obtained evidence of a potent selective force, manifesting as a spontaneous doubling in cell ploidy. Furthermore, tRNA sequencing, transcriptomics, proteomics, nucleosome mapping, replication profiling, FISH, and Hi-C were undertaken to investigate questions of tRNA neochromosome behavior and function. Its construction demonstrates the remarkable tractability of the yeast model and opens up opportunities to directly test hypotheses surrounding these essential non-coding RNAs.
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Affiliation(s)
- Daniel Schindler
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK; Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, 35032 Marburg, Germany
| | - Roy S K Walker
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EH9 3BF, Scotland; School of Natural Sciences and ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
| | - Shuangying Jiang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Aaron N Brooks
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Yun Wang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Carolin A Müller
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, UK
| | - Charlotte Cockram
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Yisha Luo
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Alicia García
- Instituto de Biología Funcional y Genómica (IBFG), CSIC, Universidad de Salamanca, Salamanca, Spain
| | - Daniel Schraivogel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Julien Mozziconacci
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Noah Pena
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Mahdi Assari
- Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | | | - Yu Zhao
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Alba Ballerini
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Benjamin A Blount
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK; Department of Bioengineering, Imperial College London, London, UK
| | - Jitong Cai
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Lois Ogunlana
- School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland
| | - Wei Liu
- School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland
| | - Katarina Jönsson
- School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland
| | - Dariusz Abramczyk
- School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, Scotland
| | - Eva Garcia-Ruiz
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Tomasz W Turowski
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5a, 02-106 Warszawa, Poland
| | - Reem Swidah
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology, Imperial College London, London, UK; Department of Bioengineering, Imperial College London, London, UK
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Francisco Antequera
- Instituto de Biología Funcional y Genómica (IBFG), CSIC, Universidad de Salamanca, Salamanca, Spain
| | - Yue Shen
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK; BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Conrad A Nieduszynski
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, UK
| | - Romain Koszul
- Institut Pasteur, CNRS UMR 3525, Université Paris Cité, Unité Régulation Spatiale des Génomes, 75015 Paris, France
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany; Department of Genetics and Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Yizhi Cai
- Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK.
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11
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Huang J, Ji X. Never a dull enzyme, RNA polymerase II. Transcription 2023; 14:49-67. [PMID: 37132022 PMCID: PMC10353340 DOI: 10.1080/21541264.2023.2208023] [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: 02/10/2023] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/04/2023] Open
Abstract
RNA polymerase II (Pol II) is composed of 12 subunits that collaborate to synthesize mRNA within the nucleus. Pol II is widely recognized as a passive holoenzyme, with the molecular functions of its subunits largely ignored. Recent studies employing auxin-inducible degron (AID) and multi-omics techniques have revealed that the functional diversity of Pol II is achieved through the differential contributions of its subunits to various transcriptional and post-transcriptional processes. By regulating these processes in a coordinated manner through its subunits, Pol II can optimize its activity for diverse biological functions. Here, we review recent progress in understanding Pol II subunits and their dysregulation in diseases, Pol II heterogeneity, Pol II clusters and the regulatory roles of RNA polymerases.
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Affiliation(s)
- Jie Huang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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12
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Lin G, Barnes CO, Weiss S, Dutagaci B, Qiu C, Feig M, Song J, Lyubimov A, Cohen AE, Kaplan CD, Calero G. Structural basis of transcription: RNA Polymerase II substrate binding and metal coordination at 3.0 Å using a free-electron laser. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.559052. [PMID: 37790421 PMCID: PMC10543002 DOI: 10.1101/2023.09.22.559052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Catalysis and translocation of multi-subunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near atomic resolution and precise arrangement of key active site components have been elusive. Here we present the free electron laser (FEL) structure of a matched ATP-bound Pol II, revealing the full active site interaction network at the highest resolution to date, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg2+, and a putative third (site C) Mg2+ analogous to that described for some DNA polymerases but not observed previously for cellular RNA polymerases. Molecular dynamics (MD) simulations of the structure indicate that the third Mg2+ is coordinated and stabilized at its observed position. TL residues provide half of the substrate binding pocket while multiple TL/bridge helix (BH) interactions induce conformational changes that could propel translocation upon substrate hydrolysis. Consistent with TL/BH communication, a FEL structure and MD simulations of the hyperactive Rpb1 T834P bridge helix mutant reveals rearrangement of some active site interactions supporting potential plasticity in active site function and long-distance effects on both the width of the central channel and TL conformation, likely underlying its increased elongation rate at the expense of fidelity.
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Affiliation(s)
- Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261 USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena CA 91125 USA
| | - Simon Weiss
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261 USA
| | - Bercem Dutagaci
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing MI 48824 USA
| | - Chenxi Qiu
- Department of Genetics, Harvard Medical School, Boston MA 02115 USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing MI 48824 USA
| | - Jihnu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Artem Lyubimov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260 USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261 USA
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13
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Tian K, Wang R, Huang J, Wang H, Ji X. Subcellular localization shapes the fate of RNA polymerase III. Cell Rep 2023; 42:112941. [PMID: 37556328 DOI: 10.1016/j.celrep.2023.112941] [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: 02/08/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/11/2023] Open
Abstract
RNA polymerase III (Pol III) plays a vital role in transcription and as a viral-DNA sensor, but how it is assembled and distributed within cells remains poorly understood. Here, we show that Pol III is assembled with chaperones in the cytoplasm and forms transcription-dependent protein clusters upon transport into the nucleus. The largest subunit (RPC1) depletion through an auxin-inducible degron leads to rapid degradation and disassembly of Pol III complex in the nucleus and cytoplasm, respectively. This generates a pool of partially assembled Pol III intermediates, which can be rapidly mobilized into the nucleus upon the restoration of RPC1. Our study highlights the critical role of subcellular localization in determining Pol III's fate and provides insight into the dynamic regulation of nuclear Pol III levels and the origin of cytoplasmic Pol III complexes involved in mediating viral immunity.
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Affiliation(s)
- Kai Tian
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Rui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jie Huang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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14
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Chen Q, Guo Y, Zhang J, Zheng N, Wang J, Liu Y, Lu J, Zhen S, Du X, Li L, Fu J, Wang G, Gu R, Wang J, Liu Y. RNA polymerase common subunit ZmRPABC5b is transcriptionally activated by Opaque2 and essential for endosperm development in maize. Nucleic Acids Res 2023; 51:7832-7850. [PMID: 37403778 PMCID: PMC10450181 DOI: 10.1093/nar/gkad571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 06/08/2023] [Accepted: 06/24/2023] [Indexed: 07/06/2023] Open
Abstract
Maize (Zea mays) kernel size is an important factor determining grain yield; although numerous genes regulate kernel development, the roles of RNA polymerases in this process are largely unclear. Here, we characterized the defective kernel 701 (dek701) mutant that displays delayed endosperm development but normal vegetative growth and flowering transition, compared to its wild type. We cloned Dek701, which encoded ZmRPABC5b, a common subunit to RNA polymerases I, II and III. Loss-of-function mutation of Dek701 impaired the function of all three RNA polymerases and altered the transcription of genes related to RNA biosynthesis, phytohormone response and starch accumulation. Consistent with this observation, loss-of-function mutation of Dek701 affected cell proliferation and phytohormone homeostasis in maize endosperm. Dek701 was transcriptionally regulated in the endosperm by the transcription factor Opaque2 through binding to the GCN4 motif within the Dek701 promoter, which was subjected to strong artificial selection during maize domestication. Further investigation revealed that DEK701 interacts with the other common RNA polymerase subunit ZmRPABC2. The results of this study provide substantial insight into the Opaque2-ZmRPABC5b transcriptional regulatory network as a central hub for regulating endosperm development in maize.
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Affiliation(s)
- Quanquan Chen
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yingmei Guo
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jie Zhang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Nannan Zheng
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jie Wang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiawen Lu
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Sihan Zhen
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xuemei Du
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Li Li
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Riliang Gu
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jianhua Wang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Maize Bio-breeding; Center for Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yunjun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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15
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Kalvelage J, Wöhlbrand L, Schoon RA, Zink FM, Correll C, Senkler J, Eubel H, Hoppenrath M, Rhiel E, Braun HP, Winklhofer M, Klingl A, Rabus R. The enigmatic nucleus of the marine dinoflagellate Prorocentrum cordatum. mSphere 2023; 8:e0003823. [PMID: 37358287 PMCID: PMC10449503 DOI: 10.1128/msphere.00038-23] [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: 01/23/2023] [Accepted: 02/20/2023] [Indexed: 06/27/2023] Open
Abstract
The marine, bloom-forming dinoflagellate Prorocentrum cordatum CCMP 1329 (formerly P. minimum) has a genome atypical of eukaryotes, with a large size of ~4.15 Gbp, organized in plentiful, highly condensed chromosomes and packed in a dinoflagellate-specific nucleus (dinokaryon). Here, we apply microscopic and proteogenomic approaches to obtain new insights into this enigmatic nucleus of axenic P. cordatum. High-resolution focused ion beam/scanning electron microscopy analysis of the flattened nucleus revealed highest density of nuclear pores in the vicinity of the nucleolus, a total of 62 tightly packed chromosomes (~0.4-6.7 µm3), and interaction of several chromosomes with the nucleolus and other nuclear structures. A specific procedure for enriching intact nuclei was developed to enable proteomic analyses of soluble and membrane protein-enriched fractions. These were analyzed with geLC and shotgun approaches employing ion-trap and timsTOF (trapped-ion-mobility-spectrometry time-of-flight) mass spectrometers, respectively. This allowed identification of 4,052 proteins (39% of unknown function), out of which 418 were predicted to serve specific nuclear functions; additional 531 proteins of unknown function could be allocated to the nucleus. Compaction of DNA despite very low histone abundance could be accomplished by highly abundant major basic nuclear proteins (HCc2-like). Several nuclear processes including DNA replication/repair and RNA processing/splicing can be fairly well explained on the proteogenomic level. By contrast, transcription and composition of the nuclear pore complex remain largely elusive. One may speculate that the large group of potential nuclear proteins with currently unknown functions may serve yet to be explored functions in nuclear processes differing from those of typical eukaryotic cells. IMPORTANCE Dinoflagellates form a highly diverse group of unicellular microalgae. They provide keystone species for the marine ecosystem and stand out among others by their very large, unusually organized genomes embedded in the nuclei markedly different from other eukaryotic cells. Functional insights into nuclear and other cell biological structures and processes of dinoflagellates have long been hampered by the paucity of available genomic sequences. The here studied cosmopolitan P. cordatum belongs to the harmful algal bloom-forming, marine dinoflagellates and has a recently de novo assembled genome. We present a detailed 3D reconstruction of the P. cordatum nucleus together with comprehensive proteogenomic insights into the protein equipment mastering the broad spectrum of nuclear processes. This study significantly advances our understanding of mechanisms and evolution of the conspicuous dinoflagellate cell biology.
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Affiliation(s)
- Jana Kalvelage
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Robin-Alexander Schoon
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Fiona-Marine Zink
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Christina Correll
- Plant Development, Botany, Ludwig-Maximilians-Universität München, Planegg, Martinsried, Germany
| | - Jennifer Senkler
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Holger Eubel
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Mona Hoppenrath
- Marine Biodiversity Research, Institute of Biology and Environmental Sciences (IBU), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Wilhelmshaven, Germany
| | - Erhard Rhiel
- Planktology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Hans-Peter Braun
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Michael Winklhofer
- Sensory Biology of Animals, Institute of Biology and Environmental Sciences (IBU), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- Research Center Neurosensory Science, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Andreas Klingl
- Plant Development, Botany, Ludwig-Maximilians-Universität München, Planegg, Martinsried, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
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16
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Belkevich AE, Pascual HG, Fakhouri AM, Ball DG, Knutson BA. Distinct Interaction Modes for the Eukaryotic RNA Polymerase Alpha-like Subunits. Mol Cell Biol 2023; 43:269-282. [PMID: 37222571 PMCID: PMC10251799 DOI: 10.1080/10985549.2023.2210023] [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: 01/31/2023] [Revised: 03/26/2023] [Accepted: 04/12/2023] [Indexed: 05/25/2023] Open
Abstract
Eukaryotic DNA-dependent RNA polymerases (Pols I-III) encode two distinct alpha-like heterodimers where one is shared between Pols I and III, and the other is unique to Pol II. Human alpha-like subunit mutations are associated with several diseases including Treacher Collins Syndrome (TCS), 4H leukodystrophy, and primary ovarian sufficiency. Yeast is commonly used to model human disease mutations, yet it remains unclear whether the alpha-like subunit interactions are functionally similar between yeast and human homologs. To examine this, we mutated several regions of the yeast and human small alpha-like subunits and used biochemical and genetic assays to establish the regions and residues required for heterodimerization with their corresponding large alpha-like subunits. Here we show that different regions of the small alpha-like subunits serve differential roles in heterodimerization, in a polymerase- and species-specific manner. We found that the small human alpha-like subunits are more sensitive to mutations, including a "humanized" yeast that we used to characterize the molecular consequence of the TCS-causingPOLR1D G52E mutation. These findings help explain why some alpha subunit associated disease mutations have little to no effect when made in their yeast orthologs and offer a better yeast model to assess the molecular basis of POLR1D associated disease mutations.
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Affiliation(s)
- Alana E. Belkevich
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Haleigh G. Pascual
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Aula M. Fakhouri
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - David G. Ball
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Bruce A. Knutson
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
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17
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Li Y, Huang J, Bao L, Zhu J, Duan W, Zheng H, Wang H, Jiang Y, Liu W, Zhang M, Yu Y, Yi C, Ji X. RNA Pol II preferentially regulates ribosomal protein expression by trapping disassociated subunits. Mol Cell 2023; 83:1280-1297.e11. [PMID: 36924766 DOI: 10.1016/j.molcel.2023.02.028] [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: 03/30/2022] [Revised: 12/12/2022] [Accepted: 02/23/2023] [Indexed: 03/17/2023]
Abstract
RNA polymerase II (RNA Pol II) has been recognized as a passively regulated multi-subunit holoenzyme. However, the extent to which RNA Pol II subunits might be important beyond the RNA Pol II complex remains unclear. Here, fractions containing disassociated RPB3 (dRPB3) were identified by size exclusion chromatography in various cells. Through a unique strategy, i.e., "specific degradation of disassociated subunits (SDDS)," we demonstrated that dRPB3 functions as a regulatory component of RNA Pol II to enable the preferential control of 3' end processing of ribosomal protein genes directly through its N-terminal domain. Machine learning analysis of large-scale genomic features revealed that the little elongation complex (LEC) helps to specialize the functions of dRPB3. Mechanistically, dRPB3 facilitates CBC-PCF11 axis activity to increase the efficiency of 3' end processing. Furthermore, RPB3 is dynamically regulated during development and diseases. These findings suggest that RNA Pol II gains specific regulatory functions by trapping disassociated subunits in mammalian cells.
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Affiliation(s)
- Yuanjun Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jie Huang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Lijun Bao
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Junyi Zhu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Wenjia Duan
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Haonan Zheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yongpeng Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Weiwei Liu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Meiling Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yang Yu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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18
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van der Zanden SY, Jongsma MLM, Neefjes ACM, Berlin I, Neefjes J. Maintaining soluble protein homeostasis between nuclear and cytoplasmic compartments across mitosis. Trends Cell Biol 2023; 33:18-29. [PMID: 35778326 DOI: 10.1016/j.tcb.2022.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/23/2022] [Accepted: 06/06/2022] [Indexed: 12/27/2022]
Abstract
The nuclear envelope (NE) is central to the architecture of eukaryotic cells, both as a physical barrier separating the nucleus from the cytoplasm and as gatekeeper of selective transport between them. However, in open mitosis, the NE fragments to allow for spindle formation and segregation of chromosomes, resulting in intermixing of nuclear and cytoplasmic soluble fractions. Recent studies have shed new light on the mechanisms driving reinstatement of soluble proteome homeostasis following NE reformation in daughter cells. Here, we provide an overview of how mitotic cells confront this challenge to ensure continuity of basic cellular functions across generations and elaborate on the implications for the proteasome - a macromolecular machine that functions in both cytoplasmic and nuclear compartments.
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Affiliation(s)
- Sabina Y van der Zanden
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands
| | - Marlieke L M Jongsma
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands
| | - Anna C M Neefjes
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands
| | - Ilana Berlin
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands.
| | - Jacques Neefjes
- Department of Cell and Chemical Biology, ONCODE Institute, Leiden University Medical Center LUMC, 2333, ZC, Leiden, The Netherlands.
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19
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Pinard M, Dastpeyman S, Poitras C, Bernard G, Gauthier MS, Coulombe B. Riluzole partially restores RNA polymerase III complex assembly in cells expressing the leukodystrophy-causative variant POLR3B R103H. Mol Brain 2022; 15:98. [PMID: 36451185 PMCID: PMC9710144 DOI: 10.1186/s13041-022-00974-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/16/2022] [Indexed: 12/12/2022] Open
Abstract
The mechanism of assembly of RNA polymerase III (Pol III), the 17-subunit enzyme that synthesizes tRNAs, 5 S rRNA, and other small-nuclear (sn) RNAs in eukaryotes, is not clearly understood. The recent discovery of the HSP90 co-chaperone PAQosome (Particle for Arrangement of Quaternary structure) revealed a function for this machinery in the biogenesis of nuclear RNA polymerases. However, the connection between Pol III subunits and the PAQosome during the assembly process remains unexplored. Here, we report the development of a mass spectrometry-based assay that allows the characterization of Pol III assembly. This assay was used to dissect the stages of Pol III assembly, to start defining the function of the PAQosome in this process, to dissect the assembly defects driven by the leukodystrophy-causative R103H substitution in POLR3B, and to discover that riluzole, an FDA-approved drug for alleviation of ALS symptoms, partly corrects these assembly defects. Together, these results shed new light on the mechanism and regulation of human nuclear Pol III biogenesis.
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Affiliation(s)
- Maxime Pinard
- grid.511547.30000 0001 2106 1695Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec Canada
| | - Samaneh Dastpeyman
- grid.511547.30000 0001 2106 1695Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec Canada
| | - Christian Poitras
- grid.511547.30000 0001 2106 1695Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec Canada
| | - Geneviève Bernard
- grid.63984.300000 0000 9064 4811Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649Department of Neurology and Neurosurgery, McGill University, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649Department of Human Genetics, McGill University, Montreal, Canada ,grid.14709.3b0000 0004 1936 8649Department of Pediatrics, McGill University, Montreal, Canada ,grid.63984.300000 0000 9064 4811Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, Canada
| | - Marie-Soleil Gauthier
- grid.511547.30000 0001 2106 1695Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec Canada
| | - Benoit Coulombe
- grid.511547.30000 0001 2106 1695Translational Proteomics Laboratory, Institut de Recherches Cliniques de Montréal, Montréal, Québec Canada ,grid.14848.310000 0001 2292 3357Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec Canada
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20
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Jiang Y, Huang J, Tian K, Yi X, Zheng H, Zhu Y, Guo T, Ji X. Cross-regulome profiling of RNA polymerases highlights the regulatory role of polymerase III on mRNA transcription by maintaining local chromatin architecture. Genome Biol 2022; 23:246. [PMID: 36443871 PMCID: PMC9703767 DOI: 10.1186/s13059-022-02812-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 11/07/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Mammalian cells have three types of RNA polymerases (Pols), Pol I, II, and III. However, the extent to which these polymerases are cross-regulated and the underlying mechanisms remain unclear. RESULTS We employ genome-wide profiling after acute depletion of Pol I, Pol II, or Pol III to assess cross-regulatory effects between these Pols. We find that these enzymes mainly affect the transcription of their own target genes, while certain genes are transcribed by the other polymerases. Importantly, the most active type of crosstalk is exemplified by the fact that Pol III depletion affects Pol II transcription. Pol II genes with transcription changes upon Pol III depletion are enriched in diverse cellular functions, and Pol III binding sites are found near their promoters. However, these Pol III binding sites do not correspond to transfer RNAs. Moreover, we demonstrate that Pol III regulates Pol II transcription and chromatin binding of the facilitates chromatin transcription (FACT) complex to alter local chromatin structures, which in turn affects the Pol II transcription rate. CONCLUSIONS Our results support a model suggesting that RNA polymerases show cross-regulatory effects: Pol III affects local chromatin structures and the FACT-Pol II axis to regulate the Pol II transcription rate at certain gene loci. This study provides a new perspective for understanding the dysregulation of Pol III in various tissues affected by developmental diseases.
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Affiliation(s)
- Yongpeng Jiang
- grid.452723.50000 0004 7887 9190Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Jie Huang
- grid.452723.50000 0004 7887 9190Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Kai Tian
- grid.452723.50000 0004 7887 9190Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Xiao Yi
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024 Zhejiang Province China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024 Zhejiang Province China ,Westlake Omics (Hangzhou) Biotechnology Co., Ltd, Hangzhou, 310024 China
| | - Haonan Zheng
- grid.452723.50000 0004 7887 9190Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Yi Zhu
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024 Zhejiang Province China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024 Zhejiang Province China ,Westlake Omics (Hangzhou) Biotechnology Co., Ltd, Hangzhou, 310024 China
| | - Tiannan Guo
- grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024 Zhejiang Province China ,grid.494629.40000 0004 8008 9315Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024 Zhejiang Province China ,Westlake Omics (Hangzhou) Biotechnology Co., Ltd, Hangzhou, 310024 China
| | - Xiong Ji
- grid.452723.50000 0004 7887 9190Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
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21
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Palumbo RJ, Belkevich AE, Pascual HG, Knutson BA. A clinically-relevant residue of POLR1D is required for Drosophila development. Dev Dyn 2022; 251:1780-1797. [PMID: 35656583 PMCID: PMC10723622 DOI: 10.1002/dvdy.505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND POLR1D is a subunit of RNA Polymerases I and III, which synthesize ribosomal RNAs. Dysregulation of these polymerases cause several types of diseases, including ribosomopathies. The craniofacial disorder Treacher Collins Syndrome (TCS) is a ribosomopathy caused by mutations in several subunits of RNA Polymerase I, including POLR1D. Here, we characterized the effect of a missense mutation in POLR1D and RNAi knockdown of POLR1D on Drosophila development. RESULTS We found that a missense mutation in Drosophila POLR1D (G30R) reduced larval rRNA levels, slowed larval growth, and arrested larval development. Remarkably, the G30R substitution is at an orthologous glycine in POLR1D that is mutated in a TCS patient (G52E). We showed that the G52E mutation in human POLR1D, and the comparable substitution (G30E) in Drosophila POLR1D, reduced their ability to heterodimerize with POLR1C in vitro. We also found that POLR1D is required early in the development of Drosophila neural cells. Furthermore, an RNAi screen revealed that POLR1D is also required for development of non-neural Drosophila cells, suggesting the possibility of defects in other cell types. CONCLUSIONS These results establish a role for POLR1D in Drosophila development, and present Drosophila as an attractive model to evaluate the molecular defects of TCS mutations in POLR1D.
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Affiliation(s)
- Ryan J Palumbo
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Alana E Belkevich
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Haleigh G Pascual
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Bruce A Knutson
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
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22
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Ma L, Wang L, Gao M, Zhang X, Zhao X, Xie D, Zhang J, Wang Z, Hou L, Zeng F. Rtr1 is required for Rpb1-Rpb2 assembly of RNAPII and prevents their cytoplasmic clump formation. FASEB J 2022; 36:e22585. [PMID: 36190433 DOI: 10.1096/fj.202200698rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 09/03/2022] [Accepted: 09/20/2022] [Indexed: 11/11/2022]
Abstract
RNA polymerase II (RNAPII) is an essential machinery for catalyzing mRNA synthesis and controlling cell fate in eukaryotes. Although the structure and function of RNAPII have been relatively defined, the molecular mechanism of its assembly process is not clear. The identification and functional analysis of assembly factors will provide new understanding to transcription regulation. In this study, we identify that RTR1, a known transcription regulator, is a new multicopy genetic suppressor of mutants of assembly factors Gpn3, Gpn2, and Rba50. We demonstrate that Rtr1 is directly required to assemble the two largest subunits of RNAPII by coordinating with Gpn3 and Npa3. Deletion of RTR1 leads to cytoplasmic clumping of RNAPII subunit and multiple copies of RTR1 can inhibit the formation of cytoplasmic clump of RNAPII subunit in gpn3-9 mutant, indicating a new layer function of Rtr1 in checking proper assembly of RNAPII. In addition, we find that disrupted activity of Rtr1 phosphatase does not trigger the formation of cytoplasmic clump of RNAPII subunit in a catalytically inactive mutant of RTR1. Based on these results, we conclude that Rtr1 cooperates with Gpn3 and Npa3 to assemble RNAPII core.
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Affiliation(s)
- Lujie Ma
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China.,College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Le Wang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Mengdi Gao
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Xinjie Zhang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Xiangdong Zhao
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Debao Xie
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Jing Zhang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Zhen Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China.,College of Science & Technology, Hebei Agricultural University, Cangzhou, China
| | - Lifeng Hou
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Fanli Zeng
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China.,College of Life Sciences, Hebei Agricultural University, Baoding, China
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23
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Li Y, Huang J, Zhu J, Bao L, Wang H, Jiang Y, Tian K, Wang R, Zheng H, Duan W, Lai W, Yi X, Zhu Y, Guo T, Ji X. Targeted protein degradation reveals RNA Pol II heterogeneity and functional diversity. Mol Cell 2022; 82:3943-3959.e11. [PMID: 36113479 DOI: 10.1016/j.molcel.2022.08.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/14/2022] [Accepted: 08/18/2022] [Indexed: 10/14/2022]
Abstract
RNA polymerase II (RNA Pol II) subunits are thought to be involved in various transcription-associated processes, but it is unclear whether they play different regulatory roles in modulating gene expression. Here, we performed nascent and mature transcript sequencing after the acute degradation of 12 mammalian RNA Pol II subunits and profiled their genomic binding sites and protein interactomes to dissect their molecular functions. We found that RNA Pol II subunits contribute differently to RNA Pol II cellular localization and transcription processes and preferentially regulate RNA processing (such as RNA splicing and 3' end maturation). Genes sensitive to the depletion of different RNA Pol II subunits tend to be involved in diverse biological functions and show different RNA half-lives. Sequences, associated protein factors, and RNA structures are correlated with RNA Pol II subunit-mediated differential gene expression. These findings collectively suggest that the heterogeneity of RNA Pol II and different genes appear to depend on some of the subunits.
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Affiliation(s)
- Yuanjun Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jie Huang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Junyi Zhu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Lijun Bao
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yongpeng Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Kai Tian
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Rui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Haonan Zheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - WenJia Duan
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Weifeng Lai
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xiao Yi
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Yi Zhu
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Tiannan Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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24
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Boguta M. Assembly of RNA polymerase III complex involves a putative co-translational mechanism. Gene 2022; 824:146394. [PMID: 35278633 DOI: 10.1016/j.gene.2022.146394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 02/28/2022] [Accepted: 03/04/2022] [Indexed: 11/04/2022]
Abstract
Detailed knowledge of structures of yeast RNA polymerases (RNAPs) contrasts with the limited information that is available on the control of their assembly. RNAP enzymes are large heteromeric complexes that function in the nucleus, but they are assembled in the cytoplasm and imported to the nucleus with help from specific auxiliary factors. Here, I review a recent study that suggests that the formation of an early-stage assembly intermediate of the RNAP III complex occurs through a co-translational mechanism. According to our hypothesis, RNAP III assembly might be seeded while the Rpb10 subunit of the enzyme core is being synthesized by cytoplasmic ribosome machinery. The co-translational assembly of RNAP III is mediated by Rbs1 protein which binds to 3'-untranslated regions in mRNA in a way that depends on the R3H domain in the Rbs1 sequence.
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Affiliation(s)
- Magdalena Boguta
- Laboratory of tRNA Transcription, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland.
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25
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Npa3-Gpn3 cooperate to assemble RNA polymerase II and prevent clump of its subunits in the cytoplasm. Int J Biol Macromol 2022; 206:837-848. [PMID: 35314265 DOI: 10.1016/j.ijbiomac.2022.03.081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/11/2022] [Accepted: 03/13/2022] [Indexed: 01/16/2023]
Abstract
RNA polymerase II (RNAPII) is an essential machinery in eukaryotes that catalyzes mRNA synthesis and controls cell fate. Although the structure and function of RNAPII are relatively well defined, the molecular mechanism of its assembly process is poorly understood. Three members of GPN-loop GTPase family Npa3/Gpn1, Gpn2, and Gpn3 participate in the biogenesis of RNAPII with non-redundant roles. In this study, we demonstrate that Gpn3 and Npa3 directly participate in the assembly of the two largest subunits during biogenesis of RNAPII. When Gpn3 is defective, assembly of RNAPII is disrupted, leading to cytoplasmic foci of RNAPII subunits. Long-term assembly factor defects will lead to the accumulation of different kind of newly synthesized RNAPII subunits in the cytoplasm to form foci, and this can be prevented by recovery of the defective assembly factor. Cytoplasmic foci of RNAPII subunits in mutants of these assembly factors reveals a new cellular rescue response named the 'RNAPII assembly stress response'.
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26
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Xie D, Zhao X, Ma L, Wang L, Li P, Cheng H, Li Z, Zeng P, Zhang J, Zeng F. Rba50 and Gpn2 recruit the second largest subunits for the assembly of RNA polymerase II and III. Int J Biol Macromol 2022; 204:565-575. [PMID: 35176321 DOI: 10.1016/j.ijbiomac.2022.02.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 11/18/2022]
Abstract
Although remarkable progress has been made toward understanding the structures of eukaryotic RNA polymerases, the pathways and factors that facilitate their assembly remain unresolved. Essential proteins Rba50 and Gpn2 are required for Rpb3 subcomplex assembly, but whether they participate in subsequent assembly steps is unknown. Herein, we performed comprehensive genetic screens to explore Rba50 function. We identified two unique extragenic rba50-3-suppressing mutations that map to genes encoding the Rba50-interacting protein Gpn2, and Rpb2, the second largest subunit of RNAPII. Both gpn2-R347S and rpb2-V1171G variants bypass Rpb1 cytoplasmic arrest and temperature-sensitive growth defects of the rba50-3 mutant. GPN2 and RPB2 were also identified as novel multicopy suppressors of the rba50-3 mutant. Rapid depletion of Rba50 affected Rpb3-Rpb2 association during RNAPII assembly. Importantly, we demonstrated that Gpn2 facilitates the association of Rba50 and Rpb2. Our results imply that Rba50-Gpn2 interaction is essential for Rpb2 recruitment during RNAPII assembly following Rpb3 subcomplex assembly. Furthermore, the Rba50-Gpn2 complex appears to play a similar role in the assembly of RNAPIII. We therefore propose a model in which Rba50 interacts with Gpn2 and thereby promotes loading of the second largest subunit of RNAP II and III onto the previously assembled subcomplex.
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Affiliation(s)
- Debao Xie
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Xiangdong Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Lujie Ma
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Le Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Pan Li
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Hongqian Cheng
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Zhaoying Li
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Pei Zeng
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Jing Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China
| | - Fanli Zeng
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, Hebei 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding, Hebei 071001, China.
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27
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Garrido-Godino AI, Cuevas-Bermúdez A, Gutiérrez-Santiago F, Mota-Trujillo MDC, Navarro F. The Association of Rpb4 with RNA Polymerase II Depends on CTD Ser5P Phosphatase Rtr1 and Influences mRNA Decay in Saccharomyces cerevisiae. Int J Mol Sci 2022; 23:2002. [PMID: 35216121 PMCID: PMC8875030 DOI: 10.3390/ijms23042002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 02/04/2023] Open
Abstract
Rtr1 is an RNA polymerase II (RNA pol II) CTD-phosphatase that influences gene expression during the transition from transcription initiation to elongation and during transcription termination. Rtr1 interacts with the RNA pol II and this interaction depends on the phosphorylation state of the CTD of Rpb1, which may influence dissociation of the heterodimer Rpb4/7 during transcription. In addition, Rtr1 was proposed as an RNA pol II import factor in RNA pol II biogenesis and participates in mRNA decay by autoregulating the turnover of its own mRNA. Our work shows that Rtr1 acts in RNA pol II assembly by mediating the Rpb4/7 association with the rest of the enzyme. RTR1 deletion alters RNA pol II assembly and increases the amount of RNA pol II associated with the chromatin that lacks Rpb4, decreasing Rpb4-mRNA imprinting and, consequently, increasing mRNA stability. Thus, Rtr1 interplays RNA pol II biogenesis and mRNA decay regulation. Our data also indicate that Rtr1 mediates mRNA decay regulation more broadly than previously proposed by cooperating with Rpb4. Interestingly, our data include new layers in the mechanisms of gene regulation and in the crosstalk between mRNA synthesis and decay by demonstrating how the association of Rpb4/7 to the RNA pol II influences mRNA decay.
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Affiliation(s)
- Ana I. Garrido-Godino
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain; (A.I.G.-G.); (A.C.-B.); (F.G.-S.); (M.d.C.M.-T.)
| | - Abel Cuevas-Bermúdez
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain; (A.I.G.-G.); (A.C.-B.); (F.G.-S.); (M.d.C.M.-T.)
| | - Francisco Gutiérrez-Santiago
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain; (A.I.G.-G.); (A.C.-B.); (F.G.-S.); (M.d.C.M.-T.)
| | - Maria del Carmen Mota-Trujillo
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain; (A.I.G.-G.); (A.C.-B.); (F.G.-S.); (M.d.C.M.-T.)
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain; (A.I.G.-G.); (A.C.-B.); (F.G.-S.); (M.d.C.M.-T.)
- Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
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28
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Ball CB, Parida M, Santana JF, Spector BM, Suarez GA, Price DH. Nuclear export restricts Gdown1 to a mitotic function. Nucleic Acids Res 2022; 50:1908-1926. [PMID: 35048979 PMCID: PMC8887472 DOI: 10.1093/nar/gkac015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/22/2021] [Accepted: 01/14/2022] [Indexed: 01/11/2023] Open
Abstract
Approximately half of purified mammalian RNA polymerase II (Pol II) is associated with a tightly interacting sub-stoichiometric subunit, Gdown1. Previous studies have established that Gdown1 inhibits transcription initiation through competitive interactions with general transcription factors and blocks the Pol II termination activity of transcription termination factor 2 (TTF2). However, the biological functions of Gdown1 remain poorly understood. Here, we utilized genetic, microscopic, and multi-omics approaches to functionally characterize Gdown1 in three human cell lines. Acute depletion of Gdown1 caused minimal direct effects on transcription. We show that Gdown1 resides predominantly in the cytoplasm of interphase cells, shuttles between the cytoplasm and nucleus, and is regulated by nuclear export. Gdown1 enters the nucleus at the onset of mitosis. Consistently, genetic ablation of Gdown1 is associated with partial de-repression of mitotic transcription, and Gdown1 KO cells present with evidence of aberrant mitoses coupled to p53 pathway activation. Evidence is presented demonstrating that Gdown1 modulates the combined functions of purified productive elongation factors PAF1C, RTF1, SPT6, DSIF and P-TEFb in vitro. Collectively, our findings support a model wherein the Pol II-regulatory function of Gdown1 occurs during mitosis and is required for genome integrity.
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Affiliation(s)
- Christopher B Ball
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Mrutyunjaya Parida
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Juan F Santana
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Benjamin M Spector
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Gustavo A Suarez
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - David H Price
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
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29
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Calvo O, Ansari A, Navarro F. Editorial: The Lesser Known World of RNA Polymerases. Front Mol Biosci 2021; 8:811413. [PMID: 34926588 PMCID: PMC8678064 DOI: 10.3389/fmolb.2021.811413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 11/17/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Olga Calvo
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Athar Ansari
- Department of Biological Science, Wayne State University, Detroit, MI, United States
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Jaén, Spain.,Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Jaén, Spain
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30
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Reprogramming mRNA Expression in Response to Defect in RNA Polymerase III Assembly in the Yeast Saccharomyces cerevisiae. Int J Mol Sci 2021; 22:ijms22147298. [PMID: 34298922 PMCID: PMC8306304 DOI: 10.3390/ijms22147298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/25/2021] [Accepted: 07/03/2021] [Indexed: 12/18/2022] Open
Abstract
The coordinated transcription of the genome is the fundamental mechanism in molecular biology. Transcription in eukaryotes is carried out by three main RNA polymerases: Pol I, II, and III. One basic problem is how a decrease in tRNA levels, by downregulating Pol III efficiency, influences the expression pattern of protein-coding genes. The purpose of this study was to determine the mRNA levels in the yeast mutant rpc128-1007 and its overdose suppressors, RBS1 and PRT1. The rpc128-1007 mutant prevents assembly of the Pol III complex and functionally mimics similar mutations in human Pol III, which cause hypomyelinating leukodystrophies. We applied RNAseq followed by the hierarchical clustering of our complete RNA-seq transcriptome and functional analysis of genes from the clusters. mRNA upregulation in rpc128-1007 cells was generally stronger than downregulation. The observed induction of mRNA expression was mostly indirect and resulted from the derepression of general transcription factor Gcn4, differently modulated by suppressor genes. rpc128-1007 mutation, regardless of the presence of suppressors, also resulted in a weak increase in the expression of ribosome biogenesis genes. mRNA genes that were downregulated by the reduction of Pol III assembly comprise the proteasome complex. In summary, our results provide the regulatory links affected by Pol III assembly that contribute differently to cellular fitness.
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31
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Fianu I, Dienemann C, Aibara S, Schilbach S, Cramer P. Cryo-EM structure of mammalian RNA polymerase II in complex with human RPAP2. Commun Biol 2021; 4:606. [PMID: 34021257 PMCID: PMC8140126 DOI: 10.1038/s42003-021-02088-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 04/08/2021] [Indexed: 11/09/2022] Open
Abstract
Nuclear import of RNA polymerase II (Pol II) involves the conserved factor RPAP2. Here we report the cryo-electron microscopy (cryo-EM) structure of mammalian Pol II in complex with human RPAP2 at 2.8 Å resolution. The structure shows that RPAP2 binds between the jaw domains of the polymerase subunits RPB1 and RPB5. RPAP2 is incompatible with binding of downstream DNA during transcription and is displaced upon formation of a transcription pre-initiation complex.
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Affiliation(s)
- Isaac Fianu
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Christian Dienemann
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Shintaro Aibara
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Sandra Schilbach
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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32
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Turowski TW, Boguta M. Specific Features of RNA Polymerases I and III: Structure and Assembly. Front Mol Biosci 2021; 8:680090. [PMID: 34055890 PMCID: PMC8160253 DOI: 10.3389/fmolb.2021.680090] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 04/16/2021] [Indexed: 12/22/2022] Open
Abstract
RNA polymerase I (RNAPI) and RNAPIII are multi-heterogenic protein complexes that specialize in the transcription of highly abundant non-coding RNAs, such as ribosomal RNA (rRNA) and transfer RNA (tRNA). In terms of subunit number and structure, RNAPI and RNAPIII are more complex than RNAPII that synthesizes thousands of different mRNAs. Specific subunits of the yeast RNAPI and RNAPIII form associated subcomplexes that are related to parts of the RNAPII initiation factors. Prior to their delivery to the nucleus where they function, RNAP complexes are assembled at least partially in the cytoplasm. Yeast RNAPI and RNAPIII share heterodimer Rpc40-Rpc19, a functional equivalent to the αα homodimer which initiates assembly of prokaryotic RNAP. In the process of yeast RNAPI and RNAPIII biogenesis, Rpc40 and Rpc19 form the assembly platform together with two small, bona fide eukaryotic subunits, Rpb10 and Rpb12. We propose that this assembly platform is co-translationally seeded while the Rpb10 subunit is synthesized by cytoplasmic ribosome machinery. The translation of Rpb10 is stimulated by Rbs1 protein, which binds to the 3′-untranslated region of RPB10 mRNA and hypothetically brings together Rpc19 and Rpc40 subunits to form the αα-like heterodimer. We suggest that such a co-translational mechanism is involved in the assembly of RNAPI and RNAPIII complexes.
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Affiliation(s)
- Tomasz W Turowski
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Magdalena Boguta
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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33
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Garrido-Godino AI, Gutiérrez-Santiago F, Navarro F. Biogenesis of RNA Polymerases in Yeast. Front Mol Biosci 2021; 8:669300. [PMID: 34026841 PMCID: PMC8136413 DOI: 10.3389/fmolb.2021.669300] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/31/2021] [Indexed: 01/25/2023] Open
Abstract
Eukaryotic RNA polymerases (RNA pols) transcriptional processes have been extensively investigated, and the structural analysis of eukaryotic RNA pols has been explored. However, the global assembly and biogenesis of these heteromultimeric complexes have been narrowly studied. Despite nuclear transcription being carried out by three RNA polymerases in eukaryotes (five in plants) with specificity in the synthesis of different RNA types, the biogenesis process has been proposed to be similar, at least for RNA pol II, to that of bacteria, which contains only one RNA pol. The formation of three different interacting subassembly complexes to conform the complete enzyme in the cytoplasm, prior to its nuclear import, has been assumed. In Saccharomyces cerevisiae, recent studies have examined in depth the biogenesis of RNA polymerases by characterizing some elements involved in the assembly of these multisubunit complexes, some of which are conserved in humans. This study reviews the latest studies governing the mechanisms and proteins described as being involved in the biogenesis of RNA polymerases in yeast.
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Affiliation(s)
- Ana I Garrido-Godino
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Jaén, Spain
| | | | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Jaén, Spain.,Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Jaén, Spain
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34
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Zhou Z, Lau OS. Dissecting the developmental roles of Pol II-associated proteins through the stomatal pores. THE NEW PHYTOLOGIST 2021; 230:11-13. [PMID: 33650186 DOI: 10.1111/nph.17157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Zimin Zhou
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117557, Singapore
| | - On Sun Lau
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117557, Singapore
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35
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Chen L, Zhao M, Wu Z, Chen S, Rojo E, Luo J, Li P, Zhao L, Chen Y, Deng J, Cheng B, He K, Gou X, Li J, Hou S. RNA polymerase II associated proteins regulate stomatal development through direct interaction with stomatal transcription factors in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2021; 230:171-189. [PMID: 33058210 DOI: 10.1111/nph.17004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/05/2020] [Indexed: 05/27/2023]
Abstract
RNA polymerase II (Pol II) associated proteins (RPAPs) have been ascribed diverse functions at the cellular level; however, their roles in developmental processes in yeasts, animals and plants are very poorly understood. Through screening for interactors of NRPB3, which encodes the third largest subunit of Pol II, we identified RIMA, the orthologue of mammalian RPAP2. A combination of genetic and biochemical assays revealed the role of RIMA and other RPAPs in stomatal development in Arabidopsis thaliana. We show that RIMA is involved in nuclear import of NRPB3 and other Pol II subunits, and is essential for restraining division and for establishing cell identity in the stomatal cell lineage. Moreover, plant RPAPs IYO/RPAP1 and QQT1/RPAP4, which interact with RIMA, are also crucial for stomatal development. Importantly, RIMA and QQT1 bind physically to stomatal transcription factors SPEECHLESS, MUTE, FAMA and SCREAMs. The RIMA-QQT1-IYO complex could work together with key stomatal transcription factors and Pol II to drive cell fate transitions in the stomatal cell lineage. Direct interactions with stomatal transcription factors provide a novel mechanism by which RPAP proteins may control differentiation of cell types and tissues in eukaryotes.
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Affiliation(s)
- Liang Chen
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Mingfeng Zhao
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Zhongliang Wu
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Sicheng Chen
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Enrique Rojo
- Centro Nacional de Biotecnología-CSIC, Cantoblanco, Madrid, E-28049, Spain
| | - Jiangwei Luo
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Ping Li
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Lulu Zhao
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yan Chen
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jianming Deng
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Bo Cheng
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Kai He
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xiaoping Gou
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jia Li
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Suiwen Hou
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
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36
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Bhargava P. Regulatory networking of the three RNA polymerases helps the eukaryotic cells cope with environmental stress. Curr Genet 2021; 67:595-603. [PMID: 33778898 DOI: 10.1007/s00294-021-01179-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 01/25/2023]
Abstract
Environmental stress influences the cellular physiology in multiple ways. Transcription by all the three RNA polymerases (Pols I, II, or III) in eukaryotes is a highly regulated process. With latest advances in technology, which have made many extensive genome-wide studies possible, it is increasingly recognized that all the cellular processes may be interconnected. A comprehensive view of the current research observations brings forward an interesting possibility that Pol II-associated factors may be directly involved in the regulation of expression from the Pol III-transcribed genes and vice versa, thus enabling a cross-talk between the two polymerases. An equally important cross-talk between the Pol I and Pol II/III has also been documented. Collectively, these observations lead to a change in the current perception that looks at the transcription of a set of genes transcribed by the three Pols in isolation. Emergence of an inclusive perspective underscores that all stress signals may converge on common mechanisms of transcription regulation, requiring an extensive cross-talk between the regulatory partners. Of the three RNA polymerases, Pol III turns out as the hub of these cross-talks, an essential component of the cellular stress-response under which the majority of the cellular transcriptional activity is shut down or re-aligned.
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Affiliation(s)
- Purnima Bhargava
- Centre for Cellular and Molecular Biology, (Council of Scientific and Industrial Research), Uppal Road, Hyderabad, 500007, India.
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37
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Cieśla M, Turowski TW, Nowotny M, Tollervey D, Boguta M. The expression of Rpb10, a small subunit common to RNA polymerases, is modulated by the R3H domain-containing Rbs1 protein and the Upf1 helicase. Nucleic Acids Res 2020; 48:12252-12268. [PMID: 33231687 PMCID: PMC7708074 DOI: 10.1093/nar/gkaa1069] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 10/05/2020] [Accepted: 10/22/2020] [Indexed: 01/07/2023] Open
Abstract
The biogenesis of eukaryotic RNA polymerases is poorly understood. The present study used a combination of genetic and molecular approaches to explore the assembly of RNA polymerase III (Pol III) in yeast. We identified a regulatory link between Rbs1, a Pol III assembly factor, and Rpb10, a small subunit that is common to three RNA polymerases. Overexpression of Rbs1 increased the abundance of both RPB10 mRNA and the Rpb10 protein, which correlated with suppression of Pol III assembly defects. Rbs1 is a poly(A)mRNA-binding protein and mutational analysis identified R3H domain to be required for mRNA interactions and genetic enhancement of Pol III biogenesis. Rbs1 also binds to Upf1 protein, a key component in nonsense-mediated mRNA decay (NMD) and levels of RPB10 mRNA were increased in a upf1Δ strain. Genome-wide RNA binding by Rbs1 was characterized by UV cross-linking based approach. We demonstrated that Rbs1 directly binds to the 3' untranslated regions (3'UTRs) of many mRNAs including transcripts encoding Pol III subunits, Rpb10 and Rpc19. We propose that Rbs1 functions by opposing mRNA degradation, at least in part mediated by NMD pathway. Orthologues of Rbs1 protein are present in other eukaryotes, including humans, suggesting that this is a conserved regulatory mechanism.
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Affiliation(s)
- Małgorzata Cieśla
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Tomasz W Turowski
- Wellcome Centre for Cell Biology, The University of Edinburgh, Edinburgh EH9 3BF, Scotland
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Ks. Trojdena 4, 02-109 Warsaw, Poland
| | - David Tollervey
- Wellcome Centre for Cell Biology, The University of Edinburgh, Edinburgh EH9 3BF, Scotland
| | - Magdalena Boguta
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland
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38
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Liu X, Xie D, Hua Y, Zeng P, Ma L, Zeng F. Npa3 interacts with Gpn3 and assembly factor Rba50 for RNA polymerase II biogenesis. FASEB J 2020; 34:15547-15558. [PMID: 32985767 DOI: 10.1096/fj.202001523r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/01/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022]
Abstract
RNA polymerase II is one of the most vital macromolecular complexes in eukaryotes and the assembly of such complete enzyme requires many factors. Three members of GPN-loop GTPase family Npa3/Gpn1, Gpn2, and Gpn3 participate in the biogenesis of RNA polymerase II with nonredundant roles. We show here that rapid degradation of each GPN protein in yeast leads to cytoplasmic accumulation of Rpb1 and defects in the assembly of RNA polymerase II, suggesting conserved functions of GPN paralogs for RNA polymerase II biogenesis as in humans. Taking advantage of a multicopy genetic screening, we identified GPN3 and assembly factor RBA50 among others as strong suppressors of npa3ts mutants. We further demonstrated that Npa3 interacts with Gpn3 and Rba50, similarly human Gpn1 physically interacts with Gpn3 and RPAP1 (human analog of Rba50). Moreover, a mutual dependency of protein levels of Npa3 and Gpn3 was also clearly presented in yeast using an auxin-inducible degron (AID) system. Interestingly, Rpb2, the second largest subunit of RNA polymerase II was determined to be the subunit that interacts with both Gpn1 and Rba50, indicating a close association of Npa3 and Rba50 in Rpb2 subcomplex assembly. Based on these results, we conclude that Npa3 interacts with Gpn3 and Rba50, for RNA polymerase II biogenesis. We therefore propose that multiple factors may coordinate through conserved regulatory mechanisms in the assembly of RNA polymerase complex.
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Affiliation(s)
- Xueqin Liu
- College of Life Sciences, Hebei Agricultural University, Baoding, China.,State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
| | - Debao Xie
- College of Life Sciences, Hebei Agricultural University, Baoding, China.,State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
| | - Yu Hua
- Peking-Tsinghua Center for Life Sciences, The National Laboratory of Protein and Plant Gene Research, The College of Life Sciences, Peking University, Beijing, China
| | - Pei Zeng
- College of Life Sciences, Hebei Agricultural University, Baoding, China.,State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
| | - Lujie Ma
- College of Life Sciences, Hebei Agricultural University, Baoding, China.,State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
| | - Fanli Zeng
- College of Life Sciences, Hebei Agricultural University, Baoding, China.,State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China.,Peking-Tsinghua Center for Life Sciences, The National Laboratory of Protein and Plant Gene Research, The College of Life Sciences, Peking University, Beijing, China
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39
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Takii R, Fujimoto M, Matsumoto M, Srivastava P, Katiyar A, Nakayama KI, Nakai A. The pericentromeric protein shugoshin 2 cooperates with HSF1 in heat shock response and RNA Pol II recruitment. EMBO J 2019; 38:e102566. [PMID: 31657478 DOI: 10.15252/embj.2019102566] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/12/2019] [Accepted: 09/12/2019] [Indexed: 12/17/2022] Open
Abstract
The recruitment of RNA polymerase II (Pol II) to core promoters is highly regulated during rapid induction of genes. In response to heat shock, heat shock transcription factor 1 (HSF1) is activated and occupies heat shock gene promoters. Promoter-bound HSF1 recruits general transcription factors and Mediator, which interact with Pol II, but stress-specific mechanisms of Pol II recruitment are unclear. Here, we show in comparative analyses of HSF1 paralogs and their mutants that HSF1 interacts with the pericentromeric adaptor protein shugoshin 2 (SGO2) during heat shock in mouse cells, in a manner dependent on inducible phosphorylation of HSF1 at serine 326, and recruits SGO2 to the HSP70 promoter. SGO2-mediated binding and recruitment of Pol II with a hypophosphorylated C-terminal domain promote expression of HSP70, implicating SGO2 as one of the coactivators that facilitate Pol II recruitment by HSF1. Furthermore, the HSF1-SGO2 complex supports cell survival and maintenance of proteostasis in heat shock conditions. These results exemplify a proteotoxic stress-specific mechanism of Pol II recruitment, which is triggered by phosphorylation of HSF1 during the heat shock response.
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Affiliation(s)
- Ryosuke Takii
- Department of Biochemistry and Molecular Biology, Yamaguchi University School of Medicine, Ube, Japan
| | - Mitsuaki Fujimoto
- Department of Biochemistry and Molecular Biology, Yamaguchi University School of Medicine, Ube, Japan
| | - Masaki Matsumoto
- Division of Proteomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Pratibha Srivastava
- Department of Biochemistry and Molecular Biology, Yamaguchi University School of Medicine, Ube, Japan
| | - Arpit Katiyar
- Department of Biochemistry and Molecular Biology, Yamaguchi University School of Medicine, Ube, Japan
| | - Keiich I Nakayama
- Division of Proteomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.,Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Akira Nakai
- Department of Biochemistry and Molecular Biology, Yamaguchi University School of Medicine, Ube, Japan
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40
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Cristóbal-Mondragón GR, Lara-Chacón B, Santiago Á, De-la-Rosa V, González-González R, Muñiz-Luna JA, Ladrón-de-Guevara E, Romero-Romero S, Rangel-Yescas GE, Fernández Velasco DA, Islas LD, Pastor N, Sánchez-Olea R, Calera MR. FRET-based analysis and molecular modeling of the human GPN-loop GTPases 1 and 3 heterodimer unveils a dominant-negative protein complex. FEBS J 2019; 286:4797-4818. [PMID: 31298811 DOI: 10.1111/febs.14996] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 05/08/2019] [Accepted: 07/09/2019] [Indexed: 01/09/2023]
Abstract
GPN-loop GTPases 1 and 3 are required for RNA polymerase II (RNAPII) nuclear import. Gpn1 and Gpn3 display some sequence similarity, physically associate, and their protein expression levels are mutually dependent in human cells. We performed here Fluorescence Resonance Energy Transfer (FRET), molecular modeling, and cell biology experiments to understand, and eventually disrupt, human Gpn1-Gpn3 interaction in live HEK293-AD cells. Transiently expressed EYFP-Gpn1 and Gpn3-CFP generated a strong FRET signal, indicative of a very close proximity, in the cytoplasm of HEK293-AD cells. Molecular modeling of the human Gpn1-Gpn3 heterodimer based on the crystallographic structure of Npa3, the Saccharomyces cerevisiae Gpn1 ortholog, revealed that human Gpn1 and Gpn3 associate through a large interaction surface formed by internal α-helix 7, insertion 2, and the GPN-loop from each protein. In site-directed mutagenesis experiments of interface residues, we identified the W132D and M227D EYFP-Gpn1 mutants as defective to produce a FRET signal when coexpressed with Gpn3-CFP. Simultaneous but not individual expression of Gpn1 and Gpn3, with either or both proteins fused to EYFP, retained RNAPII in the cytoplasm and markedly inhibited global transcription in HEK293-AD cells. Interestingly, the W132D and M227D Gpn1 mutants that showed an impaired ability to interact with Gpn3 by FRET were also unable to delocalize RNAPII in this assay, indicating that an intact Gpn1-Gpn3 interaction is required to display the dominant-negative effect on endogenous Gpn1/Gpn3 function we described here. Altogether, our results suggest that a Gpn1-Gpn3 strong interaction is critical for their cellular function.
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Affiliation(s)
| | - Bárbara Lara-Chacón
- Instituto de Física, Universidad Autónoma de San Luis Potosí, San Luis Potosí, SLP, México
| | - Ángel Santiago
- Centro de Investigación en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mor, México
| | - Víctor De-la-Rosa
- Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Coyoacán, CDMX, México
| | | | - Julio A Muñiz-Luna
- Instituto de Física, Universidad Autónoma de San Luis Potosí, San Luis Potosí, SLP, México
| | - Ernesto Ladrón-de-Guevara
- Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Coyoacán, CDMX, México
| | - Sergio Romero-Romero
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Facultad de Medicina, Universidad Nacional Autónoma de México, Coyoacán, CDMX, México
| | - Gisela E Rangel-Yescas
- Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Coyoacán, CDMX, México
| | - Daniel Alejandro Fernández Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Facultad de Medicina, Universidad Nacional Autónoma de México, Coyoacán, CDMX, México
| | - León D Islas
- Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Coyoacán, CDMX, México
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mor, México
| | - Roberto Sánchez-Olea
- Instituto de Física, Universidad Autónoma de San Luis Potosí, San Luis Potosí, SLP, México
| | - Mónica R Calera
- Instituto de Física, Universidad Autónoma de San Luis Potosí, San Luis Potosí, SLP, México
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41
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Lynch CJ, Bernad R, Calvo I, Nóbrega-Pereira S, Ruiz S, Ibarz N, Martinez-Val A, Graña-Castro O, Gómez-López G, Andrés-León E, Espinosa Angarica V, Del Sol A, Ortega S, Fernandez-Capetillo O, Rojo E, Munoz J, Serrano M. The RNA Polymerase II Factor RPAP1 Is Critical for Mediator-Driven Transcription and Cell Identity. Cell Rep 2019; 22:396-410. [PMID: 29320736 PMCID: PMC5775503 DOI: 10.1016/j.celrep.2017.12.062] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/03/2017] [Accepted: 12/18/2017] [Indexed: 01/22/2023] Open
Abstract
The RNA polymerase II-associated protein 1 (RPAP1) is conserved across metazoa and required for stem cell differentiation in plants; however, very little is known about its mechanism of action or its role in mammalian cells. Here, we report that RPAP1 is essential for the expression of cell identity genes and for cell viability. Depletion of RPAP1 triggers cell de-differentiation, facilitates reprogramming toward pluripotency, and impairs differentiation. Mechanistically, we show that RPAP1 is essential for the interaction between RNA polymerase II (RNA Pol II) and Mediator, as well as for the recruitment of important regulators, such as the Mediator-specific RNA Pol II factor Gdown1 and the C-terminal domain (CTD) phosphatase RPAP2. In agreement, depletion of RPAP1 diminishes the loading of total and Ser5-phosphorylated RNA Pol II on many genes, with super-enhancer-driven genes among the most significantly downregulated. We conclude that Mediator/RPAP1/RNA Pol II is an ancient module, conserved from plants to mammals, critical for establishing and maintaining cell identity. RPAP1 is an RNA Pol II regulator, conserved from plants to mammals RPAP1 depletion erases cell identity gene expression, triggering de-differentiation Mechanistically, RPAP1 is critical for the Mediator-RNA Pol II interaction RPAP1 preferentially contributes to enhancer-driven gene transcription
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Affiliation(s)
- Cian J Lynch
- Tumour Suppression Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain; Cellular Plasticity and Disease Group, Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
| | - Raquel Bernad
- Tumour Suppression Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain; Cellular Plasticity and Disease Group, Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
| | - Isabel Calvo
- Tumour Suppression Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Sandrina Nóbrega-Pereira
- Tumour Suppression Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain; Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Sergio Ruiz
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Nuria Ibarz
- ProteoRed-ISCIII Proteomics Unit, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Ana Martinez-Val
- ProteoRed-ISCIII Proteomics Unit, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Osvaldo Graña-Castro
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Gonzalo Gómez-López
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Eduardo Andrés-León
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain; Bioinformatics Unit, Institute of Parasitology and Biomedicine Lopez-Neyra, Granada 18016, Spain
| | - Vladimir Espinosa Angarica
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg; Cancer Science Institute, National University of Singapore, Singapore 117599, Singapore
| | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Sagrario Ortega
- Transgenic Mouse Unit, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Oscar Fernandez-Capetillo
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain; Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm 171 21, Sweden
| | - Enrique Rojo
- Department of Plant Molecular Genetics, National Center of Biotechnology (CNB-CSIC), Madrid 280049, Spain
| | - Javier Munoz
- ProteoRed-ISCIII Proteomics Unit, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Manuel Serrano
- Tumour Suppression Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain; Cellular Plasticity and Disease Group, Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain.
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42
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Hunziker M, Barandun J, Buzovetsky O, Steckler C, Molina H, Klinge S. Conformational switches control early maturation of the eukaryotic small ribosomal subunit. eLife 2019; 8:45185. [PMID: 31206356 PMCID: PMC6579516 DOI: 10.7554/elife.45185] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/05/2019] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic ribosome biogenesis is initiated with the transcription of pre-ribosomal RNA at the 5’ external transcribed spacer, which directs the early association of assembly factors but is absent from the mature ribosome. The subsequent co-transcriptional association of ribosome assembly factors with pre-ribosomal RNA results in the formation of the small subunit processome. Here we show that stable rRNA domains of the small ribosomal subunit can independently recruit their own biogenesis factors in vivo. The final assembly and compaction of the small subunit processome requires the presence of the 5’ external transcribed spacer RNA and all ribosomal RNA domains. Additionally, our cryo-electron microscopy structure of the earliest nucleolar pre-ribosomal assembly - the 5’ external transcribed spacer ribonucleoprotein – provides a mechanism for how conformational changes in multi-protein complexes can be employed to regulate the accessibility of binding sites and therefore define the chronology of maturation events during early stages of ribosome assembly.
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Affiliation(s)
- Mirjam Hunziker
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, United States
| | - Jonas Barandun
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, United States
| | - Olga Buzovetsky
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, United States
| | - Caitlin Steckler
- Proteomics Resource Center, The Rockefeller University, New York, United States
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, United States
| | - Sebastian Klinge
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, United States
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43
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Caron P, Pankotai T, Wiegant WW, Tollenaere MAX, Furst A, Bonhomme C, Helfricht A, de Groot A, Pastink A, Vertegaal ACO, Luijsterburg MS, Soutoglou E, van Attikum H. WWP2 ubiquitylates RNA polymerase II for DNA-PK-dependent transcription arrest and repair at DNA breaks. Genes Dev 2019; 33:684-704. [PMID: 31048545 PMCID: PMC6546063 DOI: 10.1101/gad.321943.118] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/25/2019] [Indexed: 11/24/2022]
Abstract
Here, Caron et al. show that the HECT E3 ubiquitin ligase WWP2 associates with components of the DNA-PK and RNAPII complexes and is recruited to DSBs at RNAPII transcribed genes. Their findings suggest that WWP2 operates in a DNA-PK-dependent shutoff circuitry for RNAPII clearance that promotes DSB repair by protecting the NHEJ machinery from collision with the transcription machinery. DNA double-strand breaks (DSBs) at RNA polymerase II (RNAPII) transcribed genes lead to inhibition of transcription. The DNA-dependent protein kinase (DNA-PK) complex plays a pivotal role in transcription inhibition at DSBs by stimulating proteasome-dependent eviction of RNAPII at these lesions. How DNA-PK triggers RNAPII eviction to inhibit transcription at DSBs remains unclear. Here we show that the HECT E3 ubiquitin ligase WWP2 associates with components of the DNA-PK and RNAPII complexes and is recruited to DSBs at RNAPII transcribed genes. In response to DSBs, WWP2 targets the RNAPII subunit RPB1 for K48-linked ubiquitylation, thereby driving DNA-PK- and proteasome-dependent eviction of RNAPII. The lack of WWP2 or expression of nonubiquitylatable RPB1 abrogates the binding of nonhomologous end joining (NHEJ) factors, including DNA-PK and XRCC4/DNA ligase IV, and impairs DSB repair. These findings suggest that WWP2 operates in a DNA-PK-dependent shutoff circuitry for RNAPII clearance that promotes DSB repair by protecting the NHEJ machinery from collision with the transcription machinery.
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Affiliation(s)
- Pierre Caron
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Tibor Pankotai
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France.,U1258, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch, France.,UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch, France.,Université de Strasbourg, 67081 Strasbourg, France
| | - Wouter W Wiegant
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Maxim A X Tollenaere
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Audrey Furst
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France.,U1258, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch, France.,UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch, France.,Université de Strasbourg, 67081 Strasbourg, France
| | - Celine Bonhomme
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France.,U1258, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch, France.,UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch, France.,Université de Strasbourg, 67081 Strasbourg, France
| | - Angela Helfricht
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Anton de Groot
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Albert Pastink
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Evi Soutoglou
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France.,U1258, Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch, France.,UMR7104, Centre National de Recherche Scientifique (CNRS), 67404 Illkirch, France.,Université de Strasbourg, 67081 Strasbourg, France
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
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44
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Płonka M, Wawrzycka D, Wysocki R, Boguta M, Cieśla M. Coupling of RNA polymerase III assembly to cell cycle progression in Saccharomyces cerevisiae. Cell Cycle 2019; 18:500-510. [PMID: 30760101 DOI: 10.1080/15384101.2019.1578134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Assembly of the RNA polymerases in both yeast and humans is proposed to occur in the cytoplasm prior to their nuclear import. Our previous studies identified a cold-sensitive mutation, rpc128-1007, in the yeast gene encoding the second largest Pol III subunit, Rpc128. rpc128-1007 is associated with defective assembly of Pol III complex and, in consequence, decreased level of tRNA synthesis. Here, we show that rpc128-1007 mutant cells remain largely unbudded and larger than wild type cells. Flow cytometry revealed that most rpc128-1007 mutant cells have G1 DNA content, suggesting that this mutation causes pronounced cell cycle delay in the G1 phase. Increased expression of gene encoding Rbs1, the Pol III assembly/import factor, could counteract G1 arrest observed in the rpc128-1007 mutant and restore wild type morphology of mutant cells. Concomitantly, cells lacking Rbs1 show a mild delay in G1 phase exit, indicating that Rbs1 is required for timely cell cycle progression. Using the double rpc128-1007 maf1Δ mutant in which tRNA synthesis is recovered, we confirmed that the Pol III assembly defect associated with rpc128-1007 is a primary cause of cell cycle arrest. Together our results indicate that impairment of Pol III complex assembly is coupled to cell cycle inhibition in the G1 phase.
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Affiliation(s)
- Marta Płonka
- a Department of Genetics, Institute of Biochemistry and Biophysics , Polish Academy of Sciences , Warsaw , Poland
| | - Donata Wawrzycka
- b Department of Genetics and Cell Physiology, Institute of Experimental Biology , University of Wrocław , Wrocław , Poland
| | - Robert Wysocki
- b Department of Genetics and Cell Physiology, Institute of Experimental Biology , University of Wrocław , Wrocław , Poland
| | - Magdalena Boguta
- a Department of Genetics, Institute of Biochemistry and Biophysics , Polish Academy of Sciences , Warsaw , Poland
| | - Małgorzata Cieśla
- a Department of Genetics, Institute of Biochemistry and Biophysics , Polish Academy of Sciences , Warsaw , Poland
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45
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Gpn2 and Rba50 Directly Participate in the Assembly of the Rpb3 Subcomplex in the Biogenesis of RNA Polymerase II. Mol Cell Biol 2018; 38:MCB.00091-18. [PMID: 29661922 DOI: 10.1128/mcb.00091-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/08/2018] [Indexed: 01/12/2023] Open
Abstract
RNA polymerase II (RNAPII) is one of the central enzymes in cell growth and organizational development. It is a large macromolecular complex consisting of 12 subunits. Relative to the clear definition of RNAPII structure and biological function, the molecular mechanism of how RNAPII is assembled is poorly understood, and thus the key assembly factors acting for the assembly of RNAPII remain elusive. In this study, we identified two factors, Gpn2 and Rba50, that directly participate in the assembly of RNAPII. Gpn2 and Rba50 were demonstrated to interact with Rpb12 and Rpb3, respectively. An interaction between Gpn2 and Rba50 was also demonstrated. When Gpn2 and Rba50 are functionally defective, the assembly of the Rpb3 subcomplex is disrupted, leading to defects in the assembly of RNAPII. Based on these results, we conclude that Gpn2 and Rba50 directly participate in the assembly of the Rpb3 subcomplex and subsequently the biogenesis of RNAPII.
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46
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Berg MD, Genereaux J, Karagiannis J, Brandl CJ. The Pseudokinase Domain of Saccharomyces cerevisiae Tra1 Is Required for Nuclear Localization and Incorporation into the SAGA and NuA4 Complexes. G3 (BETHESDA, MD.) 2018; 8:1943-1957. [PMID: 29626083 PMCID: PMC5982823 DOI: 10.1534/g3.118.200288] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 04/04/2018] [Indexed: 12/29/2022]
Abstract
Tra1 is an essential component of the SAGA/SLIK and NuA4 complexes in S. cerevisiae, recruiting these co-activator complexes to specific promoters. As a PIKK family member, Tra1 is characterized by a C-terminal phosphoinositide 3-kinase (PI3K) domain. Unlike other PIKK family members (e.g., Tor1, Tor2, Mec1, Tel1), Tra1 has no demonstrable kinase activity. We identified three conserved arginine residues in Tra1 that reside proximal or within the cleft between the N- and C-terminal subdomains of the PI3K domain. To establish a function for Tra1's PI3K domain and specifically the cleft region, we characterized a tra1 allele where these three arginine residues are mutated to glutamine. The half-life of the Tra1[Formula: see text] protein is reduced but its steady state level is maintained at near wild-type levels by a transcriptional feedback mechanism. The tra1[Formula: see text] allele results in slow growth under stress and alters the expression of genes also regulated by other components of the SAGA complex. Tra1[Formula: see text] is less efficiently transported to the nucleus than the wild-type protein. Likely related to this, Tra1[Formula: see text] associates poorly with SAGA/SLIK and NuA4. The ratio of Spt7SLIK to Spt7SAGA increases in the tra1[Formula: see text] strain and truncated forms of Spt20 become apparent upon isolation of SAGA/SLIK. Intragenic suppressor mutations of tra1[Formula: see text] map to the cleft region further emphasizing its importance. We propose that the PI3K domain of Tra1 is directly or indirectly important for incorporating Tra1 into SAGA and NuA4 and thus the biosynthesis and/or stability of the intact complexes.
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Affiliation(s)
- Matthew D Berg
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada N6A5C1
| | - Julie Genereaux
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada N6A5C1
| | - Jim Karagiannis
- Department of Biology, Western University, London, Ontario, Canada N6A5B7
| | - Christopher J Brandl
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario, Canada N6A5C1
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47
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Pan J, Meyers RM, Michel BC, Mashtalir N, Sizemore AE, Wells JN, Cassel SH, Vazquez F, Weir BA, Hahn WC, Marsh JA, Tsherniak A, Kadoch C. Interrogation of Mammalian Protein Complex Structure, Function, and Membership Using Genome-Scale Fitness Screens. Cell Syst 2018; 6:555-568.e7. [PMID: 29778836 DOI: 10.1016/j.cels.2018.04.011] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/03/2018] [Accepted: 04/24/2018] [Indexed: 11/15/2022]
Abstract
Protein complexes are assemblies of subunits that have co-evolved to execute one or many coordinated functions in the cellular environment. Functional annotation of mammalian protein complexes is critical to understanding biological processes, as well as disease mechanisms. Here, we used genetic co-essentiality derived from genome-scale RNAi- and CRISPR-Cas9-based fitness screens performed across hundreds of human cancer cell lines to assign measures of functional similarity. From these measures, we systematically built and characterized functional similarity networks that recapitulate known structural and functional features of well-studied protein complexes and resolve novel functional modules within complexes lacking structural resolution, such as the mammalian SWI/SNF complex. Finally, by integrating functional networks with large protein-protein interaction networks, we discovered novel protein complexes involving recently evolved genes of unknown function. Taken together, these findings demonstrate the utility of genetic perturbation screens alone, and in combination with large-scale biophysical data, to enhance our understanding of mammalian protein complexes in normal and disease states.
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Affiliation(s)
- Joshua Pan
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Biomedical and Biological Sciences Program, Harvard Medical School, Boston, MA 02115, USA
| | - Robin M Meyers
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Brittany C Michel
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Biomedical and Biological Sciences Program, Harvard Medical School, Boston, MA 02115, USA
| | - Nazar Mashtalir
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Ann E Sizemore
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Jonathan N Wells
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Seth H Cassel
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Biomedical and Biological Sciences Program, Harvard Medical School, Boston, MA 02115, USA; Medical Scientist Training Program, Harvard Medical School, Boston, MA 02115, USA
| | - Francisca Vazquez
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Barbara A Weir
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - William C Hahn
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Aviad Tsherniak
- Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Cigall Kadoch
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA.
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48
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Walker-Kopp N, Jackobel AJ, Pannafino GN, Morocho PA, Xu X, Knutson BA. Treacher Collins syndrome mutations in Saccharomyces cerevisiae destabilize RNA polymerase I and III complex integrity. Hum Mol Genet 2018; 26:4290-4300. [PMID: 28973381 DOI: 10.1093/hmg/ddx317] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/08/2017] [Indexed: 01/16/2023] Open
Abstract
Treacher Collins syndrome (TCS) is a craniofacial disorder that is characterized by the malformation of the facial bones. Mutations in three genes (TCOF1, POLR1C and POLR1D) involved in RNA polymerase I (Pol I) transcription account for more than 90% of disease cases. Two of these TCS-associated genes, POLR1C and POLR1D, encode for essential Pol I/III subunits that form a heterodimer necessary for Pol I/III assembly, and many TCS mutations lie along their evolutionarily conserved dimerization interface. Here we elucidate the molecular basis of TCS mutations in Saccharomyces cerevisiae, and present a new model for how TCS mutations may disrupt Pol I and III complex integrity.
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Affiliation(s)
- Nancy Walker-Kopp
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Ashleigh J Jackobel
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Gianno N Pannafino
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Paola A Morocho
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA.,Department of Clinical Laboratory Science, Medical Scholars Master in Medical Technology Program, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Xia Xu
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Bruce A Knutson
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
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Conic S, Desplancq D, Ferrand A, Fischer V, Heyer V, Reina San Martin B, Pontabry J, Oulad-Abdelghani M, Babu N K, Wright GD, Molina N, Weiss E, Tora L. Imaging of native transcription factors and histone phosphorylation at high resolution in live cells. J Cell Biol 2018; 217:1537-1552. [PMID: 29440513 PMCID: PMC5881509 DOI: 10.1083/jcb.201709153] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/15/2017] [Accepted: 01/18/2018] [Indexed: 01/16/2023] Open
Abstract
Conic et al. introduce a versatile antibody-based imaging approach to track endogenous nuclear factors in living cells. It allows efficient intracellular delivery of any fluorescent dye–conjugated antibody, or Fab fragment, into a variety of cell types. The dynamics of nuclear targets or posttranslational modifications can be monitored with high precision using confocal and super-resolution microscopy. Fluorescent labeling of endogenous proteins for live-cell imaging without exogenous expression of tagged proteins or genetic manipulations has not been routinely possible. We describe a simple versatile antibody-based imaging approach (VANIMA) for the precise localization and tracking of endogenous nuclear factors. Our protocol can be implemented in every laboratory allowing the efficient and nonharmful delivery of organic dye-conjugated antibodies, or antibody fragments, into different metazoan cell types. Live-cell imaging permits following the labeled probes bound to their endogenous targets. By using conventional and super-resolution imaging we show dynamic changes in the distribution of several nuclear transcription factors (i.e., RNA polymerase II or TAF10), and specific phosphorylated histones (γH2AX), upon distinct biological stimuli at the nanometer scale. Hence, considering the large panel of available antibodies and the simplicity of their implementation, VANIMA can be used to uncover novel biological information based on the dynamic behavior of transcription factors or posttranslational modifications in the nucleus of single live cells.
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Affiliation(s)
- Sascha Conic
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | | | - Alexia Ferrand
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Veronique Fischer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Vincent Heyer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Bernardo Reina San Martin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Julien Pontabry
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France.,Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute of Epigenetics and Stem Cells, München, Germany
| | - Mustapha Oulad-Abdelghani
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Kishore Babu N
- School of Biological Sciences, Nanyang Technological University, Singapore
| | | | - Nacho Molina
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Etienne Weiss
- Institut de Recherche de l'ESBS, UMR 7242, Illkirch, France
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France.,School of Biological Sciences, Nanyang Technological University, Singapore
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50
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Leśniewska E, Boguta M. Novel layers of RNA polymerase III control affecting tRNA gene transcription in eukaryotes. Open Biol 2017; 7:rsob.170001. [PMID: 28228471 PMCID: PMC5356446 DOI: 10.1098/rsob.170001] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 01/31/2017] [Indexed: 12/20/2022] Open
Abstract
RNA polymerase III (Pol III) transcribes a limited set of short genes in eukaryotes producing abundant small RNAs, mostly tRNA. The originally defined yeast Pol III transcriptome appears to be expanding owing to the application of new methods. Also, several factors required for assembly and nuclear import of Pol III complex have been identified recently. Models of Pol III based on cryo-electron microscopy reconstructions of distinct Pol III conformations reveal unique features distinguishing Pol III from other polymerases. Novel concepts concerning Pol III functioning involve recruitment of general Pol III-specific transcription factors and distinctive mechanisms of transcription initiation, elongation and termination. Despite the short length of Pol III transcription units, mapping of transcriptionally active Pol III with nucleotide resolution has revealed strikingly uneven polymerase distribution along all genes. This may be related, at least in part, to the transcription factors bound at the internal promoter regions. Pol III uses also a specific negative regulator, Maf1, which binds to polymerase under stress conditions; however, a subset of Pol III genes is not controlled by Maf1. Among other RNA polymerases, Pol III machinery represents unique features related to a short transcript length and high transcription efficiency.
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Affiliation(s)
- Ewa Leśniewska
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Magdalena Boguta
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
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