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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] [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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Garrido-Godino AI, Martín-Expósito M, Gutiérrez-Santiago F, Perez-Fernandez J, Navarro F. Rpb4/7, a key element of RNA pol II to coordinate mRNA synthesis in the nucleus with cytoplasmic functions in Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194846. [PMID: 35905859 DOI: 10.1016/j.bbagrm.2022.194846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/11/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Affiliation(s)
- A I Garrido-Godino
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
| | - M Martín-Expósito
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
| | - F Gutiérrez-Santiago
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain
| | - J Perez-Fernandez
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071 Jaén, Spain.
| | - F 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, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain.
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Bhardwaj V, Sharma N. Absence of the Rpb9 subunit of RNA polymerase II reduces the chronological life span in fission yeast. J Basic Microbiol 2022; 62:900-910. [PMID: 35618649 DOI: 10.1002/jobm.202200036] [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: 01/23/2022] [Revised: 04/04/2022] [Accepted: 05/14/2022] [Indexed: 11/07/2022]
Abstract
Fission yeast RNA polymerase II consists of 12 subunits, Rpb1-Rpb12. Among these subunits, Rpb9 is the only subunit whose absence does not cause lethality under optimum growth conditions in fission yeast. However, an rpb9 null fission yeast mutant exhibits a slow-growth phenotype under optimum growth conditions and a defect in survival under environmental and genotoxic stress conditions. To further gain an understanding of its physiological roles, in the present study we have elucidated the role of the Rpb9 subunit in chronological aging using fission yeast as the model organism. Our results provide evidence that the absence of Rpb9 reduces the chronological life span in fission yeast. Our data further shows that lack of Rpb9 in fission yeast causes oxidative stress sensitivity and accumulation of reactive oxygen species during the stationary phase. Our domain mapping experiments have demonstrated that the Rpb9 region encompassing its amino-terminal zinc finger domain and the central linker region is important for the role of Rpb9 in chronological aging. Finally, we also show that expression of the budding yeast or human Rpb9 ortholog can functionally complement the reduced chronological life span phenotype of the fission yeast rpb9 deletion mutant. Taken together, our study has identified a new role of the Rpb9 subunit in chronological aging.
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Affiliation(s)
- Vaibhav Bhardwaj
- University School of Biotechnology (USBT), Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India
| | - Nimisha Sharma
- University School of Biotechnology (USBT), Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, India
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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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González-Jiménez A, Campos A, Navarro F, Clemente-Blanco A, Calvo O. Regulation of Eukaryotic RNAPs Activities by Phosphorylation. Front Mol Biosci 2021; 8:681865. [PMID: 34250017 PMCID: PMC8268151 DOI: 10.3389/fmolb.2021.681865] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/07/2021] [Indexed: 01/11/2023] Open
Abstract
Evolutionarily conserved kinases and phosphatases regulate RNA polymerase II (RNAPII) transcript synthesis by modifying the phosphorylation status of the carboxyl-terminal domain (CTD) of Rpb1, the largest subunit of RNAPII. Proper levels of Rpb1-CTD phosphorylation are required for RNA co-transcriptional processing and to coordinate transcription with other nuclear processes, such as chromatin remodeling and histone modification. Whether other RNAPII subunits are phosphorylated and influences their role in gene expression is still an unanswered question. Much less is known about RNAPI and RNAPIII phosphorylation, whose subunits do not contain functional CTDs. However, diverse studies have reported that several RNAPI and RNAPIII subunits are susceptible to phosphorylation. Some of these phosphorylation sites are distributed within subunits common to all three RNAPs whereas others are only shared between RNAPI and RNAPIII. This suggests that the activities of all RNAPs might be finely modulated by phosphorylation events and raises the idea of a tight coordination between the three RNAPs. Supporting this view, the transcription by all RNAPs is regulated by signaling pathways that sense different environmental cues to adapt a global RNA transcriptional response. This review focuses on how the phosphorylation of RNAPs might regulate their function and we comment on the regulation by phosphorylation of some key transcription factors in the case of RNAPI and RNAPIII. Finally, we discuss the existence of possible common mechanisms that could coordinate their activities.
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Affiliation(s)
- Araceli González-Jiménez
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Adrián Campos
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, 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
| | - Andrés Clemente-Blanco
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
| | - Olga Calvo
- Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Salamanca, Spain
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6
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Deletion of the non-essential Rpb9 subunit of RNA polymerase II results in pleiotropic phenotypes in Schizosaccharomyces pombe. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140654. [PMID: 33775921 DOI: 10.1016/j.bbapap.2021.140654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
Schizosaccharomyces pombe RNA polymerase II comprises twelve different subunits. Its Rpb9 subunit comprises 113 amino acids, and is the only non-essential subunit of S. pombe RNA polymerase II. However, its functions have not been studied in S. pombe. The results presented in this study demonstrate that Rpb9 is involved in regulating growth under optimum and certain stress conditions in S. pombe. To further address the role (s) of various domains of this subunit in regulating these phenotypes, deletion mutant analysis was done. We observed that the region spanning 1-74 amino acids, encompassing the amino-terminal zinc finger domain and the linker region of Rpb9 was able to rescue the phenotypes associated with rpb9+deletion. We also demonstrate that the functions of this subunit are only partially conserved among yeast and humans. Our computational biology approaches provide a structural basis for the differential role of various Rpb9 domains in S. pombe. Furthermore, using these tools we show that there has been a co-evolution of the interaction residues between the Rpb9 subunit and the two largest subunits of RNA polymerase II, allowing for a more stringent organism-specific packing. Taken together, our results have provided functional and structural insights into the Rpb9 subunit of S. pombe.
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7
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RNA polymerase II subunit D is essential for zebrafish development. Sci Rep 2020; 10:13213. [PMID: 32764610 PMCID: PMC7413394 DOI: 10.1038/s41598-020-70110-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/20/2020] [Indexed: 11/09/2022] Open
Abstract
DNA-directed RNA polymerase II (pol II) is composed of ten core and two dissociable subunits. The dissociable subcomplex is a heterodimer of Rpb4/Polr2d and Rpb7/Polr2g, which are encoded by RPB4/polr2d and RPB7/polr2g genes, respectively. Functional studies of Rpb4/Polr2d in yeast have revealed that Rpb4 plays a role primarily in pol II-mediated RNA synthesis and partly in various mRNA regulations including pre-mRNA splicing, nuclear export of mRNAs and decay of mRNAs. Although Rpb4 is evolutionally highly conserved from yeast to human, it is dispensable for survival in budding yeast S. cerevisiae, whereas it was indispensable for survival in fission yeast S. pombe, slime molds and fruit fly. To elucidate whether Rpb4/Polr2d is necessary for development and survival of vertebrate animals, we generated polr2d-deficient zebrafish. The polr2d mutant embryos exhibited progressive delay of somitogenesis at the onset of 11 h postfertilization (hpf). Mutant embryos then showed increased cell death at 15 hpf, displayed hypoplasia such as small eye and cardiac edema by 48 hpf and prematurely died by 60 hpf. In accordance with these developmental defects, our RT-qPCR revealed that expression of housekeeping and zygotic genes was diminished in mutants. Collectively, we conclude that Rpb4/Polr2d is indispensable for vertebrate development.
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Calvo O. RNA polymerase II phosphorylation and gene looping: new roles for the Rpb4/7 heterodimer in regulating gene expression. Curr Genet 2020; 66:927-937. [PMID: 32508001 DOI: 10.1007/s00294-020-01084-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 12/22/2022]
Abstract
In eukaryotes, cellular RNAs are produced by three nuclear RNA polymerases (RNAPI, II, and III), which are multisubunit complexes. They share structural and functional features, although they are specialized in the synthesis of specific RNAs. RNAPII transcribes the vast majority of cellular RNAs, including mRNAs and a large number of noncoding RNAs. The structure of RNAPII is highly conserved in all eukaryotes, consisting of 12 subunits (Rpb1-12) organized into five structural modules, among which the Rpb4 and Rpb7 subunits form the stalk. Early studies suggested an accessory role for Rpb4, because is required for specific gene transcription pathways. Far from this initial hypothesis, it is now well established that the Rpb4/7 heterodimer plays much wider roles in gene expression regulation. It participates in nuclear and cytosolic processes ranging from transcription to translation and mRNA degradation in a cyclical process. For this reason, Rpb4/7 is considered a coordinator of gene expression. New functions have been added to the list of stalk functions during transcription, which will be reviewed herein: first, a role in the maintenance of proper RNAPII phosphorylation levels, and second, a role in the establishment of a looped gene architecture in actively transcribed genes.
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Affiliation(s)
- Olga Calvo
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, C/ Zacarías González 2, Salamanca, 37007, España.
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9
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A Genetic Screen for Human Genes Suppressing FUS Induced Toxicity in Yeast. G3-GENES GENOMES GENETICS 2020; 10:1843-1852. [PMID: 32276960 PMCID: PMC7263679 DOI: 10.1534/g3.120.401164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
FUS is a nucleic acid binding protein that, when mutated, cause a subset of familial amyotrophic lateral sclerosis (ALS). Expression of FUS in yeast recapitulates several pathological features of the disease-causing mutant proteins, including nuclear to cytoplasmic translocation, formation of cytoplasmic inclusions, and cytotoxicity. Genetic screens using the yeast model of FUS have identified yeast genes and their corresponding human homologs suppressing FUS induced toxicity in yeast, neurons and animal models. To expand the search for human suppressor genes of FUS induced toxicity, we carried out a genome-scale genetic screen using a newly constructed library containing 13570 human genes cloned in an inducible yeast-expression vector. Through multiple rounds of verification, we found 37 human genes that, when overexpressed, suppress FUS induced toxicity in yeast. Human genes with DNA or RNA binding functions are overrepresented among the identified suppressor genes, supporting that perturbations of RNA metabolism is a key underlying mechanism of FUS toxicity.
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10
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Verrier ER, Weiss A, Bach C, Heydmann L, Turon-Lagot V, Kopp A, El Saghire H, Crouchet E, Pessaux P, Garcia T, Pale P, Zeisel MB, Sureau C, Schuster C, Brino L, Baumert TF. Combined small molecule and loss-of-function screen uncovers estrogen receptor alpha and CAD as host factors for HDV infection and antiviral targets. Gut 2020; 69:158-167. [PMID: 30833451 PMCID: PMC6943243 DOI: 10.1136/gutjnl-2018-317065] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 01/24/2019] [Accepted: 02/10/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Hepatitis D virus (HDV) is a circular RNA virus coinfecting hepatocytes with hepatitis B virus. Chronic hepatitis D results in severe liver disease and an increased risk of liver cancer. Efficient therapeutic approaches against HDV are absent. DESIGN Here, we combined an RNAi loss-of-function and small molecule screen to uncover host-dependency factors for HDV infection. RESULTS Functional screening unravelled the hypoxia-inducible factor (HIF)-signalling and insulin-resistance pathways, RNA polymerase II, glycosaminoglycan biosynthesis and the pyrimidine metabolism as virus-hepatocyte dependency networks. Validation studies in primary human hepatocytes identified the carbamoyl-phosphatesynthetase 2, aspartate transcarbamylase and dihydroorotase (CAD) enzyme and estrogen receptor alpha (encoded by ESR1) as key host factors for HDV life cycle. Mechanistic studies revealed that the two host factors are required for viral replication. Inhibition studies using N-(phosphonoacetyl)-L-aspartic acid and fulvestrant, specific CAD and ESR1 inhibitors, respectively, uncovered their impact as antiviral targets. CONCLUSION The discovery of HDV host-dependency factors elucidates the pathogenesis of viral disease biology and opens therapeutic strategies for HDV cure.
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Affiliation(s)
- Eloi R Verrier
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000 Strasbourg, France
| | - Amélie Weiss
- IGBMC, Plateforme de Criblage Haut-débit, UMR7104 CNRS U1258 Inserm, Illkirch, France
| | - Charlotte Bach
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000 Strasbourg, France
| | - Laura Heydmann
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000 Strasbourg, France
| | - Vincent Turon-Lagot
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000 Strasbourg, France
| | - Arnaud Kopp
- IGBMC, Plateforme de Criblage Haut-débit, UMR7104 CNRS U1258 Inserm, Illkirch, France
| | - Houssein El Saghire
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000 Strasbourg, France
| | - Emilie Crouchet
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000 Strasbourg, France
| | - Patrick Pessaux
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000 Strasbourg, France,Institut Hospitalo-universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France
| | - Thomas Garcia
- Laboratoire de Synthèse, Réactivité Organiques et Catalyse, Institut de Chimie, UMR 7177 CNRS, Université de Strasbourg, Strasbourg, France
| | - Patrick Pale
- Laboratoire de Synthèse, Réactivité Organiques et Catalyse, Institut de Chimie, UMR 7177 CNRS, Université de Strasbourg, Strasbourg, France
| | - Mirjam B Zeisel
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000 Strasbourg, France
| | - Camille Sureau
- INTS, Laboratoire de Virologie Moléculaire, Paris, France
| | - Catherine Schuster
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000 Strasbourg, France
| | - Laurent Brino
- IGBMC, Plateforme de Criblage Haut-débit, UMR7104 CNRS U1258 Inserm, Illkirch, France
| | - Thomas F Baumert
- Université de Strasbourg, Inserm, Institut de Recherche sur les Maladies Virales et Hépatiques UMR_S1110, F-67000 Strasbourg, France,Institut Hospitalo-universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France,Institut Universitaire de France, Paris, France
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11
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Kumar D, Varshney S, Sengupta S, Sharma N. A comparative study of the proteome regulated by the Rpb4 and Rpb7 subunits of RNA polymerase II in fission yeast. J Proteomics 2019; 199:77-88. [PMID: 30862564 DOI: 10.1016/j.jprot.2019.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 02/12/2019] [Accepted: 03/04/2019] [Indexed: 01/13/2023]
Abstract
RNA polymerase II is a conserved multi-subunit enzyme made up of twelve different subunits. Two of these subunits, Rpb4 and Rpb7, have been shown to perform functions in both transcription as well as outside of transcription in Saccharomyces cerevisiae. However, our knowledge about the roles of these subunits in Schizosaccharomyces pombe and higher eukaryotes is still limited. Moreover, both Rpb4 and Rpb7 are indispensable for viability of S. pombe and higher eukaryotes, in comparison to S. cerevisiae where deletion of only Rpb7 results in lethality. Therefore in this study, we used S. pombe strains expressing reduced levels of these subunits to determine their impact on the S. pombe proteome employing i-TRAQ based proteomics approach. Furthermore, proteomic profiling was carried out at two different time points to gain a temporal insight into the processes regulated by Rpb4 and Rpb7. The results showed that reduced levels of either Rpb4 or Rpb7 affected the expression of proteins involved in metabolism and ribosome biogenesis at both the time points. Our polysomal profiling experiments further revealed a role of these subunits in translation. Taken together, our results suggest a key role of Rpb4 and Rpb7 subunits in ribosome biogenesis and protein translation in S. pombe. SIGNIFICANCE: Rpb4 and Rpb7 subunits of RNA polymerase II are known for their diverse roles in regulating transcription, mRNA export, mRNA decay, stress response and translation in S. cerevisiae. However, their roles in other organisms are yet to be characterized in detail. Different lines of evidence also suggest that these subunits may function independently as well as a complex in budding yeast. Therefore, in the present study we employed a genome-wide quantitative proteomics-based approach to gain deeper insights into their cellular roles, and to examine if they regulate similar or different biological pathways in fission yeast. Our results provide evidence that they are both involved in primarily regulating metabolic pathways and ribosome biogenesis and also, play a role in protein translation in S. pombe.
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Affiliation(s)
- Deepak Kumar
- University School of Biotechnology, G.G.S. Indraprastha University, Sector16C, Dwarka, New Delhi 110078, India
| | - Swati Varshney
- Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi 110020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB campus, New Delhi 110020, India
| | - Shantanu Sengupta
- Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi 110020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB campus, New Delhi 110020, India.
| | - Nimisha Sharma
- University School of Biotechnology, G.G.S. Indraprastha University, Sector16C, Dwarka, New Delhi 110078, India.
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12
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Abstract
Sub1 was initially identified as a coactivator factor with a role during transcription initiation. However, over the last years, many evidences showed that it influences processes downstream during mRNA biogenesis, such as elongation, termination, and RNAPII phosphorylation. The recent discover that Sub1 directly interacts with the RNAPII stalk adds new insights into how it achieves all these tasks.
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Affiliation(s)
- Olga Calvo
- a Instituto de Biología Funcional y Genómica (CSIC) , Salamanca , Spain
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13
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Garavís M, González-Polo N, Allepuz-Fuster P, Louro JA, Fernández-Tornero C, Calvo O. Sub1 contacts the RNA polymerase II stalk to modulate mRNA synthesis. Nucleic Acids Res 2017; 45:2458-2471. [PMID: 27924005 PMCID: PMC5389574 DOI: 10.1093/nar/gkw1206] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/18/2016] [Indexed: 12/12/2022] Open
Abstract
Biogenesis of messenger RNA is critically influenced by the phosphorylation state of the carboxy-terminal domain (CTD) in the largest RNA polymerase II (RNAPII) subunit. Several kinases and phosphatases are required to maintain proper CTD phosphorylation levels and, additionally, several other proteins modulate them, including Rpb4/7 and Sub1. The Rpb4/7 heterodimer, constituting the RNAPII stalk, promote phosphatase functions and Sub1 globally influences CTD phosphorylation, though its mechanism remains mostly unknown. Here, we show that Sub1 physically interacts with the RNAPII stalk domain, Rpb4/7, likely through its C-terminal region, and associates with Fcp1. While Rpb4 is not required for Sub1 interaction with RNAPII complex, a fully functional heterodimer is required for Sub1 association to promoters. We also demonstrate that a complete CTD is necessary for proper association of Sub1 to chromatin and to the RNAPII. Finally, genetic data show a functional relationship between Sub1 and the RNAPII clamp domain. Altogether, our results indicate that Sub1, Rpb4/7 and Fcp1 interaction modulates CTD phosphorylation. In addition, Sub1 interaction with Rpb4/7 can also modulate transcription start site selection and transcription elongation rate likely by influencing the clamp function.
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Affiliation(s)
- Miguel Garavís
- Instituto de Biología Funcional y Genómica. CSIC/Universidad de Salamanca, C/ Zacarías González 2, Salamanca 37007, Spain
| | - Noelia González-Polo
- Instituto de Biología Funcional y Genómica. CSIC/Universidad de Salamanca, C/ Zacarías González 2, Salamanca 37007, Spain
| | - Paula Allepuz-Fuster
- Instituto de Biología Funcional y Genómica. CSIC/Universidad de Salamanca, C/ Zacarías González 2, Salamanca 37007, Spain
| | - Jaime Alegrio Louro
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | | | - Olga Calvo
- Instituto de Biología Funcional y Genómica. CSIC/Universidad de Salamanca, C/ Zacarías González 2, Salamanca 37007, Spain
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14
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Sub1/PC4, a multifaceted factor: from transcription to genome stability. Curr Genet 2017; 63:1023-1035. [DOI: 10.1007/s00294-017-0715-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 05/24/2017] [Accepted: 05/26/2017] [Indexed: 10/19/2022]
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15
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Tian X, Qi W, Chen H, Zeng X, Han L, Mi D. β-Actin regulates interleukin 6-induced p21 transcription by interacting with the Rpb5 and Rpb7 subunits of RNA polymerase II. Anim Cells Syst (Seoul) 2016. [DOI: 10.1080/19768354.2016.1224204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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16
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Modulating the level of the Rpb7 subunit of RNA polymerase II affects cell separation in Schizosaccharomyces pombe. Res Microbiol 2015; 166:20-7. [DOI: 10.1016/j.resmic.2014.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 11/18/2014] [Accepted: 12/07/2014] [Indexed: 12/17/2022]
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17
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Allepuz-Fuster P, Martínez-Fernández V, Garrido-Godino AI, Alonso-Aguado S, Hanes SD, Navarro F, Calvo O. Rpb4/7 facilitates RNA polymerase II CTD dephosphorylation. Nucleic Acids Res 2014; 42:13674-88. [PMID: 25416796 PMCID: PMC4267648 DOI: 10.1093/nar/gku1227] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/04/2014] [Accepted: 11/10/2014] [Indexed: 12/11/2022] Open
Abstract
The Rpb4 and Rpb7 subunits of eukaryotic RNA polymerase II (RNAPII) participate in a variety of processes from transcription, DNA repair, mRNA export and decay, to translation regulation and stress response. However, their mechanism(s) of action remains unclear. Here, we show that the Rpb4/7 heterodimer in Saccharomyces cerevisiae plays a key role in controlling phosphorylation of the carboxy terminal domain (CTD) of the Rpb1 subunit of RNAPII. Proper phosphorylation of the CTD is critical for the synthesis and processing of RNAPII transcripts. Deletion of RPB4, and mutations that disrupt the integrity of Rpb4/7 or its recruitment to the RNAPII complex, increased phosphorylation of Ser2, Ser5, Ser7 and Thr4 within the CTD. RPB4 interacted genetically with genes encoding CTD phosphatases (SSU72, FCP1), CTD kinases (KIN28, CTK1, SRB10) and a prolyl isomerase that targets the CTD (ESS1). We show that Rpb4 is important for Ssu72 and Fcp1 phosphatases association, recruitment and/or accessibility to the CTD, and that this correlates strongly with Ser5P and Ser2P levels, respectively. Our data also suggest that Fcp1 is the Thr4P phosphatase in yeast. Based on these and other results, we suggest a model in which Rpb4/7 helps recruit and potentially stimulate the activity of CTD-modifying enzymes, a role that is central to RNAPII function.
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Affiliation(s)
- Paula Allepuz-Fuster
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca, Salamanca 37007, Spain
| | - Verónica Martínez-Fernández
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - Ana I. Garrido-Godino
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - Sergio Alonso-Aguado
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca, Salamanca 37007, Spain
| | - Steven D. Hanes
- Department of Biochemistry and Molecular Biology, Upstate Medical University, Syracuse, NY 13210, USA
| | - Francisco Navarro
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - Olga Calvo
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca, Salamanca 37007, Spain
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18
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Deshpande SM, Sadhale PP, Vijayraghavan U. Involvement of S. cerevisiae Rpb4 in subset of pathways related to transcription elongation. Gene 2014; 545:126-31. [DOI: 10.1016/j.gene.2014.04.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 04/10/2014] [Accepted: 04/25/2014] [Indexed: 11/28/2022]
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19
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Jeronimo C, Bataille AR, Robert F. The Writers, Readers, and Functions of the RNA Polymerase II C-Terminal Domain Code. Chem Rev 2013; 113:8491-522. [DOI: 10.1021/cr4001397] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
| | - Alain R. Bataille
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
| | - François Robert
- Institut de recherches cliniques de Montréal, Montréal, Québec,
Canada H2W 1R7
- Département
de Médecine,
Faculté de Médecine, Université de Montréal, Montréal, Québec,
Canada H3T 1J4
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