1
|
Amundsen SK, Smith GR. Chi hotspot Control of RecBCD Helicase-nuclease: Enzymatic Tests Support the Intramolecular Signal-transduction Model. J Mol Biol 2024; 436:168482. [PMID: 38331210 PMCID: PMC10947171 DOI: 10.1016/j.jmb.2024.168482] [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: 11/15/2023] [Revised: 01/11/2024] [Accepted: 02/02/2024] [Indexed: 02/10/2024]
Abstract
Repair of broken DNA is essential for life; the reactions involved can also promote genetic recombination to aid evolution. In Escherichia coli, RecBCD enzyme is required for the major pathway of these events. RecBCD is a complex ATP-dependent DNA helicase with nuclease activity controlled by Chi recombination hotspots (5'-GCTGGTGG-3'). During rapid DNA unwinding, when Chi is in a RecC tunnel, RecB nuclease nicks DNA at Chi. Here, we test our signal transduction model - upon binding Chi (step 1), RecC signals RecD helicase to stop unwinding (step 2); RecD then signals RecB (step 3) to nick at Chi (step 4) and to begin loading RecA DNA strand-exchange protein (step 5). We discovered that ATP-γ-S, like the small molecule RecBCD inhibitor NSAC1003, causes RecBCD to nick DNA, independent of Chi, at novel positions determined by the DNA substrate length. Two RecB ATPase-site mutants nick at novel positions determined by their RecB:RecD helicase rate ratios. In each case, we find that nicking at the novel position requires steps 3 and 4 but not step 1 or 2, as shown by mutants altered at the intersubunit contacts specific for each step; nicking also requires RecD helicase and RecB nuclease activities. Thus, altering the RecB ATPase site, by small molecules or mutation, sensitizes RecD to signal RecB to nick DNA (steps 4 and 3, respecitvely) without the signal from RecC or Chi (steps 1 and 2). These new, enzymatic results strongly support the signal transduction model and provide a paradigm for studying other complex enzymes.
Collapse
Affiliation(s)
- Susan K Amundsen
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Farview Avenue North, A1-162, Seattle, WA 98109, USA
| | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Farview Avenue North, A1-162, Seattle, WA 98109, USA.
| |
Collapse
|
2
|
Schwank K, Schmid C, Fremter T, Engel C, Milkereit P, Griesenbeck J, Tschochner H. Features of yeast RNA polymerase I with special consideration of the lobe binding subunits. Biol Chem 2023; 404:979-1002. [PMID: 37823775 DOI: 10.1515/hsz-2023-0184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/13/2023] [Indexed: 10/13/2023]
Abstract
Ribosomal RNAs (rRNAs) are structural components of ribosomes and represent the most abundant cellular RNA fraction. In the yeast Saccharomyces cerevisiae, they account for more than 60 % of the RNA content in a growing cell. The major amount of rRNA is synthesized by RNA polymerase I (Pol I). This enzyme transcribes exclusively the rRNA gene which is tandemly repeated in about 150 copies on chromosome XII. The high number of transcribed rRNA genes, the efficient recruitment of the transcription machinery and the dense packaging of elongating Pol I molecules on the gene ensure that enough rRNA is generated. Specific features of Pol I and of associated factors confer promoter selectivity and both elongation and termination competence. Many excellent reviews exist about the state of research about function and regulation of Pol I and how Pol I initiation complexes are assembled. In this report we focus on the Pol I specific lobe binding subunits which support efficient, error-free, and correctly terminated rRNA synthesis.
Collapse
Affiliation(s)
- Katrin Schwank
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Catharina Schmid
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Tobias Fremter
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Christoph Engel
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Philipp Milkereit
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Joachim Griesenbeck
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| | - Herbert Tschochner
- Regensburg Center of Biochemistry (RCB), Universität Regensburg, D-93053 Regensburg, Germany
| |
Collapse
|
3
|
Daiß JL, Griesenbeck J, Tschochner H, Engel C. Synthesis of the ribosomal RNA precursor in human cells: mechanisms, factors and regulation. Biol Chem 2023; 404:1003-1023. [PMID: 37454246 DOI: 10.1515/hsz-2023-0214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023]
Abstract
The ribosomal RNA precursor (pre-rRNA) comprises three of the four ribosomal RNAs and is synthesized by RNA polymerase (Pol) I. Here, we describe the mechanisms of Pol I transcription in human cells with a focus on recent insights gained from structure-function analyses. The comparison of Pol I-specific structural and functional features with those of other Pols and with the excessively studied yeast system distinguishes organism-specific from general traits. We explain the organization of the genomic rDNA loci in human cells, describe the Pol I transcription cycle regarding structural changes in the enzyme and the roles of human Pol I subunits, and depict human rDNA transcription factors and their function on a mechanistic level. We disentangle information gained by direct investigation from what had apparently been deduced from studies of the yeast enzymes. Finally, we provide information about how Pol I mutations may contribute to developmental diseases, and why Pol I is a target for new cancer treatment strategies, since increased rRNA synthesis was correlated with rapidly expanding cell populations.
Collapse
Affiliation(s)
- Julia L Daiß
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Joachim Griesenbeck
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Herbert Tschochner
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Christoph Engel
- Regensburg Center for Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| |
Collapse
|
4
|
Montacié C, Riondet C, Wei L, Darrière T, Weiss A, Pontvianne F, Escande ML, de Bures A, Jobet E, Barbarossa A, Carpentier MC, Aarts MGM, Attina A, Hirtz C, David A, Marchand V, Motorin Y, Curie C, Mari S, Reichheld JP, Sáez-Vásquez J. NICOTIANAMINE SYNTHASE activity affects nucleolar iron accumulation and impacts rDNA silencing and RNA methylation in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4384-4400. [PMID: 37179467 PMCID: PMC10433931 DOI: 10.1093/jxb/erad180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/11/2023] [Indexed: 05/15/2023]
Abstract
In plant cells, a large pool of iron (Fe) is contained in the nucleolus, as well as in chloroplasts and mitochondria. A central determinant for intracellular distribution of Fe is nicotianamine (NA) generated by NICOTIANAMINE SYNTHASE (NAS). Here, we used Arabidopsis thaliana plants with disrupted NAS genes to study the accumulation of nucleolar iron and understand its role in nucleolar functions and more specifically in rRNA gene expression. We found that nas124 triple mutant plants, which contained lower quantities of the iron ligand NA, also contained less iron in the nucleolus. This was concurrent with the expression of normally silenced rRNA genes from nucleolar organizer regions 2 (NOR2). Notably, in nas234 triple mutant plants, which also contained lower quantities of NA, nucleolar iron and rDNA expression were not affected. In contrast, in both nas124 and nas234, specific RNA modifications were differentially regulated in a genotype dependent manner. Taken together, our results highlight the impact of specific NAS activities in RNA gene expression. We discuss the interplay between NA and nucleolar iron with rDNA functional organization and RNA methylation.
Collapse
Affiliation(s)
- Charlotte Montacié
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Christophe Riondet
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Lili Wei
- Institut Agro, BPMP, CNRS, INRAE, Université Montpellier, 34060 Montpellier, France
| | - Tommy Darrière
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Alizée Weiss
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Frédéric Pontvianne
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Marie-Line Escande
- Observatoire Océanologique de Banyuls s/ mer, CNRS, 66650 Banyuls-sur-mer, France
- BioPIC Platform of the OOB, 66650 Banyuls-sur-mer, France
| | - Anne de Bures
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Edouard Jobet
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Adrien Barbarossa
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University & Research, 6700AA Wageningen, Netherlands
| | - Aurore Attina
- INSERM, CHU Montpellier, CNRS, IRMB, Université Montpellier, 34090Montpellier, France
| | - Christophe Hirtz
- INSERM, CHU Montpellier, CNRS, IRMB, Université Montpellier, 34090Montpellier, France
| | - Alexandre David
- IGF, CNRS, INSERM, Université Montpellier, 34090Montpellier, France
| | - Virginie Marchand
- Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, CNRS, INSERM, IBSLor (UMS2008/US40), Université de Lorraine, F-54000 Nancy, France
| | - Yuri Motorin
- Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, CNRS, INSERM, IBSLor (UMS2008/US40), Université de Lorraine, F-54000 Nancy, France
- CNRS, IMoPA (UMR 7365), Université de Lorraine, F-54000 Nancy, France
| | - Catherine Curie
- Institut Agro, BPMP, CNRS, INRAE, Université Montpellier, 34060 Montpellier, France
| | - Stéphane Mari
- Institut Agro, BPMP, CNRS, INRAE, Université Montpellier, 34060 Montpellier, France
| | - Jean-Philippe Reichheld
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Julio Sáez-Vásquez
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| |
Collapse
|
5
|
McNamar R, Freeman E, Baylor KN, Fakhouri AM, Huang S, Knutson BA, Rothblum LI. PAF49: An RNA Polymerase I subunit essential for rDNA transcription and stabilization of PAF53. J Biol Chem 2023; 299:104951. [PMID: 37356716 PMCID: PMC10365956 DOI: 10.1016/j.jbc.2023.104951] [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: 04/04/2023] [Revised: 05/30/2023] [Accepted: 06/09/2023] [Indexed: 06/27/2023] Open
Abstract
The application of genetic and biochemical techniques in yeast has informed our knowledge of transcription in mammalian cells. Such systems have allowed investigators to determine whether a gene was essential and to determine its function in rDNA transcription. However, there are significant differences in the nature of the transcription factors essential for transcription by Pol I in yeast and mammalian cells, and yeast RNA polymerase I contains 14 subunits while mammalian polymerase contains 13 subunits. We previously reported the adaptation of the auxin-dependent degron that enabled a combination of a "genetics-like" approach and biochemistry to study mammalian rDNA transcription. Using this system, we studied the mammalian orthologue of yeast RPA34.5, PAF49, and found that it is essential for rDNA transcription and cell division. The auxin-induced degradation of PAF49 induced nucleolar stress and the accumulation of P53. Interestingly, the auxin-induced degradation of AID-tagged PAF49 led to the degradation of its binding partner, PAF53, but not vice versa. A similar pattern of co-dependent expression was also found when we studied the non-essential, yeast orthologues. An analysis of the domains of PAF49 that are essential for rDNA transcription demonstrated a requirement for both the dimerization domain and an "arm" of PAF49 that interacts with PolR1B. Further, we demonstrate this interaction can be disrupted to inhibit Pol I transcription in normal and cancer cells which leads to the arrest of normal cells and cancer cell death. In summary, we have shown that both PAF53 and PAF49 are necessary for rDNA transcription and cell growth.
Collapse
Affiliation(s)
- Rachel McNamar
- Department of Cell Biology, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma, USA
| | - Emma Freeman
- Department of Cell and Development Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Kairo N Baylor
- 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
| | - Sui Huang
- Department of Cell and Development Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Bruce A Knutson
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Lawrence I Rothblum
- Department of Cell Biology, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma, USA.
| |
Collapse
|
6
|
Duval M, Yague-Sanz C, Turowski TW, Petfalski E, Tollervey D, Bachand F. The conserved RNA-binding protein Seb1 promotes cotranscriptional ribosomal RNA processing by controlling RNA polymerase I progression. Nat Commun 2023; 14:3013. [PMID: 37230993 DOI: 10.1038/s41467-023-38826-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
Transcription by RNA polymerase I (RNAPI) represents most of the transcriptional activity in eukaryotic cells and is associated with the production of mature ribosomal RNA (rRNA). As several rRNA maturation steps are coupled to RNAPI transcription, the rate of RNAPI elongation directly influences processing of nascent pre-rRNA, and changes in RNAPI transcription rate can result in alternative rRNA processing pathways in response to growth conditions and stress. However, factors and mechanisms that control RNAPI progression by influencing transcription elongation rate remain poorly understood. We show here that the conserved fission yeast RNA-binding protein Seb1 associates with the RNAPI transcription machinery and promotes RNAPI pausing states along the rDNA. The overall faster progression of RNAPI at the rDNA in Seb1-deficient cells impaired cotranscriptional pre-rRNA processing and the production of mature rRNAs. Given that Seb1 also influences pre-mRNA processing by modulating RNAPII progression, our findings unveil Seb1 as a pause-promoting factor for RNA polymerases I and II to control cotranscriptional RNA processing.
Collapse
Affiliation(s)
- Maxime Duval
- RNA group, Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Carlo Yague-Sanz
- RNA group, Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, Canada
- URPHYM-GEMO, The University of Namur, 5000, Namur, Belgium
| | - Tomasz W Turowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - David Tollervey
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - François Bachand
- RNA group, Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, Canada.
| |
Collapse
|
7
|
Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes. Nat Rev Mol Cell Biol 2023; 24:414-429. [PMID: 36732602 DOI: 10.1038/s41580-022-00573-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2022] [Indexed: 02/04/2023]
Abstract
One of the first biological machineries to be created seems to have been the ribosome. Since then, organisms have dedicated great efforts to optimize this apparatus. The ribosomal RNA (rRNA) contained within ribosomes is crucial for protein synthesis and maintenance of cellular function in all known organisms. In eukaryotic cells, rRNA is produced from ribosomal DNA clusters of tandem rRNA genes, whose organization in the nucleolus, maintenance and transcription are strictly regulated to satisfy the substantial demand for rRNA required for ribosome biogenesis. Recent studies have elucidated mechanisms underlying the integrity of ribosomal DNA and regulation of its transcription, including epigenetic mechanisms and a unique recombination and copy-number control system to stably maintain high rRNA gene copy number. In this Review, we disucss how the crucial maintenance of rRNA gene copy number through control of gene amplification and of rRNA production by RNA polymerase I are orchestrated. We also discuss how liquid-liquid phase separation controls the architecture and function of the nucleolus and the relationship between rRNA production, cell senescence and disease.
Collapse
|
8
|
Huffines AK, Engel KL, French SL, Zhang Y, Viktorovskaya OV, Schneider DA. Rate of transcription elongation and sequence-specific pausing by RNA polymerase I directly influence rRNA processing. J Biol Chem 2022; 298:102730. [PMID: 36423683 PMCID: PMC9768379 DOI: 10.1016/j.jbc.2022.102730] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/18/2022] [Accepted: 11/07/2022] [Indexed: 11/23/2022] Open
Abstract
One of the first steps in ribosome biogenesis is transcription of the ribosomal DNA by RNA polymerase I (Pol I). Processing of the resultant rRNA begins cotranscriptionally, and perturbation of Pol I transcription elongation results in defective rRNA processing. Mechanistic insight regarding the link between transcription elongation and ribosome assembly is lacking because of limited in vivo methods to assay Pol I transcription. Here, we use native elongating transcript sequencing (NET-Seq) with a strain of Saccharomyces cerevisiae containing a point mutation in Pol I, rpa190-F1205H, which results in impaired rRNA processing and ribosome assembly. We previously demonstrated that this mutation caused a mild reduction in the transcription elongation rate of Pol I in vitro; however, transcription elongation by the mutant has not been characterized in vivo. Here, our findings demonstrate that the mutant Pol I has an increased pause propensity during processive transcription elongation both in vitro and in vivo. NET-Seq reveals that rpa190-F1205H Pol I displays alternative pause site preferences in vivo. Specifically, the mutant is sensitized to A/G residues in the RNA:DNA hybrid and at the last incorporated nucleotide position. Furthermore, both NET-Seq and EM analysis of Miller chromatin spreads reveal pileups of rpa190-F1205H Pol I throughout the ribosomal DNA, particularly at the 5' end of the 35S gene. This combination of in vitro and in vivo analyses of a Pol I mutant provides novel insights into Pol I elongation properties and indicates how these properties are crucial for efficient cotranscriptional rRNA processing and ribosome assembly.
Collapse
Affiliation(s)
- Abigail K Huffines
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Krysta L Engel
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sarah L French
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Yinfeng Zhang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Olga V Viktorovskaya
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.
| |
Collapse
|
9
|
Daiß JL, Pilsl M, Straub K, Bleckmann A, Höcherl M, Heiss FB, Abascal-Palacios G, Ramsay EP, Tlučková K, Mars JC, Fürtges T, Bruckmann A, Rudack T, Bernecky C, Lamour V, Panov K, Vannini A, Moss T, Engel C. The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans. Life Sci Alliance 2022; 5:5/11/e202201568. [PMID: 36271492 PMCID: PMC9438803 DOI: 10.26508/lsa.202201568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 06/20/2022] [Accepted: 08/09/2022] [Indexed: 11/24/2022] Open
Abstract
We characterize the human RNA polymerase I by evolutionary biochemistry and cryo-EM revealing a built-in structural domain that apparently serves as transcription factor–binding platform in metazoans. Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is a major determinant of cellular growth, and dysregulation is observed in many cancer types. Here, we present the purification of human Pol I from cells carrying a genomic GFP fusion on the largest subunit allowing the structural and functional analysis of the enzyme across species. In contrast to yeast, human Pol I carries a single-subunit stalk, and in vitro transcription indicates a reduced proofreading activity. Determination of the human Pol I cryo-EM reconstruction in a close-to-native state rationalizes the effects of disease-associated mutations and uncovers an additional domain that is built into the sequence of Pol I subunit RPA1. This “dock II” domain resembles a truncated HMG box incapable of DNA binding which may serve as a downstream transcription factor–binding platform in metazoans. Biochemical analysis, in situ modelling, and ChIP data indicate that Topoisomerase 2a can be recruited to Pol I via the domain and cooperates with the HMG box domain–containing factor UBF. These adaptations of the metazoan Pol I transcription system may allow efficient release of positive DNA supercoils accumulating downstream of the transcription bubble.
Collapse
Affiliation(s)
- Julia L Daiß
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Michael Pilsl
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Kristina Straub
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Andrea Bleckmann
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Mona Höcherl
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Florian B Heiss
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Guillermo Abascal-Palacios
- Division of Structural Biology, The Institute of Cancer Research, London, UK
- Biofisika Institute (CSIC, UPV/EHU), Leioa, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Ewan P Ramsay
- Division of Structural Biology, The Institute of Cancer Research, London, UK
- Fondazione Human Technopole, Structural Biology Research Centre, Milan, Italy
| | | | - Jean-Clement Mars
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec, Canada
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, Canada
- Borden Laboratory, IRIC, Université de Montréal, Montréal, Québec, Canada
| | - Torben Fürtges
- Protein Crystallography, Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Astrid Bruckmann
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Till Rudack
- Protein Crystallography, Department of Biophysics, Faculty of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Carrie Bernecky
- Institute of Science and Technology, Klosterneuburg, Austria
| | - Valérie Lamour
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Department of Integrated Structural Biology, Illkirch, France
- Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Konstantin Panov
- School of Biological Sciences and PGJCCR, Queen’s University Belfast, Belfast, UK
| | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer Research, London, UK
- Fondazione Human Technopole, Structural Biology Research Centre, Milan, Italy
| | - Tom Moss
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec, Canada
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, Canada
| | - Christoph Engel
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| |
Collapse
|
10
|
Oborská-Oplová M, Gerhardy S, Panse VG. Orchestrating ribosomal RNA folding during ribosome assembly. Bioessays 2022; 44:e2200066. [PMID: 35751450 DOI: 10.1002/bies.202200066] [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: 03/29/2022] [Revised: 05/30/2022] [Accepted: 06/13/2022] [Indexed: 11/08/2022]
Abstract
Construction of the eukaryotic ribosome is a complex process in which a nascent ribosomal RNA (rRNA) emerging from RNA Polymerase I hierarchically folds into a native three-dimensional structure. Modular assembly of individual RNA domains through interactions with ribosomal proteins and a myriad of assembly factors permit efficient disentanglement of the error-prone RNA folding process. Following these dynamic events, long-range tertiary interactions are orchestrated to compact rRNA. A combination of genetic, biochemical, and structural studies is now providing clues into how a nascent rRNA is transformed into a functional ribosome with high precision. With this essay, we aim to draw attention to the poorly understood process of establishing correct RNA tertiary contacts during ribosome formation.
Collapse
Affiliation(s)
| | - Stefan Gerhardy
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Vikram Govind Panse
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Faculty of Science, University of Zurich, Zurich, Switzerland
| |
Collapse
|
11
|
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
| |
Collapse
|
12
|
Azouzi C, Jaafar M, Dez C, Abou Merhi R, Lesne A, Henras AK, Gadal O. Coupling Between Production of Ribosomal RNA and Maturation: Just at the Beginning. Front Mol Biosci 2021; 8:778778. [PMID: 34765647 PMCID: PMC8575686 DOI: 10.3389/fmolb.2021.778778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/12/2021] [Indexed: 01/28/2023] Open
Abstract
Ribosomal RNA (rRNA) production represents the most active transcription in the cell. Synthesis of the large rRNA precursors (35S/47S in yeast/human) is achieved by up to hundreds of RNA polymerase I (Pol I) enzymes simultaneously transcribing a single rRNA gene. In this review, we present recent advances in understanding the coupling between rRNA production and nascent rRNA folding. Mapping of the distribution of Pol I along ribosomal DNA at nucleotide resolution, using either native elongating transcript sequencing (NET-Seq) or crosslinking and analysis of cDNAs (CRAC), revealed frequent Pol I pausing, and CRAC results revealed a direct coupling between pausing and nascent RNA folding. High density of Pol I per gene imposes topological constraints that establish a defined pattern of polymerase distribution along the gene, with a persistent spacing between transcribing enzymes. RNA folding during transcription directly acts as an anti-pausing mechanism, implying that proper folding of the nascent rRNA favors elongation in vivo. Defects in co-transcriptional folding of rRNA are likely to induce Pol I pausing. We propose that premature termination of transcription, at defined positions, can control rRNA production in vivo.
Collapse
Affiliation(s)
- Chaima Azouzi
- Laboratoire de Biologie Moléculaire, Cellulaire et du Développement (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Mariam Jaafar
- Laboratoire de Biologie Moléculaire, Cellulaire et du Développement (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Christophe Dez
- Laboratoire de Biologie Moléculaire, Cellulaire et du Développement (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Raghida Abou Merhi
- Genomic Stability and Biotherapy (GSBT) Laboratory, Faculty of Sciences, Rafik Hariri Campus, Lebanese University, Beirut, Lebanon
| | - Annick Lesne
- CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, Sorbonne Université, Paris, France.,Institut de Génétique Moléculaire de Montpellier, IGMM, CNRS, Université Montpellier, Montpellier, France
| | - Anthony K Henras
- Laboratoire de Biologie Moléculaire, Cellulaire et du Développement (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Olivier Gadal
- Laboratoire de Biologie Moléculaire, Cellulaire et du Développement (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, Université de Toulouse, Toulouse, France
| |
Collapse
|
13
|
Yin X, Zhang K, Wang J, Zhou X, Zhang C, Song X, Wu Z, Du J, Chen Q, Zhang S, Deng W. RNA polymerase I subunit 12 plays opposite roles in cell proliferation and migration. Biochem Biophys Res Commun 2021; 560:112-118. [PMID: 33984768 DOI: 10.1016/j.bbrc.2021.04.091] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 11/29/2022]
Abstract
RNA polymerase I (Pol I) is responsible for the synthesis of the majority of ribosomal RNA molecules in eukaryotes. Pol I subunit 12 (RPA12) is involved in the transcriptional termination and lipid metabolism in yeast. However, its role in human cells hasn't been investigated so far. Here, we show that RPA12 is present in the nucleolus and nucleoplasm of HeLa cells. RPA12 can act as a positive factor to regulate Pol I-mediated transcription and the proliferation of 293T and HeLa cells. Unexpectedly, RPA12 can repress HeLa cell migration, indicating that RPA12 plays opposite roles in cell proliferation and migration. This study provides a novel insight into the role of RPA12 in human cells.
Collapse
Affiliation(s)
- Xiaomei Yin
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Kewei Zhang
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Juan Wang
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, 430065, China; School of Materials and Metallurgy, Wuhan University of Science and Technology, Wuhan, 430081, China
| | - Xiangyu Zhou
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Cheng Zhang
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Xiaoye Song
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Zhongyu Wu
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Jiannan Du
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Qiyue Chen
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Shihua Zhang
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, 430065, China.
| | - Wensheng Deng
- College of Life Science and Health, Wuhan University of Science and Technology, Wuhan, 430065, China.
| |
Collapse
|
14
|
The Mammalian and Yeast A49 and A34 Heterodimers: Homologous but Not the Same. Genes (Basel) 2021; 12:genes12050620. [PMID: 33921963 PMCID: PMC8143541 DOI: 10.3390/genes12050620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 11/25/2022] Open
Abstract
Ribosomal RNA synthesis is the rate-limiting step in ribosome biogenesis. In eukaryotes, RNA polymerase I (Pol I) is responsible for transcribing the ribosomal DNA genes that reside in the nucleolus. Aberrations in Pol I activity have been linked to the development of multiple cancers and other genetic diseases. Therefore, it is key that we understand the mechanisms of Pol I transcription. Recent studies have demonstrated that there are many differences between Pol I transcription in yeast and mammals. Our goal is to highlight the similarities and differences between the polymerase-associated factors (PAFs) in yeast and mammalian cells. We focus on the PAF heterodimer A49/34 in yeast and PAF53/49 in mammals. Recent studies have demonstrated that while the structures between the yeast and mammalian orthologs are very similar, they may function differently during Pol I transcription, and their patterns of regulation are different.
Collapse
|
15
|
Salim D, Bradford WD, Rubinstein B, Gerton JL. DNA replication, transcription, and H3K56 acetylation regulate copy number and stability at tandem repeats. G3-GENES GENOMES GENETICS 2021; 11:6174693. [PMID: 33729510 DOI: 10.1093/g3journal/jkab082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/26/2021] [Indexed: 11/13/2022]
Abstract
Tandem repeats are inherently unstable and exhibit extensive copy number polymorphisms. Despite mounting evidence for their adaptive potential, the mechanisms associated with regulation of the stability and copy number of tandem repeats remain largely unclear. To study copy number variation at tandem repeats, we used two well-studied repetitive arrays in the budding yeast genome, the ribosomal DNA (rDNA) locus, and the copper-inducible CUP1 gene array. We developed powerful, highly sensitive, and quantitative assays to measure repeat instability and copy number and used them in multiple high-throughput genetic screens to define pathways involved in regulating copy number variation. These screens revealed that rDNA stability and copy number are regulated by DNA replication, transcription, and histone acetylation. Through parallel studies of both arrays, we demonstrate that instability can be induced by DNA replication stress and transcription. Importantly, while changes in stability in response to stress are observed within a few cell divisions, a change in steady state repeat copy number requires selection over time. Further, H3K56 acetylation is required for regulating transcription and transcription-induced instability at the CUP1 array, and restricts transcription-induced amplification. Our work suggests that the modulation of replication and transcription is a direct, reversible strategy to alter stability at tandem repeats in response to environmental stimuli, which provides cells rapid adaptability through copy number variation. Additionally, histone acetylation may function to promote the normal adaptive program in response to transcriptional stress. Given the omnipresence of DNA replication, transcription, and chromatin marks like histone acetylation, the fundamental mechanisms we have uncovered significantly advance our understanding of the plasticity of tandem repeats more generally.
Collapse
Affiliation(s)
- Devika Salim
- Stowers Institute for Medical Research, Kansas City, MO 64110, United States of America.,Open University, Milton Keynes MK7 6BJ, United Kingdom
| | - William D Bradford
- Stowers Institute for Medical Research, Kansas City, MO 64110, United States of America
| | - Boris Rubinstein
- Stowers Institute for Medical Research, Kansas City, MO 64110, United States of America
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO 64110, United States of America.,Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, United States of America
| |
Collapse
|
16
|
Heiss FB, Daiß JL, Becker P, Engel C. Conserved strategies of RNA polymerase I hibernation and activation. Nat Commun 2021; 12:758. [PMID: 33536435 PMCID: PMC7859239 DOI: 10.1038/s41467-021-21031-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 01/05/2021] [Indexed: 11/21/2022] Open
Abstract
RNA polymerase (Pol) I transcribes the ribosomal RNA precursor in all eukaryotes. The mechanisms 'activation by cleft contraction' and 'hibernation by dimerization' are unique to the regulation of this enzyme, but structure-function analysis is limited to baker's yeast. To understand whether regulation by such strategies is specific to this model organism or conserved among species, we solve three cryo-EM structures of Pol I from Schizosaccharomyces pombe in different functional states. Comparative analysis of structural models derived from high-resolution reconstructions shows that activation is accomplished by a conserved contraction of the active center cleft. In contrast to current beliefs, we find that dimerization of the S. pombe polymerase is also possible. This dimerization is achieved independent of the 'connector' domain but relies on two previously undescribed interfaces. Our analyses highlight the divergent nature of Pol I transcription systems from their counterparts and suggest conservation of regulatory mechanisms among organisms.
Collapse
Affiliation(s)
- Florian B Heiss
- Regensburg Center for Biochemistry, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - Julia L Daiß
- Regensburg Center for Biochemistry, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - Philipp Becker
- Regensburg Center for Biochemistry, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - Christoph Engel
- Regensburg Center for Biochemistry, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany.
| |
Collapse
|
17
|
Abstract
RNA polymerase I (Pol I) specifically synthesizes ribosomal RNA. Pol I upregulation is linked to cancer, while mutations in the Pol I machinery lead to developmental disorders. Here we report the cryo-EM structure of elongating human Pol I at 2.7 Å resolution. In the exit tunnel, we observe a double-stranded RNA helix that may support Pol I processivity. Our structure confirms that human Pol I consists of 13 subunits with only one subunit forming the Pol I stalk. Additionally, the structure of human Pol I in complex with the initiation factor RRN3 at 3.1 Å resolution reveals stalk flipping upon RRN3 binding. We also observe an inactivated state of human Pol I bound to an open DNA scaffold at 3.3 Å resolution. Lastly, the high-resolution structure of human Pol I allows mapping of disease-related mutations that can aid understanding of disease etiology.
Collapse
|
18
|
Amundsen SK, Taylor AF, Smith GR. Chi hotspot control of RecBCD helicase-nuclease by long-range intramolecular signaling. Sci Rep 2020; 10:19415. [PMID: 33154402 PMCID: PMC7644769 DOI: 10.1038/s41598-020-73078-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/08/2020] [Indexed: 11/09/2022] Open
Abstract
Repair of broken DNA by homologous recombination requires coordinated enzymatic reactions to prepare it for interaction with intact DNA. The multiple activities of enterobacterial RecBCD helicase-nuclease are coordinated by Chi recombination hotspots (5′ GCTGGTGG 3′) recognized during DNA unwinding. Chi is recognized in a tunnel in RecC but activates the RecB nuclease, > 25 Ǻ away. How the Chi-dependent signal travels this long distance has been unknown. We found a Chi hotspot-deficient mutant in the RecB helicase domain located > 45 Ǻ from both the Chi-recognition site and the nuclease active site. This unexpected observation led us to find additional mutations that reduced or eliminated Chi hotspot activity in each subunit and widely scattered throughout RecBCD. Each mutation alters the intimate contact between one or another pair of subunits in crystal or cryoEM structures of RecBCD bound to DNA. Collectively, these mutations span a path about 185 Ǻ long from the Chi recognition site to the nuclease active site. We discuss these surprising results in the context of an intramolecular signal transduction accounting for many previous observations.
Collapse
Affiliation(s)
- Susan K Amundsen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrew F Taylor
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| |
Collapse
|
19
|
Knutson BA, McNamar R, Rothblum LI. Dynamics of the RNA polymerase I TFIIF/TFIIE-like subcomplex: a mini-review. Biochem Soc Trans 2020; 48:1917-1927. [PMID: 32915199 PMCID: PMC10793690 DOI: 10.1042/bst20190848] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 01/31/2023]
Abstract
RNA polymerase I (Pol I) is the most specialized eukaryotic Pol. It is only responsible for the synthesis of pre-ribosomal RNA (rRNA), the precursor of 18S, 5.8S and 28S rRNA, the most abundant cellular RNA types. Aberrant Pol I transcription is observed in a wide variety of cancers and its down-regulation is associated with several genetic disorders. The regulation and mechanism of Pol I transcription is increasing in clarity given the numerous high-resolution Pol I structures that have helped bridge seminal genetic and biochemical findings in the field. Here, we review the multifunctional roles of an important TFIIF- and TFIIE-like subcomplex composed of the Pol I subunits A34.5 and A49 in yeast, and PAF49 and PAF53 in mammals. Recent analyses have revealed a dynamic interplay between this subcomplex at nearly every step of the Pol I transcription cycle in addition to new roles in chromatin traversal and the existence of a new helix-turn-helix (HTH) within the A49/PAF53 linker domain that expands its dynamic functions during the Pol I transcription process.
Collapse
Affiliation(s)
- Bruce A. Knutson
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, U.S.A
| | - Rachel McNamar
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, U.S.A
| | - Lawrence I. Rothblum
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, U.S.A
| |
Collapse
|
20
|
Okuda EK, Gonzales-Zubiate FA, Gadal O, Oliveira CC. Nucleolar localization of the yeast RNA exosome subunit Rrp44 hints at early pre-rRNA processing as its main function. J Biol Chem 2020; 295:11195-11213. [PMID: 32554806 DOI: 10.1074/jbc.ra120.013589] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/12/2020] [Indexed: 01/12/2023] Open
Abstract
The RNA exosome is a multisubunit protein complex involved in RNA surveillance of all classes of RNA, and is essential for pre-rRNA processing. The exosome is conserved throughout evolution, present in archaea and eukaryotes from yeast to humans, where it localizes to the nucleus and cytoplasm. The catalytically active subunit Rrp44/Dis3 of the exosome in budding yeast (Saccharomyces cerevisiae) is considered a protein present in these two subcellular compartments, and here we report that it not only localizes mainly to the nucleus, but is concentrated in the nucleolus, where the early pre-rRNA processing reactions take place. Moreover, we show by confocal microscopy analysis that the core exosome subunits Rrp41 and Rrp43 also localize largely to the nucleus and strongly accumulate in the nucleolus. These results shown here shed additional light on the localization of the yeast exosome and have implications regarding the main function of this RNase complex, which seems to be primarily in early pre-rRNA processing and surveillance.
Collapse
Affiliation(s)
- Ellen K Okuda
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | | | - Olivier Gadal
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Carla C Oliveira
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| |
Collapse
|
21
|
Merkl PE, Pilsl M, Fremter T, Schwank K, Engel C, Längst G, Milkereit P, Griesenbeck J, Tschochner H. RNA polymerase I (Pol I) passage through nucleosomes depends on Pol I subunits binding its lobe structure. J Biol Chem 2020; 295:4782-4795. [PMID: 32060094 DOI: 10.1074/jbc.ra119.011827] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 02/11/2020] [Indexed: 02/02/2023] Open
Abstract
RNA polymerase I (Pol I) is a highly efficient enzyme specialized in synthesizing most ribosomal RNAs. After nucleosome deposition at each round of rDNA replication, the Pol I transcription machinery has to deal with nucleosomal barriers. It has been suggested that Pol I-associated factors facilitate chromatin transcription, but it is unknown whether Pol I has an intrinsic capacity to transcribe through nucleosomes. Here, we used in vitro transcription assays to study purified WT and mutant Pol I variants from the yeast Saccharomyces cerevisiae and compare their abilities to pass a nucleosomal barrier with those of yeast Pol II and Pol III. Under identical conditions, purified Pol I and Pol III, but not Pol II, could transcribe nucleosomal templates. Pol I mutants lacking either the heterodimeric subunit Rpa34.5/Rpa49 or the C-terminal part of the specific subunit Rpa12.2 showed a lower processivity on naked DNA templates, which was even more reduced in the presence of a nucleosome. Our findings suggest that the lobe-binding subunits Rpa34.5/Rpa49 and Rpa12.2 facilitate passage through nucleosomes, suggesting possible cooperation among these subunits. We discuss the contribution of Pol I-specific subunit domains to efficient Pol I passage through nucleosomes in the context of transcription rate and processivity.
Collapse
Affiliation(s)
- Philipp E Merkl
- Lehrstuhl Biochemie III, Universität Regensburg, Regensburg Center of Biochemistry (RCB), 93053 Regensburg, Germany
| | - Michael Pilsl
- Lehrstuhl Biochemie III, Universität Regensburg, Regensburg Center of Biochemistry (RCB), 93053 Regensburg, Germany
| | - Tobias Fremter
- Lehrstuhl Biochemie III, Universität Regensburg, Regensburg Center of Biochemistry (RCB), 93053 Regensburg, Germany
| | - Katrin Schwank
- Lehrstuhl Biochemie III, Universität Regensburg, Regensburg Center of Biochemistry (RCB), 93053 Regensburg, Germany
| | - Christoph Engel
- Lehrstuhl Biochemie III, Universität Regensburg, Regensburg Center of Biochemistry (RCB), 93053 Regensburg, Germany
| | - Gernot Längst
- Lehrstuhl Biochemie III, Universität Regensburg, Regensburg Center of Biochemistry (RCB), 93053 Regensburg, Germany
| | - Philipp Milkereit
- Lehrstuhl Biochemie III, Universität Regensburg, Regensburg Center of Biochemistry (RCB), 93053 Regensburg, Germany
| | - Joachim Griesenbeck
- Lehrstuhl Biochemie III, Universität Regensburg, Regensburg Center of Biochemistry (RCB), 93053 Regensburg, Germany
| | - Herbert Tschochner
- Lehrstuhl Biochemie III, Universität Regensburg, Regensburg Center of Biochemistry (RCB), 93053 Regensburg, Germany
| |
Collapse
|