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Ribosome synthesis in mammalian cells

English title Ribosome synthesis in mammalian cells
Applicant Kutay Ulrike
Number 166565
Funding scheme Project funding
Research institution Institut für Biochemie Departement Biologie ETH Zürich
Institution of higher education ETH Zurich - ETHZ
Main discipline Biochemistry
Start/End 01.04.2016 - 31.03.2019
Approved amount 756'000.00
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All Disciplines (2)

Discipline
Biochemistry
Cellular Biology, Cytology

Keywords (8)

RNAi screening; p53; 40S; 60S; ribosome; protein kinase; rRNA; image analysis

Lay Summary (German)

Lead
Ribosomen sind für das Leben grundlegende, makromolekulare Komplexe aller Organismen, die auch in den Zellen des menschlichen Körpers für die Synthese von Eiweißen verantwortlich sind. Der Zusammenbau menschlicher Ribosomen ist ein sehr komplizierter Prozess, der eine Vielzahl von Hilfsfaktoren benötigt. Ziel dieses Projektes ist es, derartige Hilfsfaktoren zu identifizieren und zu charakterisieren.
Lay summary

Die zwei Untereinheiten der menschlichen Ribosomen bestehen aus insgesamt 4 unterschiedlichen Ribonukleinsäuren und aus mehr als 80 verschiedenen Proteinen, die zusammen ein 4.3 MDa großen Ribonukleoproteinkomplex bilden. Der Zusammenbau der Ribosomen erfolgt entlang einem geordneten Plan und bedarf der Hilfe vieler zusätzlicher Faktoren. Die Identifizierung und funktionelle Charakterisierung dieser Hilfsfaktoren ist das Ziel dieses Forschungsprojektes. Dazu werden wir systematisch in Zellkulturmodellen jedes einzelne menschliche Protein gezielt eliminieren und mittels bildgebender Verfahren testen, ob dies die Biogenese der ribosomalen Untereinheiten beeinflusst. Für ausgewählte Faktoren werden wir untersuchen, wie sie mechanistisch die Synthese ribosomaler Komponenten oder den Zusammenbau von Ribosomen unterstützen. Da Fehler in der Ribosomenproduktion mit vererbbaren Krankheiten und unter Umständen auch mit Krebsentstehung verknüpft sein kann, erhoffen wir uns langfristig auch neue therapeutische Zielmoleküle zu entdecken.

Direct link to Lay Summary Last update: 31.03.2016

Responsible applicant and co-applicants

Employees

Publications

Publication
Structural basis for the final steps of human 40S ribosome maturation
Ameismeier Michael, Zemp Ivo, van den Heuvel Jasmin, Thoms Matthias, Berninghausen Otto, Kutay Ulrike, Beckmann Roland (2020), Structural basis for the final steps of human 40S ribosome maturation, in Nature, 587(7835), 683-687.
USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit
Montellese Christian, van den Heuvel Jasmin, Ashiono Caroline, Dörner Kerstin, Melnik André, Jonas Stefanie, Zemp Ivo, Picotti Paola, Gillet Ludovic C, Kutay Ulrike (2020), USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit, in eLife, 9, 1-27.
Influenza virus uses transportin 1 for vRNP debundling during cell entry
Miyake Yasuyuki, Keusch Jeremy J., Decamps Laure, Ho-Xuan Hung, Iketani Sho, Gut Heinz, Kutay Ulrike, Helenius Ari, Yamauchi Yohei (2019), Influenza virus uses transportin 1 for vRNP debundling during cell entry, in Nature Microbiology, 4(4), 578-586.
Observing and tracking single small ribosomal subunits in vivo
Landvogt Lisa, Ruland Jan Andreas, Montellese Christian, Siebrasse Jan Peter, Kutay Ulrike, Kubitscheck Ulrich (2019), Observing and tracking single small ribosomal subunits in vivo, in Methods, 153, 63-70.
Human AATF/Che-1 forms a nucleolar protein complex with NGDN and NOL10 required for 40S ribosomal subunit synthesis.
Lukas Bammert, Stefanie Jonas, Rosemarie Ungricht, Ulrike Kutay, Lukas Bammert, Stefanie Jonas, Rosemarie Ungricht, Ulrike Kutay (2016), Human AATF/Che-1 forms a nucleolar protein complex with NGDN and NOL10 required for 40S ribosomal subunit synthesis., in Nucleic Acids Research, 44(20), 9803-9820.
Structure of a human pre-40S particle points to a role for RACK1 in the final steps of 18S rRNA processing.
Larburu Natacha, Montellese Christian, O'Donohue Marie-Françoise, Kutay Ulrike, Gleizes Pierre-Emmanuel, Plisson-Chastang Célia, Larburu Natacha, Montellese Christian, O'Donohue Marie-Françoise, Kutay Ulrike, Gleizes Pierre-Emmanuel, Plisson-Chastang Célia (2016), Structure of a human pre-40S particle points to a role for RACK1 in the final steps of 18S rRNA processing., in Nucleic acids research, 44(17), 8465-78.
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Collaboration

Group / person Country
Types of collaboration
Pierre-Emmanuel Gleizes, Celia Plisson-Chastang/CNRS Toulouse France (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Richard Pearson/Peter Mac CallumCancer Center, Melboure Australia (Oceania)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Sebastian Leidel, MPI Münster, Germany Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
Peter Horvath/Hungarian Academy of Science Szeged Hungary (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Exchange of personnel
Jens Pfannstiel/ University Hohenheim Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Paola Picotti/ Institute of Biochemistry, ETH Zurich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Austrian Swiss RNA Meeting Poster Processing of the Ubiquitin-like Ribosomal Fusion Protein FUBI-eS30 is Required for 40S Subunit Maturation in Human Cells 30.01.2019 Hof bei Salzburg, Austria Van den Heuvel Jasmin;
Austrian Swiss RNA Meeting Talk given at a conference Not everyone is treated equally – turnover of excess ribosomal proteins 30.01.2019 Hof bei Salzburg, Austria Zemp Ivo;
Swiss RNA Workshop 2019 Poster Processing of the Ubiquitin-like Ribosomal Fusion Protein FUBIeS30 is Required for 40S Subunit Maturation in Human Cells 25.01.2019 Bern, Switzerland Van den Heuvel Jasmin;
EMBO Meeting 'Endoplasmic reticulum function in health and disease' Talk given at a conference Breaking membrane-chromatin contacts in preparation of cells for mitosis 21.10.2018 Lucca, Italy Kutay Ulrike;
Horizons in Molecular Biology Symposium Talk given at a conference Taking apart the nuclear envelope during open mitosis 11.09.2018 Göttingen, Germany Kutay Ulrike;
Colloqium DKFZ-ZMBH Alliance Individual talk Taking apart the nuclear envelope during open mitosis 21.06.2018 ZMBH Heidelberg, Germany Kutay Ulrike;
RNA Society 23rd Annual Meeting Poster Processing of the Ubiquitin-like Ribosomal Fusion Protein FUBI-eS30 is Required for 40S Subunit Maturation in Human Cells 29.05.2018 Berkeley, United States of America Van den Heuvel Jasmin;
Monday Lecture Series Individual talk Taking apart the nuclear envelope during open mitosis 09.04.2018 Lisbon, Instituto de Medicina Molecular, Portugal Kutay Ulrike;
Life Science Seminar Series Individual talk Cellular Reorganization for Open Mitosis 13.02.2018 Geneva, Switzerland Kutay Ulrike;
ASCB EMBO Meeting Talk given at a conference Taking Apart the Nuclear Envelope during Open Mitosis 06.12.2017 Philadelphia, United States of America Kutay Ulrike;
EMBO Conference ‘Nuclear structure and dynamics’ Talk given at a conference Nuclear Dynamics 08.10.2017 L’Isle sur la Sorgue, France, France Kutay Ulrike;
Mechanisms of Nuclear Transport Talk given at a conference Taking apart the nuclear envelope during open mitosis 23.09.2017 Sant Feliu de Guixols, Spain Kutay Ulrike;
Biochemical Society Meeting Talk given at a conference Nuclear Pore Complex Disassembly during Open Mitosis 25.08.2017 Edinburgh, Great Britain and Northern Ireland Kutay Ulrike;
Gordon Research Conference Talk given at a conference Targeting of membrane proteins from the ER to the inner nuclear membrane 16.07.2017 Andover, United States of America Kutay Ulrike;
68. Mosbacher Kolloquium Talk given at a conference Taking apart the nuclear envelope during open mitosis 30.03.2017 Mosbach, Germany Kutay Ulrike;
Swiss RNA Workshop 2017 Poster Processing of the Ubiquitin-like Ribosomal Fusion Protein FUBI-eS30/FAU in Human Cells 27.01.2017 Bern, Switzerland Van den Heuvel Jasmin;


Knowledge transfer events

Active participation

Title Type of contribution Date Place Persons involved
Studienwochen für Gymnasiastinnen und Gymnasiasten Performances, exhibitions (e.g. for education institutions) 05.06.2017 ETH Zürich, Switzerland Zemp Ivo;
Studienwochen für Gymnasiastinnen und Gymnasiasten Performances, exhibitions (e.g. for education institutions) 06.06.2016 ETH Zürich, Switzerland Zemp Ivo;


Associated projects

Number Title Start Funding scheme
141735 NCCR RNA & disease: Understanding the role of RNA biology in disease mechanisms (phase I) 01.05.2014 National Centres of Competence in Research (NCCRs)
170810 A single molecule imaging system for super-resolution and tracking experiments 01.10.2017 R'EQUIP
144221 Ribosome synthesis in mammalian cells 01.10.2012 Project funding

Abstract

The coding information contained in messenger RNAs is translated into proteins by sophisticated ribonucleoprotein particles called ribosomes in all living cells. Ribosomes are composed of two subunits of distinct structure, size, composition and function. The human 80S ribosome, built by the small 40S and the large 60S subunit, is altogether 4.3 MDa in size and composed of 4 ribosomal RNAs (rRNAs) and about 80 ribosomal proteins (RPs). To be functional in protein translation, the ribosomal subunits must be correctly assembled, following a well-ordered pathway during which a long precursor rRNA (pre-rRNA) is processed, modified and folded and the RPs are placed at their designated positions. The synthesis of ribosomal subunits in eukaryotes proceeds along a complex assembly line starting with pre-rRNA synthesis in nucleoli, followed by many intermediate nuclear steps up to their final maturation in the cytoplasm. Proteomic approaches and genetic screens in yeast drove the identification of more than 250 trans-acting factors that assist ribosomal subunit production. These factors associate with pre-ribosomal particles either transiently or as structural components of precursor particles, and are continuously recycled to assist consecutive rounds of ribosome assembly. Although the basic aspects of ribosome biogenesis are conserved between yeast and man, our knowledge on the even more complex process of human ribosome biogenesis is far less complete. This increased complexity not only arises from the larger size of mammalian ribosomes and the more intricate pre-rRNA processing pathway, but also from the highly multifaceted regulatory networks and surveillance pathways linked to ribosome production in vertebrate cells. Since deregulation of ribosome biogenesis manifests in a variety of genetically inherited ribosomopathies and is associated with tumorigenesis, there is great demand to obtain a comprehensive understanding of the process in human cells. As defects in ribosome synthesis activate the p53 stress response pathway leading to cell cycle arrest and apoptosis, factors involved in the making of ribosomes have emerged as attractive targets for cancer therapy.In this grant application, we propose to address some key, unresolved questions related to ribosome biogenesis. As a broad approach, we will further pursue imaging-based RNA interference screening campaigns to comprehensively identify factors involved in human ribosome synthesis. Here, we will give focus on the completion of a genome-wide RNAi screen on 60S subunit synthesis. In parallel, we will exploit data derived from a completed screen on 40S subunit synthesis to specifically address the function of a newly identified protein complex in early steps of pre-rRNA processing, and its role in governing p53 activation. Further, by exploiting the screening data, we will study the recycling of trans-acting factors as well as the role of selected factors in ribosome synthesis. Collectively, this research will not only provide a comprehensive analysis of the machinery involved in human ribosome synthesis, but will also advance the mechanistic understanding of key processes in the making of a fundamental macromolecular complex.
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