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Analysis of eukaryotic ribosome biogenesis in the model system Saccharomyces cerevisiae

English title Analysis of eukaryotic ribosome biogenesis in the model system Saccharomyces cerevisiae
Applicant Kressler Dieter
Number 175547
Funding scheme Project funding (Div. I-III)
Research institution Département de Biologie Faculté des Sciences Université de Fribourg
Institution of higher education University of Fribourg - FR
Main discipline Biochemistry
Start/End 01.10.2017 - 31.12.2021
Approved amount 700'000.00
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All Disciplines (4)

Discipline
Biochemistry
Genetics
Molecular Biology
Cellular Biology, Cytology

Keywords (6)

Ribosome biogenesis; co-translational regulation; Saccharomyces cerevisiae; yeast genetics; chaperones; ribosomal proteins

Lay Summary (German)

Lead
Die Herstellung von Ribosomen ist ein fundamentaler Prozess, welcher den Zellen die molekularen Maschinen der Proteinsynthese zur Verfügung stellt. Der Zusammenbau der Ribosomen wird mit Hilfe einer Vielzahl (= 200) sogenannter Biogenese-Faktoren bewerkstelligt. Unter anderem werden diese Biogenese-Faktoren dazu benötigt, die reifenden Prä-Ribosomen vom Ort ihrer Entstehung (Nukleolus) bis zum Ort der Proteinsynthese (Zytoplasma) zu begleiten und sie dabei in ihre aktive Struktur zu formen.
Lay summary
Inhalt und Ziel des Forschungsprojekts
Bedingt durch die enorme Komplexität des Prozesses, studiert meine Arbeitsgruppe selektive Aspekte der eukaryotischen Ribosomenbiogenese im Modellorganismus Saccharomyces cerevisiae (Bierhefe). Im Speziellen untersuchen wir (i) die frühen Reifungsschritte von prä-60S Ribosomen und (ii) wie spezifische 'Chaperon' Proteine einzelne ribosomale Protein schützen und zu ihrem Assemblierungsort auf den Prä-Ribosomen begleiten. Zudem möchten wir verstehen (iii) wie die Expression gewisser ribosomaler Proteine während der Translation reguliert wird. Um unsere Forschungsziele zu erreichen, verwenden wir eine Vielfalt an biochemischen, zellbiologischen und hefe-genetischen Methoden.

Wissenschaftlicher und gesellschaftlicher Kontext des Forschungsprojekts
Bei unserer Arbeit handelt es sich um reine Grundlagenforschung. Die gewonnenen Erkenntnisse tragen möglicherweise zum Verständnis und, zu einem späteren Zeitpunkt, eventuell zur Behandlung von Ribosomopathien, das heisst mit Ribosomendefekten assoziierte Krankheiten (wie zum Beispiel die Diamond-Blackfan Anämie), bei. Die Ergebnisse unserer Forschungsarbeiten werden, nach Evaluation durch anerkannte Experten, in internationalen Fachjournalen veröffentlicht und dadurch anderen Wissenschaftlern und der Allgemeinheit zugänglich gemacht.
Direct link to Lay Summary Last update: 30.09.2017

Responsible applicant and co-applicants

Employees

Project partner

Publications

Publication
Conformational proofreading of distant 40S ribosomal subunit maturation events by a long-range communication mechanism
Mitterer Valentin, Shayan Ramtin, Ferreira-Cerca Sébastien, Murat Guillaume, Enne Tanja, Rinaldi Dana, Weigl Sarah, Omanic Hajrija, Gleizes Pierre-Emmanuel, Kressler Dieter, Plisson-Chastang Celia, Pertschy Brigitte (2019), Conformational proofreading of distant 40S ribosomal subunit maturation events by a long-range communication mechanism, in Nature Communications, 10(1), 2754-2754.
Ubiquitin release from eL 40 is required for cytoplasmic maturation and function of 60S ribosomal subunits in Saccharomyces cerevisiae
Martín‐Villanueva Sara, Fernández‐Pevida Antonio, Fernández‐Fernández José, Kressler Dieter, de la Cruz Jesús (2019), Ubiquitin release from eL 40 is required for cytoplasmic maturation and function of 60S ribosomal subunits in Saccharomyces cerevisiae, in The FEBS Journal, 287(2), 345-360.
The Ubiquitin Moiety of Ubi1 Is Required for Productive Expression of Ribosomal Protein eL40 in Saccharomyces cerevisiae
Martín-Villanueva Sara, Fernández-Pevida Antonio, Kressler Dieter, de la Cruz Jesús (2019), The Ubiquitin Moiety of Ubi1 Is Required for Productive Expression of Ribosomal Protein eL40 in Saccharomyces cerevisiae, in Cells, 8(8), 850-850.
Tsr4 and Nap1, two novel members of the ribosomal protein chaperOME
Rössler Ingrid, Embacher Julia, Pillet Benjamin, Murat Guillaume, Liesinger Laura, Hafner Jutta, Unterluggauer Julia Judith, Birner-Gruenberger Ruth, Kressler Dieter, Pertschy Brigitte (2019), Tsr4 and Nap1, two novel members of the ribosomal protein chaperOME, in Nucleic Acids Research, 47(13), 6984-7002.
Suppressor mutations in Rpf2–Rrs1 or Rpl5 bypass the Cgr1 function for pre-ribosomal 5S RNP-rotation
Thoms Matthias, Mitterer Valentin, Kater Lukas, Falquet Laurent, Beckmann Roland, Kressler Dieter, Hurt Ed (2018), Suppressor mutations in Rpf2–Rrs1 or Rpl5 bypass the Cgr1 function for pre-ribosomal 5S RNP-rotation, in Nature Communications, 9(1), 4094-4094.

Collaboration

Group / person Country
Types of collaboration
Jesús de la Cruz / University of Sevilla Spain (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Brigitte Pertschy / University of Graz Austria (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Ribosome 2019 Poster Functional characterization of a new Prp43-binding protein containing a G-patch domain 06.01.2019 Mérida, Mexico Méndez-Godoy Alfonso;
11th International Conference on Ribosome Synthesis Poster Towards the identification of novel dedicated chaperones of ribosomal proteins 01.08.2018 Orford, Québec, Canada Kressler Dieter; Pillet Benjamin;


Associated projects

Number Title Start Funding scheme
156764 Analysis of eukaryotic ribosome biogenesis in the model system Saccharomyces cerevisiae 01.10.2014 Project funding (Div. I-III)
101445 Analysis of the functional environment and the mechanism of action of the putative AAA-type ATPase Rix7p during ribosome biogenesis in Saccharomyces cerevisiae 01.06.2004 Fellowships for advanced researchers
146344 Analysis of eukaryotic ribosome biogenesis in the model system Saccharomyces cerevisiae 01.10.2013 SNSF Professorships
204801 Role of dedicated chaperones of ribosomal proteins in eukaryotic ribosome biogenesis 01.01.2022 Project funding (Div. I-III)
123341 Analysis of eukaryotic ribosome biogenesis in the model system Saccharomyces cerevisiae 01.10.2009 SNSF Professorships
156764 Analysis of eukaryotic ribosome biogenesis in the model system Saccharomyces cerevisiae 01.10.2014 Project funding (Div. I-III)

Abstract

The process of ribosome biogenesis is evolutionarily conserved among eukaryotes and constitutes a main cellular activity. Most of our current knowledge about this complicated process comes from studies with the yeast Saccharomyces cerevisiae. Research over the last 30 years has revealed that numerous biogenesis factors (>200), including many energy-consuming enzymes and quality-controlling checkpoint factors, are required for the accurate and efficient maturation of pre-ribosomal particles as they travel from the nucleolus to the cytoplasm. Fueled by recent advances in cryo-electron microscopy, a structural view of ribosome assembly has begun to emerge with the first, near-atomic snapshots of different assembly intermediates. Moreover, we have only recently learnt that dedicated chaperones, which in many cases already capture their client in a co-translational manner, selectively protect and facilitate the assembly of individual ribosomal proteins (r-proteins). Despite the enormous progress in understanding how this gigantic molecular jigsaw puzzle is put together, the precise role of a large number of biogenesis factors and the molecular mechanisms driving ribosome assembly have remained in many instances largely elusive.The aim of this proposal is to provide molecular insight into selected aspects of eukaryotic ribosome biogenesis. To this end, we combine unique and extremely powerful yeast genetic approaches with biochemical, cell biological, and, in the framework of collaborations, structural methods.Specifically, I propose the following projects:1) Investigation of early pre-60S maturation eventsThe early steps of pre-60S maturation, partly owing to the lack of structural information, are still poorly understood. We have previously shown that the AAA-type ATPase Rix7 is required for the release of Nsa1 from a nucleolar pre-60S particle. By performing an ‘in vivo structure probing’ approach, based on the isolation of suppressor mutations that bypass the requirement for the essential Nsa1, we have identified several early-acting pre-60S biogenesis factors. Here, we propose to decipher their functional and physical interaction network and to unveil the assembly alterations that compensate for the lack of Nsa1 recruitment in order to illuminate the early phase of pre-60S formation and maturation.2) Identification and characterization of novel dedicated chaperones of r-proteinsSo far only eight of the 79 r-proteins have been shown to be associated with dedicated chaperones. Anticipating a more widespread requirement for dedicated chaperones, we propose to identify novel dedicated chaperones and to subsequently define their relevance for the life cycle of their r-protein client. By determining the co-translational capturing potential and the structural basis of the interaction, we expect to obtain insight into the timing and mode of r-protein recognition as well as the mechanism of r-protein assembly into pre-ribosomes.3) Co-translational regulation of Rpl4 expressionWe have previously shown that Acl4 is a dedicated chaperone of Rpl4. Our analysis of ?acl4 suppressors revealed an unexpected connection between the ribosome-associated chaperone NAC and the Ccr4/Not complex for the regulation of Rpl4 expression. With this project, we aim to provide detailed insight into this co-translational control mechanism by investigating how the regulatory module is recruited to the RPL4 mRNA and how it affects its translation and degradation. Moreover, we will determine the subset of mRNAs that are regulated by this quality control mechanism.
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