Dieter Kressler
dieter.kressler@unifr.ch
+41 26 300 8645
https://orcid.org/0000-0003-4855-3563
PhD, group leader, head of proteomics platform
Senior Researcher
Department of Biology
PER 05 bu. 0.316d
Ch. du Musée 10
1700 Fribourg
Ch. du Musée 10
1700 Fribourg
PER 05, 0.316d
Research and publications
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Publications
60 publications
The Beak of Eukaryotic Ribosomes: Life, Work and Miracles
Biomolecules (2024) | Journal articlePolar confinement of a macromolecular machine by an SRP-type GTPase
Nature Communications (2024) | Journal article -
Research projects
Role of dedicated chaperones of ribosomal proteins in eukaryotic ribosome biogenesis
Status: OngoingStart 01.01.2022 End 31.12.2025 Funding SNSF Open project sheet Our current knowledge about the highly conserved process of eukaryotic ribosome assembly is mainly derived from studies with the yeast Saccharomyces cerevisiae. In a simplistic view, the making of ribosomes consists in the accurate piecing together of the four ribosomal RNAs and the 79 ribosomal proteins (r-proteins); however, this process has turned out to be of outstanding complexity. Research over the last 30 years has identified a myriad of biogenesis factors (>200) that are specifically associated with distinct pre-ribosomal particles in order to permit their unidirectional and efficient shaping, as they travel from the nucleolus to the cytoplasm, into mature ribosomal subunits. Only recently, the field has entered a new era as groundbreaking advances in cryo-electron microscopy have enabled the visualization of different assembly stages at high resolution. However, less is known about how the r-protein building blocks are synthesized in sufficient, assembly-competent amounts to sustain the high rate of ribosome assembly. Recent research from my laboratory has significantly contributed to the identification of selective binding partners of r-proteins, referred to as dedicated chaperones, which enable their safe transfer to the pre-ribosomal assembly site. The aim of this proposal is to provide molecular insight into the precise functional roles of dedicated chaperones in supplying assembly-competent r-proteins. To this end, we combine powerful yeast genetic approaches with biochemical, cell biological, and, in the framework of collaborations, structural methods. Specifically, I propose the following projects: 1) Identification and functional characterization of novel dedicated chaperones of r-proteins Up to now, an association with a bona fide dedicated chaperone could be revealed for only nine of the 79 r-proteins. In line with a more widespread requirement for dedicated chaperones, we have already been able to identify binding partners of additional r-proteins. While the previously uncharacterized Ylr287c likely serves as a dedicated chaperone of Rpp0, the related histone chaperones Nap1 and Vps75 interact with either Rpl24 or its ribosomal-like counterpart Rlp24. Since it is our aim to obtain a comprehensive inventory of the transient interaction partners of all r-proteins, we have also started to implement a promising proximity-labeling approach, which has already enabled the identification of a validated candidate dedicated chaperone for Rpl1. Here, we propose to continue with the biochemical identification of novel dedicated chaperones and, in parallel, proceed with the functional characterization of the already identified binding partners in order to define their relevance for the life cycle of their r-protein client. Moreover, we aim to unveil the molecular details of the binary interactions, which is expected to provide mechanistic insight into how r-proteins get incorporated into pre-ribosomal particles. 2) Relevance and mechanistic dissection of co-translational regulation of Rpl3 and Rpl4 expression Our recent work has unveiled the existence of a novel mechanism enabling the tight co-translational regulation of Rpl3 and Rpl4 de novo synthesis. According to our current model, the identified regulatory machinery competes with Rrb1 or Acl4 for binding to nascent Rpl3 or Rpl4, respectively, and, if these are not captured in a timely manner by their dedicated chaperone, negatively regulates the levels of the encoding mRNA. Coupling regulation to the availability of the dedicated chaperone represents an elegant mechanism to adjust the expression levels of the two r-proteins to their actual consumption during ribosome assembly. However, several aspects remain to be explored in order to obtain a complete mechanistic understanding of the regulatory process and its physiological relevance. Therefore, the proposed research is aimed at revealing: 1) the importance of this regulation for proteostasis maintenance, 2) the elusive component mediating mRNA degradation, and 3) the order of events and the mechanism of substrate recognition. Analysis of eukaryotic ribosome biogenesis in the model system Saccharomyces cerevisiae
Status: CompletedStart 01.10.2017 End 31.12.2021 Funding SNSF Open project sheet 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 events The 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-proteins So 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 expression We 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. Analysis of eukaryotic ribosome biogenesis in the model system Saccharomyces cerevisiae
Status: CompletedStart 01.10.2014 End 30.09.2017 Funding SNSF Open project sheet The process of ribosome biogenesis is evolutionarily conserved among eukaryotes and it constitutes a main cellular activity. Most of our current knowledge concerning this highly dynamic multi-step process comes from studies with the yeast Saccharomyces cerevisiae. The combined use of proteomic, genetic, and cell biological methods has revealed that a multitude of protein trans-acting factors (>200) are required for the assembly and maturation of pre-ribosomal particles as they travel from the nucleolus to the cytoplasm. Amongst these are, in agreement with the dynamic nature of the process, energy-consuming enzymes such as AAA-type ATPases, ATP-dependent RNA helicases and GTPases. This suggests that the energy derived from nucleotide hydrolysis confers directionality to ribosome assembly and that such a large number of trans-acting factors is required to ensure accurate and efficient synthesis of ribosomal subunits. However, the molecular mechanisms driving ribosome assembly remain largely elusive. Current challenges in the field consist in the identification of the specific substrates of energy-consuming enzymes and in the understanding of their mechanism and timing of action. In order to understand the process at a molecular level, it will be necessary to gain structural insight into the trans-acting factors and the pre-ribosomal particles that they are associated with and acting on. Finally, we will have to understand how ribosomal proteins contribute to ribosome biogenesis and how ribosomal proteins and trans-acting factors get from their site of cytoplasmic synthesis to their mostly nucle(ol)ar assembly site. The aim of this proposal is to provide molecular insight into selected aspects of eukaryotic ribosome biogenesis. To this end, we will use S. cerevisiae as a model system, which is especially amenable to the application of a wide variety of biochemical, cell biological and unique genetic methods. Specifically, I propose the following projects: 1) Analysis of the Nsa1/pre-ribosome interaction We have previously shown that the AAA-type ATPase Rix7 is required for the release of Nsa1 from pre-60S ribosomal particles, thereby triggering the progression of 60S biogenesis. Here, we will exploit the recently solved Nsa1 crystal structure in order to identify by mutational analysis the Nsa1 surface that mediates binding to the pre-60S ribosome. In a complementary approach, we will determine by electron microscopy the binding site of Nsa1 on pre-60S ribosomes. 2) Investigation of assembly alterations that bypass the requirement for pre-60S association of Nsa1 Our recent studies revealed that the requirement for pre-60S association of the essential Nsa1 is bypassed by reduced functionality of several 60S biogenesis factors (Ebp2, Mak5, Nop1, and Nop4). In order to obtain a comprehensive inventory of assembly alterations that render Nsa1 binding dispensable, we will further exploit this ’in vivo structure probing’ approach by isolating and characterizing novel ?nsa1 suppressors. Alterations of local (pre-)rRNP structures within these pre-60S particles will then be experimentally determined by chemical probing. 3) Identification of additional nuclear and/or pre-60S substrates of the AAA-type ATPase Rix7 Our observation that dominant-negative alleles of RIX7 retain their phenotype in the absence of Nsa1 strongly suggests that Rix7 may have additional nuclear substrates besides Nsa1. Moreover, over-expression of wild-type Rix7 has a negative effect on growth of mak5 and ebp2 mutant cells, both in the absence and presence of Nsa1, indicating that Rix7 may act on structurally defective pre-60S subunits and subject these to degradation. To further explore these exciting possibilities, the power of yeast genetics will be exploited to identify additional nuclear substrates of Rix7 and to unveil how Rix7 recognizes structurally defective pre-60S subunits. 4) Co-translational recruitment of ‘chaperones’ to nascent ribosomal proteins Recent evidence suggests that certain ribosomal proteins require distinct ‘chaperone’ proteins in order to be stably expressed and delivered to their site of assembly. We have already revealed for a set of four ribosomal proteins (Rps3, Rpl3, Rpl5, and Rpl10) that the ‘chaperone’ partners (Yar1, Rrb1, Syo1, and Sqt1) recognize their very N-terminal residues, notably implicated in rRNA binding. Therefore, we aim to demonstrate that these ‘chaperones’ are recruited to nascent ribosomal proteins, thus establishing a novel step of ribosome assembly, commencing with the recognition of ribosomal proteins during translation. We will complement this study by structural and functional analyses of the ‘chaperone’/ribosomal protein interactions. 5) Functional role of ubiquitin in the ubiquitin-fusion protein Rpl40 This project should elucidate the effects on 60S subunit maturation due to impaired cleavage or the absence of the ubiquitin moiety from the natural ubiquitin-Rpl40 fusion protein Ubi1. Specifically, we aim to understand whether the ubiquitin moiety of Ubi1 serves principally as a cis-acting ‘chaperone’ for Rpl40 or whether it may fulfil additional roles during cytoplasmic pre-60S maturation events. Analysis of eukaryotic ribosome biogenesis in the model system Saccharomyces cerevisiae
Status: CompletedAnalysis of eukaryotic ribosome biogenesis in the model system Saccharomyces cerevisiae
Status: Completed