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Wettstein R, Hugener J, Gillet L, Hernández-Armenta Y, Henggeler A, Xu J, van Gerwen J, Wollweber F, Arter M, Aebersold R, Beltrao P, Pilhofer M, Matos J. Waves of regulated protein expression and phosphorylation rewire the proteome to drive gametogenesis in budding yeast. Dev Cell 2024; 59:1764-1782.e8. [PMID: 38906138 DOI: 10.1016/j.devcel.2024.05.025] [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: 09/24/2023] [Revised: 02/25/2024] [Accepted: 05/20/2024] [Indexed: 06/23/2024]
Abstract
Sexually reproducing eukaryotes employ a developmentally regulated cell division program-meiosis-to generate haploid gametes from diploid germ cells. To understand how gametes arise, we generated a proteomic census encompassing the entire meiotic program of budding yeast. We found that concerted waves of protein expression and phosphorylation modify nearly all cellular pathways to support meiotic entry, meiotic progression, and gamete morphogenesis. Leveraging this comprehensive resource, we pinpointed dynamic changes in mitochondrial components and showed that phosphorylation of the FoF1-ATP synthase complex is required for efficient gametogenesis. Furthermore, using cryoET as an orthogonal approach to visualize mitochondria, we uncovered highly ordered filament arrays of Ald4ALDH2, a conserved aldehyde dehydrogenase that is highly expressed and phosphorylated during meiosis. Notably, phosphorylation-resistant mutants failed to accumulate filaments, suggesting that phosphorylation regulates context-specific Ald4ALDH2 polymerization. Overall, this proteomic census constitutes a broad resource to guide the exploration of the unique sequence of events underpinning gametogenesis.
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Affiliation(s)
- Rahel Wettstein
- Max Perutz Laboratories, University of Vienna, 1030 Vienna, Austria; Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Jannik Hugener
- Max Perutz Laboratories, University of Vienna, 1030 Vienna, Austria; Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland; Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Ludovic Gillet
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Yi Hernández-Armenta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Adrian Henggeler
- Max Perutz Laboratories, University of Vienna, 1030 Vienna, Austria; Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Jingwei Xu
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Julian van Gerwen
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Florian Wollweber
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Meret Arter
- Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Pedro Beltrao
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK.
| | - Martin Pilhofer
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.
| | - Joao Matos
- Max Perutz Laboratories, University of Vienna, 1030 Vienna, Austria; Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland.
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2
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LaPeruta AJ, Hedayati S, Micic J, Fitzgerald F, Kim D, Oualline G, Woolford JL. Yeast ribosome biogenesis factors Puf6 and Nog2 and ribosomal proteins uL2 and eL43 act in concert to facilitate the release of nascent large ribosomal subunits from the nucleolus. Nucleic Acids Res 2023; 51:11277-11290. [PMID: 37811893 PMCID: PMC10639061 DOI: 10.1093/nar/gkad794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 09/11/2023] [Accepted: 09/22/2023] [Indexed: 10/10/2023] Open
Abstract
Large ribosomal subunit precursors (pre-LSUs) are primarily synthesized in the nucleolus. At an undetermined step in their assembly, they are released into the nucleoplasm. Structural models of yeast pre-LSUs at various stages of assembly have been collected using cryo-EM. However, which cryo-EM model is closest to the final nucleolar intermediate of the LSU has yet to be determined. To elucidate the mechanisms of the release of pre-LSUs from the nucleolus, we assayed effects of depleting or knocking out two yeast ribosome biogenesis factors (RiBi factors), Puf6 and Nog2, and two ribosomal proteins, uL2 and eL43. These proteins function during or stabilize onto pre-LSUs between the late nucleolar stages to early nucleoplasmic stages of ribosome biogenesis. By characterizing the phenotype of these four mutants, we determined that a particle that is intermediate between the cryo-EM model State NE1 and State NE2 likely represents the final nucleolar assembly intermediate of the LSU. We conclude that the release of the RiBi factors Nip7, Nop2 and Spb1 and the subsequent stabilization of rRNA domains IV and V may be key triggers for the release of pre-LSUs from the nucleolus.
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Affiliation(s)
- Amber J LaPeruta
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Stefanie Hedayati
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jelena Micic
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Fiona Fitzgerald
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - David Kim
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Grace Oualline
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - John L Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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3
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Lau B, Huang Z, Kellner N, Niu S, Berninghausen O, Beckmann R, Hurt E, Cheng J. Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis. EMBO Rep 2023; 24:e56910. [PMID: 37129998 PMCID: PMC10328080 DOI: 10.15252/embr.202356910] [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: 01/30/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023] Open
Abstract
Ribosome biogenesis proceeds along a multifaceted pathway from the nucleolus to the cytoplasm that is extensively coupled to several quality control mechanisms. However, the mode by which 5S ribosomal RNA is incorporated into the developing pre-60S ribosome, which in humans links ribosome biogenesis to cell proliferation by surveillance by factors such as p53-MDM2, is poorly understood. Here, we report nine nucleolar pre-60S cryo-EM structures from Chaetomium thermophilum, one of which clarifies the mechanism of 5S RNP incorporation into the early pre-60S. Successive assembly states then represent how helicases Dbp10 and Spb4, and the Pumilio domain factor Puf6 act in series to surveil the gradual folding of the nearby 25S rRNA domain IV. Finally, the methyltransferase Spb1 methylates a universally conserved guanine nucleotide in the A-loop of the peptidyl transferase center, thereby licensing further maturation. Our findings provide insight into the hierarchical action of helicases in safeguarding rRNA tertiary structure folding and coupling to surveillance mechanisms that culminate in local RNA modification.
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Affiliation(s)
- Benjamin Lau
- Heidelberg University Biochemistry Center (BZH)HeidelbergGermany
| | - Zixuan Huang
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co‐laboratory of Medical Epigenetics and MetabolismFudan UniversityShanghaiChina
| | - Nikola Kellner
- Heidelberg University Biochemistry Center (BZH)HeidelbergGermany
| | | | | | - Roland Beckmann
- Gene CenterLudwig‐Maximilians‐Universität MünchenMunichGermany
| | - Ed Hurt
- Heidelberg University Biochemistry Center (BZH)HeidelbergGermany
| | - Jingdong Cheng
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co‐laboratory of Medical Epigenetics and MetabolismFudan UniversityShanghaiChina
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4
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Dörner K, Ruggeri C, Zemp I, Kutay U. Ribosome biogenesis factors-from names to functions. EMBO J 2023; 42:e112699. [PMID: 36762427 PMCID: PMC10068337 DOI: 10.15252/embj.2022112699] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/13/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
The assembly of ribosomal subunits is a highly orchestrated process that involves a huge cohort of accessory factors. Most eukaryotic ribosome biogenesis factors were first identified by genetic screens and proteomic approaches of pre-ribosomal particles in Saccharomyces cerevisiae. Later, research on human ribosome synthesis not only demonstrated that the requirement for many of these factors is conserved in evolution, but also revealed the involvement of additional players, reflecting a more complex assembly pathway in mammalian cells. Yet, it remained a challenge for the field to assign a function to many of the identified factors and to reveal their molecular mode of action. Over the past decade, structural, biochemical, and cellular studies have largely filled this gap in knowledge and led to a detailed understanding of the molecular role that many of the players have during the stepwise process of ribosome maturation. Such detailed knowledge of the function of ribosome biogenesis factors will be key to further understand and better treat diseases linked to disturbed ribosome assembly, including ribosomopathies, as well as different types of cancer.
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Affiliation(s)
- Kerstin Dörner
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,Molecular Life Sciences Ph.D. Program, Zurich, Switzerland
| | - Chiara Ruggeri
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,RNA Biology Ph.D. Program, Zurich, Switzerland
| | - Ivo Zemp
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Ulrike Kutay
- Department of Biology, Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
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5
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King GA, Wettstein R, Varberg JM, Chetlapalli K, Walsh ME, Gillet LC, Hernández-Armenta C, Beltrao P, Aebersold R, Jaspersen SL, Matos J, Ünal E. Meiotic nuclear pore complex remodeling provides key insights into nuclear basket organization. J Cell Biol 2023; 222:e202204039. [PMID: 36515990 PMCID: PMC9754704 DOI: 10.1083/jcb.202204039] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 09/12/2022] [Accepted: 11/05/2022] [Indexed: 12/15/2022] Open
Abstract
Nuclear pore complexes (NPCs) are large proteinaceous assemblies that mediate nuclear compartmentalization. NPCs undergo large-scale structural rearrangements during mitosis in metazoans and some fungi. However, our understanding of NPC remodeling beyond mitosis remains limited. Using time-lapse fluorescence microscopy, we discovered that NPCs undergo two mechanistically separable remodeling events during budding yeast meiosis in which parts or all of the nuclear basket transiently dissociate from the NPC core during meiosis I and II, respectively. Meiosis I detachment, observed for Nup60 and Nup2, is driven by Polo kinase-mediated phosphorylation of Nup60 at its interface with the Y-complex. Subsequent reattachment of Nup60-Nup2 to the NPC core is facilitated by a lipid-binding amphipathic helix in Nup60. Preventing Nup60-Nup2 reattachment causes misorganization of the entire nuclear basket in gametes. Strikingly, meiotic nuclear basket remodeling also occurs in the distantly related fission yeast, Schizosaccharomyces pombe. Our study reveals a conserved and developmentally programmed aspect of NPC plasticity, providing key mechanistic insights into the nuclear basket organization.
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Affiliation(s)
- Grant A. King
- Department of Molecular and Cell Biology, University of California, Berkeley, CA
| | - Rahel Wettstein
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
- Max Perutz Labs, University of Vienna, Vienna, Austria
| | | | | | - Madison E. Walsh
- Department of Molecular and Cell Biology, University of California, Berkeley, CA
| | - Ludovic C.J. Gillet
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Claudia Hernández-Armenta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Pedro Beltrao
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Sue L. Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS
| | - Joao Matos
- Institute of Biochemistry, ETH Zürich, Zürich, Switzerland
- Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California, Berkeley, CA
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6
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Rössler I, Weigl S, Fernández-Fernández J, Martín-Villanueva S, Strauss D, Hurt E, de la Cruz J, Pertschy B. The C-terminal tail of ribosomal protein Rps15 is engaged in cytoplasmic pre-40S maturation. RNA Biol 2021; 19:560-574. [PMID: 35438042 PMCID: PMC9037480 DOI: 10.1080/15476286.2022.2064073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 04/04/2022] [Indexed: 11/22/2022] Open
Abstract
The small ribosomal subunit protein Rps15/uS19 is involved in early nucleolar ribosome biogenesis and subsequent nuclear export of pre-40S particles to the cytoplasm. In addition, the C-terminal tail of Rps15 was suggested to play a role in mature ribosomes, namely during translation elongation. Here, we show that Rps15 not only functions in nucleolar ribosome assembly but also in cytoplasmic pre-40S maturation, which is indicated by a strong genetic interaction between Rps15 and the 40S assembly factor Ltv1. Specifically, mutations either in the globular or C-terminal domain of Rps15 when combined with the non-essential ltv1 null allele are lethal or display a strong growth defect. However, not only rps15 ltv1 double mutants but also single rps15 C-terminal deletion mutants exhibit an accumulation of the 20S pre-rRNA in the cytoplasm, indicative of a cytoplasmic pre-40S maturation defect. Since in pre-40S particles, the C-terminal tail of Rps15 is positioned between assembly factors Rio2 and Tsr1, we further tested whether Tsr1 is genetically linked to Rps15, which indeed could be demonstrated. Thus, the integrity of the Rps15 C-terminal tail plays an important role during late pre-40S maturation, perhaps in a quality control step to ensure that only 40S ribosomal subunits with functional Rps15 C-terminal tail can efficiently enter translation. As mutations in the C-terminal tail of human RPS15 have been observed in connection with chronic lymphocytic leukaemia, it is possible that apart from defects in translation, an impaired late pre-40S maturation step in the cytoplasm could also be a reason for this disease.
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Affiliation(s)
- Ingrid Rössler
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Sarah Weigl
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - José Fernández-Fernández
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Sara Martín-Villanueva
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Daniela Strauss
- Biochemistry Center BZH, Heidelberg University, Heidelberg, Germany
| | - Ed Hurt
- Biochemistry Center BZH, Heidelberg University, Heidelberg, Germany
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Brigitte Pertschy
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
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