1
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Anastas V, Chavdoula E, La Ferlita A, Soysal B, Cosentini I, Nigita G, Kearse MG, Tsichlis PN. KDM2B is required for ribosome biogenesis and its depletion unequally affects mRNA translation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595403. [PMID: 38826406 PMCID: PMC11142201 DOI: 10.1101/2024.05.22.595403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
KDM2B is a JmjC domain lysine demethylase, which promotes cell immortalization, stem cell self-renewal and tumorigenesis. Here we employed a multi-omics strategy to address its role in ribosome biogenesis and mRNA translation. These processes are required to sustain cell proliferation, an important cancer hallmark. Contrary to earlier observations, KDM2B promotes ribosome biogenesis by stimulating the transcription of genes encoding ribosome biogenesis factors and ribosomal proteins, particularly those involved in the biogenesis of the 40S ribosomal subunits. Knockdown of KDM2B impaired the assembly of the small and large subunit processomes, as evidenced by specific defects in pre-ribosomal RNA processing. The final outcome was a decrease in the rate of ribosome assembly and in the abundance of ribosomes, and inhibition of mRNA translation. The inhibition of translation was distributed unequally among mRNAs with different features, suggesting that mRNA-embedded properties influence how mRNAs interpret ribosome abundance. This study identified a novel mechanism contributing to the regulation of translation and provided evidence for a rich biology elicited by a pathway that depends on KDM2B, and perhaps other regulators of translation.
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Affiliation(s)
- Vollter Anastas
- Tufts Graduate School of Biomedical Sciences, Program in Genetics, Boston, MA, United States
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
| | - Evangelia Chavdoula
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
| | - Alessandro La Ferlita
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
| | - Burak Soysal
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
| | - Ilaria Cosentini
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
- Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy (CNR), Palermo, Italy
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
| | - Michael G Kearse
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Philip N Tsichlis
- Tufts Graduate School of Biomedical Sciences, Program in Genetics, Boston, MA, United States
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, United States
- The Ohio State University, Comprehensive Cancer Center, Columbus, OH, United States
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2
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Remines M, Schoonover MG, Knox Z, Kenwright K, Hoffert KM, Coric A, Mead J, Ampfer J, Seye S, Strome ED. Profiling the compendium of changes in Saccharomyces cerevisiae due to mutations that alter availability of the main methyl donor S-Adenosylmethionine. G3 (BETHESDA, MD.) 2024; 14:jkae002. [PMID: 38184845 PMCID: PMC10989883 DOI: 10.1093/g3journal/jkae002] [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: 11/17/2023] [Revised: 11/17/2023] [Accepted: 12/16/2023] [Indexed: 01/09/2024]
Abstract
The SAM1 and SAM2 genes encode for S-Adenosylmethionine (AdoMet) synthetase enzymes, with AdoMet serving as the main cellular methyl donor. We have previously shown that independent deletion of these genes alters chromosome stability and AdoMet concentrations in opposite ways in Saccharomyces cerevisiae. To characterize other changes occurring in these mutants, we grew wildtype, sam1Δ/sam1Δ, and sam2Δ/sam2Δ strains in 15 different Phenotypic Microarray plates with different components and measured growth variations. RNA-Sequencing was also carried out on these strains and differential gene expression determined for each mutant. We explored how the phenotypic growth differences are linked to the altered gene expression, and hypothesize mechanisms by which loss of the SAM genes and subsequent AdoMet level changes, impact pathways and processes. We present 6 stories, discussing changes in sensitivity or resistance to azoles, cisplatin, oxidative stress, arginine biosynthesis perturbations, DNA synthesis inhibitors, and tamoxifen, to demonstrate the power of this novel methodology to broadly profile changes due to gene mutations. The large number of conditions that result in altered growth, as well as the large number of differentially expressed genes with wide-ranging functionality, speaks to the broad array of impacts that altering methyl donor abundance can impart. Our findings demonstrate that some cellular changes are directly related to AdoMet-dependent methyltransferases and AdoMet availability, some are directly linked to the methyl cycle and its role in production of several important cellular components, and others reveal impacts of SAM gene mutations on previously unconnected pathways.
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Affiliation(s)
- McKayla Remines
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA
| | - Makailyn G Schoonover
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA
| | - Zoey Knox
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA
| | - Kailee Kenwright
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA
| | - Kellyn M Hoffert
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA
| | - Amila Coric
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA
| | - James Mead
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA
| | - Joseph Ampfer
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA
| | - Serigne Seye
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA
| | - Erin D Strome
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099, USA
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3
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Dodel M, Guiducci G, Dermit M, Krishnamurthy S, Alard EL, Capraro F, Rekad Z, Stojic L, Mardakheh FK. TREX reveals proteins that bind to specific RNA regions in living cells. Nat Methods 2024; 21:423-434. [PMID: 38374261 PMCID: PMC10927567 DOI: 10.1038/s41592-024-02181-1] [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: 08/21/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024]
Abstract
Different regions of RNA molecules can often engage in specific interactions with distinct RNA-binding proteins (RBPs), giving rise to diverse modalities of RNA regulation and function. However, there are currently no methods for unbiased identification of RBPs that interact with specific RNA regions in living cells and under endogenous settings. Here we introduce TREX (targeted RNase H-mediated extraction of crosslinked RBPs)-a highly sensitive approach for identifying proteins that directly bind to specific RNA regions in living cells. We demonstrate that TREX outperforms existing methods in identifying known interactors of U1 snRNA, and reveals endogenous region-specific interactors of NORAD long noncoding RNA. Using TREX, we generated a comprehensive region-by-region interactome for 45S rRNA, uncovering both established and previously unknown interactions that regulate ribosome biogenesis. With its applicability to different cell types, TREX is an RNA-centric tool for unbiased positional mapping of endogenous RNA-protein interactions in living cells.
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Affiliation(s)
- Martin Dodel
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Giulia Guiducci
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Maria Dermit
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Sneha Krishnamurthy
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Emilie L Alard
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Federica Capraro
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Zeinab Rekad
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Lovorka Stojic
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
| | - Faraz K Mardakheh
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
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4
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Mitterer V, Hamze H, Kunowska N, Stelzl U, Henras A, Hurt E. The RNA helicase Dbp10 coordinates assembly factor association with PTC maturation during ribosome biogenesis. Nucleic Acids Res 2024; 52:1975-1987. [PMID: 38113283 PMCID: PMC10899779 DOI: 10.1093/nar/gkad1206] [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: 03/30/2023] [Revised: 11/08/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023] Open
Abstract
During ribosome biogenesis a plethora of assembly factors and essential enzymes drive the unidirectional maturation of nascent pre-ribosomal subunits. The DEAD-box RNA helicase Dbp10 is suggested to restructure pre-ribosomal rRNA of the evolving peptidyl-transferase center (PTC) on nucleolar ribosomal 60S assembly intermediates. Here, we show that point mutations within conserved catalytic helicase-core motifs of Dbp10 yield a dominant-lethal growth phenotype. Such dbp10 mutants, which stably associate with pre-60S intermediates, impair pre-60S biogenesis at a nucleolar stage prior to the release of assembly factor Rrp14 and stable integration of late nucleolar factors such as Noc3. Furthermore, the binding of the GTPase Nug1 to particles isolated directly via mutant Dbp10 bait proteins is specifically inhibited. The N-terminal domain of Nug1 interacts with Dbp10 and the methyltransferase Spb1, whose pre-60S incorporation is also reduced in absence of functional Dbp10 resulting in decreased methylation of 25S rRNA nucleotide G2922. Our data suggest that Dbp10's helicase activity generates the necessary framework for assembly factor docking thereby permitting PTC rRNA methylation and the progression of pre-60S maturation.
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Affiliation(s)
- Valentin Mitterer
- Biochemistry Center, University of Heidelberg, 69120 Heidelberg, Germany
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Hussein Hamze
- Molecular, Cellular and Developmental Biology Unit (MCD), Center for Integrative Biology (CBI), CNRS, University of Toulouse, 31062 Toulouse, France
| | - Natalia Kunowska
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, 8010 Graz, Austria
| | - Ulrich Stelzl
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
| | - Anthony K Henras
- Molecular, Cellular and Developmental Biology Unit (MCD), Center for Integrative Biology (CBI), CNRS, University of Toulouse, 31062 Toulouse, France
| | - Ed Hurt
- Biochemistry Center, University of Heidelberg, 69120 Heidelberg, Germany
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5
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Fernández-Fernández J, Martín-Villanueva S, Perez-Fernandez J, de la Cruz J. The Role of Ribosomal Proteins eL15 and eL36 in the Early Steps of Yeast 60S Ribosomal Subunit Assembly. J Mol Biol 2023; 435:168321. [PMID: 37865285 DOI: 10.1016/j.jmb.2023.168321] [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: 08/25/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 10/23/2023]
Abstract
Ribosomal proteins have important roles in maintaining the structure and function of mature ribosomes, but they also drive crucial rearrangement reactions during ribosome biogenesis. The contribution of most, but not all, ribosomal proteins to ribosome synthesis has been previously analyzed in the yeast Saccharomyces cerevisiae. Herein, we characterize the role of yeast eL15 during 60S ribosomal subunit formation. In vivo depletion of eL15 results in a shortage of 60S subunits and the appearance of half-mer polysomes. This is likely due to defective processing of the 27SA3 to the 27SBS pre-rRNA and impaired subsequent processing of both forms of 27SB pre-rRNAs to mature 25S and 5.8S rRNAs. Indeed, eL15 depletion leads to the efficient turnover of the de novo formed 27S pre-rRNAs. Additionally, depletion of eL15 blocks nucleocytoplasmic export of pre-60S particles. Moreover, we have analyzed the impact of depleting either eL15 or eL36 on the composition of early pre-60S particles, thereby revealing that the depletion of eL15 or eL36 not only affects each other's assembly into pre-60S particles but also that of neighboring ribosomal proteins, including eL8. These intermediates also lack most ribosome assembly factors required for 27SA3 and 27SB pre-rRNA processing, named A3- and B-factors, respectively. Importantly, our results recapitulate previous ones obtained upon eL8 depletion. We conclude that assembly of eL15, together with that of eL8 and eL36, is a prerequisite to shape domain I of 5.8S/25S rRNA within early pre-60S particles, through their binding to this rRNA domain and the recruitment of specific groups of assembly factors.
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Affiliation(s)
- José Fernández-Fernández
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Seville, Spain
| | - Sara Martín-Villanueva
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain
| | - Jorge Perez-Fernandez
- Department of Biochemistry III, University of Regensburg, D-93051 Regensburg, Germany.
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, E-41012 Seville, Spain.
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6
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Mishra PK, Au WC, Castineira PG, Ali N, Stanton J, Boeckmann L, Takahashi Y, Costanzo M, Boone C, Bloom KS, Thorpe PH, Basrai MA. Misregulation of cell cycle-dependent methylation of budding yeast CENP-A contributes to chromosomal instability. Mol Biol Cell 2023; 34:ar99. [PMID: 37436802 PMCID: PMC10551700 DOI: 10.1091/mbc.e23-03-0108] [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: 03/23/2023] [Revised: 06/15/2023] [Accepted: 07/06/2023] [Indexed: 07/13/2023] Open
Abstract
Centromere (CEN) identity is specified epigenetically by specialized nucleosomes containing evolutionarily conserved CEN-specific histone H3 variant CENP-A (Cse4 in Saccharomyces cerevisiae, CENP-A in humans), which is essential for faithful chromosome segregation. However, the epigenetic mechanisms that regulate Cse4 function have not been fully defined. In this study, we show that cell cycle-dependent methylation of Cse4-R37 regulates kinetochore function and high-fidelity chromosome segregation. We generated a custom antibody that specifically recognizes methylated Cse4-R37 and showed that methylation of Cse4 is cell cycle regulated with maximum levels of methylated Cse4-R37 and its enrichment at the CEN chromatin occur in the mitotic cells. Methyl-mimic cse4-R37F mutant exhibits synthetic lethality with kinetochore mutants, reduced levels of CEN-associated kinetochore proteins and chromosome instability (CIN), suggesting that mimicking the methylation of Cse4-R37 throughout the cell cycle is detrimental to faithful chromosome segregation. Our results showed that SPOUT methyltransferase Upa1 contributes to methylation of Cse4-R37 and overexpression of UPA1 leads to CIN phenotype. In summary, our studies have defined a role for cell cycle-regulated methylation of Cse4 in high-fidelity chromosome segregation and highlight an important role of epigenetic modifications such as methylation of kinetochore proteins in preventing CIN, an important hallmark of human cancers.
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Affiliation(s)
- Prashant K. Mishra
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Wei-Chun Au
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Pedro G. Castineira
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Nazrin Ali
- Queen Mary University of London, E1 4NS, UK
| | - John Stanton
- University of North Carolina, Chapel Hill, NC 27599
| | - Lars Boeckmann
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Yoshimitsu Takahashi
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Michael Costanzo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | | | | | - Munira A. Basrai
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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7
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Seidel M, Romanov N, Obarska-Kosinska A, Becker A, Trevisan Doimo de Azevedo N, Provaznik J, Nagaraja SR, Landry JJM, Benes V, Beck M. Co-translational binding of importins to nascent proteins. Nat Commun 2023; 14:3418. [PMID: 37296145 PMCID: PMC10256725 DOI: 10.1038/s41467-023-39150-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Various cellular quality control mechanisms support proteostasis. While, ribosome-associated chaperones prevent the misfolding of nascent chains during translation, importins were shown to prevent the aggregation of specific cargoes in a post-translational mechanism prior the import into the nucleoplasm. Here, we hypothesize that importins may already bind ribosome-associated cargo in a co-translational manner. We systematically measure the nascent chain association of all importins in Saccharomyces cerevisiae by selective ribosome profiling. We identify a subset of importins that bind to a wide range of nascent, often uncharacterized cargoes. This includes ribosomal proteins, chromatin remodelers and RNA binding proteins that are aggregation prone in the cytosol. We show that importins act consecutively with other ribosome-associated chaperones. Thus, the nuclear import system is directly intertwined with nascent chain folding and chaperoning.
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Affiliation(s)
- Maximilian Seidel
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
- Faculty of Bioscience, Heidelberg University, Heidelberg, Germany
| | - Natalie Romanov
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | | | - Anja Becker
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | | | - Jan Provaznik
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Sankarshana R Nagaraja
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Jonathan J M Landry
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Martin Beck
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany.
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt, Germany.
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8
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Hamey JJ, Wilkins MR. The protein methylation network in yeast: A landmark in completeness for a eukaryotic post-translational modification. Proc Natl Acad Sci U S A 2023; 120:e2215431120. [PMID: 37252976 PMCID: PMC10265986 DOI: 10.1073/pnas.2215431120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
Defining all sites for a post-translational modification in the cell, and identifying their upstream modifying enzymes, is essential for a complete understanding of a modification's function. However, the complete mapping of a modification in the proteome and definition of its associated enzyme-substrate network is rarely achieved. Here, we present the protein methylation network for Saccharomyces cerevisiae. Through a formal process of defining and quantifying all potential sources of incompleteness, for both the methylation sites in the proteome and also protein methyltransferases, we prove that this protein methylation network is now near-complete. It contains 33 methylated proteins and 28 methyltransferases, comprising 44 enzyme-substrate relationships, and a predicted further three enzymes. While the precise molecular function of most methylation sites is unknown, and it remains possible that other sites and enzymes remain undiscovered, the completeness of this protein modification network is unprecedented and allows us to holistically explore the role and evolution of protein methylation in the eukaryotic cell. We show that while no single protein methylation event is essential in yeast, the vast majority of methylated proteins are themselves essential, being primarily involved in the core cellular processes of transcription, RNA processing, and translation. This suggests that protein methylation in lower eukaryotes exists to fine-tune proteins whose sequences are evolutionarily constrained, providing an improvement in the efficiency of their cognate processes. The approach described here, for the construction and evaluation of post-translational modification networks and their constituent enzymes and substrates, defines a formal process of utility for other post-translational modifications.
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Affiliation(s)
- Joshua J. Hamey
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW2052, Australia
| | - Marc R. Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW2052, Australia
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9
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Bohnsack KE, Henras AK, Nielsen H, Bohnsack MT. Making ends meet: a universal driver of large ribosomal subunit biogenesis. Trends Biochem Sci 2023; 48:213-215. [PMID: 36207216 DOI: 10.1016/j.tibs.2022.09.003] [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: 06/15/2022] [Revised: 09/10/2022] [Accepted: 09/14/2022] [Indexed: 11/07/2022]
Abstract
A common aspect of ribosome assembly, conserved across all domains of life, is the establishment of connections between the 5' and 3' ends of the large subunit (LSU) ribosomal RNA (rRNA) to initiate rRNA domain compaction and subunit assembly. We discuss the diverse mechanisms employed in different organisms to accomplish this important event.
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Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany.
| | - Anthony K Henras
- Molecular, Cellular and Developmental Biology Unit, University of Toulouse, Toulouse, France
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany; Göttingen Center for Molecular Biosciences, Georg-August University, Göttingen, Germany.
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10
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Inhibition of Ribosome Assembly and Ribosome Translation Has Distinctly Different Effects on Abundance and Paralogue Composition of Ribosomal Protein mRNAs in Saccharomyces cerevisiae. mSystems 2023; 8:e0109822. [PMID: 36651729 PMCID: PMC9948716 DOI: 10.1128/msystems.01098-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Many mutations in genes for ribosomal proteins (r-proteins) and assembly factors cause cell stress and altered cell fate, resulting in congenital diseases collectively called ribosomopathies. Even though all such mutations depress the cell's protein synthesis capacity, they generate many different phenotypes, suggesting that the diseases are not due simply to insufficient protein synthesis capacity. To learn more, we investigated how the global transcriptome in Saccharomyces cerevisiae responds to reduced protein synthesis generated in two different ways: abolishing the assembly of new ribosomes and inhibiting ribosomal function. Our results showed that the mechanism by which protein synthesis is obstructed affects the ribosomal protein transcriptome differentially: ribosomal protein mRNA abundance increases during the abolition of ribosome formation but decreases during the inhibition of ribosome function. Interestingly, the ratio between mRNAs from some, but not all, pairs of paralogous ribosomal protein genes encoding slightly different versions of a given r-protein changed differently during the two types of stress, suggesting that expression of specific ribosomal protein paralogous mRNAs may contribute to the stress response. Unexpectedly, the abundance of transcripts for ribosome assembly factors and translation factors remained relatively unaffected by the stresses. On the other hand, the state of the translation apparatus did affect cell physiology: mRNA levels for some other proteins not directly related to the translation apparatus also changed differentially, though not coordinately with the r-protein genes, in response to the stresses. IMPORTANCE Mutations in genes for ribosomal proteins or assembly factors cause a variety of diseases called ribosomopathies. These diseases are typically ascribed to a reduction in the cell's capacity for protein synthesis. Paradoxically, ribosomal mutations result in a wide variety of disease phenotypes, even though they all reduce protein synthesis. Here, we show that the transcriptome changes differently depending on how the protein synthesis capacity is reduced. Most strikingly, inhibiting ribosome formation and ribosome function had opposite effects on the abundance of mRNA for ribosomal proteins, while genes for ribosome translation and assembly factors showed no systematic responses. Thus, the process by which the protein synthesis capacity is reduced contributes decisively to global mRNA composition. This emphasis on process is a new concept in understanding ribosomopathies and other stress responses.
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11
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Parker MD, Karbstein K. Quality control ensures fidelity in ribosome assembly and cellular health. J Cell Biol 2023; 222:213871. [PMID: 36790396 PMCID: PMC9960125 DOI: 10.1083/jcb.202209115] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/09/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
The coordinated integration of ribosomal RNA and protein into two functional ribosomal subunits is safeguarded by quality control checkpoints that ensure ribosomes are correctly assembled and functional before they engage in translation. Quality control is critical in maintaining the integrity of ribosomes and necessary to support healthy cell growth and prevent diseases associated with mistakes in ribosome assembly. Its importance is demonstrated by the finding that bypassing quality control leads to misassembled, malfunctioning ribosomes with altered translation fidelity, which change gene expression and disrupt protein homeostasis. In this review, we outline our understanding of quality control within ribosome synthesis and how failure to enforce quality control contributes to human disease. We first provide a definition of quality control to guide our investigation, briefly present the main assembly steps, and then examine stages of assembly that test ribosome function, establish a pass-fail system to evaluate these functions, and contribute to altered ribosome performance when bypassed, and are thus considered "quality control."
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Affiliation(s)
- Melissa D. Parker
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA,University of Florida—Scripps Biomedical Research, Jupiter, FL, USA
| | - Katrin Karbstein
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA,University of Florida—Scripps Biomedical Research, Jupiter, FL, USA,Howard Hughes Medical Institute Faculty Scholar, Howard Hughes Medical Institute, Chevy Chase, MD, USA,Correspondence to Katrin Karbstein:
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12
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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: 26] [Impact Index Per Article: 26.0] [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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13
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Khreiss A, Capeyrou R, Lebaron S, Albert B, Bohnsack K, Bohnsack M, Henry Y, Henras A, Humbert O. The DEAD-box protein Dbp6 is an ATPase and RNA annealase interacting with the peptidyl transferase center (PTC) of the ribosome. Nucleic Acids Res 2023; 51:744-764. [PMID: 36610750 PMCID: PMC9881158 DOI: 10.1093/nar/gkac1196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/21/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
Ribosomes are ribozymes, hence correct folding of the rRNAs during ribosome biogenesis is crucial to ensure catalytic activity. RNA helicases, which can modulate RNA-RNA and RNA/protein interactions, are proposed to participate in rRNA tridimensional folding. Here, we analyze the biochemical properties of Dbp6, a DEAD-box RNA helicase required for the conversion of the initial 90S pre-ribosomal particle into the first pre-60S particle. We demonstrate that in vitro, Dbp6 shows ATPase as well as annealing and clamping activities negatively regulated by ATP. Mutations in Dbp6 core motifs involved in ATP binding and ATP hydrolysis are lethal and impair Dbp6 ATPase activity but increase its RNA binding and RNA annealing activities. These data suggest that correct regulation of these activities is important for Dbp6 function in vivo. Using in vivo cross-linking (CRAC) experiments, we show that Dbp6 interacts with 25S rRNA sequences located in the 5' domain I and in the peptidyl transferase center (PTC), and also crosslinks to snoRNAs hybridizing to the immature PTC. We propose that the ATPase and RNA clamping/annealing activities of Dbp6 modulate interactions of snoRNAs with the immature PTC and/or contribute directly to the folding of this region.
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Affiliation(s)
- Ali Khreiss
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Régine Capeyrou
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Simon Lebaron
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Benjamin Albert
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, 37073 Göttingen, Germany,Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Yves Henry
- Correspondence may also be addressed to Yves Henry. Tel: +33 5 61 33 59 53; Fax: +33 5 61 33 58 86;
| | - Anthony K Henras
- Correspondence may also be addressed to Anthony Henras. Tel: +33 5 61 33 59 55; Fax: +33 5 61 33 58 86;
| | - Odile Humbert
- To whom correspondence should be addressed. Tel: +33 5 61 33 59 52; Fax: +33 5 61 33 58 86;
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14
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Bhutada P, Favre S, Jaafar M, Hafner J, Liesinger L, Unterweger S, Bischof K, Darnhofer B, Siva Sankar D, Rechberger G, Abou Merhi R, Lebaron S, Birner-Gruenberger R, Kressler D, Henras AK, Pertschy B. Rbp95 binds to 25S rRNA helix H95 and cooperates with the Npa1 complex during early pre-60S particle maturation. Nucleic Acids Res 2022; 50:10053-10077. [PMID: 36018804 PMCID: PMC9508819 DOI: 10.1093/nar/gkac724] [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: 12/02/2021] [Revised: 08/05/2022] [Accepted: 08/12/2022] [Indexed: 11/21/2022] Open
Abstract
Eukaryotic ribosome synthesis involves more than 200 assembly factors, which promote ribosomal RNA (rRNA) processing, modification and folding, and assembly of ribosomal proteins. The formation and maturation of the earliest pre-60S particles requires structural remodeling by the Npa1 complex, but is otherwise still poorly understood. Here, we introduce Rbp95 (Ycr016w), a constituent of early pre-60S particles, as a novel ribosome assembly factor. We show that Rbp95 is both genetically and physically linked to most Npa1 complex members and to ribosomal protein Rpl3. We demonstrate that Rbp95 is an RNA-binding protein containing two independent RNA-interacting domains. In vivo, Rbp95 associates with helix H95 in the 3′ region of the 25S rRNA, in close proximity to the binding sites of Npa1 and Rpl3. Additionally, Rbp95 interacts with several snoRNAs. The absence of Rbp95 results in alterations in the protein composition of early pre-60S particles. Moreover, combined mutation of Rbp95 and Npa1 complex members leads to a delay in the maturation of early pre-60S particles. We propose that Rbp95 acts together with the Npa1 complex during early pre-60S maturation, potentially by promoting pre-rRNA folding events within pre-60S particles.
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Affiliation(s)
- Priya Bhutada
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Sébastien Favre
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Mariam Jaafar
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France.,Genomic Stability and Biotherapy (GSBT) Laboratory, Faculty of Sciences, Rafik Hariri Campus, Lebanese University, Beirut, Lebanon
| | - Jutta Hafner
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Laura Liesinger
- BioTechMed-Graz, Graz, Austria.,Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria
| | - Stefan Unterweger
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Karin Bischof
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Barbara Darnhofer
- BioTechMed-Graz, Graz, Austria.,Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria
| | - Devanarayanan Siva Sankar
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Gerald Rechberger
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Raghida Abou Merhi
- Genomic Stability and Biotherapy (GSBT) Laboratory, Faculty of Sciences, Rafik Hariri Campus, Lebanese University, Beirut, Lebanon
| | - Simon Lebaron
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Ruth Birner-Gruenberger
- BioTechMed-Graz, Graz, Austria.,Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria.,Institute of Chemical Technologies and Analytics, Technische Universität Wien, Getreidemarkt 9/E164, 1060 Vienna, Austria
| | - Dieter Kressler
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Anthony K Henras
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Brigitte Pertschy
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria.,BioTechMed-Graz, Graz, Austria
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