1
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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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2
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Deryabin A, Moraleva A, Dobrochaeva K, Kovaleva D, Rubtsova M, Dontsova O, Rubtsov Y. Human RPF1 and ESF1 in Pre-rRNA Processing and the Assembly of Pre-Ribosomal Particles: A Functional Study. Cells 2024; 13:326. [PMID: 38391939 PMCID: PMC10886481 DOI: 10.3390/cells13040326] [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: 08/08/2023] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 02/24/2024] Open
Abstract
Ribosome biogenesis is essential for the functioning of living cells. In higher eukaryotes, this multistep process is tightly controlled and involves a variety of specialized proteins and RNAs. This pool of so-called ribosome biogenesis factors includes diverse proteins with enzymatic and structural functions. Some of them have homologs in yeast S. cerevisiae, and their function can be inferred from the structural and biochemical data obtained for the yeast counterparts. The functions of human proteins RPF1 and ESF1 remain largely unclear, although RPF1 has been recently shown to participate in 60S biogenesis. Both proteins have drawn our attention since they contribute to the early stages of ribosome biogenesis, which are far less studied than the later stages. In this study, we employed the loss-of-function shRNA/siRNA-based approach to the human cell line HEK293 to determine the role of RPF1 and ESF1 in ribosome biogenesis. Downregulating RPF1 and ESF1 significantly changed the pattern of RNA products derived from 47S pre-rRNA. Our findings demonstrate that RPF1 and ESF1 are associated with different pre-ribosomal particles, pre-60S, and pre-40S particles, respectively. Our results allow for speculation about the particular steps of pre-rRNA processing, which highly rely on the RPF1 and ESF1 functions. We suggest that both factors are not directly involved in pre-rRNA cleavage but rather help pre-rRNA to acquire the conformation favoring its cleavage.
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Affiliation(s)
- Alexander Deryabin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 119997 Moscow, Russia
| | - Anastasiia Moraleva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 119997 Moscow, Russia
- Department of Applied Mathematics, MIREA-Russian Technological University, 119454 Moscow, Russia
| | - Kira Dobrochaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 119997 Moscow, Russia
| | - Diana Kovaleva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 119997 Moscow, Russia
| | - Maria Rubtsova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Olga Dontsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 119997 Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Yury Rubtsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 119997 Moscow, Russia
- N.N.Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, 115478 Moscow, Russia
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3
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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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4
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Thoms M, Lau B, Cheng J, Fromm L, Denk T, Kellner N, Flemming D, Fischer P, Falquet L, Berninghausen O, Beckmann R, Hurt E. Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation. EMBO Rep 2023; 24:e57984. [PMID: 37921038 DOI: 10.15252/embr.202357984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/11/2023] [Accepted: 10/14/2023] [Indexed: 11/04/2023] Open
Abstract
The rixosome defined in Schizosaccharomyces pombe and humans performs diverse roles in pre-ribosomal RNA processing and gene silencing. Here, we isolate and describe the conserved rixosome from Chaetomium thermophilum, which consists of two sub-modules, the sphere-like Rix1-Ipi3-Ipi1 and the butterfly-like Las1-Grc3 complex, connected by a flexible linker. The Rix1 complex of the rixosome utilizes Sda1 as landing platform on nucleoplasmic pre-60S particles to wedge between the 5S rRNA tip and L1-stalk, thereby facilitating the 180° rotation of the immature 5S RNP towards its mature conformation. Upon rixosome positioning, the other sub-module with Las1 endonuclease and Grc3 polynucleotide-kinase can reach a strategic position at the pre-60S foot to cleave and 5' phosphorylate the nearby ITS2 pre-rRNA. Finally, inward movement of the L1 stalk permits the flexible Nop53 N-terminus with its AIM motif to become positioned at the base of the L1-stalk to facilitate Mtr4 helicase-exosome participation for completing ITS2 removal. Thus, the rixosome structure elucidates the coordination of two central ribosome biogenesis events, but its role in gene silencing may adapt similar strategies.
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Affiliation(s)
- Matthias Thoms
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Benjamin Lau
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Jingdong Cheng
- Minhang Hospital & Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, Fudan University, Shanghai, China
| | - Lisa Fromm
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Timo Denk
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Nikola Kellner
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Dirk Flemming
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Paulina Fischer
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Laurent Falquet
- University of Fribourg and Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | | | - Roland Beckmann
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ed Hurt
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
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5
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LaPeruta AJ, Micic J, Woolford Jr. JL. Additional principles that govern the release of pre-ribosomes from the nucleolus into the nucleoplasm in yeast. Nucleic Acids Res 2023; 51:10867-10883. [PMID: 35736211 PMCID: PMC10639060 DOI: 10.1093/nar/gkac430] [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: 10/16/2021] [Revised: 05/05/2022] [Accepted: 06/20/2022] [Indexed: 11/14/2022] Open
Abstract
During eukaryotic ribosome biogenesis, pre-ribosomes travel from the nucleolus, where assembly is initiated, to the nucleoplasm and then are exported to the cytoplasm, where assembly concludes. Although nuclear export of pre-ribosomes has been extensively investigated, the release of pre-ribosomes from the nucleolus is an understudied phenomenon. Initial data indicate that unfolded rRNA interacts in trans with nucleolar components and that, when rRNA folds due to ribosomal protein (RP) binding, the number of trans interactions drops below the threshold necessary for nucleolar retention. To validate and expand on this idea, we performed a bioinformatic analysis of the protein components of the Saccharomyces cerevisiae ribosome assembly pathway. We found that ribosome biogenesis factors (RiBi factors) contain significantly more predicted trans interacting regions than RPs. We also analyzed cryo-EM structures of ribosome assembly intermediates to determine how nucleolar pre-ribosomes differ from post-nucleolar pre-ribosomes, specifically the capacity of RPs, RiBi factors, and rRNA components to interact in trans. We observed a significant decrease in the theoretical trans-interacting capability of pre-ribosomes between nucleolar and post-nucleolar stages of assembly due to the release of RiBi factors from particles and the folding of rRNA. Here, we provide a mechanism for the release of pre-ribosomes from the nucleolus.
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Affiliation(s)
- Amber J LaPeruta
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Jelena Micic
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - John L Woolford Jr.
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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6
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Bohnsack KE, Yi S, Venus S, Jankowsky E, Bohnsack MT. Cellular functions of eukaryotic RNA helicases and their links to human diseases. Nat Rev Mol Cell Biol 2023; 24:749-769. [PMID: 37474727 DOI: 10.1038/s41580-023-00628-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2023] [Indexed: 07/22/2023]
Abstract
RNA helicases are highly conserved proteins that use nucleoside triphosphates to bind or remodel RNA, RNA-protein complexes or both. RNA helicases are classified into the DEAD-box, DEAH/RHA, Ski2-like, Upf1-like and RIG-I families, and are the largest class of enzymes active in eukaryotic RNA metabolism - virtually all aspects of gene expression and its regulation involve RNA helicases. Mutation and dysregulation of these enzymes have been linked to a multitude of diseases, including cancer and neurological disorders. In this Review, we discuss the regulation and functional mechanisms of RNA helicases and their roles in eukaryotic RNA metabolism, including in transcription regulation, pre-mRNA splicing, ribosome assembly, translation and RNA decay. We highlight intriguing models that link helicase structure, mechanisms of function (such as local strand unwinding, translocation, winching, RNA clamping and displacing RNA-binding proteins) and biological roles, including emerging connections between RNA helicases and cellular condensates formed through liquid-liquid phase separation. We also discuss associations of RNA helicases with human diseases and recent efforts towards the design of small-molecule inhibitors of these pivotal regulators of eukaryotic gene expression.
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Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
| | - Soon Yi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Sarah Venus
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Moderna, Cambridge, MA, USA.
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
- Göttingen Centre for Molecular Biosciences, University of Göttingen, Göttingen, Germany.
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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7
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Khreiss A, Bohnsack KE, Bohnsack MT. Molecular functions of RNA helicases during ribosomal subunit assembly. Biol Chem 2023; 404:781-789. [PMID: 37233600 DOI: 10.1515/hsz-2023-0135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/09/2023] [Indexed: 05/27/2023]
Abstract
During their biogenesis, the ribosomal subunits undergo numerous structural and compositional changes to achieve their final architecture. RNA helicases are a key driving force of such remodelling events but deciphering their particular functions has long been challenging due to lack of knowledge of their molecular functions and RNA substrates. Advances in the biochemical characterisation of RNA helicase activities together with new insights into RNA helicase binding sites on pre-ribosomes and structural snapshots of pre-ribosomal complexes containing RNA helicases now open the door to a deeper understanding of precisely how different RNA helicases contribute to ribosomal subunit maturation.
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Affiliation(s)
- Ali Khreiss
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, D-37073 Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, D-37073 Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, D-37073 Göttingen, Germany
- Göttingen Centre for Molecular Biosciences, Georg-August University, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
- Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
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8
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Vanden Broeck A, Klinge S. Principles of human pre-60 S biogenesis. Science 2023; 381:eadh3892. [PMID: 37410842 DOI: 10.1126/science.adh3892] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/20/2023] [Indexed: 07/08/2023]
Abstract
During the early stages of human large ribosomal subunit (60S) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60S particles by an unknown mechanism. Here, we report a series of cryo-electron microscopy structures of human nucleolar and nuclear pre-60S assembly intermediates at resolutions of 2.5 to 3.2 angstroms. These structures show how protein interaction hubs tether assembly factor complexes to nucleolar particles and how guanosine triphosphatases and adenosine triphosphatase couple irreversible nucleotide hydrolysis steps to the installation of functional centers. Nuclear stages highlight how a conserved RNA-processing complex, the rixosome, couples large-scale RNA conformational changes with pre-ribosomal RNA processing by the RNA degradation machinery. Our ensemble of human pre-60S particles provides a rich foundation with which to elucidate the molecular principles of ribosome formation.
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Affiliation(s)
- Arnaud Vanden Broeck
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Sebastian Klinge
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA
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9
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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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10
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Sanghai ZA, Piwowarczyk R, Broeck AV, Klinge S. A co-transcriptional ribosome assembly checkpoint controls nascent large ribosomal subunit maturation. Nat Struct Mol Biol 2023; 30:594-599. [PMID: 37037974 DOI: 10.1038/s41594-023-00947-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/24/2023] [Indexed: 04/12/2023]
Abstract
During transcription of eukaryotic ribosomal DNA in the nucleolus, assembly checkpoints exist that guarantee the formation of stable precursors of small and large ribosomal subunits. While the formation of an early large subunit assembly checkpoint precedes the separation of small and large subunit maturation, its mechanism of action and function remain unknown. Here, we report the cryo-electron microscopy structure of the yeast co-transcriptional large ribosomal subunit assembly intermediate that serves as a checkpoint. The structure provides the mechanistic basis for how quality-control pathways are established through co-transcriptional ribosome assembly factors, that structurally interrogate, remodel and, together with ribosomal proteins, cooperatively stabilize correctly folded pre-ribosomal RNA. Our findings thus provide a molecular explanation for quality control during eukaryotic ribosome assembly in the nucleolus.
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Affiliation(s)
- Zahra A Sanghai
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York, USA
| | - Rafal Piwowarczyk
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York, USA
| | - Arnaud Vanden Broeck
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York, USA
| | - Sebastian Klinge
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York, USA.
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11
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Amin A, Wu R, Khan MA, Cheung MH, Liang Y, Liu C, Zhu G, Yu ZL, Liang C. An essential Noc3p dimerization cycle mediates ORC double-hexamer formation in replication licensing. Life Sci Alliance 2023; 6:e202201594. [PMID: 36599624 PMCID: PMC9813392 DOI: 10.26508/lsa.202201594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 01/05/2023] Open
Abstract
Replication licensing, a prerequisite of DNA replication, helps to ensure once-per-cell-cycle genome duplication. Some DNA replication-initiation proteins are sequentially loaded onto replication origins to form pre-replicative complexes (pre-RCs). ORC and Noc3p bind replication origins throughout the cell cycle, providing a platform for pre-RC assembly. We previously reported that cell cycle-dependent ORC dimerization is essential for the chromatin loading of the symmetric MCM double-hexamers. Here, we used Saccharomyces cerevisiae separation-of-function NOC3 mutants to confirm the separable roles of Noc3p in DNA replication and ribosome biogenesis. We also show that an essential and cell cycle-dependent Noc3p dimerization cycle regulates the ORC dimerization cycle. Noc3p dimerizes at the M-to-G1 transition and de-dimerizes in S-phase. The Noc3p dimerization cycle coupled with the ORC dimerization cycle enables replication licensing, protects nascent sister replication origins after replication initiation, and prevents re-replication. This study has revealed a new mechanism of replication licensing and elucidated the molecular mechanism of Noc3p as a mediator of ORC dimerization in pre-RC formation.
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Affiliation(s)
- Aftab Amin
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Rentian Wu
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Muhammad Ajmal Khan
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Man Hei Cheung
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Yanting Liang
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Changdong Liu
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Guang Zhu
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Zhi-Ling Yu
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Chun Liang
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- EnKang Pharmaceuticals (Guangzhou), Ltd., Guangzhou, China
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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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Hariharan N, Ghosh S, Palakodeti D. The story of rRNA expansion segments: Finding functionality amidst diversity. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1732. [PMID: 35429135 DOI: 10.1002/wrna.1732] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 02/24/2022] [Accepted: 03/19/2022] [Indexed: 01/31/2023]
Abstract
Expansion segments (ESs) are multinucleotide insertions present across phyla at specific conserved positions in eukaryotic rRNAs. ESs are generally absent in bacterial rRNAs with some exceptions, while the archaeal rRNAs have microexpansions at regions that coincide with those of eukaryotic ESs. Although there is an increasing prominence of ribosomes, especially the ribosomal proteins, in fine-tuning gene expression through translation regulation, the role of rRNA ESs is relatively underexplored. While rRNAs have been established as the major catalytic hub in ribosome function, the presence of ESs widens their scope as a species-specific regulatory hub of protein synthesis. In this comprehensive review, we have elaborately discussed the current understanding of the functional aspects of rRNA ESs of cytoplasmic eukaryotic ribosomes and discuss their past, present, and future. This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems Translation > Ribosome Structure/Function Translation > Regulation.
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Affiliation(s)
- Nivedita Hariharan
- Technologies for the Advancement of Science, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India.,The University of Trans-disciplinary Health Sciences and Technology, Bangalore, India
| | - Sumana Ghosh
- Manipal Academy of Higher Education, Manipal, India
| | - Dasaradhi Palakodeti
- Technologies for the Advancement of Science, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
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15
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Meier UT. The daunting task of modifying ribosomal RNA. RNA (NEW YORK, N.Y.) 2022; 28:1555-1557. [PMID: 36109161 PMCID: PMC9670813 DOI: 10.1261/rna.079391.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
One of the most basic tasks of every cell is the synthesis of ribosomes, yet the process is so complex that we are only beginning to comprehend it. In human cells, the final product contains four RNAs and 79 proteins forming a large ribonucleoprotein, the ribosome. About twice as many factors are involved in assembly of these protein synthesizing machines. Additionally, some 200 small nucleolar ribonucleoproteins (snoRNPs) function in the modification of pre-ribosomal RNA (pre-rRNA) at a similar number of ribonucleotides. Modification is essential for proper function and biogenesis of ribosomes (Decatur and Fournier 2002; Sloan et al. 2016). While abrogation of individual modifications has little to no measurable effects, removal of a combination of modifications or of all causes severe to lethal effects. Modifications mostly cluster around the functional centers of the ribosome and some modifications are important for ribosome assembly. The subject of this perspective is to raise awareness to how modification at so many sites can be achieved while the pre-rRNA is being processed, folded and re-folded, and assembled with ribosomal proteins to yield the pre-ribosomal subunits in the nucleolus (Baßler and Hurt 2019). This is not a comprehensive review but a simplification of complex issues providing access to the general reader.
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Affiliation(s)
- U Thomas Meier
- Albert Einstein College of Medicine, Bronx, New York 10461, USA
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16
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Cheng J, Lau B, Thoms M, Ameismeier M, Berninghausen O, Hurt E, Beckmann R. The nucleoplasmic phase of pre-40S formation prior to nuclear export. Nucleic Acids Res 2022; 50:11924-11937. [PMID: 36321656 PMCID: PMC9723619 DOI: 10.1093/nar/gkac961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/04/2022] [Accepted: 10/21/2022] [Indexed: 11/07/2022] Open
Abstract
Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural transitions of assembly intermediates from human and yeast cells during the nucleoplasmic maturation phase. After dissociation of all 90S factors, the 40S body adopts a close-to-mature conformation, whereas the 3' major domain, later forming the 40S head, remains entirely immature. A first coordination is facilitated by the assembly factors TSR1 and BUD23-TRMT112, followed by re-positioning of RRP12 that is already recruited early to the 90S for further head rearrangements. Eventually, the uS2 cluster, CK1 (Hrr25 in yeast) and the export factor SLX9 associate with the pre-40S to provide export competence. These exemplary findings reveal the evolutionary conserved mechanism of how yeast and humans assemble the 40S ribosomal subunit, but reveal also a few minor differences.
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Affiliation(s)
- Jingdong Cheng
- Gene Center and Department of Biochemistry, University of Munich LMU, Feodor-Lynen-Str. 25, 81377 Munich, Germany,Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Dong’an Road 131, 200032 Shanghai, China
| | - Benjamin Lau
- BZH, University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Matthias Thoms
- Gene Center and Department of Biochemistry, University of Munich LMU, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Michael Ameismeier
- Gene Center and Department of Biochemistry, University of Munich LMU, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Otto Berninghausen
- Gene Center and Department of Biochemistry, University of Munich LMU, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Ed Hurt
- Correspondence may also be addressed to Ed Hurt.
| | - Roland Beckmann
- To whom correspondence should be addressed. Tel: +49 89 218076900; Fax: +49 89 218076945;
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17
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Moraleva AA, Deryabin AS, Rubtsov YP, Rubtsova MP, Dontsova OA. Eukaryotic Ribosome Biogenesis: The 60S Subunit. Acta Naturae 2022; 14:39-49. [PMID: 35925480 PMCID: PMC9307984 DOI: 10.32607/actanaturae.11541] [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: 07/29/2021] [Accepted: 02/11/2022] [Indexed: 11/20/2022] Open
Abstract
Ribosome biogenesis is consecutive coordinated maturation of ribosomal precursors in the nucleolus, nucleoplasm, and cytoplasm. The formation of mature ribosomal subunits involves hundreds of ribosomal biogenesis factors that ensure ribosomal RNA processing, tertiary structure, and interaction with ribosomal proteins. Although the main features and stages of ribosome biogenesis are conservative among different groups of eukaryotes, this process in human cells has become more complicated due to the larger size of the ribosomes and pre-ribosomes and intricate regulatory pathways affecting their assembly and function. Many of the factors involved in the biogenesis of human ribosomes have been identified using genome-wide screening based on RNA interference. A previous part of this review summarized recent data on the processing of the primary rRNA transcript and compared the maturation of the small 40S subunit in yeast and human cells. This part of the review focuses on the biogenesis of the large 60S subunit of eukaryotic ribosomes.
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Affiliation(s)
- A. A. Moraleva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - A. S. Deryabin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - Yu. P. Rubtsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - M. P. Rubtsova
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991 Russia
| | - O. A. Dontsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991 Russia
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
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18
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Micic J, Rodríguez-Galán O, Babiano R, Fitzgerald F, Fernández-Fernández J, Zhang Y, Gao N, Woolford JL, de la Cruz J. Ribosomal protein eL39 is important for maturation of the nascent polypeptide exit tunnel and proper protein folding during translation. Nucleic Acids Res 2022; 50:6453-6473. [PMID: 35639884 PMCID: PMC9226512 DOI: 10.1093/nar/gkac366] [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: 08/19/2021] [Revised: 04/04/2022] [Accepted: 05/12/2022] [Indexed: 11/29/2022] Open
Abstract
During translation, nascent polypeptide chains travel from the peptidyl transferase center through the nascent polypeptide exit tunnel (NPET) to emerge from 60S subunits. The NPET includes portions of five of the six 25S/5.8S rRNA domains and ribosomal proteins uL4, uL22, and eL39. Internal loops of uL4 and uL22 form the constriction sites of the NPET and are important for both assembly and function of ribosomes. Here, we investigated the roles of eL39 in tunnel construction, 60S biogenesis, and protein synthesis. We show that eL39 is important for proper protein folding during translation. Consistent with a delay in processing of 27S and 7S pre-rRNAs, eL39 functions in pre-60S assembly during middle nucleolar stages. Our biochemical assays suggest the presence of eL39 in particles at these stages, although it is not visualized in them by cryo-electron microscopy. This indicates that eL39 takes part in assembly even when it is not fully accommodated into the body of pre-60S particles. eL39 is also important for later steps of assembly, rotation of the 5S ribonucleoprotein complex, likely through long range rRNA interactions. Finally, our data strongly suggest the presence of alternative pathways of ribosome assembly, previously observed in the biogenesis of bacterial ribosomal subunits.
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Affiliation(s)
- Jelena Micic
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Olga Rodríguez-Galán
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Reyes Babiano
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Fiona Fitzgerald
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - José Fernández-Fernández
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Yunyang Zhang
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - John L Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
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19
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Tseng YT, Sung YC, Liu CY, Lo KY. Translation initiation factor eIF4G1 modulates assembly of the polypeptide exit tunnel region in yeast ribosome biogenesis. J Cell Sci 2022; 135:275526. [PMID: 35615984 DOI: 10.1242/jcs.259540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/12/2022] [Indexed: 01/24/2023] Open
Abstract
eIF4G is an important eukaryotic translation initiation factor. In this study, eIF4G1, one of the eIF4G isoforms, was shown to directly participate in biogenesis of the large (60S) ribosomal subunit in Saccharomyces cerevisiae cells. Mutation of eIF4G1 decreased the amount 60S ribosomal subunits significantly. The C-terminal fragment of eIF4G1 could complement the function in 60S biogenesis. Analyses of its purified complex with mass spectrometry indicated that eIF4G1 associated with the pre-60S form directly. Strong genetic and direct protein-protein interactions were observed between eIF4G1 and Ssf1 protein. Upon deletion of eIF4G1, Ssf1, Rrp15, Rrp14 and Mak16 were abnormally retained on the pre-60S complex. This purturbed the loading of Arx1 and eL31 at the polypeptide exit tunnel (PET) site and the transition to a Nog2 complex. Our data indicate that eIF4G1 is important in facilitating PET maturation and 27S processing correctly. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Yun-Ting Tseng
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Yu-Cheng Sung
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Ching-Yu Liu
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Kai-Yin Lo
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
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20
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Ismail S, Flemming D, Thoms M, Gomes-Filho JV, Randau L, Beckmann R, Hurt E. Emergence of the primordial pre-60S from the 90S pre-ribosome. Cell Rep 2022; 39:110640. [PMID: 35385737 PMCID: PMC8994135 DOI: 10.1016/j.celrep.2022.110640] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/01/2022] [Accepted: 03/16/2022] [Indexed: 01/03/2023] Open
Abstract
Synthesis of ribosomes begins in the nucleolus with formation of the 90S pre-ribosome, during which the pre-40S and pre-60S pathways diverge by pre-rRNA cleavage. However, it remains unclear how, after this uncoupling, the earliest pre-60S subunit continues to develop. Here, we reveal a large-subunit intermediate at the beginning of its construction when still linked to the 90S, the precursor to the 40S subunit. This primordial pre-60S is characterized by the SPOUT domain methyltransferase Upa1-Upa2, large α-solenoid scaffolds, Mak5, one of several RNA helicases, and two small nucleolar RNA (snoRNAs), C/D box snR190 and H/ACA box snR37. The emerging pre-60S does not efficiently disconnect from the 90S pre-ribosome in a dominant mak5 helicase mutant, allowing a 70-nm 90S-pre-60S bipartite particle to be visualized by electron microscopy. Our study provides insight into the assembly pathway when the still-connected nascent 40S and 60S subunits are beginning to separate.
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Affiliation(s)
- Sherif Ismail
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Dirk Flemming
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Matthias Thoms
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | | | - Lennart Randau
- Philipps-Universität Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany
| | - Roland Beckmann
- Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany.
| | - Ed Hurt
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.
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21
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Sarnowski CP, Bikaki M, Leitner A. Cross-linking and mass spectrometry as a tool for studying the structural biology of ribonucleoproteins. Structure 2022; 30:441-461. [PMID: 35366400 DOI: 10.1016/j.str.2022.03.003] [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: 07/29/2021] [Revised: 02/03/2022] [Accepted: 03/01/2022] [Indexed: 11/17/2022]
Abstract
Cross-linking and mass spectrometry (XL-MS) workflows represent an increasingly popular technique for low-resolution structural studies of macromolecular complexes. Cross-linking reactions take place in the solution state, capturing contact sites between components of a complex that represent the native, functionally relevant structure. Protein-protein XL-MS protocols are widely adopted, providing precise localization of cross-linking sites to single amino acid positions within a pair of cross-linked peptides. In contrast, protein-RNA XL-MS workflows are evolving rapidly and differ in their ability to localize interaction regions within the RNA sequence. Here, we review protein-protein and protein-RNA XL-MS workflows, and discuss their applications in studies of protein-RNA complexes. The examples highlight the complementary value of XL-MS in structural studies of protein-RNA complexes, where more established high-resolution techniques might be unable to produce conclusive data.
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Affiliation(s)
- Chris P Sarnowski
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zurich, Switzerland; Systems Biology PhD Program, University of Zürich and ETH Zürich, Zurich, Switzerland
| | - Maria Bikaki
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zurich, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, 8093 Zurich, Switzerland.
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22
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Sailer C, Jansen J, Sekulski K, Cruz VE, Erzberger JP, Stengel F. A comprehensive landscape of 60S ribosome biogenesis factors. Cell Rep 2022; 38:110353. [PMID: 35139378 PMCID: PMC8884084 DOI: 10.1016/j.celrep.2022.110353] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/02/2021] [Accepted: 01/19/2022] [Indexed: 01/03/2023] Open
Abstract
Eukaryotic ribosome biogenesis is facilitated and regulated by numerous ribosome biogenesis factors (RBFs). High-resolution cryoelectron microscopy (cryo-EM) maps have defined the molecular interactions of RBFs during maturation, but many transient and dynamic interactions, particularly during early assembly, remain uncharacterized. Using quantitative proteomics and crosslinking coupled to mass spectrometry (XL-MS) data from an extensive set of pre-ribosomal particles, we derive a comprehensive and time-resolved interaction map of RBF engagement during 60S maturation. We localize 22 previously unmapped RBFs to specific biogenesis intermediates and validate our results by mapping the catalytic activity of the methyltransferases Bmt2 and Rcm1 to their predicted nucleolar 60S intermediates. Our analysis reveals the interaction sites for the RBFs Noc2 and Ecm1 and elucidates the interaction map and timing of 60S engagement by the DEAD-box ATPases Dbp9 and Dbp10. Our data provide a powerful resource for future studies of 60S ribosome biogenesis. In this study, Sailer et al. generate a comprehensive and precise timeline of ribosome biogenesis factor (RBF) engagement during 60S maturation and localize previously unmapped RBFs in the yeast Saccharomyces cerevisiae. Overall, their data represent an essential resource for future structural studies of large subunit ribosome biogenesis.
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Affiliation(s)
- Carolin Sailer
- Department of Biology, University of Konstanz, Universitätsstrae 10, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrae 10, 78457 Konstanz, Germany
| | - Jasmin Jansen
- Department of Biology, University of Konstanz, Universitätsstrae 10, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrae 10, 78457 Konstanz, Germany
| | - Kamil Sekulski
- Department of Biophysics, UT Southwestern Medical Center - ND10.124B, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Victor E Cruz
- Department of Biophysics, UT Southwestern Medical Center - ND10.124B, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA
| | - Jan P Erzberger
- Department of Biophysics, UT Southwestern Medical Center - ND10.124B, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816, USA.
| | - Florian Stengel
- Department of Biology, University of Konstanz, Universitätsstrae 10, 78457 Konstanz, Germany; Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrae 10, 78457 Konstanz, Germany.
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23
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Karbstein K. Attacking a DEAD problem: The role of DEAD-box ATPases in ribosome assembly and beyond. Methods Enzymol 2022; 673:19-38. [PMID: 35965007 PMCID: PMC10154911 DOI: 10.1016/bs.mie.2022.03.033] [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] [Indexed: 11/30/2022]
Abstract
DEAD-box proteins are a subfamily of ATPases with similarity to RecA-type helicases that are involved in all aspects of RNA Biology. Despite their potential to regulate these processes via their RNA-dependent ATPase activity, their roles remain poorly characterized. Here I describe a roadmap to study these proteins in the context of ribosome assembly, the process that utilizes more than half of all DEAD-box proteins encoded in the yeast genome.
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Affiliation(s)
- Katrin Karbstein
- Department of Integrative Structural and Computational Biology, Scripps Florida, Jupiter, FL, United States; HHMI Faculty Scholar, Chevy Chase, MD, United States; The Skaggs Graduate School of Chemical and Biological Sciences, Scripps Florida, Jupiter, FL, United States.
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24
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Mitterer V, Pertschy B. RNA folding and functions of RNA helicases in ribosome biogenesis. RNA Biol 2022; 19:781-810. [PMID: 35678541 PMCID: PMC9196750 DOI: 10.1080/15476286.2022.2079890] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic ribosome biogenesis involves the synthesis of ribosomal RNA (rRNA) and its stepwise folding into the unique structure present in mature ribosomes. rRNA folding starts already co-transcriptionally in the nucleolus and continues when pre-ribosomal particles further maturate in the nucleolus and upon their transit to the nucleoplasm and cytoplasm. While the approximate order of folding of rRNA subdomains is known, especially from cryo-EM structures of pre-ribosomal particles, the actual mechanisms of rRNA folding are less well understood. Both small nucleolar RNAs (snoRNAs) and proteins have been implicated in rRNA folding. snoRNAs hybridize to precursor rRNAs (pre-rRNAs) and thereby prevent premature folding of the respective rRNA elements. Ribosomal proteins (r-proteins) and ribosome assembly factors might have a similar function by binding to rRNA elements and preventing their premature folding. Besides that, a small group of ribosome assembly factors are thought to play a more active role in rRNA folding. In particular, multiple RNA helicases participate in individual ribosome assembly steps, where they are believed to coordinate RNA folding/unfolding events or the release of proteins from the rRNA. In this review, we summarize the current knowledge on mechanisms of RNA folding and on the specific function of the individual RNA helicases involved. As the yeast Saccharomyces cerevisiae is the organism in which ribosome biogenesis and the role of RNA helicases in this process is best studied, we focused our review on insights from this model organism, but also make comparisons to other organisms where applicable.
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Affiliation(s)
- Valentin Mitterer
- Biochemistry Center, Heidelberg University, Im Neuenheimer Feld 328, Heidelberg, Germany
- BioTechMed-Graz, Graz, Austria
| | - Brigitte Pertschy
- BioTechMed-Graz, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, Graz, Austria
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25
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Oborská-Oplová M, Fischer U, Altvater M, Panse VG. Eukaryotic Ribosome assembly and Nucleocytoplasmic Transport. Methods Mol Biol 2022; 2533:99-126. [PMID: 35796985 PMCID: PMC9761919 DOI: 10.1007/978-1-0716-2501-9_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The process of eukaryotic ribosome assembly stretches across the nucleolus, the nucleoplasm and the cytoplasm, and therefore relies on efficient nucleocytoplasmic transport. In yeast, the import machinery delivers ~140,000 ribosomal proteins every minute to the nucleus for ribosome assembly. At the same time, the export machinery facilitates translocation of ~2000 pre-ribosomal particles every minute through ~200 nuclear pore complexes (NPC) into the cytoplasm. Eukaryotic ribosome assembly also requires >200 conserved assembly factors, which transiently associate with pre-ribosomal particles. Their site(s) of action on maturing pre-ribosomes are beginning to be elucidated. In this chapter, we outline protocols that enable rapid biochemical isolation of pre-ribosomal particles for single particle cryo-electron microscopy (cryo-EM) and in vitro reconstitution of nuclear transport processes. We discuss cell-biological and genetic approaches to investigate how the ribosome assembly and the nucleocytoplasmic transport machineries collaborate to produce functional ribosomes.
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Affiliation(s)
- Michaela Oborská-Oplová
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Ute Fischer
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | | | - Vikram Govind Panse
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
- Faculty of Science, University of Zurich, Zurich, Switzerland.
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26
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Pöll G, Pilsl M, Griesenbeck J, Tschochner H, Milkereit P. Analysis of subunit folding contribution of three yeast large ribosomal subunit proteins required for stabilisation and processing of intermediate nuclear rRNA precursors. PLoS One 2021; 16:e0252497. [PMID: 34813592 PMCID: PMC8610266 DOI: 10.1371/journal.pone.0252497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/17/2021] [Indexed: 11/19/2022] Open
Abstract
In yeast and human cells many of the ribosomal proteins (r-proteins) are required for the stabilisation and productive processing of rRNA precursors. Functional coupling of r-protein assembly with the stabilisation and maturation of subunit precursors potentially promotes the production of ribosomes with defined composition. To further decipher mechanisms of such an intrinsic quality control pathway we analysed here the contribution of three yeast large ribosomal subunit r-proteins rpL2 (uL2), rpL25 (uL23) and rpL34 (eL34) for intermediate nuclear subunit folding steps. Structure models obtained from single particle cryo-electron microscopy analyses provided evidence for specific and hierarchic effects on the stable positioning and remodelling of large ribosomal subunit domains. Based on these structural and previous biochemical data we discuss possible mechanisms of r-protein dependent hierarchic domain arrangement and the resulting impact on the stability of misassembled subunits.
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Affiliation(s)
- Gisela Pöll
- Chair of Biochemistry III, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Michael Pilsl
- Structural Biochemistry Unit, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Joachim Griesenbeck
- Chair of Biochemistry III, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
- * E-mail: (JG); (HT); (PM)
| | - Herbert Tschochner
- Chair of Biochemistry III, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
- * E-mail: (JG); (HT); (PM)
| | - Philipp Milkereit
- Chair of Biochemistry III, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
- * E-mail: (JG); (HT); (PM)
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27
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Aquino GRR, Hackert P, Krogh N, Pan KT, Jaafar M, Henras AK, Nielsen H, Urlaub H, Bohnsack KE, Bohnsack MT. The RNA helicase Dbp7 promotes domain V/VI compaction and stabilization of inter-domain interactions during early 60S assembly. Nat Commun 2021; 12:6152. [PMID: 34686661 PMCID: PMC8536713 DOI: 10.1038/s41467-021-26208-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 09/22/2021] [Indexed: 02/07/2023] Open
Abstract
Early pre-60S ribosomal particles are poorly characterized, highly dynamic complexes that undergo extensive rRNA folding and compaction concomitant with assembly of ribosomal proteins and exchange of assembly factors. Pre-60S particles contain numerous RNA helicases, which are likely regulators of accurate and efficient formation of appropriate rRNA structures. Here we reveal binding of the RNA helicase Dbp7 to domain V/VI of early pre-60S particles in yeast and show that in the absence of this protein, dissociation of the Npa1 scaffolding complex, release of the snR190 folding chaperone, recruitment of the A3 cluster factors and binding of the ribosomal protein uL3 are impaired. uL3 is critical for formation of the peptidyltransferase center (PTC) and is responsible for stabilizing interactions between the 5′ and 3′ ends of the 25S, an essential pre-requisite for subsequent pre-60S maturation events. Highlighting the importance of pre-ribosome remodeling by Dbp7, our data suggest that in the absence of Dbp7 or its catalytic activity, early pre-ribosomal particles are targeted for degradation. Early steps of large 60S ribosomal subunit biogenesis are not well understood. Here, the authors combine biochemical experiments with protein-RNA crosslinking and mass spectrometry to show that the RNA helicase Dbp7 is key player during early 60S ribosomal assembly. Dbp7 regulates a series of events driving compaction of domain V/VI in early pre60S ribosomal particles.
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Affiliation(s)
- Gerald Ryan R Aquino
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200N, Copenhagen, Denmark
| | - Kuan-Ting Pan
- Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, 37077, Göttingen, Germany.,Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590, Frankfurt am Main, Germany.,Frankfurt Cancer Institute, Goethe University, 60596, Frankfurt am Main, Germany
| | - Mariam Jaafar
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062, Toulouse, France
| | - Anthony K Henras
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062, Toulouse, France
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200N, Copenhagen, Denmark.,Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Henning Urlaub
- Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, 37077, Göttingen, Germany.,Institute for Clinical Chemistry, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany. .,Göttingen Centre for Molecular Biosciences, Georg-August-University, Justus-von-Liebig Weg 11, 37077, Göttingen, Germany.
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28
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Bagatelli FFM, de Luna Vitorino FN, da Cunha JPC, Oliveira CC. The ribosome assembly factor Nop53 has a structural role in the formation of nuclear pre-60S intermediates, affecting late maturation events. Nucleic Acids Res 2021; 49:7053-7074. [PMID: 34125911 PMCID: PMC8266606 DOI: 10.1093/nar/gkab494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/18/2021] [Accepted: 05/24/2021] [Indexed: 12/19/2022] Open
Abstract
Eukaryotic ribosome biogenesis is an elaborate process during which ribosomal proteins assemble with the pre-rRNA while it is being processed and folded. Hundreds of assembly factors (AF) are required and transiently recruited to assist the sequential remodeling events. One of the most intricate ones is the stepwise removal of the internal transcribed spacer 2 (ITS2), between the 5.8S and 25S rRNAs, that constitutes together with five AFs the pre-60S ‘foot’. In the transition from nucleolus to nucleoplasm, Nop53 replaces Erb1 at the basis of the foot and recruits the RNA exosome for the ITS2 cleavage and foot disassembly. Here we comprehensively analyze the impact of Nop53 recruitment on the pre-60S compositional changes. We show that depletion of Nop53, different from nop53 mutants lacking the exosome-interacting motif, not only causes retention of the unprocessed foot in late pre-60S intermediates but also affects the transition from nucleolar state E particle to subsequent nuclear stages. Additionally, we reveal that Nop53 depletion causes the impairment of late maturation events such as Yvh1 recruitment. In light of recently described pre-60S cryo-EM structures, our results provide biochemical evidence for the structural role of Nop53 rearranging and stabilizing the foot interface to assist the Nog2 particle formation.
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Affiliation(s)
- Felipe F M Bagatelli
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-000, Brazil
| | - Francisca N de Luna Vitorino
- Laboratory of Cell Cycle, Butantan Institute, São Paulo, SP 05503-900, Brazil.,Center of Toxins, Immune-Response and Cell Signaling, Butantan Institute, São Paulo, SP 05503-900, Brazil
| | - Julia P C da Cunha
- Laboratory of Cell Cycle, Butantan Institute, São Paulo, SP 05503-900, Brazil.,Center of Toxins, Immune-Response and Cell Signaling, Butantan Institute, São Paulo, SP 05503-900, Brazil
| | - Carla C Oliveira
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP 05508-000, Brazil
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29
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Tartakoff AM, Chen L, Raghavachari S, Gitiforooz D, Dhinakaran A, Ni CL, Pasadyn C, Mahabeleshwar GH, Pasadyn V, Woolford JL. The nucleolus as a polarized coaxial cable in which the rDNA axis is surrounded by dynamic subunit-specific phases. Curr Biol 2021; 31:2507-2519.e4. [PMID: 33862007 PMCID: PMC8222187 DOI: 10.1016/j.cub.2021.03.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/18/2021] [Accepted: 03/11/2021] [Indexed: 12/24/2022]
Abstract
In ribosomal DNA (rDNA) repeats, sequences encoding small-subunit (SSU) rRNA precede those encoding large-subunit (LSU) rRNAs. Processing the composite transcript and subunit assembly requires >100 subunit-specific nucleolar assembly factors (AFs). To investigate the functional organization of the nucleolus, we localized AFs in S. cerevisiae in which the rDNA axis was "linearized" to reduce its dimensionality, thereby revealing its coaxial organization. In this situation, rRNA synthesis and processing continue. The axis is embedded in an inner layer/phase of SSU AFs that is surrounded by an outer layer/phase of LSU AFs. When subunit production is inhibited, subsets of AFs differentially relocate between the inner and outer layers, as expected if there is a cycle of repeated relocation whereby "latent" AFs become "operative" when recruited to nascent subunits. Recognition of AF cycling and localization of segments of rRNA make it possible to infer the existence of assembly intermediates that span between the inner and outer layers and to chart the cotranscriptional assembly of each subunit. AF cycling also can explain how having more than one protein phase in the nucleolus makes possible "vectorial 2-phase partitioning" as a driving force for relocation of nascent rRNPs. Because nucleoplasmic AFs are also present in the outer layer, we propose that critical surface remodeling occurs at this site, thereby partitioning subunit precursors into the nucleoplasm for post-transcriptional maturation. Comparison to observations on higher eukaryotes shows that the coaxial paradigm is likely to be applicable for the many other organisms that have rDNA repeats.
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Affiliation(s)
- Alan M Tartakoff
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA.
| | - Lan Chen
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - Shashank Raghavachari
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - Daria Gitiforooz
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - Akshyasri Dhinakaran
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - Chun-Lun Ni
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | | | - Ganapati H Mahabeleshwar
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - Vanessa Pasadyn
- Department of Pathology and Cell Biology Program, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH 44106, USA
| | - John L Woolford
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
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30
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Wang X, Yue Z, Xu F, Wang S, Hu X, Dai J, Zhao G. Coevolution of ribosomal RNA expansion segment 7L and assembly factor Noc2p specializes the ribosome biogenesis pathway between Saccharomyces cerevisiae and Candida albicans. Nucleic Acids Res 2021; 49:4655-4667. [PMID: 33823547 PMCID: PMC8096215 DOI: 10.1093/nar/gkab218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 03/01/2021] [Accepted: 03/20/2021] [Indexed: 01/20/2023] Open
Abstract
Ribosomes of different species share an evolutionarily conserved core, exhibiting flexible shells formed partially by the addition of species-specific ribosomal RNAs (rRNAs) with largely unexplored functions. In this study, we showed that by swapping the Saccharomyces cerevisiae 25S rRNA genes with non-S. cerevisiae homologs, species-specific rRNA variations caused moderate to severe pre-rRNA processing defects. Specifically, rRNA substitution by the Candida albicans caused severe growth defects and deficient pre-rRNA processing. We observed that such defects could be attributed primarily to variations in expansion segment 7L (ES7L) and could be restored by an assembly factor Noc2p mutant (Noc2p-K384R). We showed that swapping ES7L attenuated the incorporation of Noc2p and other proteins (Erb1p, Rrp1p, Rpl6p and Rpl7p) into pre-ribosomes, and this effect could be compensated for by Noc2p-K384R. Furthermore, replacement of Noc2p with ortholog from C. albicans could also enhance the incorporation of Noc2p and the above proteins into pre-ribosomes and consequently restore normal growth. Taken together, our findings help to elucidate the roles played by the species-specific rRNA variations in ribosomal biogenesis and further provide evidence that coevolution of rRNA expansion segments and cognate assembly factors specialized the ribosome biogenesis pathway, providing further insights into the function and evolution of ribosome.
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Affiliation(s)
- Xiangxiang Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, China
| | - Zhiyong Yue
- School of Medicine, Xi'an International University, Xi'an 710077, China
| | - Feifei Xu
- Department of Anesthesiology and Perioperative Medicine, Xijing Hospital, the Fourth Military Medical University, Xi'an 710032, China
| | - Sufang Wang
- School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xin Hu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, China
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guanghou Zhao
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, China
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31
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Cragnolini T, Sahota H, Joseph AP, Sweeney A, Malhotra S, Vasishtan D, Topf M. TEMPy2: a Python library with improved 3D electron microscopy density-fitting and validation workflows. Acta Crystallogr D Struct Biol 2021; 77:41-47. [PMID: 33404524 PMCID: PMC7787107 DOI: 10.1107/s2059798320014928] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/10/2020] [Indexed: 11/10/2022] Open
Abstract
Structural determination of molecular complexes by cryo-EM requires large, often complex processing of the image data that are initially obtained. Here, TEMPy2, an update of the TEMPy package to process, optimize and assess cryo-EM maps and the structures fitted to them, is described. New optimization routines, comprehensive automated checks and workflows to perform these tasks are described.
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Affiliation(s)
- Tristan Cragnolini
- Institute of Structural and Molecular Biology, Birkbeck, University College London, London, United Kingdom
| | - Harpal Sahota
- Institute of Structural and Molecular Biology, Birkbeck, University College London, London, United Kingdom
| | - Agnel Praveen Joseph
- Institute of Structural and Molecular Biology, Birkbeck, University College London, London, United Kingdom
| | - Aaron Sweeney
- Institute of Structural and Molecular Biology, Birkbeck, University College London, London, United Kingdom
| | - Sony Malhotra
- Institute of Structural and Molecular Biology, Birkbeck, University College London, London, United Kingdom
| | - Daven Vasishtan
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck, University College London, London, United Kingdom
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32
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Lacoux C, Wacheul L, Saraf K, Pythoud N, Huvelle E, Figaro S, Graille M, Carapito C, Lafontaine DLJ, Heurgué-Hamard V. The catalytic activity of the translation termination factor methyltransferase Mtq2-Trm112 complex is required for large ribosomal subunit biogenesis. Nucleic Acids Res 2020; 48:12310-12325. [PMID: 33166396 PMCID: PMC7708063 DOI: 10.1093/nar/gkaa972] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 01/14/2023] Open
Abstract
The Mtq2-Trm112 methyltransferase modifies the eukaryotic translation termination factor eRF1 on the glutamine side chain of a universally conserved GGQ motif that is essential for release of newly synthesized peptides. Although this modification is found in the three domains of life, its exact role in eukaryotes remains unknown. As the deletion of MTQ2 leads to severe growth impairment in yeast, we have investigated its role further and tested its putative involvement in ribosome biogenesis. We found that Mtq2 is associated with nuclear 60S subunit precursors, and we demonstrate that its catalytic activity is required for nucleolar release of pre-60S and for efficient production of mature 5.8S and 25S rRNAs. Thus, we identify Mtq2 as a novel ribosome assembly factor important for large ribosomal subunit formation. We propose that Mtq2-Trm112 might modify eRF1 in the nucleus as part of a quality control mechanism aimed at proof-reading the peptidyl transferase center, where it will subsequently bind during translation termination.
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Affiliation(s)
- Caroline Lacoux
- UMR8261 (CNRS, Université de Paris), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Ludivine Wacheul
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles Cancer Research Center (U-CRC), Center for Microscopy and Molecular Imaging (CMMI), Gosselies, Belgium
| | - Kritika Saraf
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles Cancer Research Center (U-CRC), Center for Microscopy and Molecular Imaging (CMMI), Gosselies, Belgium
| | - Nicolas Pythoud
- Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), UMR 7178, IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Emmeline Huvelle
- UMR8261 (CNRS, Université de Paris), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Sabine Figaro
- UMR8261 (CNRS, Université de Paris), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, F-91128 Palaiseau, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), UMR 7178, IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Denis L J Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles Cancer Research Center (U-CRC), Center for Microscopy and Molecular Imaging (CMMI), Gosselies, Belgium
| | - Valérie Heurgué-Hamard
- UMR8261 (CNRS, Université de Paris), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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33
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Mutational Analysis of the Nsa2 N-Terminus Reveals Its Essential Role in Ribosomal 60S Subunit Assembly. Int J Mol Sci 2020; 21:ijms21239108. [PMID: 33266193 PMCID: PMC7730687 DOI: 10.3390/ijms21239108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 11/23/2022] Open
Abstract
The ribosome assembly factor Nsa2 is part of the Rea1-Rsa4-Nsa2 interconnected relay on nuclear pre-60S particles that is essential for 60S ribosome biogenesis. Cryo-EM structures depict Nsa2 docked via its C-terminal β-barrel domain to nuclear pre-60S particles, whereas the extended N-terminus, consisting of three α-helical segments, meanders between various 25S rRNA helices with the extreme N-terminus in close vicinity to the Nog1 GTPase center. Here, we tested whether this unappreciated proximity between Nsa2 and Nog1 is of functional importance. Our findings demonstrate that a conservative mutation, Nsa2 Q3N, abolished cell growth and impaired 60S biogenesis. Subsequent genetic and biochemical analyses verified that the Nsa2 N-terminus is required to target Nsa2 to early pre-60S particles. However, overexpression of the Nsa2 N-terminus abolished cytoplasmic recycling of the Nog1 GTPase, and both Nog1 and the Nsa2-N (1-58) construct, but not the respective Nsa2-N (1-58) Q3N mutant, were found arrested on late cytoplasmic pre-60S particles. These findings point to specific roles of the different Nsa2 domains for 60S ribosome biogenesis.
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34
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Structure of the mature kinetoplastids mitoribosome and insights into its large subunit biogenesis. Proc Natl Acad Sci U S A 2020; 117:29851-29861. [PMID: 33168716 PMCID: PMC7703582 DOI: 10.1073/pnas.2011301117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Kinetoplastids is a group of flagellated unicellular eukaryotic parasites including human pathogens, such as Trypanosoma cruzi and Leishmania spp., etiologic agents of Chagas disease and leishmaniasis. They are potentially lethal, affecting more than 20 million people worldwide. Therapeutic strategies are extremely limited and highly toxic. The finding of new molecular targets represents one venue for the development of new therapeutic strategies. In this work, we present the structure of the full mitoribosomes from two kinetoplastids, Leishmania tarentolae and T. cruzi, thus far uncharacterized. We also reveal the structure of an large subunit assembly intermediate harboring 16 different factors. In addition to defining a subset of novel kinetoplastid-specific factors, our results shed light on the mitochondrial ribosomal RNA maturation process. Kinetoplastids are unicellular eukaryotic parasites responsible for such human pathologies as Chagas disease, sleeping sickness, and leishmaniasis. They have a single large mitochondrion, essential for the parasite survival. In kinetoplastid mitochondria, most of the molecular machineries and gene expression processes have significantly diverged and specialized, with an extreme example being their mitochondrial ribosomes. These large complexes are in charge of translating the few essential mRNAs encoded by mitochondrial genomes. Structural studies performed in Trypanosoma brucei already highlighted the numerous peculiarities of these mitoribosomes and the maturation of their small subunit. However, several important aspects mainly related to the large subunit (LSU) remain elusive, such as the structure and maturation of its ribosomal RNA. Here we present a cryo-electron microscopy study of the protozoans Leishmania tarentolae and Trypanosoma cruzi mitoribosomes. For both species, we obtained the structure of their mature mitoribosomes, complete rRNA of the LSU, as well as previously unidentified ribosomal proteins. In addition, we introduce the structure of an LSU assembly intermediate in the presence of 16 identified maturation factors. These maturation factors act on both the intersubunit and the solvent sides of the LSU, where they refold and chemically modify the rRNA and prevent early translation before full maturation of the LSU.
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35
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Micic J, Li Y, Wu S, Wilson D, Tutuncuoglu B, Gao N, Woolford JL. Coupling of 5S RNP rotation with maturation of functional centers during large ribosomal subunit assembly. Nat Commun 2020; 11:3751. [PMID: 32719344 PMCID: PMC7385084 DOI: 10.1038/s41467-020-17534-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 06/29/2020] [Indexed: 12/29/2022] Open
Abstract
The protein composition and structure of assembling 60S ribosomal subunits undergo numerous changes as pre-ribosomes transition from the nucleolus to the nucleoplasm. This includes stable anchoring of the Rpf2 subcomplex containing 5S rRNA, rpL5, rpL11, Rpf2 and Rrs1, which initially docks onto the flexible domain V of rRNA at earlier stages of assembly. In this work, we tested the function of the C-terminal domain (CTD) of Rpf2 during these anchoring steps, by truncating this extension and assaying effects on middle stages of subunit maturation. The rpf2Δ255-344 mutation affects proper folding of rRNA helices H68-70 during anchoring of the Rpf2 subcomplex. In addition, several assembly factors (AFs) are absent from pre-ribosomes or in altered conformations. Consequently, major remodeling events fail to occur: rotation of the 5S RNP, maturation of the peptidyl transferase center (PTC) and the nascent polypeptide exit tunnel (NPET), and export of assembling subunits to the cytoplasm. As assembling 60S subunits transit from the nucleolus to the nucleoplasm, they undergo significant changes in protein composition and structure. Here, the authors provide a structural view of interconnected events during the middle steps of assembly that include the maturation of the central protuberance, the peptidyltransferase center and the nascent polypeptide exit tunnel.
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Affiliation(s)
- Jelena Micic
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yu Li
- State Key Laboratory of Membrane Biology, School of Life Science, Tsinghua University, Beijing, China.,Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Beijing, China
| | - Shan Wu
- State Key Laboratory of Membrane Biology, School of Life Science, Tsinghua University, Beijing, China.,State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, China
| | - Daniel Wilson
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Beril Tutuncuoglu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China.
| | - John L Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA.
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Kater L, Mitterer V, Thoms M, Cheng J, Berninghausen O, Beckmann R, Hurt E. Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis. Mol Cell 2020; 79:615-628.e5. [PMID: 32668200 DOI: 10.1016/j.molcel.2020.06.032] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/13/2020] [Accepted: 06/18/2020] [Indexed: 12/15/2022]
Abstract
Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering poorly understood large-scale structural transitions that we analyzed by cryo-electron microscopy. Two nuclear pre-60S intermediates were discovered that represent previously unknown states after Rea1-mediated removal of the Ytm1-Erb1 complex and reveal how the L1 stalk develops from a pre-mature nucleolar to a mature-like nucleoplasmic state. A later pre-60S intermediate shows how the central protuberance arises, assisted by the nearby Rix1-Rea1 machinery, which was solved in its pre-ribosomal context to molecular resolution. This revealed a Rix12-Ipi32 tetramer anchored to the pre-60S via Ipi1, strategically positioned to monitor this decisive remodeling. These results are consistent with a general underlying principle that temporarily stabilized immature RNA domains are successively remodeled by assembly factors, thereby ensuring failsafe assembly progression.
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Affiliation(s)
- Lukas Kater
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany
| | - Valentin Mitterer
- Biochemie-Zentrum der Universität Heidelberg, 69120 Heidelberg, Germany
| | - Matthias Thoms
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany; Biochemie-Zentrum der Universität Heidelberg, 69120 Heidelberg, Germany
| | - Jingdong Cheng
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany
| | - Otto Berninghausen
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany
| | - Roland Beckmann
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany.
| | - Ed Hurt
- Biochemie-Zentrum der Universität Heidelberg, 69120 Heidelberg, Germany.
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37
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From Snapshots to Flipbook-Resolving the Dynamics of Ribosome Biogenesis with Chemical Probes. Int J Mol Sci 2020; 21:ijms21082998. [PMID: 32340379 PMCID: PMC7215809 DOI: 10.3390/ijms21082998] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 12/27/2022] Open
Abstract
The synthesis of ribosomes is one of the central and most resource demanding processes in each living cell. As ribosome biogenesis is tightly linked with the regulation of the cell cycle, perturbation of ribosome formation can trigger severe diseases, including cancer. Eukaryotic ribosome biogenesis starts in the nucleolus with pre-rRNA transcription and the initial assembly steps, continues in the nucleoplasm and is finished in the cytoplasm. From start to end, this process is highly dynamic and finished within few minutes. Despite the tremendous progress made during the last decade, the coordination of the individual maturation steps is hard to unravel by a conventional methodology. In recent years small molecular compounds were identified that specifically block either rDNA transcription or distinct steps within the maturation pathway. As these inhibitors diffuse into the cell rapidly and block their target proteins within seconds, they represent excellent tools to investigate ribosome biogenesis. Here we review how the inhibitors affect ribosome biogenesis and discuss how these effects can be interpreted by taking the complex self-regulatory mechanisms of the pathway into account. With this we want to highlight the potential of low molecular weight inhibitors to approach the dynamic nature of the ribosome biogenesis pathway.
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Abstract
In the past 25 years, genetic and biochemical analyses of ribosome assembly in yeast have identified most of the factors that participate in this complex pathway and have generated models for the mechanisms driving the assembly. More recently, the publication of numerous cryo-electron microscopy structures of yeast ribosome assembly intermediates has provided near-atomic resolution snapshots of ribosome precursor particles. Satisfyingly, these structural data support the genetic and biochemical models and provide additional mechanistic insight into ribosome assembly. In this Review, we discuss the mechanisms of assembly of the yeast small ribosomal subunit and large ribosomal subunit in the nucleolus, nucleus and cytoplasm. Particular emphasis is placed on concepts such as the mechanisms of RNA compaction, the functions of molecular switches and molecular mimicry, the irreversibility of assembly checkpoints and the roles of structural and functional proofreading of pre-ribosomal particles.
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Gnanasundram SV, Kos-Braun IC, Koš M. At least two molecules of the RNA helicase Has1 are simultaneously present in pre-ribosomes during ribosome biogenesis. Nucleic Acids Res 2019; 47:10852-10864. [PMID: 31511893 PMCID: PMC6846684 DOI: 10.1093/nar/gkz767] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 11/20/2022] Open
Abstract
The RNA helicase Has1 is involved in the biogenesis of both small and large ribosomal subunits. How it performs these separate roles is not fully understood. Here we provide evidence that at least two molecules of Has1 are temporarily present at the same time in 90S pre-ribosomes. We identified multiple Has1 binding sites in the 18S, 5.8S and 25S rRNAs. We show that while the Has1 catalytic activity is not required for binding to 5.8S/25S region in pre-rRNA, it is essential for binding to 18S sites. After the cleavage of pre-rRNA at the A2 site, Has1 remains associated not only with pre-60S but, unexpectedly, also with pre-40S ribosomes. The recruitment to 90S/pre-40S and pre-60S ribosomes is mutually independent. Our data provides insight into how Has1 performs its separate functions in the synthesis of both ribosomal subunits.
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Affiliation(s)
- Sivakumar Vadivel Gnanasundram
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
- Inserm UMR1131, Institute Universitaire d’Hématologie, Hôpital St. Louis, F-75010 Paris, France
| | - Isabelle C Kos-Braun
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Martin Koš
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
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40
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Shaping the Nascent Ribosome: AAA-ATPases in Eukaryotic Ribosome Biogenesis. Biomolecules 2019; 9:biom9110715. [PMID: 31703473 PMCID: PMC6920918 DOI: 10.3390/biom9110715] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 02/08/2023] Open
Abstract
AAA-ATPases are molecular engines evolutionarily optimized for the remodeling of proteins and macromolecular assemblies. Three AAA-ATPases are currently known to be involved in the remodeling of the eukaryotic ribosome, a megadalton range ribonucleoprotein complex responsible for the translation of mRNAs into proteins. The correct assembly of the ribosome is performed by a plethora of additional and transiently acting pre-ribosome maturation factors that act in a timely and spatially orchestrated manner. Minimal disorder of the assembly cascade prohibits the formation of functional ribosomes and results in defects in proliferation and growth. Rix7, Rea1, and Drg1, which are well conserved across eukaryotes, are involved in different maturation steps of pre-60S ribosomal particles. These AAA-ATPases provide energy for the efficient removal of specific assembly factors from pre-60S particles after they have fulfilled their function in the maturation cascade. Recent structural and functional insights have provided the first glimpse into the molecular mechanism of target recognition and remodeling by Rix7, Rea1, and Drg1. Here we summarize current knowledge on the AAA-ATPases involved in eukaryotic ribosome biogenesis. We highlight the latest insights into their mechanism of mechano-chemical complex remodeling driven by advanced cryo-EM structures and the use of highly specific AAA inhibitors.
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Chikne V, Shanmugha Rajan K, Shalev-Benami M, Decker K, Cohen-Chalamish S, Madmoni H, Biswas VK, Kumar Gupta S, Doniger T, Unger R, Tschudi C, Ullu E, Michaeli S. Small nucleolar RNAs controlling rRNA processing in Trypanosoma brucei. Nucleic Acids Res 2019; 47:2609-2629. [PMID: 30605535 PMCID: PMC6411936 DOI: 10.1093/nar/gky1287] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 12/04/2018] [Accepted: 12/20/2018] [Indexed: 12/19/2022] Open
Abstract
In trypanosomes, in contrast to most eukaryotes, the large subunit (LSU) ribosomal RNA is fragmented into two large and four small ribosomal RNAs (srRNAs) pieces, and this additional processing likely requires trypanosome-specific factors. Here, we examined the role of 10 abundant small nucleolar RNAs (snoRNAs) involved in rRNA processing. We show that each snoRNA involved in LSU processing associates with factors engaged in either early or late biogenesis steps. Five of these snoRNAs interact with the intervening sequences of rRNA precursor, whereas the others only guide rRNA modifications. The function of the snoRNAs was explored by silencing snoRNAs. The data suggest that the LSU rRNA processing events do not correspond to the order of rRNA transcription, and that srRNAs 2, 4 and 6 which are part of LSU are processed before srRNA1. Interestingly, the 6 snoRNAs that affect srRNA1 processing guide modifications on rRNA positions that span locations from the protein exit tunnel to the srRNA1, suggesting that these modifications may serve as check-points preceding the liberation of srRNA1. This study identifies the highest number of snoRNAs so far described that are involved in rRNA processing and/or rRNA folding and highlights their function in the unique trypanosome rRNA maturation events.
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Affiliation(s)
- Vaibhav Chikne
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - K Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Moran Shalev-Benami
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Kathryn Decker
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Smadar Cohen-Chalamish
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Hava Madmoni
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Viplov K Biswas
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Sachin Kumar Gupta
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Ron Unger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
| | - Christian Tschudi
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06536, USA
| | - Elisabetta Ullu
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06536, USA
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900 Israel
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42
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Sleiman S, Dragon F. Recent Advances on the Structure and Function of RNA Acetyltransferase Kre33/NAT10. Cells 2019; 8:cells8091035. [PMID: 31491951 PMCID: PMC6770127 DOI: 10.3390/cells8091035] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/23/2019] [Accepted: 08/25/2019] [Indexed: 02/07/2023] Open
Abstract
Ribosome biogenesis is one of the most energy demanding processes in the cell. In eukaryotes, the main steps of this process occur in the nucleolus and include pre-ribosomal RNA (pre-rRNA) processing, post-transcriptional modifications, and assembly of many non-ribosomal factors and ribosomal proteins in order to form mature and functional ribosomes. In yeast and humans, the nucleolar RNA acetyltransferase Kre33/NAT10 participates in different maturation events, such as acetylation and processing of 18S rRNA, and assembly of the 40S ribosomal subunit. Here, we review the structural and functional features of Kre33/NAT10 RNA acetyltransferase, and we underscore the importance of this enzyme in ribosome biogenesis, as well as in acetylation of non-ribosomal targets. We also report on the role of human NAT10 in Hutchinson-Gilford progeria syndrome.
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Affiliation(s)
- Sophie Sleiman
- Département des Sciences Biologiques and Centre d'Excellence en Recherche sur les Maladies Orphelines-Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, QC H3C 3P8, Canada.
| | - Francois Dragon
- Département des Sciences Biologiques and Centre d'Excellence en Recherche sur les Maladies Orphelines-Fondation Courtois (CERMO-FC), Université du Québec à Montréal, Montréal, QC H3C 3P8, Canada.
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43
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Thermophile 90S Pre-ribosome Structures Reveal the Reverse Order of Co-transcriptional 18S rRNA Subdomain Integration. Mol Cell 2019; 75:1256-1269.e7. [DOI: 10.1016/j.molcel.2019.06.032] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 06/11/2019] [Accepted: 06/21/2019] [Indexed: 11/23/2022]
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44
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Correll CC, Bartek J, Dundr M. The Nucleolus: A Multiphase Condensate Balancing Ribosome Synthesis and Translational Capacity in Health, Aging and Ribosomopathies. Cells 2019; 8:cells8080869. [PMID: 31405125 PMCID: PMC6721831 DOI: 10.3390/cells8080869] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/31/2019] [Accepted: 08/06/2019] [Indexed: 12/21/2022] Open
Abstract
The nucleolus is the largest membrane-less structure in the eukaryotic nucleus. It is involved in the biogenesis of ribosomes, essential macromolecular machines responsible for synthesizing all proteins required by the cell. The assembly of ribosomes is evolutionarily conserved and is the most energy-consuming cellular process needed for cell growth, proliferation, and homeostasis. Despite the significance of this process, the intricate pathophysiological relationship between the nucleolus and protein synthesis has only recently begun to emerge. Here, we provide perspective on new principles governing nucleolar formation and the resulting multiphase organization driven by liquid-liquid phase separation. With recent advances in the structural analysis of ribosome formation, we highlight the current understanding of the step-wise assembly of pre-ribosomal subunits and the quality control required for proper function. Finally, we address how aging affects ribosome genesis and how genetic defects in ribosome formation cause ribosomopathies, complex diseases with a predisposition to cancer.
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Affiliation(s)
- Carl C Correll
- Center for Proteomics and Molecular Therapeutics, Rosalind Franklin University of Medicine & Science, North Chicago, IL 60064, USA.
| | - Jiri Bartek
- Danish Cancer Society Research Center, Genome Integrity Unit, DK-2100 Copenhagen, Denmark
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Miroslav Dundr
- Center for Cancer Cell Biology Immunology and Infection, Rosalind Franklin University of Medicine & Science, North Chicago, IL 60064, USA.
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45
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Awad D, Prattes M, Kofler L, Rössler I, Loibl M, Pertl M, Zisser G, Wolinski H, Pertschy B, Bergler H. Inhibiting eukaryotic ribosome biogenesis. BMC Biol 2019; 17:46. [PMID: 31182083 PMCID: PMC6558755 DOI: 10.1186/s12915-019-0664-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/14/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Ribosome biogenesis is a central process in every growing cell. In eukaryotes, it requires more than 250 non-ribosomal assembly factors, most of which are essential. Despite this large repertoire of potential targets, only very few chemical inhibitors of ribosome biogenesis are known so far. Such inhibitors are valuable tools to study this highly dynamic process and elucidate mechanistic details of individual maturation steps. Moreover, ribosome biogenesis is of particular importance for fast proliferating cells, suggesting its inhibition could be a valid strategy for treatment of tumors or infections. RESULTS We systematically screened ~ 1000 substances for inhibitory effects on ribosome biogenesis using a microscopy-based screen scoring ribosomal subunit export defects. We identified 128 compounds inhibiting maturation of either the small or the large ribosomal subunit or both. Northern blot analysis demonstrates that these inhibitors cause a broad spectrum of different rRNA processing defects. CONCLUSIONS Our findings show that the individual inhibitors affect a wide range of different maturation steps within the ribosome biogenesis pathway. Our results provide for the first time a comprehensive set of inhibitors to study ribosome biogenesis by chemical inhibition of individual maturation steps and establish the process as promising druggable pathway for chemical intervention.
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Affiliation(s)
- Dominik Awad
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/EG, A-8010, Graz, Austria.,Present address: Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Prattes
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/EG, A-8010, Graz, Austria
| | - Lisa Kofler
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/EG, A-8010, Graz, Austria
| | - Ingrid Rössler
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/EG, A-8010, Graz, Austria
| | - Mathias Loibl
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/EG, A-8010, Graz, Austria
| | - Melanie Pertl
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/EG, A-8010, Graz, Austria
| | - Gertrude Zisser
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/EG, A-8010, Graz, Austria
| | - Heimo Wolinski
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/EG, A-8010, Graz, Austria
| | - Brigitte Pertschy
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/EG, A-8010, Graz, Austria.
| | - Helmut Bergler
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/EG, A-8010, Graz, Austria.
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46
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Co-Assembly of 40S and 60S Ribosomal Proteins in Early Steps of Eukaryotic Ribosome Assembly. Int J Mol Sci 2019; 20:ijms20112806. [PMID: 31181743 PMCID: PMC6600400 DOI: 10.3390/ijms20112806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/28/2019] [Accepted: 06/06/2019] [Indexed: 01/21/2023] Open
Abstract
In eukaryotes three of the four ribosomal RNA (rRNA) molecules are transcribed as a long precursor that is processed into mature rRNAs concurrently with the assembly of ribosomal subunits. However, the relative timing of association of ribosomal proteins with the ribosomal precursor particles and the cleavage of the precursor rRNA into the subunit-specific moieties is not known. To address this question, we searched for ribosomal precursors containing components from both subunits. Particles containing specific ribosomal proteins were targeted by inducing synthesis of epitope-tagged ribosomal proteins followed by pull-down with antibodies targeting the tagged protein. By identifying other ribosomal proteins and internal rRNA transcribed spacers (ITS1 and ITS2) in the immuno-purified ribosomal particles, we showed that eS7/S7 and uL4/L4 bind to nascent ribosomes prior to the separation of 40S and 60S specific segments, while uS4/S9, uL22, and eL13/L13 are bound after, or simultaneously with, the separation. Thus, the incorporation of ribosomal proteins from the two subunits begins as a co-assembly with a single rRNA molecule, but is finished as an assembly onto separate precursors for the two subunits.
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47
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Chaker-Margot M, Klinge S. Assembly and early maturation of large subunit precursors. RNA (NEW YORK, N.Y.) 2019; 25:465-471. [PMID: 30670483 PMCID: PMC6426289 DOI: 10.1261/rna.069799.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/19/2019] [Indexed: 06/09/2023]
Abstract
The eukaryotic ribosome is assembled through a complex process involving more than 200 factors. As preribosomal RNA is transcribed, assembly factors bind the nascent pre-rRNA and guide its correct folding, modification, and cleavage. While these early events in the assembly of the small ribosomal subunit have been relatively well characterized, assembly of the large subunit precursors, or pre-60S, is less well understood. Recent structures of nucleolar intermediates of large subunit assembly have shed light on the role of many early large subunit assembly factors, but how these particles emerge is still unknown. Here, we use the expression and purification of truncated pre-rRNAs to examine the initial assembly of pre-60S particles. Using this approach, we can recapitulate the early recruitment of large subunit assembly factors mainly to the domains I, II, and VI of the assembling 25S rRNA.
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MESH Headings
- Aptamers, Nucleotide/chemical synthesis
- Aptamers, Nucleotide/metabolism
- Cloning, Molecular
- Organelle Biogenesis
- Plasmids/chemistry
- Plasmids/metabolism
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosome Subunits, Large, Eukaryotic/genetics
- Ribosome Subunits, Large, Eukaryotic/metabolism
- Ribosome Subunits, Large, Eukaryotic/ultrastructure
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Staining and Labeling/methods
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Affiliation(s)
- Malik Chaker-Margot
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York 10065, USA
- Tri-Institutional Training Program in Chemical Biology, The Rockefeller University, New York, New York 10065, USA
| | - Sebastian Klinge
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York 10065, USA
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48
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RNA helicases mediate structural transitions and compositional changes in pre-ribosomal complexes. Nat Commun 2018; 9:5383. [PMID: 30568249 PMCID: PMC6300602 DOI: 10.1038/s41467-018-07783-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 11/28/2018] [Indexed: 01/31/2023] Open
Abstract
Production of eukaryotic ribosomal subunits is a highly dynamic process; pre-ribosomes undergo numerous structural rearrangements that establish the architecture present in mature complexes and serve as key checkpoints, ensuring the fidelity of ribosome assembly. Using in vivo crosslinking, we here identify the pre-ribosomal binding sites of three RNA helicases. Our data support roles for Has1 in triggering release of the U14 snoRNP, a critical event during early 40S maturation, and in driving assembly of domain I of pre-60S complexes. Binding of Mak5 to domain II of pre-60S complexes promotes recruitment of the ribosomal protein Rpl10, which is necessary for subunit joining and ribosome function. Spb4 binds to a molecular hinge at the base of ES27 facilitating binding of the export factor Arx1, thereby promoting pre-60S export competence. Our data provide important insights into the driving forces behind key structural remodelling events during ribosomal subunit assembly.
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49
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Thoms M, Mitterer V, Kater L, Falquet L, Beckmann R, Kressler D, Hurt E. Suppressor mutations in Rpf2-Rrs1 or Rpl5 bypass the Cgr1 function for pre-ribosomal 5S RNP-rotation. Nat Commun 2018; 9:4094. [PMID: 30291245 PMCID: PMC6173701 DOI: 10.1038/s41467-018-06660-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 09/17/2018] [Indexed: 12/03/2022] Open
Abstract
During eukaryotic 60S biogenesis, the 5S RNP requires a large rotational movement to achieve its mature position. Cryo-EM of the Rix1-Rea1 pre-60S particle has revealed the post-rotation stage, in which a gently undulating α-helix corresponding to Cgr1 becomes wedged between Rsa4 and the relocated 5S RNP, but the purpose of this insertion was unknown. Here, we show that cgr1 deletion in yeast causes a slow-growth phenotype and reversion of the pre-60S particle to the pre-rotation stage. However, spontaneous extragenic suppressors could be isolated, which restore growth and pre-60S biogenesis in the absence of Cgr1. Whole-genome sequencing reveals that the suppressor mutations map in the Rpf2–Rrs1 module and Rpl5, which together stabilize the unrotated stage of the 5S RNP. Thus, mutations in factors stabilizing the pre-rotation stage facilitate 5S RNP relocation upon deletion of Cgr1, but Cgr1 itself could stabilize the post-rotation stage. During biogenesis of the eukaryotic 60S ribosome, a large rotational movement of the 5S RNP is required to achieve its mature position. By analyzing extragenic suppressors of crg1—a key factor required for rotation—the authors provide mechanistic insight into a key step of ribosome biogenesis.
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Affiliation(s)
- Matthias Thoms
- Biochemistry Centre, University of Heidelberg, Heidelberg, 69120, Germany.
| | - Valentin Mitterer
- Biochemistry Centre, University of Heidelberg, Heidelberg, 69120, Germany
| | - Lukas Kater
- Gene Center, University of Munich, Munich, 81377, Germany
| | - Laurent Falquet
- University of Fribourg and Swiss Institute of Bioinformatics, Fribourg, 1700, Switzerland
| | | | - Dieter Kressler
- University of Fribourg and Swiss Institute of Bioinformatics, Fribourg, 1700, Switzerland
| | - Ed Hurt
- Biochemistry Centre, University of Heidelberg, Heidelberg, 69120, Germany.
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Joret C, Capeyrou R, Belhabich-Baumas K, Plisson-Chastang C, Ghandour R, Humbert O, Fribourg S, Leulliot N, Lebaron S, Henras AK, Henry Y. The Npa1p complex chaperones the assembly of the earliest eukaryotic large ribosomal subunit precursor. PLoS Genet 2018; 14:e1007597. [PMID: 30169518 PMCID: PMC6136799 DOI: 10.1371/journal.pgen.1007597] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 09/13/2018] [Accepted: 07/30/2018] [Indexed: 11/18/2022] Open
Abstract
The early steps of the production of the large ribosomal subunit are probably the least understood stages of eukaryotic ribosome biogenesis. The first specific precursor to the yeast large ribosomal subunit, the first pre-60S particle, contains 30 assembly factors (AFs), including 8 RNA helicases. These helicases, presumed to drive conformational rearrangements, usually lack substrate specificity in vitro. The mechanisms by which they are targeted to their correct substrate within pre-ribosomal particles and their precise molecular roles remain largely unknown. We demonstrate that the Dbp6p helicase, essential for the normal accumulation of the first pre-60S pre-ribosomal particle in S. cerevisiae, associates with a complex of four AFs, namely Npa1p, Npa2p, Nop8p and Rsa3p, prior to their incorporation into the 90S pre-ribosomal particles. By tandem affinity purifications using yeast extracts depleted of one component of the complex, we show that Npa1p forms the backbone of the complex. We provide evidence that Npa1p and Npa2p directly bind Dbp6p and we demonstrate that Npa1p is essential for the insertion of the Dbp6p helicase within 90S pre-ribosomal particles. In addition, by an in vivo cross-linking analysis (CRAC), we map Npa1p rRNA binding sites on 25S rRNA adjacent to the root helices of the first and last secondary structure domains of 25S rRNA. This finding supports the notion that Npa1p and Dbp6p function in the formation and/or clustering of root helices of large subunit rRNAs which creates the core of the large ribosomal subunit RNA structure. Npa1p also crosslinks to snoRNAs involved in decoding center and peptidyl transferase center modifications and in the immediate vicinity of the binding sites of these snoRNAs on 25S rRNA. Our data suggest that the Dbp6p helicase and the Npa1p complex play key roles in the compaction of the central core of 25S rRNA and the control of snoRNA-pre-rRNA interactions. Ribosomes, the molecular machines synthesizing proteins, are composed of a small and large subunit, formed by the binding of numerous ribosomal proteins (RPs) to properly folded ribosomal RNAs (rRNAs). RP incorporation as well as processing and folding of rRNAs occur within a succession of pre-ribosomal particles. Formation of the initial pre-60S particle, the first precursor to the large ribosomal subunit, is the least understood step of ribosome biogenesis in eukaryotes. This pre-ribosomal particle contains several assembly factors (AFs), including RNA helicases believed to catalyse key conformational rearrangements. These helicases usually lack substrate specificity on their own. Here, we show that the Dbp6p helicase, a component of the first pre-60S particle and essential for its normal accumulation, associates with a complex of four AFs, including Npa1p. We demonstrate that Npa1p directly binds Dbp6p, forms the backbone of the complex and is required for the integration of Dbp6p within pre-ribosomal particles. We show that Npa1p binds to sequences forming the core of large subunit rRNAs as well as small nucleolar RNAs required for chemical modification of large subunit rRNAs. Altogether our results suggest that the Npa1p complex plays a crucial role in the chemical modification and folding of large subunit rRNAs.
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Affiliation(s)
- Clément Joret
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Régine Capeyrou
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Kamila Belhabich-Baumas
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Célia Plisson-Chastang
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Rabea Ghandour
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Odile Humbert
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | | | - Nicolas Leulliot
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, Paris, France
| | - Simon Lebaron
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
- * E-mail: (SL); (AKH); (YH)
| | - Anthony K. Henras
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
- * E-mail: (SL); (AKH); (YH)
| | - Yves Henry
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
- * E-mail: (SL); (AKH); (YH)
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