1
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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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2
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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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3
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Parker MD, Karbstein K. Quality control ensures fidelity in ribosome assembly and cellular health. J Cell Biol 2023; 222:213871. [PMID: 36790396 PMCID: PMC9960125 DOI: 10.1083/jcb.202209115] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/09/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
The coordinated integration of ribosomal RNA and protein into two functional ribosomal subunits is safeguarded by quality control checkpoints that ensure ribosomes are correctly assembled and functional before they engage in translation. Quality control is critical in maintaining the integrity of ribosomes and necessary to support healthy cell growth and prevent diseases associated with mistakes in ribosome assembly. Its importance is demonstrated by the finding that bypassing quality control leads to misassembled, malfunctioning ribosomes with altered translation fidelity, which change gene expression and disrupt protein homeostasis. In this review, we outline our understanding of quality control within ribosome synthesis and how failure to enforce quality control contributes to human disease. We first provide a definition of quality control to guide our investigation, briefly present the main assembly steps, and then examine stages of assembly that test ribosome function, establish a pass-fail system to evaluate these functions, and contribute to altered ribosome performance when bypassed, and are thus considered "quality control."
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Affiliation(s)
- Melissa D. Parker
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA,University of Florida—Scripps Biomedical Research, Jupiter, FL, USA
| | - Katrin Karbstein
- The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA,University of Florida—Scripps Biomedical Research, Jupiter, FL, USA,Howard Hughes Medical Institute Faculty Scholar, Howard Hughes Medical Institute, Chevy Chase, MD, USA,Correspondence to Katrin Karbstein:
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4
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Dörner K, Ruggeri C, Zemp I, Kutay U. Ribosome biogenesis factors-from names to functions. EMBO J 2023; 42:e112699. [PMID: 36762427 PMCID: PMC10068337 DOI: 10.15252/embj.2022112699] [Citation(s) in RCA: 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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5
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Webster SF, Ghalei H. Maturation of small nucleolar RNAs: from production to function. RNA Biol 2023; 20:715-736. [PMID: 37796118 PMCID: PMC10557570 DOI: 10.1080/15476286.2023.2254540] [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] [Accepted: 08/28/2023] [Indexed: 10/06/2023] Open
Abstract
Small Nucleolar RNAs (snoRNAs) are an abundant group of non-coding RNAs with well-defined roles in ribosomal RNA processing, folding and chemical modification. Besides their classic roles in ribosome biogenesis, snoRNAs are also implicated in several other cellular activities including regulation of splicing, transcription, RNA editing, cellular trafficking, and miRNA-like functions. Mature snoRNAs must undergo a series of processing steps tightly regulated by transiently associating factors and coordinated with other cellular processes including transcription and splicing. In addition to their mature forms, snoRNAs can contribute to gene expression regulation through their derivatives and degradation products. Here, we review the current knowledge on mechanisms of snoRNA maturation, including the different pathways of processing, and the regulatory mechanisms that control snoRNA levels and complex assembly. We also discuss the significance of studying snoRNA maturation, highlight the gaps in the current knowledge and suggest directions for future research in this area.
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Affiliation(s)
- Sarah F. Webster
- Biochemistry, Cell, and Developmental Biology Graduate Program, Emory University, Atlanta, Georgia, USA
- Department of Biochemistry, Emory University, Atlanta, Georgia, USA
| | - Homa Ghalei
- Department of Biochemistry, Emory University, Atlanta, Georgia, USA
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6
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Bhutada P, Favre S, Jaafar M, Hafner J, Liesinger L, Unterweger S, Bischof K, Darnhofer B, Siva Sankar D, Rechberger G, Abou Merhi R, Lebaron S, Birner-Gruenberger R, Kressler D, Henras AK, Pertschy B. Rbp95 binds to 25S rRNA helix H95 and cooperates with the Npa1 complex during early pre-60S particle maturation. Nucleic Acids Res 2022; 50:10053-10077. [PMID: 36018804 PMCID: PMC9508819 DOI: 10.1093/nar/gkac724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 08/05/2022] [Accepted: 08/12/2022] [Indexed: 11/21/2022] Open
Abstract
Eukaryotic ribosome synthesis involves more than 200 assembly factors, which promote ribosomal RNA (rRNA) processing, modification and folding, and assembly of ribosomal proteins. The formation and maturation of the earliest pre-60S particles requires structural remodeling by the Npa1 complex, but is otherwise still poorly understood. Here, we introduce Rbp95 (Ycr016w), a constituent of early pre-60S particles, as a novel ribosome assembly factor. We show that Rbp95 is both genetically and physically linked to most Npa1 complex members and to ribosomal protein Rpl3. We demonstrate that Rbp95 is an RNA-binding protein containing two independent RNA-interacting domains. In vivo, Rbp95 associates with helix H95 in the 3′ region of the 25S rRNA, in close proximity to the binding sites of Npa1 and Rpl3. Additionally, Rbp95 interacts with several snoRNAs. The absence of Rbp95 results in alterations in the protein composition of early pre-60S particles. Moreover, combined mutation of Rbp95 and Npa1 complex members leads to a delay in the maturation of early pre-60S particles. We propose that Rbp95 acts together with the Npa1 complex during early pre-60S maturation, potentially by promoting pre-rRNA folding events within pre-60S particles.
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Affiliation(s)
- Priya Bhutada
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Sébastien Favre
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Mariam Jaafar
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France.,Genomic Stability and Biotherapy (GSBT) Laboratory, Faculty of Sciences, Rafik Hariri Campus, Lebanese University, Beirut, Lebanon
| | - Jutta Hafner
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Laura Liesinger
- BioTechMed-Graz, Graz, Austria.,Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria
| | - Stefan Unterweger
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Karin Bischof
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Barbara Darnhofer
- BioTechMed-Graz, Graz, Austria.,Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria
| | - Devanarayanan Siva Sankar
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Gerald Rechberger
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Raghida Abou Merhi
- Genomic Stability and Biotherapy (GSBT) Laboratory, Faculty of Sciences, Rafik Hariri Campus, Lebanese University, Beirut, Lebanon
| | - Simon Lebaron
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Ruth Birner-Gruenberger
- BioTechMed-Graz, Graz, Austria.,Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria.,Institute of Chemical Technologies and Analytics, Technische Universität Wien, Getreidemarkt 9/E164, 1060 Vienna, Austria
| | - Dieter Kressler
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Anthony K Henras
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Brigitte Pertschy
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria.,BioTechMed-Graz, Graz, Austria
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7
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Chen J, Huang Y, Zhang K. The DEAD-Box Protein Rok1 Coordinates Ribosomal RNA Processing in Association with Rrp5 in Drosophila. Int J Mol Sci 2022; 23:ijms23105685. [PMID: 35628496 PMCID: PMC9146779 DOI: 10.3390/ijms23105685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/09/2022] [Accepted: 05/17/2022] [Indexed: 02/04/2023] Open
Abstract
Ribosome biogenesis and processing involve the coordinated action of many components. The DEAD-box RNA helicase (Rok1) is essential for cell viability, and the depletion of Rok1 inhibits pre-rRNA processing. Previous research on Rok1 and its cofactor Rrp5 has been performed primarily in yeast. Few functional studies have been performed in complex multicellular eukaryotes. Here, we used a combination of genetics and developmental experiments to show that Rok1 and Rrp5, which localize to the nucleolus, play key roles in the pre-rRNA processing and ribosome assembly in D. melanogaster. The accumulation of pre-rRNAs caused by Rok1 depletion can result in developmental defects. The loss of Rok1 enlarged the nucleolus and led to stalled ribosome assembly and pre-rRNA processing in the nucleolus, thereby blocking rRNA maturation and exacerbating the inhibition of mitosis in the brain. We also discovered that rrp54-2/4-2 displayed significantly increased ITS1 signaling by fluorescence in situ hybridization, and a reduction in ITS2. Rrp5 signal was highly enriched in the core of the nucleolus in the rok1167/167 mutant, suggesting that Rok1 is required for the accurate cellular localization of Rrp5 in the nucleolus. We have thus uncovered functions of Rok1 that reveal important implications for ribosome processing in eukaryotes.
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Affiliation(s)
- Jie Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
- Correspondence: (J.C.); (Y.H.); Tel.: +86-20-87597440 (J.C.)
| | - Yuantai Huang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
- Correspondence: (J.C.); (Y.H.); Tel.: +86-20-87597440 (J.C.)
| | - Kang Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
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8
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Yang YM, Karbstein K. The chaperone Tsr2 regulates Rps26 release and reincorporation from mature ribosomes to enable a reversible, ribosome-mediated response to stress. SCIENCE ADVANCES 2022; 8:eabl4386. [PMID: 35213229 PMCID: PMC8880767 DOI: 10.1126/sciadv.abl4386] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 01/13/2022] [Indexed: 05/04/2023]
Abstract
Although ribosome assembly is quality controlled to maintain protein homeostasis, different ribosome populations have been described. How these form, especially under stress conditions that affect energy levels and stop the energy-intensive production of ribosomes, remains unknown. Here, we demonstrate how a physiologically relevant ribosome population arises during high Na+, sorbitol, or pH stress via dissociation of Rps26 from fully assembled ribosomes to enable a translational response to these stresses. The chaperone Tsr2 releases Rps26 in the presence of high Na+ or pH in vitro and is required for Rps26 release in vivo. Moreover, Tsr2 stores free Rps26 and promotes reincorporation of the protein, thereby repairing the subunit after the Na+ stress subsides. Our data implicate a residue in Rps26 involved in Diamond Blackfan Anemia in mediating the effects of Na+. These data demonstrate how different ribosome populations can arise rapidly, without major energy input and without bypass of quality control mechanisms.
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Affiliation(s)
- Yoon-Mo Yang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Katrin Karbstein
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
- HHMI Faculty Scholar, Chevy Chase, MD 20815, USA
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9
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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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10
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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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11
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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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12
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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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13
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Tseng TL, Wang YT, Tsao CY, Ke YT, Lee YC, Hsu HJ, Poss KD, Chen CH. The RNA helicase Ddx52 functions as a growth switch in juvenile zebrafish. Development 2021; 148:271093. [PMID: 34323273 DOI: 10.1242/dev.199578] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/30/2021] [Indexed: 12/18/2022]
Abstract
Vertebrate animals usually display robust growth trajectories during juvenile stages, and reversible suspension of this growth momentum by a single genetic determinant has not been reported. Here, we report a single genetic factor that is essential for juvenile growth in zebrafish. Using a forward genetic screen, we recovered a temperature-sensitive allele, pan (after Peter Pan), that suspends whole-organism growth at juvenile stages. Remarkably, even after growth is halted for a full 8-week period, pan mutants are able to resume a robust growth trajectory after release from the restrictive temperature, eventually growing into fertile adults without apparent adverse phenotypes. Positional cloning and complementation assays revealed that pan encodes a probable ATP-dependent RNA helicase (DEAD-Box Helicase 52; ddx52) that maintains the level of 47S precursor ribosomal RNA. Furthermore, genetic silencing of ddx52 and pharmacological inhibition of bulk RNA transcription similarly suspend the growth of flies, zebrafish and mice. Our findings reveal evidence that safe, reversible pauses of juvenile growth can be mediated by targeting the activity of a single gene, and that its pausing mechanism has high evolutionary conservation.
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Affiliation(s)
- Tzu-Lun Tseng
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ying-Ting Wang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chang-Yu Tsao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Teng Ke
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Ching Lee
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hwei-Jan Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Kenneth D Poss
- Department of Cell Biology, Regeneration Next, Duke University Medical Center, Durham, NC 27710, USA
| | - Chen-Hui Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
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14
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Barik S. An Analytical Review of the Structural Features of Pentatricopeptide Repeats: Strategic Amino Acids, Repeat Arrangements and Superhelical Architecture. Int J Mol Sci 2021; 22:ijms22105407. [PMID: 34065603 PMCID: PMC8160929 DOI: 10.3390/ijms22105407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/27/2022] Open
Abstract
Tricopeptide repeats are common in natural proteins, and are exemplified by 34- and 35-residue repeats, known respectively as tetratricopeptide repeats (TPRs) and pentatricopeptide repeats (PPRs). In both classes, each repeat unit forms an antiparallel bihelical structure, so that multiple such units in a polypeptide are arranged in a parallel fashion. The primary structures of the motifs are nonidentical, but amino acids of similar properties occur in strategic positions. The focus of the present work was on PPR, but TPR, its better-studied cousin, is often included for comparison. The analyses revealed that critical amino acids, namely Gly, Pro, Ala and Trp, were placed at distinct locations in the higher order structure of PPR domains. While most TPRs occur in repeats of three, the PPRs exhibited a much greater diversity in repeat numbers, from 1 to 30 or more, separated by spacers of various sequences and lengths. Studies of PPR strings in proteins showed that the majority of PPR units are single, and that the longer tandems (i.e., without space in between) occurred in decreasing order. The multi-PPR domains also formed superhelical vortices, likely governed by interhelical angles rather than the spacers. These findings should be useful in designing and understanding the PPR domains.
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Affiliation(s)
- Sailen Barik
- EonBio, 3780 Pelham Drive, Mobile, AL 36619, USA
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15
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Moore AT, de Victoria AL, Koculi E. Interactions of the C-Terminal Truncated DEAD-Box Protein DDX3X With RNA and Nucleotide Substrates. ACS OMEGA 2021; 6:12640-12646. [PMID: 34056415 PMCID: PMC8154130 DOI: 10.1021/acsomega.1c00700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
DDX3X is a human DEAD-box RNA helicase implicated in many important cellular processes. In addition to the RecA-like catalytic core, DDX3X contains N- and C-terminal domains. The ancillary domains of DEAD-box RNA helicases have been shown to modulate their interactions with RNA and nucleotide substrates. Here, with the goal of understanding the role of N- and C-terminal domains of DDX3X on the DDX3X catalytic activity, we examined the interactions of RNA substrates and nucleotides with a DDX3X construct possessing the entire N-terminal domain and the catalytic core but lacking 80 residues from its C-terminal domain. Next, we compared our results with previously investigated DDX3X constructs. Our data show that the C-terminal truncated DDX3X does not bind to a blunt-ended double-helix RNA. This conclusion agrees with the data obtained on the wild-type LAF-1 protein, the DDX3X ortholog in Caenorhabditis elegans, and disagrees with the data obtained on the minimally active DDX3X construct, which misses 131 residues from its N-terminal domain and 80 residues from its C-terminal domain. The minimally active DDX3X construct was able to bind to the blunt-ended RNA construct. Combined, the previous studies and our results indicate that the N-terminal of DDX3X modulates the choice of DDX3X-RNA substrates. Furthermore, a previous study showed that the wild-type DDX3X construct hydrolyzes all four nucleotides and deoxynucleotides, both in the presence and absence of RNA. The C-terminal truncated DDX3X investigated here hydrolyzes only cytidine triphosphate (CTP) in the absence of RNA and CTP, adenosine triphosphate (ATP), and deoxyribose adenosine triphosphate (dATP) in the presence of RNA. Hence, the C-terminal truncated DDX3X has a more stringent nucleotide specificity than wild-type DDX3X.
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Affiliation(s)
- Anthony
F. T. Moore
- Department
of Chemistry, University of Central Florida, Orlando, Florida 32816, United States
| | | | - Eda Koculi
- Department
of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
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16
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Aquino GRR, Krogh N, Hackert P, Martin R, Gallesio JD, van Nues RW, Schneider C, Watkins NJ, Nielsen H, Bohnsack KE, Bohnsack MT. RNA helicase-mediated regulation of snoRNP dynamics on pre-ribosomes and rRNA 2'-O-methylation. Nucleic Acids Res 2021; 49:4066-4084. [PMID: 33721027 PMCID: PMC8053091 DOI: 10.1093/nar/gkab159] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 12/18/2022] Open
Abstract
RNA helicases play important roles in diverse aspects of RNA metabolism through their functions in remodelling ribonucleoprotein complexes (RNPs), such as pre-ribosomes. Here, we show that the DEAD box helicase Dbp3 is required for efficient processing of the U18 and U24 intron-encoded snoRNAs and 2′-O-methylation of various sites within the 25S ribosomal RNA (rRNA) sequence. Furthermore, numerous box C/D snoRNPs accumulate on pre-ribosomes in the absence of Dbp3. Many snoRNAs guiding Dbp3-dependent rRNA modifications have overlapping pre-rRNA basepairing sites and therefore form mutually exclusive interactions with pre-ribosomes. Analysis of the distribution of these snoRNAs between pre-ribosome-associated and ‘free’ pools demonstrated that many are almost exclusively associated with pre-ribosomal complexes. Our data suggest that retention of such snoRNPs on pre-ribosomes when Dbp3 is lacking may impede rRNA 2′-O-methylation by reducing the recycling efficiency of snoRNPs and by inhibiting snoRNP access to proximal target sites. The observation of substoichiometric rRNA modification at adjacent sites suggests that the snoRNPs guiding such modifications likely interact stochastically rather than hierarchically with their pre-rRNA target sites. Together, our data provide new insights into the dynamics of snoRNPs on pre-ribosomal complexes and the remodelling events occurring during the early stages of ribosome assembly.
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Affiliation(s)
- Gerald Ryan R Aquino
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, 3B Blegdamsvej, 2200N Copenhagen, Denmark
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Roman Martin
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Jimena Davila Gallesio
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Robert W van Nues
- Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Claudia Schneider
- Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nicholas J Watkins
- Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, 3B Blegdamsvej, 2200N Copenhagen, Denmark.,Genomics group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
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17
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Bamberger C, Pankow S, Martínez-Bartolomé S, Ma M, Diedrich J, Rissman RA, Yates JR. Protein Footprinting via Covalent Protein Painting Reveals Structural Changes of the Proteome in Alzheimer's Disease. J Proteome Res 2021; 20:2762-2771. [PMID: 33872013 PMCID: PMC8477671 DOI: 10.1021/acs.jproteome.0c00912] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Misfolding and aggregation of amyloid-β peptide and hyperphosphorylated tau are molecular markers of Alzheimer's disease (AD), and although the 3D structures of these aberrantly folded proteins have been visualized in exquisite detail, no method has been able to survey protein folding across the proteome in AD. Here, we present covalent protein painting (CPP), a mass spectrometry-based protein footprinting approach to quantify the accessibility of lysine ε-amines for covalent modification at the surface of natively folded proteins. We used CPP to survey the reactivity of 2645 lysine residues and therewith the structural proteome of HEK293T cells and found that reactivity increased upon mild heat shock. CPP revealed that the accessibility of lysine residues for covalent modification in tubulin-β (TUBB), in succinate dehydrogenase (SHDB), and in amyloid-β peptide (Aβ) is altered in human postmortem brain samples of patients with neurodegenerative diseases. The structural alterations of TUBB and SHDB in patients with AD, dementia with Lewy bodies (DLB), or both point to broader perturbations of the 3D proteome beyond Aβ and hyperphosphorylated tau.
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Affiliation(s)
- Casimir Bamberger
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sandra Pankow
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Salvador Martínez-Bartolomé
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Michelle Ma
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jolene Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Robert A. Rissman
- Department of Neurosciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Veterans Affairs San Diego Healthcare System, San Diego, CA, 92161, USA
| | - John R. Yates
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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18
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Hypoxia: Uncharged tRNA to the Rescue! Curr Biol 2021; 31:R25-R27. [PMID: 33434482 DOI: 10.1016/j.cub.2020.10.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new study has identified genes that protect Caenorhabditis elegans from hypoxic stress. Genomic approaches and whole-organism proteomics reveal a regulatory interaction between a threonyl-tRNA synthetase and ribosome biogenesis that modulates global translation and hypoxic sensitivity.
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19
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Itani OA, Zhong X, Tang X, Scott BA, Yan JY, Flibotte S, Lim Y, Hsieh AC, Bruce JE, Van Gilst M, Crowder CM. Coordinate Regulation of Ribosome and tRNA Biogenesis Controls Hypoxic Injury and Translation. Curr Biol 2020; 31:128-137.e5. [PMID: 33157031 DOI: 10.1016/j.cub.2020.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 08/21/2020] [Accepted: 10/01/2020] [Indexed: 01/01/2023]
Abstract
The translation machinery is composed of a myriad of proteins and RNAs whose levels must be coordinated to efficiently produce proteins without wasting energy or substrate. However, protein synthesis is clearly not always perfectly tuned to its environment, as disruption of translation machinery components can lengthen lifespan and stress survival. While much has been learned from bacteria and yeast about translational regulation, much less is known in metazoans. In a screen for mutations protecting C. elegans from hypoxic stress, we isolated multiple genes impacting protein synthesis: a ribosomal RNA helicase gene, tRNA biosynthesis genes, and a gene controlling amino acid availability. To define better the mechanisms by which these genes impact protein synthesis, we performed a second screen for suppressors of the conditional developmental arrest phenotype of the RNA helicase mutant and identified genes involved in ribosome biogenesis. Surprisingly, these suppressor mutations restored normal hypoxic sensitivity and protein synthesis to the tRNA biogenesis mutants, but not to the mutant reducing amino acid uptake. Proteomic analysis demonstrated that reduced tRNA biosynthetic activity produces a selective homeostatic reduction in ribosomal subunits, thereby offering a mechanism for the suppression results. Our study uncovers an unrecognized higher-order-translation regulatory mechanism in a metazoan whereby ribosome biogenesis genes communicate with genes controlling tRNA abundance matching the global rate of protein synthesis with available resources.
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Affiliation(s)
- Omar A Itani
- Department of Anesthesiology and Pain Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195-6540, USA; Mitochondria and Metabolism Center, University of Washington, 850 Republican Street, Seattle, WA 98105, USA
| | - Xuefei Zhong
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98105, USA
| | - Xiaoting Tang
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98105, USA
| | - Barbara A Scott
- Department of Anesthesiology and Pain Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195-6540, USA; Mitochondria and Metabolism Center, University of Washington, 850 Republican Street, Seattle, WA 98105, USA
| | - Jun Yi Yan
- Department of Anesthesiology and Pain Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195-6540, USA; Mitochondria and Metabolism Center, University of Washington, 850 Republican Street, Seattle, WA 98105, USA; Department of Anesthesiology, Central Hospital of Changdian, Dandong, Liaoning 118214, China
| | - Stephane Flibotte
- Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall Vancouver, BC V6T 1Z3, Canada
| | - Yiting Lim
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA
| | - Andrew C Hsieh
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98105, USA; Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA; Department of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195-6420, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98105, USA
| | - Marc Van Gilst
- Department of Anesthesiology and Pain Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195-6540, USA; Mitochondria and Metabolism Center, University of Washington, 850 Republican Street, Seattle, WA 98105, USA
| | - C Michael Crowder
- Department of Anesthesiology and Pain Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195-6540, USA; Mitochondria and Metabolism Center, University of Washington, 850 Republican Street, Seattle, WA 98105, USA; Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98105, USA.
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20
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Choudhury P, Kretschmer J, Hackert P, Bohnsack KE, Bohnsack MT. The DExD box ATPase DDX55 is recruited to domain IV of the 28S ribosomal RNA by its C-terminal region. RNA Biol 2020; 18:1124-1135. [PMID: 33048000 PMCID: PMC8244758 DOI: 10.1080/15476286.2020.1829366] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
RNA helicases contribute to diverse aspects of RNA metabolism through their functions in re-arranging RNA structures. Identification of the remodelling targets of RNA helicases is a critical step in elucidating their cellular functions. Here, we show that, in contrast to many other ribosome biogenesis factors, the DExD box ATPase DDX55 predominantly localizes to the nucleoplasm and we identify a nuclear localization signal within the C-terminal region of the protein. DDX55 associates with pre-ribosomal subunits in human cells and is required for maturation of large subunit pre-rRNAs. Interestingly, in vitro analyses show that DDX55 selectively associates with double-stranded RNA substrates, which also stimulate its ATPase activity, and our data suggest that the C-terminal region of DDX55 contributes to this substrate specificity. The C-terminal region of DDX55 is also necessary for recruitment of the helicase to pre-ribosomes and, using in vivo crosslinking, we reveal a binding site for DDX55 in helix H62 of the 28S ribosomal RNA. Taken together, these data highlight the importance of the C-terminal region of DDX55 in substrate specificity and recruitment, and identify domain IV as a potential remodelling target of DDX55 during LSU biogenesis.
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Affiliation(s)
- Priyanka Choudhury
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany
| | - Jens Kretschmer
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August University, Göttingen, Germany
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21
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Vos TJ, Kothe U. snR30/U17 Small Nucleolar Ribonucleoprotein: A Critical Player during Ribosome Biogenesis. Cells 2020; 9:cells9102195. [PMID: 33003357 PMCID: PMC7601244 DOI: 10.3390/cells9102195] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/26/2020] [Accepted: 09/28/2020] [Indexed: 11/29/2022] Open
Abstract
The small nucleolar RNA snR30 (U17 in humans) plays a unique role during ribosome synthesis. Unlike most members of the H/ACA class of guide RNAs, the small nucleolar ribonucleoprotein (snoRNP) complex assembled on snR30 does not direct pseudouridylation of ribosomal RNA (rRNA), but instead snR30 is critical for 18S rRNA processing during formation of the small subunit (SSU) of the ribosome. Specifically, snR30 is essential for three pre-rRNA cleavages at the A0/01, A1/1, and A2/2a sites in yeast and humans, respectively. Accordingly, snR30 is the only essential H/ACA guide RNA in yeast. Here, we summarize our current knowledge about the interactions and functions of snR30, discuss what remains to be elucidated, and present two non-exclusive hypotheses on the possible molecular function of snR30 during ribosome biogenesis. First, snR30 might be responsible for recruiting other proteins including endonucleases to the SSU processome. Second, snR30 may contribute to the refolding of pre-rRNA into a required conformation that serves as a checkpoint during ribosome biogenesis facilitating pre-rRNA cleavage. In both scenarios, the snR30 snoRNP may have scaffolding and RNA chaperoning activity. In conclusion, the snR30 snoRNP is a crucial player with an unknown molecular mechanism during ribosome synthesis, posing many interesting future research questions.
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Affiliation(s)
| | - Ute Kothe
- Correspondence: ; Tel.: +1-403-332-5274
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22
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Clerget G, Bourguignon-Igel V, Marmier-Gourrier N, Rolland N, Wacheul L, Manival X, Charron C, Kufel J, Méreau A, Senty-Ségault V, Tollervey D, Lafontaine DLJ, Branlant C, Rederstorff M. Synergistic defects in pre-rRNA processing from mutations in the U3-specific protein Rrp9 and U3 snoRNA. Nucleic Acids Res 2020; 48:3848-3868. [PMID: 31996908 PMCID: PMC7144924 DOI: 10.1093/nar/gkaa066] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 01/17/2020] [Accepted: 01/22/2020] [Indexed: 01/24/2023] Open
Abstract
U3 snoRNA and the associated Rrp9/U3-55K protein are essential for 18S rRNA production by the SSU-processome complex. U3 and Rrp9 are required for early pre-rRNA cleavages at sites A0, A1 and A2, but the mechanism remains unclear. Substitution of Arg 289 in Rrp9 to Ala (R289A) specifically reduced cleavage at sites A1 and A2. Surprisingly, R289 is located on the surface of the Rrp9 β-propeller structure opposite to U3 snoRNA. To understand this, we first characterized the protein-protein interaction network of Rrp9 within the SSU-processome. This identified a direct interaction between the Rrp9 β-propeller domain and Rrp36, the strength of which was reduced by the R289A substitution, implicating this interaction in the observed processing phenotype. The Rrp9 R289A mutation also showed strong synergistic negative interactions with mutations in U3 that destabilize the U3/pre-rRNA base-pair interactions or reduce the length of their linking segments. We propose that the Rrp9 β-propeller and U3/pre-rRNA binding cooperate in the structure or stability of the SSU-processome. Additionally, our analysis of U3 variants gave insights into the function of individual segments of the 5′-terminal 72-nt sequence of U3. We interpret these data in the light of recently reported SSU-processome structures.
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Affiliation(s)
| | | | | | | | - Ludivine Wacheul
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S/FNRS), Université Libre de Bruxelles (ULB), and Center for Microscopy and Molecular Imaging (CMMI), B-6041 Charleroi-Gosselies, Belgium
| | - Xavier Manival
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | | | - Joanna Kufel
- Wellcome Center for Cell Biology, University of Edinburgh, Scotland, UK
| | - Agnès Méreau
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | | | - David Tollervey
- Wellcome Center for Cell Biology, University of Edinburgh, Scotland, UK
| | - Denis L J Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S/FNRS), Université Libre de Bruxelles (ULB), and Center for Microscopy and Molecular Imaging (CMMI), B-6041 Charleroi-Gosselies, Belgium
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23
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Braun CM, Hackert P, Schmid CE, Bohnsack MT, Bohnsack KE, Perez-Fernandez J. Pol5 is required for recycling of small subunit biogenesis factors and for formation of the peptide exit tunnel of the large ribosomal subunit. Nucleic Acids Res 2020; 48:405-420. [PMID: 31745560 PMCID: PMC7145529 DOI: 10.1093/nar/gkz1079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 01/24/2023] Open
Abstract
More than 200 assembly factors (AFs) are required for the production of ribosomes in yeast. The stepwise association and dissociation of these AFs with the pre-ribosomal subunits occurs in a hierarchical manner to ensure correct maturation of the pre-rRNAs and assembly of the ribosomal proteins. Although decades of research have provided a wealth of insights into the functions of many AFs, others remain poorly characterized. Pol5 was initially classified with B-type DNA polymerases, however, several lines of evidence indicate the involvement of this protein in ribosome assembly. Here, we show that depletion of Pol5 affects the processing of pre-rRNAs destined for the both the large and small subunits. Furthermore, we identify binding sites for Pol5 in the 5' external transcribed spacer and within domain III of the 25S rRNA sequence. Consistent with this, we reveal that Pol5 is required for recruitment of ribosomal proteins that form the polypeptide exit tunnel in the LSU and that depletion of Pol5 impairs the release of 5' ETS fragments from early pre-40S particles. The dual functions of Pol5 in 60S assembly and recycling of pre-40S AFs suggest that this factor could contribute to ensuring the stoichiometric production of ribosomal subunits.
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Affiliation(s)
- Christina M Braun
- Department of Biochemistry III, University of Regensburg, Universitätstrasse 31, 93053 Regensburg, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Catharina E Schmid
- Department of Biochemistry III, University of Regensburg, Universitätstrasse 31, 93053 Regensburg, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August University, Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Jorge Perez-Fernandez
- Department of Biochemistry III, University of Regensburg, Universitätstrasse 31, 93053 Regensburg, Germany
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24
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Li JL, Chen C, Chen W, Zhao LF, Xu XK, Li Y, Yuan HY, Lin JR, Pan JP, Jin BL, Li FC. Integrative genomic analyses identify WDR12 as a novel oncogene involved in glioblastoma. J Cell Physiol 2020; 235:7344-7355. [PMID: 32180229 DOI: 10.1002/jcp.29635] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 01/09/2020] [Indexed: 01/16/2023]
Abstract
Glioblastoma (GBM) is the most malignant primary brain tumor in adults. Due to its invasive nature, it cannot be thoroughly eliminated. WD repeat domain 12 (WDR12) processes the 32S precursor rRNA but cannot affect the synthesis of the 45S/47S primary transcript. In this study, we found that WDR12 is highly expressed in GBM according to the analysis results of mRNA expression by The Cancer Genome Atlas database. The high expression level of WDR12 is dramatically related to shorter overall survival and reduced disease-free survival. Next, we knocked down WDR12 and found that knockdown of WDR12 promoted the apoptosis and inhibited the proliferation by cell biology experiments. Differential expression genes in gene-chip revealed that WDR12 knockdown mainly inhibited cell cycle. Finally, we also found that WDR12 is associated with PLK1 and EZH2 in cell proliferation of GBM. Resumptively, this report showed a possible evidence that WDR12 drove malignant behavior of GBM, whose expression may present a neoteric independent prognostic biomarker in GBM.
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Affiliation(s)
- Jun-Liang Li
- Department of Neurosurgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Cheng Chen
- Department of Neurosurgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Wei Chen
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Ling-Feng Zhao
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Xin-Ke Xu
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Yang Li
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Hong-Yao Yuan
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Jin-Rong Lin
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Jun-Ping Pan
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Bi-Lian Jin
- Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Fang-Cheng Li
- Department of Neurosurgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Neurosurgery, Guangzhou Women and Children's Medical Center, Guangzhou, China.,Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
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25
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Davila Gallesio J, Hackert P, Bohnsack KE, Bohnsack MT. Sgd1 is an MIF4G domain-containing cofactor of the RNA helicase Fal1 and associates with the 5' domain of the 18S rRNA sequence. RNA Biol 2020; 17:539-553. [PMID: 31994962 PMCID: PMC7237134 DOI: 10.1080/15476286.2020.1716540] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Assembly of eukaryotic ribosomal subunits is a complex and dynamic process involving the action of more than 200 trans-acting assembly factors. Although recent cryo-electron microscopy structures have provided information on architecture of several pre-ribosomal particles and the binding sites of many AFs, the RNA and protein interactions of many other AFs not captured in these snapshots still remain elusive. RNA helicases are key regulators of structural rearrangements within pre-ribosomal complexes and here we have analysed the eIF4A-like RNA helicase Fal1 and its putative cofactor Sgd1. Our data show that these proteins interact directly via the MIF4G domain of Sgd1 and that the MIF4G domain of Sgd1 stimulates the catalytic activity of Fal1 in vitro. The catalytic activity of Fal1, and the interaction between Fal1 and Sgd1, are required for efficient pre-rRNA processing at the A0, A1 and A2 sites. Furthermore, Sgd1 co-purifies the early small subunit biogenesis factors Lcp5 and Rok1, suggesting that the Fal1-Sgd1 complex likely functions within the SSU processome. In vivo crosslinking data reveal that Sgd1 binds to helix H12 of the 18S rRNA sequence and we further demonstrate that this interaction is formed by the C-terminal region of the protein, which is essential for its function in ribosome biogenesis.
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Affiliation(s)
- Jimena Davila Gallesio
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August University, Göttingen, Germany
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26
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Khoshnevis S, Liu X, Dattolo MD, Karbstein K. Rrp5 establishes a checkpoint for 60S assembly during 40S maturation. RNA (NEW YORK, N.Y.) 2019; 25:1164-1176. [PMID: 31217256 PMCID: PMC6800521 DOI: 10.1261/rna.071225.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/16/2019] [Indexed: 06/09/2023]
Abstract
Even though the RNAs contained in the small (40S) and large (60S) ribosomal subunits are cotranscribed, their assembly proceeds largely separately, involving entirely distinct machineries. Nevertheless, separation of the two subunits, an event that is critical for assembly of the small subunit, is delayed until domain I of the large subunit is transcribed, indicating crosstalk between the two assembly pathways. Here we show that this crosstalk is mediated by the assembly factor Rrp5, one of only three proteins required for assembly of both ribosomal subunits. Quantitative RNA binding and cleavage data demonstrate that early on, Rrp5 blocks separation of the two subunits, and thus 40S maturation by inhibiting the access of Rcl1 to promote cleavage of the nascent rRNA. Upon transcription of domain I of 25S rRNA, the 60S assembly factors Noc1/Noc2 bind both this RNA and Rrp5 to change the Rrp5 RNA binding mode to enable pre-40S rRNA processing. Mutants in the HEAT-repeat domain of Noc1 are deficient in the separation of the subunits, which is rescued by overexpression of wild-type but not inactive Rcl1 in vivo. Thus, Rrp5 establishes a checkpoint for 60S assembly during 40S maturation to ensure balanced levels of the two subunits.
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Affiliation(s)
- Sohail Khoshnevis
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Xin Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Maria D Dattolo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
| | - Katrin Karbstein
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida 33458, USA
- HHMI Faculty Scholar
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27
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Abstract
Ribosomes, which synthesize the proteins of a cell, comprise ribosomal RNA and ribosomal proteins, which coassemble hierarchically during a process termed ribosome biogenesis. Historically, biochemical and molecular biology approaches have revealed how preribosomal particles form and mature in consecutive steps, starting in the nucleolus and terminating after nuclear export into the cytoplasm. However, only recently, due to the revolution in cryo-electron microscopy, could pseudoatomic structures of different preribosomal particles be obtained. Together with in vitro maturation assays, these findings shed light on how nascent ribosomes progress stepwise along a dynamic biogenesis pathway. Preribosomes assemble gradually, chaperoned by a myriad of assembly factors and small nucleolar RNAs, before they reach maturity and enter translation. This information will lead to a better understanding of how ribosome synthesis is linked to other cellular pathways in humans and how it can cause diseases, including cancer, if disturbed.
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Affiliation(s)
- Jochen Baßler
- Biochemistry Center, University of Heidelberg, 69120 Heidelberg, Germany; ,
| | - Ed Hurt
- Biochemistry Center, University of Heidelberg, 69120 Heidelberg, Germany; ,
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28
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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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29
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Pérébaskine N, Thore S, Fribourg S. Structural and interaction analysis of the Rrp5 C-terminal region. FEBS Open Bio 2018; 8:1605-1614. [PMID: 30338212 PMCID: PMC6168700 DOI: 10.1002/2211-5463.12495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/05/2018] [Accepted: 07/14/2018] [Indexed: 11/18/2022] Open
Abstract
Rrp5 is an essential factor during the ribosome biogenesis process. The protein contains a series of 12 S1 RNA-binding domains followed by a TetratricoPeptide Repeat (TPR) domain. In the past, several studies aiming at defining the function of the TPR domain have used nonequivalent Rrp5 constructs, as these protein fragments include not only the TPR module, but also three or four S1 domains. We solved the structure of the Rrp5 TPR module and demonstrated in vitro that the TPR region alone does not bind RNA, while the three S1 domains preceding the TPR module can associate with homopolymeric RNA. Finally, we tested the association of our Rrp5 constructs with several proposed interactors, in support of cryo-EM-based models. COORDINATES Atomic coordinates and structure factors have been deposited to the Protein Data Bank under the accession number 5NLG.
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30
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Barandun J, Chaker-Margot M, Hunziker M, Molloy KR, Chait BT, Klinge S. The complete structure of the small-subunit processome. Nat Struct Mol Biol 2017; 24:944-953. [PMID: 28945246 DOI: 10.1038/nsmb.3472] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 08/25/2017] [Indexed: 01/24/2023]
Abstract
The small-subunit processome represents the earliest stable precursor of the eukaryotic small ribosomal subunit. Here we present the cryo-EM structure of the Saccharomyces cerevisiae small-subunit processome at an overall resolution of 3.8 Å, which provides an essentially complete near-atomic model of this assembly. In this nucleolar superstructure, 51 ribosome-assembly factors and two RNAs encapsulate the 18S rRNA precursor and 15 ribosomal proteins in a state that precedes pre-rRNA cleavage at site A1. Extended flexible proteins are employed to connect distant sites in this particle. Molecular mimicry and steric hindrance, as well as protein- and RNA-mediated RNA remodeling, are used in a concerted fashion to prevent the premature formation of the central pseudoknot and its surrounding elements within the small ribosomal subunit.
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Affiliation(s)
- Jonas Barandun
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York, USA
| | - Malik Chaker-Margot
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York, USA
- Tri-Institutional Training Program in Chemical Biology, The Rockefeller University, New York, New York, USA
| | - Mirjam Hunziker
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York, USA
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion 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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31
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Memet I, Doebele C, Sloan KE, Bohnsack MT. The G-patch protein NF-κB-repressing factor mediates the recruitment of the exonuclease XRN2 and activation of the RNA helicase DHX15 in human ribosome biogenesis. Nucleic Acids Res 2017; 45:5359-5374. [PMID: 28115624 PMCID: PMC5435916 DOI: 10.1093/nar/gkx013] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/04/2017] [Indexed: 01/05/2023] Open
Abstract
In eukaryotes, the synthesis of ribosomal subunits, which involves the maturation of the ribosomal (r)RNAs and assembly of ribosomal proteins, requires the co-ordinated action of a plethora of ribosome biogenesis factors. Many of these cofactors remain to be characterized in human cells. Here, we demonstrate that the human G-patch protein NF-κB-repressing factor (NKRF) forms a pre-ribosomal subcomplex with the DEAH-box RNA helicase DHX15 and the 5΄-3΄ exonuclease XRN2. Using UV crosslinking and analysis of cDNA (CRAC), we reveal that NKRF binds to the transcribed spacer regions of the pre-rRNA transcript. Consistent with this, we find that depletion of NKRF, XRN2 or DHX15 impairs an early pre-rRNA cleavage step (A’). The catalytic activity of DHX15, which we demonstrate is stimulated by NKRF functioning as a cofactor, is required for efficient A’ cleavage, suggesting that a structural remodelling event may facilitate processing at this site. In addition, we show that depletion of NKRF or XRN2 also leads to the accumulation of excised pre-rRNA spacer fragments and that NKRF is essential for recruitment of the exonuclease to nucleolar pre-ribosomal complexes. Our findings therefore reveal a novel pre-ribosomal subcomplex that plays distinct roles in the processing of pre-rRNAs and the turnover of excised spacer fragments.
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Affiliation(s)
- Indira Memet
- Institute for Molecular Biology, University Medical Center Göttingen, Georg-August-University, 37073 Göttingen, Germany
| | - Carmen Doebele
- Institute for Molecular Biology, University Medical Center Göttingen, Georg-August-University, 37073 Göttingen, Germany
| | - Katherine E Sloan
- Institute for Molecular Biology, University Medical Center Göttingen, Georg-August-University, 37073 Göttingen, Germany
| | - Markus T Bohnsack
- Institute for Molecular Biology, University Medical Center Göttingen, Georg-August-University, 37073 Göttingen, Germany.,Göttingen Centre for Molecular Biosciences, Georg-August-University, 37073 Göttingen, Germany
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32
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Wells GR, Weichmann F, Sloan KE, Colvin D, Watkins NJ, Schneider C. The ribosome biogenesis factor yUtp23/hUTP23 coordinates key interactions in the yeast and human pre-40S particle and hUTP23 contains an essential PIN domain. Nucleic Acids Res 2017; 45:4796-4809. [PMID: 28082392 PMCID: PMC5416842 DOI: 10.1093/nar/gkw1344] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/22/2016] [Indexed: 11/30/2022] Open
Abstract
Two proteins with PIN endonuclease domains, yUtp24(Fcf1)/hUTP24 and yUtp23/hUTP23 are essential for early pre-ribosomal (r)RNA cleavages at sites A0, A1/1 and A2/2a in yeast and humans. The yUtp24/hUTP24 PIN endonuclease is proposed to cleave at sites A1/1 and A2/2a, but the enzyme cleaving at site A0 is not known. Yeast yUtp23 contains a degenerate, non-essential PIN domain and functions together with the snR30 snoRNA, while human hUTP23 is associated with U17, the human snR30 counterpart. Using in vivo RNA–protein crosslinking and gel shift experiments, we reveal that yUtp23/hUTP23 makes direct contacts with expansion sequence 6 (ES6) in the 18S rRNA sequence and that yUtp23 interacts with the 3΄ half of the snR30 snoRNA. Protein–protein interaction studies further demonstrated that yeast yUtp23 and human hUTP23 directly interact with the H/ACA snoRNP protein yNhp2/hNHP2, the RNA helicase yRok1/hROK1(DDX52), the ribosome biogenesis factor yRrp7/hRRP7 and yUtp24/hUTP24. yUtp23/hUTP23 could therefore be central to the coordinated integration and release of ES6 binding factors and likely plays a pivotal role in remodeling this pre-rRNA region in both yeast and humans. Finally, studies using RNAi-rescue systems in human cells revealed that intact PIN domain and Zinc finger motifs in human hUTP23 are essential for 18S rRNA maturation.
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Affiliation(s)
- Graeme R Wells
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Franziska Weichmann
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Katherine E Sloan
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - David Colvin
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Nicholas J Watkins
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Claudia Schneider
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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33
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Sun Q, Zhu X, Qi J, An W, Lan P, Tan D, Chen R, Wang B, Zheng S, Zhang C, Chen X, Zhang W, Chen J, Dong MQ, Ye K. Molecular architecture of the 90S small subunit pre-ribosome. eLife 2017; 6. [PMID: 28244370 PMCID: PMC5354517 DOI: 10.7554/elife.22086] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/26/2017] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of Saccharomyces cerevisiae 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors. DOI:http://dx.doi.org/10.7554/eLife.22086.001
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Affiliation(s)
- Qi Sun
- PTN Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China.,Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Xing Zhu
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China
| | - Jia Qi
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China.,Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Weidong An
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China.,College of Biological Sciences, China Agricultural University, Beijing, China
| | - Pengfei Lan
- National Institute of Biological Sciences, Beijing, China
| | - Dan Tan
- National Institute of Biological Sciences, Beijing, China
| | - Rongchang Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China
| | - Bing Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Sanduo Zheng
- National Institute of Biological Sciences, Beijing, China
| | - Cheng Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Xining Chen
- National Institute of Biological Sciences, Beijing, China
| | - Wei Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Jing Chen
- PTN Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China.,Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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