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Noh C, Kang Y, Heo S, Kim T, Kim H, Chang J, Sundharbaabu PR, Shim S, Lim K, Lee JH, Jo K. Scanning Electron Microscopy Imaging of Large DNA Molecules Using a Metal-Free Electro-Stain Composed of DNA-Binding Proteins and Synthetic Polymers. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309702. [PMID: 38704672 PMCID: PMC11267313 DOI: 10.1002/advs.202309702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/19/2024] [Indexed: 05/06/2024]
Abstract
This paper presents the first scanning electron microscopy (SEM)-based DNA imaging in biological samples. This novel approach incorporates a metal-free electro-stain reagent, formulated by combining DNA-binding proteins and synthetic polymers to enhance the visibility of 2-nm-thick DNA under SEM. Notably, DNA molecules stain with proteins and polymers appear as dark lines under SEM. The resulting DNA images exhibit a thickness of 15.0±4.0 nm. As SEM is the primary platform, it integrates seamlessly with various chemically functionalized large surfaces with the aid of microfluidic devices. The approach allows high-resolution imaging of various DNA structures including linear, circular, single-stranded DNA and RNA, originating from nuclear and mitochondrial genomes. Furthermore, quantum dots are successfully visualized as bright labels that are sequence-specifically incorporated into DNA molecules, which highlights the potential for SEM-based optical DNA mapping. In conclusion, DNA imaging using SEM with the novel electro-stain offers electron microscopic resolution with the ease of optical microscopy.
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Affiliation(s)
- Chanyoung Noh
- Department of ChemistrySogang UniversitySeoul04107South Korea
| | - Yoonjung Kang
- Department of ChemistrySogang UniversitySeoul04107South Korea
| | - Sujung Heo
- Department of ChemistrySogang UniversitySeoul04107South Korea
| | - Taesoo Kim
- Department of ChemistrySogang UniversitySeoul04107South Korea
| | - Hayeon Kim
- Department of ChemistrySogang UniversitySeoul04107South Korea
| | - Junhyuck Chang
- School of Advanced Materials Science and EngineeringDepartment of MetaBioHealth Sungkyunkwan University (SKKU)Suwon16419South Korea
| | - Priyannth Ramasami Sundharbaabu
- School of Advanced Materials Science and EngineeringDepartment of MetaBioHealth Sungkyunkwan University (SKKU)Suwon16419South Korea
| | - Sanghee Shim
- Department of ChemistryKorea UniversitySeoul02841South Korea
| | - Kwang‐il Lim
- Department of Chemical and Biological EngineeringSookmyung Women's UniversitySeoul04312South Korea
| | - Jung Heon Lee
- School of Advanced Materials Science and EngineeringDepartment of MetaBioHealth Sungkyunkwan University (SKKU)Suwon16419South Korea
| | - Kyubong Jo
- Department of ChemistrySogang UniversitySeoul04107South Korea
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2
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Shine M, Gordon J, Schärfen L, Zigackova D, Herzel L, Neugebauer KM. Co-transcriptional gene regulation in eukaryotes and prokaryotes. Nat Rev Mol Cell Biol 2024; 25:534-554. [PMID: 38509203 PMCID: PMC11199108 DOI: 10.1038/s41580-024-00706-2] [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] [Accepted: 01/19/2024] [Indexed: 03/22/2024]
Abstract
Many steps of RNA processing occur during transcription by RNA polymerases. Co-transcriptional activities are deemed commonplace in prokaryotes, in which the lack of membrane barriers allows mixing of all gene expression steps, from transcription to translation. In the past decade, an extraordinary level of coordination between transcription and RNA processing has emerged in eukaryotes. In this Review, we discuss recent developments in our understanding of co-transcriptional gene regulation in both eukaryotes and prokaryotes, comparing methodologies and mechanisms, and highlight striking parallels in how RNA polymerases interact with the machineries that act on nascent RNA. The development of RNA sequencing and imaging techniques that detect transient transcription and RNA processing intermediates has facilitated discoveries of transcription coordination with splicing, 3'-end cleavage and dynamic RNA folding and revealed physical contacts between processing machineries and RNA polymerases. Such studies indicate that intron retention in a given nascent transcript can prevent 3'-end cleavage and cause transcriptional readthrough, which is a hallmark of eukaryotic cellular stress responses. We also discuss how coordination between nascent RNA biogenesis and transcription drives fundamental aspects of gene expression in both prokaryotes and eukaryotes.
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Affiliation(s)
- Morgan Shine
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jackson Gordon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Leonard Schärfen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Dagmar Zigackova
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Lydia Herzel
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin, Germany.
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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3
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Yang J, Wang Y, Huang Z, Jiang Y, Pan X, Dong X, Yang G. Roles of rRNA N-methyladenosine modification in the function of ribosomes. Cell Biochem Funct 2023; 41:1106-1114. [PMID: 38041420 DOI: 10.1002/cbf.3891] [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: 07/10/2023] [Revised: 10/19/2023] [Accepted: 11/17/2023] [Indexed: 12/03/2023]
Abstract
The N-methyladenosine (m6A) modification of ribosomal RNA (rRNA) plays critical roles in regulating the function of ribosomes, the essential molecular machines that translate genetic information from mRNA into proteins. Specifically, m6A modification affects ribosome biogenesis, stability, and function by regulating the processing and maturation of rRNA, the assembly and composition of ribosomes, and the accuracy and efficiency of translation. Furthermore, m6A modification allows for dynamic regulation of translation in response to environmental and cellular signals. Therefore, a deeper understanding of the mechanisms and functions of m6A modification in rRNA will advance our knowledge of ribosome-mediated gene expression and facilitate the development of new therapeutic strategies for ribosome-related diseases.
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Affiliation(s)
- Jingyi Yang
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Yameng Wang
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Zekai Huang
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Yashuang Jiang
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Xiaolei Pan
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Xiaowei Dong
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, China
| | - Geng Yang
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, China
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4
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Riback JA, Eeftens JM, Lee DSW, Quinodoz SA, Donlic A, Orlovsky N, Wiesner L, Beckers L, Becker LA, Strom AR, Rana U, Tolbert M, Purse BW, Kleiner R, Kriwacki R, Brangwynne CP. Viscoelasticity and advective flow of RNA underlies nucleolar form and function. Mol Cell 2023; 83:3095-3107.e9. [PMID: 37683610 PMCID: PMC11089468 DOI: 10.1016/j.molcel.2023.08.006] [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: 09/22/2022] [Revised: 04/20/2023] [Accepted: 08/08/2023] [Indexed: 09/10/2023]
Abstract
The nucleolus is the largest biomolecular condensate and facilitates transcription, processing, and assembly of ribosomal RNA (rRNA). Although nucleolar function is thought to require multiphase liquid-like properties, nucleolar fluidity and its connection to the highly coordinated transport and biogenesis of ribosomal subunits are poorly understood. Here, we use quantitative imaging, mathematical modeling, and pulse-chase nucleotide labeling to examine nucleolar material properties and rRNA dynamics. The mobility of rRNA is several orders of magnitude slower than that of nucleolar proteins, with rRNA steadily moving away from the transcriptional sites in a slow (∼1 Å/s), radially directed fashion. This constrained but directional mobility, together with polymer physics-based calculations, suggests that nascent rRNA forms an entangled gel, whose constant production drives outward flow. We propose a model in which progressive maturation of nascent rRNA reduces its initial entanglement, fluidizing the nucleolar periphery to facilitate the release of assembled pre-ribosomal particles.
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Affiliation(s)
- Joshua A Riback
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Jorine M Eeftens
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Daniel S W Lee
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, Princeton, NJ 08544, USA
| | - Sofia A Quinodoz
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Anita Donlic
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Natalia Orlovsky
- Department of Molecular Biology, Princeton University, Princeton, Princeton, NJ 08544, USA
| | - Lennard Wiesner
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Lien Beckers
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, Princeton, NJ 08544, USA
| | - Lindsay A Becker
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, Princeton, NJ 08544, USA
| | - Amy R Strom
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Ushnish Rana
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Michele Tolbert
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA
| | - Byron W Purse
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Ralph Kleiner
- Department of Chemistry, Princeton University, Princeton, Princeton, NJ 08544, USA
| | - Richard Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA
| | - Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, Princeton, NJ 08544, USA; Howard Hughes Medical Institute, Princeton University, Princeton, Princeton, NJ 08544, USA; Omenn-Darling Bioengineering Institute, Princeton University, Princeton, NJ 08544, USA.
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5
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Wu S, Chen J, Teo BHD, Wee SYK, Wong MHM, Cui J, Chen J, Leong KP, Lu J. The axis of complement C1 and nucleolus in antinuclear autoimmunity. Front Immunol 2023; 14:1196544. [PMID: 37359557 PMCID: PMC10288996 DOI: 10.3389/fimmu.2023.1196544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/19/2023] [Indexed: 06/28/2023] Open
Abstract
Antinuclear autoantibodies (ANA) are heterogeneous self-reactive antibodies that target the chromatin network, the speckled, the nucleoli, and other nuclear regions. The immunological aberration for ANA production remains partially understood, but ANA are known to be pathogenic, especially, in systemic lupus erythematosus (SLE). Most SLE patients exhibit a highly polygenic disease involving multiple organs, but in rare complement C1q, C1r, or C1s deficiencies, the disease can become largely monogenic. Increasing evidence point to intrinsic autoimmunogenicity of the nuclei. Necrotic cells release fragmented chromatins as nucleosomes and the alarmin HMGB1 is associated with the nucleosomes to activate TLRs and confer anti-chromatin autoimmunogenecity. In speckled regions, the major ANA targets Sm/RNP and SSA/Ro contain snRNAs that confer autoimmunogenecity to Sm/RNP and SSA/Ro antigens. Recently, three GAR/RGG-containing alarmins have been identified in the nucleolus that helps explain its high autoimmunogenicity. Interestingly, C1q binds to the nucleoli exposed by necrotic cells to cause protease C1r and C1s activation. C1s cleaves HMGB1 to inactive its alarmin activity. C1 proteases also degrade many nucleolar autoantigens including nucleolin, a major GAR/RGG-containing autoantigen and alarmin. It appears that the different nuclear regions are intrinsically autoimmunogenic by containing autoantigens and alarmins. However, the extracellular complement C1 complex function to dampen nuclear autoimmunogenecity by degrading these nuclear proteins.
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Affiliation(s)
- Shan Wu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Junjie Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Boon Heng Dennis Teo
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Seng Yin Kelly Wee
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Ming Hui Millie Wong
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jianzhou Cui
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jinmiao Chen
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
| | - Khai Pang Leong
- Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore, Singapore
| | - Jinhua Lu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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6
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Gerber A, van Otterdijk S, Bruggeman FJ, Tutucci E. Understanding spatiotemporal coupling of gene expression using single molecule RNA imaging technologies. Transcription 2023; 14:105-126. [PMID: 37050882 PMCID: PMC10807504 DOI: 10.1080/21541264.2023.2199669] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/30/2023] [Accepted: 04/01/2023] [Indexed: 04/14/2023] Open
Abstract
Across all kingdoms of life, gene regulatory mechanisms underlie cellular adaptation to ever-changing environments. Regulation of gene expression adjusts protein synthesis and, in turn, cellular growth. Messenger RNAs are key molecules in the process of gene expression. Our ability to quantitatively measure mRNA expression in single cells has improved tremendously over the past decades. This revealed an unexpected coordination between the steps that control the life of an mRNA, from transcription to degradation. Here, we provide an overview of the state-of-the-art imaging approaches for measurement and quantitative understanding of gene expression, starting from the early visualizations of single genes by electron microscopy to current fluorescence-based approaches in single cells, including live-cell RNA-imaging approaches to FISH-based spatial transcriptomics across model organisms. We also highlight how these methods have shaped our current understanding of the spatiotemporal coupling between transcriptional and post-transcriptional events in prokaryotes. We conclude by discussing future challenges of this multidisciplinary field.Abbreviations: mRNA: messenger RNA; rRNA: ribosomal rDNA; tRNA: transfer RNA; sRNA: small RNA; FISH: fluorescence in situ hybridization; RNP: ribonucleoprotein; smFISH: single RNA molecule FISH; smiFISH: single molecule inexpensive FISH; HCR-FISH: Hybridization Chain-Reaction-FISH; RCA: Rolling Circle Amplification; seqFISH: Sequential FISH; MERFISH: Multiplexed error robust FISH; UTR: Untranslated region; RBP: RNA binding protein; FP: fluorescent protein; eGFP: enhanced GFP, MCP: MS2 coat protein; PCP: PP7 coat protein; MB: Molecular beacons; sgRNA: single guide RNA.
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Affiliation(s)
- Alan Gerber
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Sander van Otterdijk
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank J. Bruggeman
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Evelina Tutucci
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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7
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Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes. Nat Rev Mol Cell Biol 2023; 24:414-429. [PMID: 36732602 DOI: 10.1038/s41580-022-00573-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2022] [Indexed: 02/04/2023]
Abstract
One of the first biological machineries to be created seems to have been the ribosome. Since then, organisms have dedicated great efforts to optimize this apparatus. The ribosomal RNA (rRNA) contained within ribosomes is crucial for protein synthesis and maintenance of cellular function in all known organisms. In eukaryotic cells, rRNA is produced from ribosomal DNA clusters of tandem rRNA genes, whose organization in the nucleolus, maintenance and transcription are strictly regulated to satisfy the substantial demand for rRNA required for ribosome biogenesis. Recent studies have elucidated mechanisms underlying the integrity of ribosomal DNA and regulation of its transcription, including epigenetic mechanisms and a unique recombination and copy-number control system to stably maintain high rRNA gene copy number. In this Review, we disucss how the crucial maintenance of rRNA gene copy number through control of gene amplification and of rRNA production by RNA polymerase I are orchestrated. We also discuss how liquid-liquid phase separation controls the architecture and function of the nucleolus and the relationship between rRNA production, cell senescence and disease.
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8
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Huffines AK, Engel KL, French SL, Zhang Y, Viktorovskaya OV, Schneider DA. Rate of transcription elongation and sequence-specific pausing by RNA polymerase I directly influence rRNA processing. J Biol Chem 2022; 298:102730. [PMID: 36423683 PMCID: PMC9768379 DOI: 10.1016/j.jbc.2022.102730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/18/2022] [Accepted: 11/07/2022] [Indexed: 11/23/2022] Open
Abstract
One of the first steps in ribosome biogenesis is transcription of the ribosomal DNA by RNA polymerase I (Pol I). Processing of the resultant rRNA begins cotranscriptionally, and perturbation of Pol I transcription elongation results in defective rRNA processing. Mechanistic insight regarding the link between transcription elongation and ribosome assembly is lacking because of limited in vivo methods to assay Pol I transcription. Here, we use native elongating transcript sequencing (NET-Seq) with a strain of Saccharomyces cerevisiae containing a point mutation in Pol I, rpa190-F1205H, which results in impaired rRNA processing and ribosome assembly. We previously demonstrated that this mutation caused a mild reduction in the transcription elongation rate of Pol I in vitro; however, transcription elongation by the mutant has not been characterized in vivo. Here, our findings demonstrate that the mutant Pol I has an increased pause propensity during processive transcription elongation both in vitro and in vivo. NET-Seq reveals that rpa190-F1205H Pol I displays alternative pause site preferences in vivo. Specifically, the mutant is sensitized to A/G residues in the RNA:DNA hybrid and at the last incorporated nucleotide position. Furthermore, both NET-Seq and EM analysis of Miller chromatin spreads reveal pileups of rpa190-F1205H Pol I throughout the ribosomal DNA, particularly at the 5' end of the 35S gene. This combination of in vitro and in vivo analyses of a Pol I mutant provides novel insights into Pol I elongation properties and indicates how these properties are crucial for efficient cotranscriptional rRNA processing and ribosome assembly.
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Affiliation(s)
- Abigail K Huffines
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Krysta L Engel
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sarah L French
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Yinfeng Zhang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Olga V Viktorovskaya
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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9
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Oborská-Oplová M, Gerhardy S, Panse VG. Orchestrating ribosomal RNA folding during ribosome assembly. Bioessays 2022; 44:e2200066. [PMID: 35751450 DOI: 10.1002/bies.202200066] [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: 03/29/2022] [Revised: 05/30/2022] [Accepted: 06/13/2022] [Indexed: 11/08/2022]
Abstract
Construction of the eukaryotic ribosome is a complex process in which a nascent ribosomal RNA (rRNA) emerging from RNA Polymerase I hierarchically folds into a native three-dimensional structure. Modular assembly of individual RNA domains through interactions with ribosomal proteins and a myriad of assembly factors permit efficient disentanglement of the error-prone RNA folding process. Following these dynamic events, long-range tertiary interactions are orchestrated to compact rRNA. A combination of genetic, biochemical, and structural studies is now providing clues into how a nascent rRNA is transformed into a functional ribosome with high precision. With this essay, we aim to draw attention to the poorly understood process of establishing correct RNA tertiary contacts during ribosome formation.
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Affiliation(s)
| | - Stefan Gerhardy
- Institute of Medical Microbiology, University of 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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10
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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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11
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Zannino L, Biggiogera M. How to stain nucleic acids and proteins in Miller spreads. Eur J Histochem 2022; 66. [PMID: 35212500 PMCID: PMC8883610 DOI: 10.4081/ejh.2022.3364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/12/2022] [Indexed: 11/23/2022] Open
Abstract
The spread technique proposed by Miller and Beatty in 1969 allowed for the first time the visualization at transmission electron microscopy of nucleic acids and chromatin in an isolated and distended conformation. The final step of staining the spread chromatin is of critical importance because it can strongly influence the interpretation of the results. We evaluated different staining techniques and the most part of them provided a good result. Specifically, well contrasted micrographs were obtained when staining with H3PW12O40 (PTA), as originally proposed by Miller and Beatty, and with two alternatives proposed here: uranyl acetate or terbium citrate staining. Quite good contrast of the spread DNA could be achieved also by using Osmium Ammine; while no or few contrast of nucleic acids was observed by staining with KMnO₄ and H3PMo12O40 (PMA) respectively.
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Affiliation(s)
- Lorena Zannino
- Laboratory of Cell Biology and Neurobiology, Department of Biology and Biotechnology, University of Pavia.
| | - Marco Biggiogera
- Laboratory of Cell Biology and Neurobiology, Department of Biology and Biotechnology, University of Pavia.
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12
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Schächner C, Merkl PE, Pilsl M, Schwank K, Hergert K, Kruse S, Milkereit P, Tschochner H, Griesenbeck J. Establishment and Maintenance of Open Ribosomal RNA Gene Chromatin States in Eukaryotes. Methods Mol Biol 2022; 2533:25-38. [PMID: 35796980 PMCID: PMC9761505 DOI: 10.1007/978-1-0716-2501-9_2] [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
In growing eukaryotic cells, nuclear ribosomal (r)RNA synthesis by RNA polymerase (RNAP) I accounts for the vast majority of cellular transcription. This high output is achieved by the presence of multiple copies of rRNA genes in eukaryotic genomes transcribed at a high rate. In contrast to most of the other transcribed genomic loci, actively transcribed rRNA genes are largely devoid of nucleosomes adapting a characteristic "open" chromatin state, whereas a significant fraction of rRNA genes resides in a transcriptionally inactive nucleosomal "closed" chromatin state. Here, we review our current knowledge about the nature of open rRNA gene chromatin and discuss how this state may be established.
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Affiliation(s)
- Christopher Schächner
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Philipp E Merkl
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
- TUM ForTe, Technische Universität München, Munich, Germany
| | - Michael Pilsl
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Katrin Schwank
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Kristin Hergert
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Sebastian Kruse
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Philipp Milkereit
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany.
| | - Herbert Tschochner
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany.
| | - Joachim Griesenbeck
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany.
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13
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Erdmann PS, Hou Z, Klumpe S, Khavnekar S, Beck F, Wilfling F, Plitzko JM, Baumeister W. In situ cryo-electron tomography reveals gradient organization of ribosome biogenesis in intact nucleoli. Nat Commun 2021; 12:5364. [PMID: 34508074 PMCID: PMC8433212 DOI: 10.1038/s41467-021-25413-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 08/09/2021] [Indexed: 02/08/2023] Open
Abstract
Ribosomes comprise a large (LSU) and a small subunit (SSU) which are synthesized independently in the nucleolus before being exported into the cytoplasm, where they assemble into functional ribosomes. Individual maturation steps have been analyzed in detail using biochemical methods, light microscopy and conventional electron microscopy (EM). In recent years, single particle analysis (SPA) has yielded molecular resolution structures of several pre-ribosomal intermediates. It falls short, however, of revealing the spatiotemporal sequence of ribosome biogenesis in the cellular context. Here, we present our study on native nucleoli in Chlamydomonas reinhardtii, in which we follow the formation of LSU and SSU precursors by in situ cryo-electron tomography (cryo-ET) and subtomogram averaging (STA). By combining both positional and molecular data, we reveal gradients of ribosome maturation within the granular component (GC), offering a new perspective on how the liquid-liquid-phase separation of the nucleolus supports ribosome biogenesis.
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Affiliation(s)
- Philipp S Erdmann
- Max Planck Institute of Biochemistry, Martinsried, Germany.
- Fondazione Human Technopole, Milano, Italy.
| | - Zhen Hou
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sven Klumpe
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - Florian Beck
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Wilfling
- Max Planck Institute of Biochemistry, Martinsried, Germany
- Max Planck Institute of Biophysics, Frankfurt, Germany
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14
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Jarrous N, Mani D, Ramanathan A. Coordination of transcription and processing of tRNA. FEBS J 2021; 289:3630-3641. [PMID: 33929081 DOI: 10.1111/febs.15904] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/02/2021] [Accepted: 04/28/2021] [Indexed: 12/17/2022]
Abstract
Coordination of transcription and processing of RNA is a basic principle in regulation of gene expression in eukaryotes. In the case of mRNA, coordination is primarily founded on a co-transcriptional processing mechanism by which a nascent precursor mRNA undergoes maturation via cleavage and modification by the transcription machinery. A similar mechanism controls the biosynthesis of rRNA. However, the coordination of transcription and processing of tRNA, a rather short transcript, remains unknown. Here, we present a model for high molecular weight initiation complexes of human RNA polymerase III that assemble on tRNA genes and process precursor transcripts to mature forms. These multifunctional initiation complexes may support co-transcriptional processing, such as the removal of the 5' leader of precursor tRNA by RNase P. Based on this model, maturation of tRNA is predetermined prior to transcription initiation.
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Affiliation(s)
- Nayef Jarrous
- Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Dhivakar Mani
- Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Aravind Ramanathan
- Microbiology and Molecular Genetics, Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
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15
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Ojha S, Malla S, Lyons SM. snoRNPs: Functions in Ribosome Biogenesis. Biomolecules 2020; 10:biom10050783. [PMID: 32443616 PMCID: PMC7277114 DOI: 10.3390/biom10050783] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/10/2020] [Accepted: 05/13/2020] [Indexed: 01/18/2023] Open
Abstract
Ribosomes are perhaps the most critical macromolecular machine as they are tasked with carrying out protein synthesis in cells. They are incredibly complex structures composed of protein components and heavily chemically modified RNAs. The task of assembling mature ribosomes from their component parts consumes a massive amount of energy and requires greater than 200 assembly factors. Among the most critical of these are small nucleolar ribonucleoproteins (snoRNPs). These are small RNAs complexed with diverse sets of proteins. As suggested by their name, they localize to the nucleolus, the site of ribosome biogenesis. There, they facilitate multiple roles in ribosomes biogenesis, such as pseudouridylation and 2′-O-methylation of ribosomal (r)RNA, guiding pre-rRNA processing, and acting as molecular chaperones. Here, we reviewed their activity in promoting the assembly of ribosomes in eukaryotes with regards to chemical modification and pre-rRNA processing.
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Affiliation(s)
- Sandeep Ojha
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
| | - Sulochan Malla
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
| | - Shawn M. Lyons
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02115, USA; (S.O.); (S.M.)
- The Genome Science Institute, Boston University School of Medicine, Boston, MA 02115, USA
- Correspondence: ; Tel.: +1-617-358-4280
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16
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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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17
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Rederstorff M. Une mutation ponctuelle dans la protéine Rrp9 de la particule U3 entraîne un découplage des clivages précoces de l’ARN pré-ribosomique. Med Sci (Paris) 2020; 36:329-331. [DOI: 10.1051/medsci/2020054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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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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19
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Bennison DJ, Irving SE, Corrigan RM. The Impact of the Stringent Response on TRAFAC GTPases and Prokaryotic Ribosome Assembly. Cells 2019; 8:cells8111313. [PMID: 31653044 PMCID: PMC6912228 DOI: 10.3390/cells8111313] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/17/2019] [Accepted: 10/23/2019] [Indexed: 12/24/2022] Open
Abstract
Many facets of ribosome biogenesis and function, including ribosomal RNA (rRNA) transcription, 70S assembly and protein translation, are negatively impacted upon induction of a nutrient stress-sensing signalling pathway termed the stringent response. This stress response is mediated by the alarmones guanosine tetra- and penta-phosphate ((p)ppGpp), the accumulation of which leads to a massive cellular response that slows growth and aids survival. The 70S bacterial ribosome is an intricate structure, with assembly both complex and highly modular. Presiding over the assembly process is a group of P-loop GTPases within the TRAFAC (Translation Factor Association) superclass that are crucial for correct positioning of both early and late stage ribosomal proteins (r-proteins) onto the rRNA. Often described as 'molecular switches', members of this GTPase superfamily readily bind and hydrolyse GTP to GDP in a cyclic manner that alters the propensity of the GTPase to carry out a function. TRAFAC GTPases are considered to act as checkpoints to ribosome assembly, involved in binding to immature sections in the GTP-bound state, preventing further r-protein association until maturation is complete. Here we review our current understanding of the impact of the stringent response and (p)ppGpp production on ribosome maturation in prokaryotic cells, focusing on the inhibition of (p)ppGpp on GTPase-mediated subunit assembly, but also touching upon the inhibition of rRNA transcription and protein translation.
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Affiliation(s)
- Daniel J Bennison
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
| | - Sophie E Irving
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
| | - Rebecca M Corrigan
- The Florey Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
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20
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Matos-Perdomo E, Machín F. Nucleolar and Ribosomal DNA Structure under Stress: Yeast Lessons for Aging and Cancer. Cells 2019; 8:cells8080779. [PMID: 31357498 PMCID: PMC6721496 DOI: 10.3390/cells8080779] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/15/2019] [Accepted: 07/24/2019] [Indexed: 02/06/2023] Open
Abstract
Once thought a mere ribosome factory, the nucleolus has been viewed in recent years as an extremely sensitive gauge of diverse cellular stresses. Emerging concepts in nucleolar biology include the nucleolar stress response (NSR), whereby a series of cell insults have a special impact on the nucleolus. These insults include, among others, ultra-violet radiation (UV), nutrient deprivation, hypoxia and thermal stress. While these stresses might influence nucleolar biology directly or indirectly, other perturbances whose origin resides in the nucleolar biology also trigger nucleolar and systemic stress responses. Among the latter, we find mutations in nucleolar and ribosomal proteins, ribosomal RNA (rRNA) processing inhibitors and ribosomal DNA (rDNA) transcription inhibition. The p53 protein also mediates NSR, leading ultimately to cell cycle arrest, apoptosis, senescence or differentiation. Hence, NSR is gaining importance in cancer biology. The nucleolar size and ribosome biogenesis, and how they connect with the Target of Rapamycin (TOR) signalling pathway, are also becoming important in the biology of aging and cancer. Simple model organisms like the budding yeast Saccharomyces cerevisiae, easy to manipulate genetically, are useful in order to study nucleolar and rDNA structure and their relationship with stress. In this review, we summarize the most important findings related to this topic.
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Affiliation(s)
- Emiliano Matos-Perdomo
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
- Escuela de Doctorado y Estudios de Postgrado, Universidad de La Laguna, 38200 Tenerife, Spain
| | - Félix Machín
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain.
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna, 38200 Tenerife, Spain.
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, 35450 Santa María de Guía, Gran Canaria, Spain.
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21
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Potapova TA, Gerton JL. Ribosomal DNA and the nucleolus in the context of genome organization. Chromosome Res 2019; 27:109-127. [PMID: 30656516 DOI: 10.1007/s10577-018-9600-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/13/2018] [Accepted: 12/17/2018] [Indexed: 12/12/2022]
Abstract
The nucleolus constitutes a prominent nuclear compartment, a membraneless organelle that was first documented in the 1830s. The fact that specific chromosomal regions were present in the nucleolus was recognized by Barbara McClintock in the 1930s, and these regions were termed nucleolar organizing regions, or NORs. The primary function of ribosomal DNA (rDNA) is to produce RNA components of ribosomes. Yet, ribosomal DNA also plays a pivotal role in nuclear organization by assembling the nucleolus. This review is focused on the rDNA and associated proteins in the context of genome organization. Recent advances in understanding chromatin organization suggest that chromosomes are organized into topological domains by a DNA loop extrusion process. We discuss the perspective that rDNA may also be organized in topological domains constrained by structural maintenance of chromosome protein complexes such as cohesin and condensin. Moreover, biophysical studies indicate that the nucleolar compartment may be formed by active processes as well as phase separation, a perspective that lends further insight into nucleolar organization. The application of the latest perspectives and technologies to this organelle help further elucidate its role in nuclear structure and function.
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Affiliation(s)
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
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22
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Cenik ES, Meng X, Tang NH, Hall RN, Arribere JA, Cenik C, Jin Y, Fire A. Maternal Ribosomes Are Sufficient for Tissue Diversification during Embryonic Development in C. elegans. Dev Cell 2019; 48:811-826.e6. [PMID: 30799226 DOI: 10.1016/j.devcel.2019.01.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 11/06/2018] [Accepted: 01/21/2019] [Indexed: 12/20/2022]
Abstract
Caenorhabditis elegans provides an amenable system to explore whether newly composed ribosomes are required to progress through development. Despite the complex pattern of tissues that are formed during embryonic development, we found that null homozygotes lacking any of the five different ribosomal proteins (RPs) can produce fully functional first-stage larvae, with similar developmental competence seen upon complete deletion of the multi-copy ribosomal RNA locus. These animals, relying on maternal but not zygotic contribution of ribosomal components, are capable of completing embryogenesis. In the absence of new ribosomal components, the resulting animals are arrested before progression from the first larval stage and fail in two assays for postembryonic plasticity of neuronal structure. Mosaic analyses of larvae that are a mixture of ribosome-competent and non-competent cells suggest a global regulatory mechanism in which ribosomal insufficiency in a subset of cells triggers organism-wide growth arrest.
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Affiliation(s)
- Elif Sarinay Cenik
- Department of Pathology, Stanford University Medical School, Stanford, CA, USA; Department of Molecular Biosciences, University of Texas Austin, Austin, TX, USA
| | - Xuefeng Meng
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Ngang Heok Tang
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, San Diego, CA, USA
| | | | - Joshua A Arribere
- Department of MCD Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas Austin, Austin, TX, USA
| | - Yishi Jin
- Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, San Diego, CA, USA
| | - Andrew Fire
- Department of Pathology, Stanford University Medical School, Stanford, CA, USA.
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23
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Chen J, Teo BHD, Cai Y, Wee SYK, Lu J. The linker histone H1.2 is a novel component of the nucleolar organizer regions. J Biol Chem 2018; 293:2358-2369. [PMID: 29301938 DOI: 10.1074/jbc.m117.810184] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 12/18/2017] [Indexed: 01/27/2023] Open
Abstract
The nucleoli accumulate rRNA genes and are the sites of rRNA synthesis and rRNA assembly into ribosomes. During mitosis, nucleoli dissociate, but nucleolar remnants remain on the rRNA gene loci, forming distinct nucleolar organizer regions (NORs). Little is known about the composition and structure of NORs, but upstream binding factor (UBF) has been established as its master organizer. In this study, we sought to establish new proteins in NORs. Using UBF-Sepharose to isolate UBF-binding proteins, we identified histone H1.2 as a candidate partner but were puzzled by this observation, given that UBF is known to be located predominantly in nucleoli, whereas H1.2 distributed broadly among the chromatins in interphase nuclei. We then examined cells undergoing mitosis and saw that both H1.2 and UBF were recruited into NORs in this state, reconciling the results of our UBF pulldowns. Inhibiting rRNA synthesis in interphase nuclei also induced NOR-like structures containing both UBF and H1.2. When chromosomes were isolated and spread on coverslips, NORs appeared separated from the chromosomes containing both UBF and H1.2. After chromosomes were fragmented by homogenization, intact NORs remained visible. Results collectively suggest that NORs are independent structures and that the linker histone H1.2 is a novel component of this structure.
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Affiliation(s)
- Junjie Chen
- From the Department of Microbiology and Immunology, Yong Loo Lin School of Medicine and Immunology Programme, National University of Singapore, Singapore 117697
| | - Boon Heng Dennis Teo
- From the Department of Microbiology and Immunology, Yong Loo Lin School of Medicine and Immunology Programme, National University of Singapore, Singapore 117697
| | - Yitian Cai
- From the Department of Microbiology and Immunology, Yong Loo Lin School of Medicine and Immunology Programme, National University of Singapore, Singapore 117697
| | - Seng Yin Kelly Wee
- From the Department of Microbiology and Immunology, Yong Loo Lin School of Medicine and Immunology Programme, National University of Singapore, Singapore 117697
| | - Jinhua Lu
- From the Department of Microbiology and Immunology, Yong Loo Lin School of Medicine and Immunology Programme, National University of Singapore, Singapore 117697
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24
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Davis JH, Williamson JR. Structure and dynamics of bacterial ribosome biogenesis. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0181. [PMID: 28138067 DOI: 10.1098/rstb.2016.0181] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 01/28/2023] Open
Abstract
Bacterial ribosome biogenesis has been an active area of research for more than 30 years and has served as a test-bed for the development of new biochemical, biophysical and structural techniques to understand macromolecular assembly generally. Recent work inspecting the process in vivo has advanced our understanding of the role of ribosome biogenesis factors, the co-transcriptional nature of assembly, the kinetics of the process under sub-optimal conditions, and the rRNA folding and ribosome protein binding pathways. Additionally, new structural work enabled by single-particle electron microscopy has helped to connect in vitro ribosomal protein binding maps to the underlying RNA. This review summarizes the state of these in vivo studies, provides a kinetic model for ribosome assembly under sub-optimal conditions, and describes a framework to compare newly emerging assembly intermediate structures.This article is part of the themed issue 'Perspectives on the ribosome'.
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Affiliation(s)
- Joseph H Davis
- Department of Integrative Structural and Computational Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA .,Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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25
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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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26
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de la Cruz J, Gómez-Herreros F, Rodríguez-Galán O, Begley V, de la Cruz Muñoz-Centeno M, Chávez S. Feedback regulation of ribosome assembly. Curr Genet 2017; 64:393-404. [PMID: 29022131 DOI: 10.1007/s00294-017-0764-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/06/2017] [Accepted: 10/07/2017] [Indexed: 12/12/2022]
Abstract
Ribosome biogenesis is a crucial process for growth and constitutes the major consumer of cellular resources. This pathway is subjected to very stringent regulation to ensure correct ribosome manufacture with a wide variety of environmental and metabolic changes, and intracellular insults. Here we summarise our current knowledge on the regulation of ribosome biogenesis in Saccharomyces cerevisiae by particularly focusing on the feedback mechanisms that maintain ribosome homeostasis. Ribosome biogenesis in yeast is controlled mainly at the level of the production of both pre-rRNAs and ribosomal proteins through the transcriptional and post-transcriptional control of the TORC1 and protein kinase A signalling pathways. Pre-rRNA processing can occur before or after the 35S pre-rRNA transcript is completed; the switch between these two alternatives is regulated by growth conditions. The expression of both ribosomal proteins and the large family of transacting factors involved in ribosome biogenesis is co-regulated. Recently, it has been shown that the synthesis of rRNA and ribosomal proteins, but not of trans-factors, is coupled. Thus the so-called CURI complex sequesters specific transcription factor Ifh1 to repress ribosomal protein genes when rRNA transcription is impaired. We recently found that an analogue system should operate to control the expression of transacting factor genes in response to actual ribosome assembly performance. Regulation of ribosome biogenesis manages situations of imbalanced ribosome production or misassembled ribosomal precursors and subunits, which have been closely linked to distinct human diseases.
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Affiliation(s)
- Jesús de la Cruz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain. .,Departamento de Genética, Universidad de Sevilla, Seville, Spain.
| | - Fernando Gómez-Herreros
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Olga Rodríguez-Galán
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Victoria Begley
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - María de la Cruz Muñoz-Centeno
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain. .,Departamento de Genética, Universidad de Sevilla, Seville, Spain.
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27
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Cheng J, Kellner N, Berninghausen O, Hurt E, Beckmann R. 3.2-Å-resolution structure of the 90S preribosome before A1 pre-rRNA cleavage. Nat Struct Mol Biol 2017; 24:954-964. [PMID: 28967883 DOI: 10.1038/nsmb.3476] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/04/2017] [Indexed: 12/15/2022]
Abstract
The 40S small ribosomal subunit is cotranscriptionally assembled in the nucleolus as part of a large chaperone complex called the 90S preribosome or small-subunit processome. Here, we present the 3.2-Å-resolution structure of the Chaetomium thermophilum 90S preribosome, which allowed us to build atomic structures for 34 assembly factors, including the Mpp10 complex, Bms1, Utp14 and Utp18, and the complete U3 small nucleolar ribonucleoprotein. Moreover, we visualized the U3 RNA heteroduplexes with a 5' external transcribed spacer (5' ETS) and pre-18S RNA, and their stabilization by 90S factors. Overall, the structure explains how a highly intertwined network of assembly factors and pre-rRNA guide the sequential, independent folding of the individual pre-40S domains while the RNA regions forming the 40S active sites are kept immature. Finally, by identifying the unprocessed A1 cleavage site and the nearby Utp24 endonuclease, we suggest a proofreading model for regulated 5'-ETS separation and 90S-pre-40S transition.
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Affiliation(s)
- Jingdong Cheng
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, University of Munich, Munich, Germany
| | - Nikola Kellner
- Biochemie-Zentrum der Universität Heidelberg, Heidelberg, Germany
| | - Otto Berninghausen
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, University of Munich, Munich, Germany
| | - Ed Hurt
- Biochemie-Zentrum der Universität Heidelberg, Heidelberg, Germany
| | - Roland Beckmann
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, University of Munich, Munich, Germany
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High-throughput RNA structure probing reveals critical folding events during early 60S ribosome assembly in yeast. Nat Commun 2017; 8:714. [PMID: 28959008 PMCID: PMC5620067 DOI: 10.1038/s41467-017-00761-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 07/26/2017] [Indexed: 11/25/2022] Open
Abstract
While the protein composition of various yeast 60S ribosomal subunit assembly intermediates has been studied in detail, little is known about ribosomal RNA (rRNA) structural rearrangements that take place during early 60S assembly steps. Using a high-throughput RNA structure probing method, we provide nucleotide resolution insights into rRNA structural rearrangements during nucleolar 60S assembly. Our results suggest that many rRNA-folding steps, such as folding of 5.8S rRNA, occur at a very specific stage of assembly, and propose that downstream nuclear assembly events can only continue once 5.8S folding has been completed. Our maps of nucleotide flexibility enable making predictions about the establishment of protein–rRNA interactions, providing intriguing insights into the temporal order of protein–rRNA as well as long-range inter-domain rRNA interactions. These data argue that many distant domains in the rRNA can assemble simultaneously during early 60S assembly and underscore the enormous complexity of 60S synthesis. Ribosome biogenesis is a dynamic process that involves the ordered assembly of ribosomal proteins and numerous RNA structural rearrangements. Here the authors apply ChemModSeq, a high-throughput RNA structure probing method, to quantitatively measure changes in RNA flexibility during the nucleolar stages of 60S assembly in yeast.
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29
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Eukaryotic ribosome assembly, transport and quality control. Nat Struct Mol Biol 2017; 24:689-699. [PMID: 28880863 DOI: 10.1038/nsmb.3454] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/27/2017] [Indexed: 12/18/2022]
Abstract
Eukaryotic ribosome synthesis is a complex, energy-consuming process that takes place across the nucleolus, nucleoplasm and cytoplasm and requires more than 200 conserved assembly factors. Here, we discuss mechanisms by which the ribosome assembly and nucleocytoplasmic transport machineries collaborate to produce functional ribosomes. We also highlight recent cryo-EM studies that provided unprecedented snapshots of ribosomes during assembly and quality control.
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30
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Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome. Cell 2017; 166:380-393. [PMID: 27419870 DOI: 10.1016/j.cell.2016.06.014] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/05/2016] [Accepted: 06/01/2016] [Indexed: 12/13/2022]
Abstract
The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that associate with nascent pre-rRNA. We report the cryo-EM structure of the Chaetomium thermophilum 90S pre-ribosome, revealing how a network of biogenesis factors including 19 β-propellers and large α-solenoid proteins engulfs the pre-rRNA. Within the 90S pre-ribosome, we identify the UTP-A, UTP-B, Mpp10-Imp3-Imp4, Bms1-Rcl1, and U3 snoRNP modules, which are organized around 5'-ETS and partially folded 18S rRNA. The U3 snoRNP is strategically positioned at the center of the 90S particle to perform its multiple tasks during pre-rRNA folding and processing. The architecture of the elusive 90S pre-ribosome gives unprecedented structural insight into the early steps of pre-rRNA maturation. Nascent rRNA that is co-transcriptionally folded and given a particular shape by encapsulation within a dedicated mold-like structure is reminiscent of how polypeptides use chaperone chambers for their protein folding.
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31
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Chaker-Margot M, Barandun J, Hunziker M, Klinge S. Architecture of the yeast small subunit processome. Science 2016; 355:science.aal1880. [PMID: 27980088 DOI: 10.1126/science.aal1880] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/05/2016] [Indexed: 12/21/2022]
Abstract
The small subunit (SSU) processome, a large ribonucleoprotein particle, organizes the assembly of the eukaryotic small ribosomal subunit by coordinating the folding, cleavage, and modification of nascent pre-ribosomal RNA (rRNA). Here, we present the cryo-electron microscopy structure of the yeast SSU processome at 5.1-angstrom resolution. The structure reveals how large ribosome biogenesis complexes assist the 5' external transcribed spacer and U3 small nucleolar RNA in providing an intertwined RNA-protein assembly platform for the separate maturation of 18S rRNA domains. The strategic placement of a molecular motor at the center of the particle further suggests a mechanism for mediating conformational changes within this giant particle. This study provides a structural framework for a mechanistic understanding of eukaryotic ribosome assembly in the model organism Saccharomyces cerevisiae.
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Affiliation(s)
- Malik Chaker-Margot
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA.,Tri-Institutional Training Program in Chemical Biology, The Rockefeller University, New York, NY 10065, USA
| | - Jonas Barandun
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Mirjam Hunziker
- 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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32
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Talkish J, Biedka S, Jakovljevic J, Zhang J, Tang L, Strahler JR, Andrews PC, Maddock JR, Woolford JL. Disruption of ribosome assembly in yeast blocks cotranscriptional pre-rRNA processing and affects the global hierarchy of ribosome biogenesis. RNA (NEW YORK, N.Y.) 2016; 22:852-66. [PMID: 27036125 PMCID: PMC4878612 DOI: 10.1261/rna.055780.115] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/18/2016] [Indexed: 05/11/2023]
Abstract
In higher eukaryotes, pre-rRNA processing occurs almost exclusively post-transcriptionally. This is not the case in rapidly dividing yeast, as the majority of nascent pre-rRNAs are processed cotranscriptionally, with cleavage at the A2 site first releasing a pre-40S ribosomal subunit followed by release of a pre-60S ribosomal subunit upon transcription termination. Ribosome assembly is driven in part by hierarchical association of assembly factors and r-proteins. Groups of proteins are thought to associate with pre-ribosomes cotranscriptionally during early assembly steps, whereas others associate later, after transcription is completed. Here we describe a previously uncharacterized phenotype observed upon disruption of ribosome assembly, in which normally late-binding proteins associate earlier, with pre-ribosomes containing 35S pre-rRNA. As previously observed by many other groups, we show that disruption of 60S subunit biogenesis results in increased amounts of 35S pre-rRNA, suggesting that a greater fraction of pre-rRNAs are processed post-transcriptionally. Surprisingly, we found that early pre-ribosomes containing 35S pre-rRNA also contain proteins previously thought to only associate with pre-ribosomes after early pre-rRNA processing steps have separated maturation of the two subunits. We believe the shift to post-transcriptional processing is ultimately due to decreased cellular division upon disruption of ribosome assembly. When cells are grown under stress or to high density, a greater fraction of pre-rRNAs are processed post-transcriptionally and follow an alternative processing pathway. Together, these results affirm the principle that ribosome assembly occurs through different, parallel assembly pathways and suggest that there is a kinetic foot-race between the formation of protein binding sites and pre-rRNA processing events.
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Affiliation(s)
- Jason Talkish
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA The Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Stephanie Biedka
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA The Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Jelena Jakovljevic
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA The Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Jingyu Zhang
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Lan Tang
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - John R Strahler
- Department of Biological Chemistry, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Philip C Andrews
- Department of Biological Chemistry, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Janine R Maddock
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - John L Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA The Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
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Smirnov E, Hornáček M, Kováčik L, Mazel T, Schröfel A, Svidenská S, Skalníková M, Bartová E, Cmarko D, Raška I. Reproduction of the FC/DFC units in nucleoli. Nucleus 2016; 7:203-15. [PMID: 26934002 DOI: 10.1080/19491034.2016.1157674] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The essential structural components of the nucleoli, Fibrillar Centers (FC) and Dense Fibrillar Components (DFC), together compose FC/DFC units, loci of rDNA transcription and early RNA processing. In the present study we followed cell cycle related changes of these units in 2 human sarcoma derived cell lines with stable expression of RFP-PCNA (the sliding clamp protein) and GFP-RPA43 (a subunit of RNA polymerase I, pol I) or GFP-fibrillarin. Correlative light and electron microscopy analysis showed that the pol I and fibrillarin positive nucleolar beads correspond to individual FC/DFC units. In vivo observations showed that at early S phase, when transcriptionally active ribosomal genes were replicated, the number of the units in each cell increased by 60-80%. During that period the units transiently lost pol I, but not fibrillarin. Then, until the end of interphase, number of the units did not change, and their duplication was completed only after the cell division, by mid G1 phase. This peculiar mode of reproduction suggests that a considerable subset of ribosomal genes remain transcriptionally silent from mid S phase to mitosis, but become again active in the postmitotic daughter cells.
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Affiliation(s)
- Evgeny Smirnov
- a Charles University in Prague , First Faculty of Medicine , Institute of Cellular Biology and Pathology , Prague , Czech Republic
| | - Matúš Hornáček
- a Charles University in Prague , First Faculty of Medicine , Institute of Cellular Biology and Pathology , Prague , Czech Republic
| | - Lubomír Kováčik
- a Charles University in Prague , First Faculty of Medicine , Institute of Cellular Biology and Pathology , Prague , Czech Republic
| | - Tomáš Mazel
- a Charles University in Prague , First Faculty of Medicine , Institute of Cellular Biology and Pathology , Prague , Czech Republic
| | - Adam Schröfel
- a Charles University in Prague , First Faculty of Medicine , Institute of Cellular Biology and Pathology , Prague , Czech Republic
| | - Silvie Svidenská
- a Charles University in Prague , First Faculty of Medicine , Institute of Cellular Biology and Pathology , Prague , Czech Republic
| | - Magdalena Skalníková
- a Charles University in Prague , First Faculty of Medicine , Institute of Cellular Biology and Pathology , Prague , Czech Republic
| | - Eva Bartová
- a Charles University in Prague , First Faculty of Medicine , Institute of Cellular Biology and Pathology , Prague , Czech Republic.,b Institute of Biophysics of the CAS , Brno , Czech Republic
| | - Dušan Cmarko
- a Charles University in Prague , First Faculty of Medicine , Institute of Cellular Biology and Pathology , Prague , Czech Republic
| | - Ivan Raška
- a Charles University in Prague , First Faculty of Medicine , Institute of Cellular Biology and Pathology , Prague , Czech Republic
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34
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Wang D, Qin B, Li X, Tang D, Zhang Y, Cheng Z, Xue Y. Nucleolar DEAD-Box RNA Helicase TOGR1 Regulates Thermotolerant Growth as a Pre-rRNA Chaperone in Rice. PLoS Genet 2016; 12:e1005844. [PMID: 26848586 PMCID: PMC4743921 DOI: 10.1371/journal.pgen.1005844] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/13/2016] [Indexed: 11/18/2022] Open
Abstract
Plants have evolved a considerable number of intrinsic tolerance strategies to acclimate to ambient temperature increase. However, their molecular mechanisms remain largely obscure. Here we report a DEAD-box RNA helicase, TOGR1 (Thermotolerant Growth Required1), prerequisite for rice growth themotolerance. Regulated by both temperature and the circadian clock, its expression is tightly coupled to daily temperature fluctuations and its helicase activities directly promoted by temperature increase. Located in the nucleolus and associated with the small subunit (SSU) pre-rRNA processome, TOGR1 maintains a normal rRNA homeostasis at high temperature. Natural variation in its transcript level is positively correlated with plant height and its overexpression significantly improves rice growth under hot conditions. Our findings reveal a novel molecular mechanism of RNA helicase as a key chaperone for rRNA homeostasis required for rice thermotolerant growth and provide a potential strategy to breed heat-tolerant crops by modulating the expression of TOGR1 and its orthologs. Global warming is increasingly posing negative impacts on crop productivity. In this study, we report a nucleolar-located RNA helicase TOGR1 for thermotolerant growth in rice. TOGR1 maintains pre-rRNA homeostasis under high temperature by securing a proper pre-rRNA structure via elevating its helicase activity. Its expression is high temperature inducible with an afternoon peak expression, consistent with a high temperature anticipation of the circadian clock. Transcriptome analysis revealed that TOGR1 is essential in coordinating primary metabolisms to support thermotolerant growth. Importantly, an enhanced expression of TOGR1 significantly increased biomass of rice. Our findings reveal a novel role of a RNA helicase in thermotolerance and provide a potential strategy to breed heat-tolerant rice cultivars and possibly other heat-tolerant crops.
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Affiliation(s)
- Dong Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
| | - Baoxiang Qin
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
| | - Xiang Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
| | - Ding Tang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
| | - Yu’e Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
- Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Yongbiao Xue
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China
- Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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35
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Abstract
Nucleoli are formed on the basis of ribosomal genes coding for RNAs of ribosomal particles, but also include a great variety of other DNA regions. In this article, we discuss the characteristics of ribosomal DNA: the structure of the rDNA locus, complex organization and functions of the intergenic spacer, multiplicity of gene copies in one cell, selective silencing of genes and whole gene clusters, relation to components of nucleolar ultrastructure, specific problems associated with replication. We also review current data on the role of non-ribosomal DNA in the organization and function of nucleoli. Finally, we discuss probable causes preventing efficient visualization of DNA in nucleoli.
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36
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Stępiński D. Functional ultrastructure of the plant nucleolus. PROTOPLASMA 2014; 251:1285-306. [PMID: 24756369 PMCID: PMC4209244 DOI: 10.1007/s00709-014-0648-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 04/08/2014] [Indexed: 05/23/2023]
Abstract
Nucleoli are nuclear domains present in almost all eukaryotic cells. They not only specialize in the production of ribosomal subunits but also play roles in many fundamental cellular activities. Concerning ribosome biosynthesis, particular stages of this process, i.e., ribosomal DNA transcription, primary RNA transcript processing, and ribosome assembly proceed in precisely defined nucleolar subdomains. Although eukaryotic nucleoli are conservative in respect of their main function, clear morphological differences between these structures can be noticed between individual kingdoms. In most cases, a plant nucleolus shows well-ordered structure in which four main ultrastructural components can be distinguished: fibrillar centers, dense fibrillar component, granular component, and nucleolar vacuoles. Nucleolar chromatin is an additional crucial structural component of this organelle. Nucleolonema, although it is not always an unequivocally distinguished nucleolar domain, has often been described as a well-grounded morphological element, especially of plant nucleoli. The ratios and morphology of particular subcompartments of a nucleolus can change depending on its metabolic activity which in turn is correlated with the physiological state of a cell, cell type, cell cycle phase, as well as with environmental influence. Precise attribution of functions to particular nucleolar subregions in the process of ribosome biosynthesis is now possible using various approaches. The presented description of plant nucleolar morphology summarizes previous knowledge regarding the function of nucleoli as well as of their particular subdomains not only in the course of ribosome biosynthesis.
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Affiliation(s)
- Dariusz Stępiński
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Łódź, Pomorska 141/143, 90-236, Łódź, Poland,
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Henras AK, Plisson-Chastang C, O'Donohue MF, Chakraborty A, Gleizes PE. An overview of pre-ribosomal RNA processing in eukaryotes. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:225-42. [PMID: 25346433 PMCID: PMC4361047 DOI: 10.1002/wrna.1269] [Citation(s) in RCA: 391] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 08/04/2014] [Accepted: 08/29/2014] [Indexed: 12/23/2022]
Abstract
Ribosomal RNAs are the most abundant and universal noncoding RNAs in living organisms. In eukaryotes, three of the four ribosomal RNAs forming the 40S and 60S subunits are borne by a long polycistronic pre-ribosomal RNA. A complex sequence of processing steps is required to gradually release the mature RNAs from this precursor, concomitant with the assembly of the 79 ribosomal proteins. A large set of trans-acting factors chaperone this process, including small nucleolar ribonucleoparticles. While yeast has been the gold standard for studying the molecular basis of this process, recent technical advances have allowed to further define the mechanisms of ribosome biogenesis in animals and plants. This renewed interest for a long-lasting question has been fueled by the association of several genetic diseases with mutations in genes encoding both ribosomal proteins and ribosome biogenesis factors, and by the perspective of new anticancer treatments targeting the mechanisms of ribosome synthesis. A consensus scheme of pre-ribosomal RNA maturation is emerging from studies in various kinds of eukaryotic organisms. However, major differences between mammalian and yeast pre-ribosomal RNA processing have recently come to light. WIREs RNA 2015, 6:225–242. doi: 10.1002/wrna.1269
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Affiliation(s)
- Anthony K Henras
- Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse-Paul Sabatier CNRS, UMR 5099, Toulouse, France
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Turowski TW, Tollervey D. Cotranscriptional events in eukaryotic ribosome synthesis. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:129-39. [PMID: 25176256 DOI: 10.1002/wrna.1263] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/16/2014] [Accepted: 07/23/2014] [Indexed: 12/13/2022]
Abstract
Eukaryotic ribosomes are synthesized in a complex, multistep pathway. This begins with transcription of the rDNA genes by a specialized RNA polymerase, accompanied by the cotranscriptional binding of large numbers of ribosome synthesis factors, small nucleolar RNAs and ribosomal proteins. Cleavage of the nascent transcript releases the early pre-40S and pre-60S particles, which acquire export competence in the nucleoplasm prior to translocation through the nuclear pore complexes and final maturation to functional ribosomal subunits in the cytoplasm. This review will focus on the many and complex interactions occurring during pre-rRNA synthesis, particularly in budding yeast in which the pathway is best understood.
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Affiliation(s)
- Tomasz W Turowski
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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Sloan KE, Bohnsack MT, Schneider C, Watkins NJ. The roles of SSU processome components and surveillance factors in the initial processing of human ribosomal RNA. RNA (NEW YORK, N.Y.) 2014; 20:540-50. [PMID: 24550520 PMCID: PMC3964915 DOI: 10.1261/rna.043471.113] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 12/19/2013] [Indexed: 05/19/2023]
Abstract
During eukaryotic ribosome biogenesis, three of the mature ribosomal (r)RNAs are released from a single precursor transcript (pre-rRNA) by an ordered series of endonucleolytic cleavages and exonucleolytic processing steps. Production of the 18S rRNA requires the removal of the 5' external transcribed spacer (5'ETS) by endonucleolytic cleavages at sites A0 and A1/site 1. In metazoans, an additional cleavage in the 5'ETS, at site A', upstream of A0, has also been reported. Here, we have investigated how A' processing is coordinated with assembly of the early preribosomal complex. We find that only the tUTP (UTP-A) complex is critical for A' cleavage, while components of the bUTP (UTP-B) and U3 snoRNP are important, but not essential, for efficient processing at this site. All other factors involved in the early stages of 18S rRNA processing that were tested here function downstream from this processing step. Interestingly, we show that the RNA surveillance factors XRN2 and MTR4 are also involved in A' cleavage in humans. A' cleavage is largely bypassed when XRN2 is depleted, and we also discover that A' cleavage is not always the initial processing event in all cell types. Together, our data suggest that A' cleavage is not a prerequisite for downstream pre-rRNA processing steps and may, in fact, represent a quality control step for initial pre-rRNA transcripts. Furthermore, we show that components of the RNA surveillance machinery, including the exosome and TRAMP complexes, also play key roles in the recycling of excised spacer fragments and degradation of aberrant pre-rRNAs in human cells.
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Affiliation(s)
- Katherine E. Sloan
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- Centre for Biochemistry and Molecular Cell Biology, Georg-August University, 37073 Göttingen, Germany
| | - Markus T. Bohnsack
- Centre for Biochemistry and Molecular Cell Biology, Georg-August University, 37073 Göttingen, Germany
| | - Claudia Schneider
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nicholas J. Watkins
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- Corresponding authorE-mail
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Srivastava A, Ahamad J, Ray AK, Kaur D, Bhattacharya A, Bhattacharya S. Analysis of U3 snoRNA and small subunit processome components in the parasitic protist Entamoeba histolytica. Mol Biochem Parasitol 2014; 193:82-92. [PMID: 24631428 DOI: 10.1016/j.molbiopara.2014.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 02/27/2014] [Accepted: 03/01/2014] [Indexed: 10/25/2022]
Abstract
In the early branching parasitic protist Entamoeba histolytica, pre-rRNA synthesis continues when cells are subjected to growth stress, but processing slows down and unprocessed pre-rRNA accumulates. To gain insight into the regulatory mechanisms leading to accumulation, it is necessary to define the pre-rRNA processing machinery in E. histolytica. We searched the E. histolytica genome sequence for homologs of the SSU processome, which contains the U3snoRNA, and 72 proteins in yeast. We could identify 57 of the proteins with high confidence. Of the rest, 6 were absent in human, and 4 were non-essential in yeast. The remaining 5 were absent in other parasite genomes as well. Analysis of U3snoRNA showed that the E. histolytica U3snoRNA adopted the same conserved secondary structure as seen in yeast and human. The predicted structure was verified by chemical modification followed by primer extension (SHAPE). Further we showed that the predicted interactions of Eh_U3snoRNA boxes A and A' with pre-18S rRNA were highly conserved both in position and sequence. The predicted interactions of 5'-hinge and 3'-hinge sequences of Eh_U3 snoRNA with the 5'-ETS sequences were conserved in position but not in sequence. Transcription of selected genes of SSU processome was tested by northern analysis, and transcripts of predicted sizes were obtained. During serum starvation, when unprocessed pre-RNA accumulated, the transcript levels of some of these genes declined. This is the first report on pre-rRNA processing machinery in E. histolytica, and shows that the components are well conserved with respect to yeast and human.
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Affiliation(s)
- Ankita Srivastava
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Jamaluddin Ahamad
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Ashwini Kumar Ray
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Devinder Kaur
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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Hamperl S, Brown CR, Garea AV, Perez-Fernandez J, Bruckmann A, Huber K, Wittner M, Babl V, Stoeckl U, Deutzmann R, Boeger H, Tschochner H, Milkereit P, Griesenbeck J. Compositional and structural analysis of selected chromosomal domains from Saccharomyces cerevisiae. Nucleic Acids Res 2013; 42:e2. [PMID: 24106087 PMCID: PMC3874202 DOI: 10.1093/nar/gkt891] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Chromatin is the template for replication and transcription in the eukaryotic nucleus, which needs to be defined in composition and structure before these processes can be fully understood. We report an isolation protocol for the targeted purification of specific genomic regions in their native chromatin context from Saccharomyces cerevisiae. Subdomains of the multicopy ribosomal DNA locus containing transcription units of RNA polymerases I, II or III or an autonomous replication sequence were independently purified in sufficient amounts and purity to analyze protein composition and histone modifications by mass spectrometry. We present and discuss the proteomic data sets obtained for chromatin in different functional states. The native chromatin was further amenable to electron microscopy analysis yielding information about nucleosome occupancy and positioning at the single-molecule level. We also provide evidence that chromatin from virtually every single copy genomic locus of interest can be purified and analyzed by this technique.
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Affiliation(s)
- Stephan Hamperl
- Universität Regensburg, Biochemie-Zentrum Regensburg (BZR), Lehrstuhl für Biochemie III, 93053 Regensburg, Germany and Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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42
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Sardana R, White JP, Johnson AW. The rRNA methyltransferase Bud23 shows functional interaction with components of the SSU processome and RNase MRP. RNA (NEW YORK, N.Y.) 2013; 19:828-40. [PMID: 23604635 PMCID: PMC3683916 DOI: 10.1261/rna.037671.112] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 03/14/2013] [Indexed: 05/25/2023]
Abstract
Bud23 is responsible for the conserved methylation of G1575 of 18S rRNA, in the P-site of the small subunit of the ribosome. bud23Δ mutants have severely reduced small subunit levels and show a general failure in cleavage at site A2 during rRNA processing. Site A2 is the primary cleavage site for separating the precursors of 18S and 25S rRNAs. Here, we have taken a genetic approach to identify the functional environment of BUD23. We found mutations in UTP2 and UTP14, encoding components of the SSU processome, as spontaneous suppressors of a bud23Δ mutant. The suppressors improved growth and subunit balance and restored cleavage at site A2. In a directed screen of 50 ribosomal trans-acting factors, we identified strong positive and negative genetic interactions with components of the SSU processome and strong negative interactions with components of RNase MRP. RNase MRP is responsible for cleavage at site A3 in pre-rRNA, an alternative cleavage site for separating the precursor rRNAs. The strong negative genetic interaction between RNase MRP mutants and bud23Δ is likely due to the combined defects in cleavage at A2 and A3. Our results suggest that Bud23 plays a role at the time of A2 cleavage, earlier than previously thought. The genetic interaction with the SSU processome suggests that Bud23 could be involved in triggering disassembly of the SSU processome, or of particular subcomplexes of the processome.
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Hamperl S, Wittner M, Babl V, Perez-Fernandez J, Tschochner H, Griesenbeck J. Chromatin states at ribosomal DNA loci. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:405-17. [PMID: 23291532 DOI: 10.1016/j.bbagrm.2012.12.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 11/16/2012] [Accepted: 12/21/2012] [Indexed: 12/29/2022]
Abstract
Eukaryotic transcription of ribosomal RNAs (rRNAs) by RNA polymerase I can account for more than half of the total cellular transcripts depending on organism and growth condition. To support this level of expression, eukaryotic rRNA genes are present in multiple copies. Interestingly, these genes co-exist in different chromatin states that may differ significantly in their nucleosome content and generally correlate well with transcriptional activity. Here we review how these chromatin states have been discovered and characterized focusing particularly on their structural protein components. The establishment and maintenance of rRNA gene chromatin states and their impact on rRNA synthesis are discussed. This article is part of a Special Issue entitled: Transcription by Odd Pols.
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Affiliation(s)
- Stephan Hamperl
- Lehrstuhl Biochemie III, Universität Regensburg, 93053 Regensburg, Germany
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44
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Hierlmeier T, Merl J, Sauert M, Perez-Fernandez J, Schultz P, Bruckmann A, Hamperl S, Ohmayer U, Rachel R, Jacob A, Hergert K, Deutzmann R, Griesenbeck J, Hurt E, Milkereit P, Baßler J, Tschochner H. Rrp5p, Noc1p and Noc2p form a protein module which is part of early large ribosomal subunit precursors in S. cerevisiae. Nucleic Acids Res 2012. [PMID: 23209026 PMCID: PMC3553968 DOI: 10.1093/nar/gks1056] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Eukaryotic ribosome biogenesis requires more than 150 auxiliary proteins, which transiently interact with pre-ribosomal particles. Previous studies suggest that several of these biogenesis factors function together as modules. Using a heterologous expression system, we show that the large ribosomal subunit (LSU) biogenesis factor Noc1p of Saccharomyces cerevisiae can simultaneously interact with the LSU biogenesis factor Noc2p and Rrp5p, a factor required for biogenesis of the large and the small ribosomal subunit. Proteome analysis of RNA polymerase-I-associated chromatin and chromatin immunopurification experiments indicated that all members of this protein module and a specific set of LSU biogenesis factors are co-transcriptionally recruited to nascent ribosomal RNA (rRNA) precursors in yeast cells. Further ex vivo analyses showed that all module members predominantly interact with early pre-LSU particles after the initial pre-rRNA processing events have occurred. In yeast strains depleted of Noc1p, Noc2p or Rrp5p, levels of the major LSU pre-rRNAs decreased and the respective other module members were associated with accumulating aberrant rRNA fragments. Therefore, we conclude that the module exhibits several binding interfaces with pre-ribosomes. Taken together, our results suggest a co- and post-transcriptional role of the yeast Rrp5p-Noc1p-Noc2p module in the structural organization of early LSU precursors protecting them from non-productive RNase activity.
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Affiliation(s)
- Thomas Hierlmeier
- Universität Regensburg, Biochemie-Zentrum Regensburg (BZR), Lehrstuhl Biochemie III, 93053 Regensburg, Germany
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45
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Hochstatter J, Hölzel M, Rohrmoser M, Schermelleh L, Leonhardt H, Keough R, Gonda TJ, Imhof A, Eick D, Längst G, Németh A. Myb-binding protein 1a (Mybbp1a) regulates levels and processing of pre-ribosomal RNA. J Biol Chem 2012; 287:24365-77. [PMID: 22645127 DOI: 10.1074/jbc.m111.303719] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Ribosomal RNA gene transcription, co-transcriptional processing, and ribosome biogenesis are highly coordinated processes that are tightly regulated during cell growth. In this study we discovered that Mybbp1a is associated with both the RNA polymerase I complex and the ribosome biogenesis machinery. Using a reporter assay that uncouples transcription and RNA processing, we show that Mybbp1a represses rRNA gene transcription. In addition, overexpression of the protein reduces RNA polymerase I loading on endogenous rRNA genes as revealed by chromatin immunoprecipitation experiments. Accordingly, depletion of Mybbp1a results in an accumulation of the rRNA precursor in vivo but surprisingly also causes growth arrest of the cells. This effect can be explained by the observation that the modulation of Mybbp1a protein levels results in defects in pre-rRNA processing within the cell. Therefore, the protein may play a dual role in the rRNA metabolism, potentially linking and coordinating ribosomal DNA transcription and pre-rRNA processing to allow for the efficient synthesis of ribosomes.
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Affiliation(s)
- Julia Hochstatter
- Biochemistry Center Regensburg, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
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Phipps KR, Charette JM, Baserga SJ. The small subunit processome in ribosome biogenesis—progress and prospects. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 2:1-21. [PMID: 21318072 DOI: 10.1002/wrna.57] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The small subunit (SSU) processome is a 2.2-MDa ribonucleoprotein complex involved in the processing, assembly, and maturation of the SSU of eukaryotic ribosomes. The identities of many of the factors involved in SSU biogenesis have been elucidated over the past 40 years. However, as our understanding increases, so do the number of questions about the nature of this complicated process. Cataloging the components is the first step toward understanding the molecular workings of a system. This review will focus on how identifying components of ribosome biogenesis has led to the knowledge of how these factors, protein and RNA alike, associate with one another into subcomplexes, with a concentration on the small ribosomal subunit. We will also explore how this knowledge of subcomplex assembly has informed our understanding of the workings of the ribosome synthesis system as a whole.
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Affiliation(s)
- Kathleen R Phipps
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
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Stepiński D. Organization of the nucleoli of soybean root meristematic cells at different states of their activity. Micron 2010; 41:283-8. [PMID: 20071186 DOI: 10.1016/j.micron.2009.11.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Revised: 11/23/2009] [Accepted: 11/25/2009] [Indexed: 10/20/2022]
Abstract
Internal organization of a nucleolus changes along with rRNA transcriptional activity. These changes mainly concern qualitative and quantitative alternations of three main nucleolar components: fibrillar centres (FC), dense fibrillar component (DFC) and granular component (GC). In the present work quantitative measurements of the number and sizes of FCs and DFCs in nucleoli of root meristematic cells of soybean seedlings grown at (1) chilling conditions that reduce transcriptional activity of soybean nucleoli (temp. of 10 degrees C) and at (2) conditions that increase this activity (recovery at optimal temp. of 25 degrees C after previous chilling), even more than (3) the control, have been carried out. Morphometric measurements showed that the highest number of FCs and DFCs was in the most active nucleoli, while the smallest number - in those with the lowest activity. The average size of an individual FC was similar in all nucleoli regardless of their transcriptional activity, that of the individual DFC varied, being bigger in the nucleoli of the chilled plants and smallest in those of the recovered plants. The numbers of FCs and DFCs seem to be indicators of transcriptional activity of plant nucleoli - the higher number of FCs and DFCs the more active nucleoli.
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Affiliation(s)
- Dariusz Stepiński
- Department of Cytophysiology, University of Łódź, Pilarskiego 14, 90-321 Łódź, Poland.
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Hokii Y, Sasano Y, Sato M, Sakamoto H, Sakata K, Shingai R, Taneda A, Oka S, Himeno H, Muto A, Fujiwara T, Ushida C. A small nucleolar RNA functions in rRNA processing in Caenorhabditis elegans. Nucleic Acids Res 2010; 38:5909-18. [PMID: 20460460 PMCID: PMC2943600 DOI: 10.1093/nar/gkq335] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
CeR-2 RNA is one of the newly identified Caenorhabditis elegans noncoding RNAs (ncRNAs). The characterization of CeR-2 by RNomic studies has failed to classify it into any known ncRNA family. In this study, we examined the spatiotemporal expression patterns of CeR-2 to gain insight into its function. CeR-2 is expressed in most cells from the early embryo to adult stages. The subcellular localization of this RNA is analogous to that of fibrillarin, a major protein of the nucleolus. It was observed that knockdown of C/D small nucleolar ribonucleoproteins (snoRNPs), but not of H/ACA snoRNPs, resulted in the aberrant nucleolar localization of CeR-2 RNA. A mutant worm with a reduced amount of cellular CeR-2 RNA showed changes in its pre-rRNA processing pattern compared with that of the wild-type strain N2. These results suggest that CeR-2 RNA is a C/D snoRNA involved in the processing of rRNAs.
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Affiliation(s)
- Yusuke Hokii
- Functional Genomics and Technology, United Graduate School of Agricultural Science, Iwate University, 18-8 Ueda 3-chome, Morioka 020-8550
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Mrd1p is required for release of base-paired U3 snoRNA within the preribosomal complex. Mol Cell Biol 2009; 29:5763-74. [PMID: 19704003 DOI: 10.1128/mcb.00428-09] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In eukaryotes, ribosomes are made from precursor rRNA (pre-rRNA) and ribosomal proteins in a maturation process that requires a large number of snoRNPs and processing factors. A fundamental problem is how the coordinated and productive folding of the pre-rRNA and assembly of successive pre-rRNA-protein complexes is achieved cotranscriptionally. The conserved protein Mrd1p, which contains five RNA binding domains (RBDs), is essential for processing events leading to small ribosomal subunit synthesis. We show that full function of Mrd1p requires all five RBDs and that the RBDs are functionally distinct and needed during different steps in processing. Mrd1p mutations trap U3 snoRNA in pre-rRNP complexes both in base-paired and non-base-paired interactions. A single essential RBD, RBD5, is involved in both types of interactions, but its conserved RNP1 motif is not needed for releasing the base-paired interactions. RBD5 is also required for the late pre-rRNP compaction preceding A(2) cleavage. Our results suggest that Mrd1p modulates successive conformational rearrangements within the pre-rRNP that influence snoRNA-pre-rRNA contacts and couple U3 snoRNA-pre-rRNA remodeling and late steps in pre-rRNP compaction that are essential for cleavage at A(0) to A(2). Mrd1p therefore coordinates key events in biosynthesis of small ribosome subunits.
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50
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Wery M, Ruidant S, Schillewaert S, Leporé N, Lafontaine DLJ. The nuclear poly(A) polymerase and Exosome cofactor Trf5 is recruited cotranscriptionally to nucleolar surveillance. RNA (NEW YORK, N.Y.) 2009; 15:406-419. [PMID: 19141608 PMCID: PMC2657017 DOI: 10.1261/rna.1402709] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2008] [Accepted: 11/25/2008] [Indexed: 05/27/2023]
Abstract
Terminal balls detected at the 5'-end of nascent ribosomal transcripts act as pre-rRNA processing complexes and are detected in all eukaryotes examined, resulting in illustrious Christmas tree images. Terminal balls (also known as SSU-processomes) compaction reflects the various stages of cotranscriptional ribosome assembly. Here, we have followed SSU-processome compaction in vivo by use of a chromatin immunoprecipitation (Ch-IP) approach and shown, in agreement with electron microscopy analysis of Christmas trees, that it progressively condenses to come in close proximity to the 5'-end of the 25S rRNA gene. The SSU-processome is comprised of independent autonomous building blocks that are loaded onto nascent pre-rRNAs and assemble into catalytically active pre-rRNA processing complexes in a stepwise and highly hierarchical process. Failure to assemble SSU-processome subcomplexes with proper kinetics triggers a nucleolar surveillance pathway that targets misassembled pre-rRNAs otherwise destined to mature into small subunit 18S rRNA for polyadenylation, preferentially by TRAMP5, and degradation by the 3' to 5' exoribonucleolytic activity of the Exosome. Trf5 colocalized with nascent pre-rRNPs, indicating that this nucleolar surveillance initiates cotranscriptionally.
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Affiliation(s)
- Maxime Wery
- Fonds de la Recherche Scientifique (FRS-FNRS), AcadémieWallonie-Bruxelles, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, Charleroi-Gosselies, B-6041 Belgium
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