Viscoelastic RNA entanglement and advective flow underlie nucleolar form and function

The nucleolus facilitates transcription, processing, and assembly of ribosomal RNA (rRNA), the most abundant RNA in cells. Nucleolar function is facilitated by its multiphase liquid properties, but nucleolar fluidity and its connection to ribosome biogenesis remain unclear. Here, we used quantitative imaging, mathematical modeling, and pulse-chase nucleotide labelling to map nucleolar rRNA dynamics. Inconsistent with a purely diffusive process, rRNA steadily expands away from the transcriptional sites, moving in a slow (~1 Å/s), radially-directed fashion. This motion reflects the viscoelastic properties of a highly concentrated gel of entangled rRNA, whose constant polymerization drives steady outward flow. We propose a new viscoelastic rRNA release model, where nucleolar rRNA cleavage and processing reduce entanglement, fluidizing the nucleolar periphery to facilitate release of mature pre-ribosomal particles.

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Controlling the material properties and rRNA processing function of the nucleolus using light

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1903870116 ◽

2019 ◽

Vol 116 (35) ◽

pp. 17330-17335 ◽

Cited By ~ 17

Author(s):

Lian Zhu ◽

Tiffany M. Richardson ◽

Ludivine Wacheul ◽

Ming-Tzo Wei ◽

Marina Feric ◽

...

Keyword(s):

Phase Behavior ◽

Ribosomal Rna ◽

Material Properties ◽

Viscoelastic Properties ◽

Ribosome Biogenesis ◽

Threshold Concentration ◽

Rrna Processing ◽

Small Proteins ◽

Nucleolar Material ◽

Processing Steps

The nucleolus is a prominent nuclear condensate that plays a central role in ribosome biogenesis by facilitating the transcription and processing of nascent ribosomal RNA (rRNA). A number of studies have highlighted the active viscoelastic nature of the nucleolus, whose material properties and phase behavior are a consequence of underlying molecular interactions. However, the ways in which the material properties of the nucleolus impact its function in rRNA biogenesis are not understood. Here we utilize the Cry2olig optogenetic system to modulate the viscoelastic properties of the nucleolus. We show that above a threshold concentration of Cry2olig protein, the nucleolus can be gelled into a tightly linked, low mobility meshwork. Gelled nucleoli no longer coalesce and relax into spheres but nonetheless permit continued internal molecular mobility of small proteins. These changes in nucleolar material properties manifest in specific alterations in rRNA processing steps, including a buildup of larger rRNA precursors and a depletion of smaller rRNA precursors. We propose that the flux of processed rRNA may be actively tuned by the cell through modulating nucleolar material properties, which suggests the potential of materials-based approaches for therapeutic intervention in ribosomopathies.

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Functional ribosome biogenesis is a prerequisite for p53 destabilization: impact of chemotherapy on nucleolar functions and RNA metabolism

Biological Chemistry ◽

10.1515/hsz-2013-0153 ◽

2013 ◽

Vol 394 (9) ◽

pp. 1133-1143 ◽

Cited By ~ 17

Author(s):

Kaspar Burger ◽

Dirk Eick

Keyword(s):

Ribosomal Rna ◽

Ribosome Biogenesis ◽

Rna Metabolism ◽

Chemotherapeutic Drugs ◽

Tumor Suppressor P53 ◽

Nucleolar Structure ◽

Highly Sensitive ◽

Important Regulator ◽

Sensitive Sensor ◽

And Function

Abstract The production and processing of ribosomal RNA is a complex and well-coordinated nucleolar process for ribosome biogenesis. Progress in understanding nucleolar structure and function has lead to the unexpected discovery of the nucleolus as a highly sensitive sensor of cellular stress and an important regulator of the tumor suppressor p53. Inhibition of ribosomal RNA metabolism has been shown to activate a signaling pathway for p53 induction. This review elucidates the potential of classical and recently developed chemotherapeutic drugs to stabilize p53 by inhibiting nucleolar functions.

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Structure and function of ribosomal RNA gene chromatin

Biochemical Society Transactions ◽

10.1042/bst0360619 ◽

2008 ◽

Vol 36 (4) ◽

pp. 619-624 ◽

Cited By ~ 40

Author(s):

Joanna L. Birch ◽

Joost C.B.M. Zomerdijk

Keyword(s):

Ribosomal Rna ◽

Ribosome Biogenesis ◽

Rna Polymerase I ◽

Rrna Genes ◽

Rrna Gene ◽

Pol I ◽

And Function ◽

Polymerase I ◽

Cell Growth And Proliferation ◽

Cellular Control

Transcription of the major ribosomal RNAs by Pol I (RNA polymerase I) is a key determinant of ribosome biogenesis, driving cell growth and proliferation in eukaryotes. Hundreds of copies of rRNA genes are present in each cell, and there is evidence that the cellular control of Pol I transcription involves adjustments to the number of rRNA genes actively engaged in transcription, as well as to the rate of transcription from each active gene. Chromatin structure is inextricably linked to rRNA gene activity, and the present review highlights recent advances in this area.

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2′-O-Methylation of Ribosomal RNA: Towards an Epitranscriptomic Control of Translation?

Biomolecules ◽

10.3390/biom8040106 ◽

2018 ◽

Vol 8 (4) ◽

pp. 106 ◽

Cited By ~ 29

Author(s):

Piero Monaco ◽

Virginie Marcel ◽

Jean-Jacques Diaz ◽

Frédéric Catez

Keyword(s):

Ribosomal Rna ◽

Translational Control ◽

Ribosome Biogenesis ◽

In Vitro Translation ◽

Ribosome Structure ◽

Quantitative Mapping ◽

And Function ◽

The Impact ◽

First Time

Ribosomal RNA (rRNA) undergoes post-transcriptional modification of over 200 nucleotides, predominantly 2′-O-methylation (2′-O-Me). 2′-O-Methylation protects RNA from hydrolysis and modifies RNA strand flexibility but does not contribute to Watson-Crick base pairing. The contribution of 2′-O-Me to the translational capacity of ribosomes has been established. Yet, how 2′-O-Me participates in ribosome biogenesis and ribosome functioning remains unclear. The development of 2′-O-Me quantitative mapping methods has contributed to the demonstration that these modifications are not constitutive but rather provide heterogeneity to the ribosomal population. Moreover, recent advances in ribosome structure analysis and in vitro translation assays have proven, for the first time, that 2′-O-Me contributes to regulating protein synthesis. This review highlights the recent data exploring the impact of 2′-O-Me on ribosome structure and function, and the emerging idea that the rRNA epitranscriptome is involved in translational control.

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Cohesion promotes nucleolar structure and function

Molecular Biology of the Cell ◽

10.1091/mbc.e13-07-0377 ◽

2014 ◽

Vol 25 (3) ◽

pp. 337-346 ◽

Cited By ~ 29

Author(s):

Bethany Harris ◽

Tania Bose ◽

Kenneth K. Lee ◽

Fei Wang ◽

Shuai Lu ◽

...

Keyword(s):

Ribosome Biogenesis ◽

Molecular Mechanisms ◽

Human Cells ◽

Rna Polymerase I ◽

Nucleolar Structure ◽

Roberts Syndrome ◽

Evolutionarily Conserved ◽

Rrna Cleavage ◽

And Function ◽

Polymerase I

The cohesin complex contributes to ribosome function, although the molecular mechanisms involved are unclear. Compromised cohesin function is associated with a class of diseases known as cohesinopathies. One cohesinopathy, Roberts syndrome (RBS), occurs when a mutation reduces acetylation of the cohesin Smc3 subunit. Mutation of the cohesin acetyltransferase is associated with impaired rRNA production, ribosome biogenesis, and protein synthesis in yeast and human cells. Cohesin binding to the ribosomal DNA (rDNA) is evolutionarily conserved from bacteria to human cells. We report that the RBS mutation in yeast (eco1-W216G) exhibits a disorganized nucleolus and reduced looping at the rDNA. RNA polymerase I occupancy of the genes remains normal, suggesting that recruitment is not impaired. Impaired rRNA production in the RBS mutant coincides with slower rRNA cleavage. In addition to the RBS mutation, mutations in any subunit of the cohesin ring are associated with defects in ribosome biogenesis. Depletion or artificial destruction of cohesion in a single cell cycle is associated with loss of nucleolar integrity, demonstrating that the defects at the rDNA can be directly attributed to loss of cohesion. Our results strongly suggest that organization of the rDNA provided by cohesion is critical for formation and function of the nucleolus.

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The Ribosome Biogenesis—Cancer Connection

Cells ◽

10.3390/cells8010055 ◽

2019 ◽

Vol 8 (1) ◽

pp. 55 ◽

Cited By ~ 33

Author(s):

Marianna Penzo ◽

Lorenzo Montanaro ◽

Davide Treré ◽

Massimo Derenzini

Keyword(s):

Cell Proliferation ◽

Cancer Cells ◽

Cancer Chemotherapy ◽

Ribosome Biogenesis ◽

Structure And Function ◽

Tumor Pathology ◽

And Function ◽

Nucleolar Function

Multifaceted relations link ribosome biogenesis to cancer. Ribosome biogenesis takes place in the nucleolus. Clarifying the mechanisms involved in this nucleolar function and its relationship with cell proliferation: 1) allowed the understanding of the reasons for the nucleolar changes in cancer cells and their exploitation in tumor pathology, 2) defined the importance of the inhibition of ribosome biogenesis in cancer chemotherapy and 3) focused the attention on alterations of ribosome biogenesis in the pathogenesis of cancer. This review summarizes the research milestones regarding these relevant relationships between ribosome biogenesis and cancer. The structure and function of the nucleolus will also be briefly described.

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A versatile cis-acting element reporter system to study the function, maturation and stability of ribosomal RNA mutants in archaea

Nucleic Acids Research ◽

10.1093/nar/gkz1156 ◽

2019 ◽

Vol 48 (4) ◽

pp. 2073-2090 ◽

Cited By ~ 4

Author(s):

Michael Jüttner ◽

Matthias Weiß ◽

Nina Ostheimer ◽

Corinna Reglin ◽

Michael Kern ◽

...

Keyword(s):

Ribosomal Rna ◽

Ribosome Biogenesis ◽

Reporter System ◽

Ribosome Synthesis ◽

Cis Acting ◽

Phylogenetic Studies ◽

Molecular Determinants ◽

Ribosomal Rna Processing ◽

And Function

Abstract General molecular principles of ribosome biogenesis have been well explored in bacteria and eukaryotes. Collectively, these studies have revealed important functional differences and few similarities between these processes. Phylogenetic studies suggest that the information processing machineries from archaea and eukaryotes are evolutionary more closely related than their bacterial counterparts. These observations raise the question of how ribosome synthesis in archaea may proceed in vivo. In this study, we describe a versatile plasmid-based cis-acting reporter system allowing to analyze in vivo the consequences of ribosomal RNA mutations in the model archaeon Haloferax volcanii. Applying this system, we provide evidence that the bulge-helix-bulge motif enclosed within the ribosomal RNA processing stems is required for the formation of archaeal-specific circular-pre-rRNA intermediates and mature rRNAs. In addition, we have collected evidences suggesting functional coordination of the early steps of ribosome synthesis in H. volcanii. Together our investigation describes a versatile platform allowing to generate and functionally analyze the fate of diverse rRNA variants, thereby paving the way to better understand the cis-acting molecular determinants necessary for archaeal ribosome synthesis, maturation, stability and function.

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Scanning tunneling microscopy (STM) of DNA and RNA

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100152148 ◽

1989 ◽

Vol 47 ◽

pp. 34-35

Author(s):

Patricia G. Arscott ◽

Gil Lee ◽

Victor A. Bloomfield ◽

D. Fennell Evans

Keyword(s):

Molecular Structures ◽

Inorganic Materials ◽

Resolving Power ◽

Scanning Tunneling ◽

Tunneling Microscopy ◽

Form And Function ◽

Dna And Rna ◽

Calf Thymus ◽

And Function ◽

The Relationship

STM is one of the most promising techniques available for visualizing the fine details of biomolecular structure. It has been used to map the surface topography of inorganic materials in atomic dimensions, and thus has the resolving power not only to determine the conformation of small molecules but to distinguish site-specific features within a molecule. That level of detail is of critical importance in understanding the relationship between form and function in biological systems. The size, shape, and accessibility of molecular structures can be determined much more accurately by STM than by electron microscopy since no staining, shadowing or labeling with heavy metals is required, and there is no exposure to damaging radiation by electrons. Crystallography and most other physical techniques do not give information about individual molecules.We have obtained striking images of DNA and RNA, using calf thymus DNA and two synthetic polynucleotides, poly(dG-me5dC)·poly(dG-me5dC) and poly(rA)·poly(rU).

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