scholarly journals Nascent ribosomal RNA acts as surfactant that suppresses growth of fibrillar centers in nucleolus

2021 ◽  
Author(s):  
Tetsuya Yamamoto ◽  
Tomohiro Yamazaki ◽  
Kensuke Ninomiya ◽  
Tetsuro Hirose
Keyword(s):  
Ribosomal Rna ◽  
Size Control ◽  
Nuclear Bodies ◽  
General Mechanism ◽  
Optimal Size ◽  
Ribosomal Biogenesis ◽  
Assembly Mechanism ◽  
Transcription Inhibitor ◽  
Polymerase I ◽  
Liquid Liquid Phase Separation

ABSTRACTLiquid-liquid phase separation (LLPS) has been thought to be the assembly mechanism of the multiphase structure of nucleolus, the site of ribosomal biogenesis. Condensates assembled by LLPS increase their size to minimize the surface energy as far as their components are available. However, multiple microphases, fibrillar centers (FCs), dispersed in a nucleolus are stable and their size does not grow unless the transcription of pre-ribosomal RNA (pre-rRNA) is inhibited. To understand the mechanism of the suppression of the growth of FCs, we here construct a minimal theoretical model by taking into account the nascent pre-rRNA transcripts tethered to the surfaces of FCs by RNA polymerase I. Our theory predicts that nascent pre-rRNA transcripts generate the lateral osmotic pressure that counteracts the surface tension of the microphases and this suppresses the growth of the microphases over the optimal size. The optimal size of the microphases decreases with increasing the transcription rate and decreasing the rate of RNA processing. This prediction is supported by our experiments showing that the size of FCs increased with increasing the dose of transcription inhibitor. This theory may provide insight in the general mechanism of the size control of nuclear bodies.

scholarly journals BLM helicase facilitates RNA polymerase I-mediated ribosomal RNA transcription

2011 ◽  
Vol 21 (5) ◽  
pp. 1172-1183 ◽  
Author(s):  
Patrick M. Grierson ◽  
Kate Lillard ◽  
Gregory K. Behbehani ◽  
Kelly A. Combs ◽  
Saumitri Bhattacharyya ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Ribosomal Rna ◽  
Rna Polymerase I ◽  
Rna Transcription ◽  
Blm Helicase ◽  
Polymerase I

Particle size-control enables extraordinary activity of ruthenium nanoparticles/multiwalled carbon nanotube catalysts towards the oxygen reduction reaction

Nanoscale ◽  
2019 ◽  
Vol 11 (29) ◽  
pp. 13968-13976 ◽  
Author(s):  
Chang Liu ◽  
Gailing Bai ◽  
Zhifeng Jiao ◽  
Baoying Lv ◽  
Yunwei Wang ◽  
...  
Keyword(s):  
Particle Size ◽  
Fuel Cells ◽  
Carbon Nanotube ◽  
Oxygen Reduction Reaction ◽  
Oxygen Reduction ◽  
Size Control ◽  
Reduction Reaction ◽  
Optimal Size ◽  
Ruthenium Nanoparticles ◽  
Multiwalled Carbon

Catalysts with optimal size for the oxygen reduction reaction (ORR) play a vital important role in fuel cells and metal–air batteries.

scholarly journals PhaSePro: the database of proteins driving liquid–liquid phase separation

2019 ◽  
Author(s):  
Bálint Mészáros ◽  
Gábor Erdős ◽  
Beáta Szabó ◽  
Éva Schád ◽  
Ágnes Tantos ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Ribosome Biogenesis ◽  
Weak Interactions ◽  
Experimental Studies ◽  
Rna Degradation ◽  
Liquid Phase Separation ◽  
General Mechanism ◽  
Open Questions ◽  
Liquid Liquid Phase Separation

Abstract Membraneless organelles (MOs) are dynamic liquid condensates that host a variety of specific cellular processes, such as ribosome biogenesis or RNA degradation. MOs form through liquid–liquid phase separation (LLPS), a process that relies on multivalent weak interactions of the constituent proteins and other macromolecules. Since the first discoveries of certain proteins being able to drive LLPS, it emerged as a general mechanism for the effective organization of cellular space that is exploited in all kingdoms of life. While numerous experimental studies report novel cases, the computational identification of LLPS drivers is lagging behind, and many open questions remain about the sequence determinants, composition, regulation and biological relevance of the resulting condensates. Our limited ability to overcome these issues is largely due to the lack of a dedicated LLPS database. Therefore, here we introduce PhaSePro (https://phasepro.elte.hu), an openly accessible, comprehensive, manually curated database of experimentally validated LLPS driver proteins/protein regions. It not only provides a wealth of information on such systems, but improves the standardization of data by introducing novel LLPS-specific controlled vocabularies. PhaSePro can be accessed through an appealing, user-friendly interface and thus has definite potential to become the central resource in this dynamically developing field.

scholarly journals Exploiting mammalian low-complexity domains for liquid-liquid phase separation–driven underwater adhesive coatings

2019 ◽  
Vol 5 (8) ◽  
pp. eaax3155 ◽  
Author(s):  
Mengkui Cui ◽  
Xinyu Wang ◽  
Bolin An ◽  
Chen Zhang ◽  
Xinrui Gui ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Soft Materials ◽  
Low Complexity ◽  
Liquid Phase Separation ◽  
Biologically Inspired ◽  
Underwater Adhesion ◽  
Assembly Mechanism ◽  
Adhesion Performance ◽  
Liquid Liquid Phase Separation

Many biological materials form via liquid-liquid phase separation (LLPS), followed by maturation into a solid-like state. Here, using a biologically inspired assembly mechanism designed to recapitulate these sequential assemblies, we develop ultrastrong underwater adhesives made from engineered proteins containing mammalian low-complexity (LC) domains. We show that LC domain–mediated LLPS and maturation substantially promotes the wetting, adsorption, priming, and formation of dense, uniform amyloid nanofiber coatings on diverse surfaces (e.g., Teflon), and even penetrating difficult-to-access locations such as the interiors of microfluidic devices. Notably, these coatings can be deposited on substrates over a broad range of pH values (3 to 11) and salt concentrations (up to 1 M NaCl) and exhibit strong underwater adhesion performance. Beyond demonstrating the utility of mammalian LC domains for driving LLPS in soft materials applications, our study illustrates a powerful example of how combining LLPS with subsequent maturation steps can be harnessed for engineering protein-based materials.

scholarly journals In vitroevidence that eukaryotic ribosomal RNA transcription is regulated by modification of RNA polymerase I

1984 ◽  
Vol 12 (21) ◽  
pp. 8161-8180 ◽  
Author(s):  
Marvin R. Paule ◽  
Calvin T. Iida ◽  
Peter J. Perna ◽  
Guy H. Harris ◽  
Deborah A. Knoll ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Ribosomal Rna ◽  
Rna Polymerase I ◽  
Rna Transcription ◽  
Polymerase I

scholarly journals Targeting RNA Polymerase I with an Oral Small Molecule CX-5461 Inhibits Ribosomal RNA Synthesis and Solid Tumor Growth

2010 ◽  
Vol 71 (4) ◽  
pp. 1418-1430 ◽  
Author(s):  
Denis Drygin ◽  
Amy Lin ◽  
Josh Bliesath ◽  
Caroline B. Ho ◽  
Sean E. O'Brien ◽  
...  
Keyword(s):  
Tumor Growth ◽  
Rna Polymerase ◽  
Small Molecule ◽  
Ribosomal Rna ◽  
Solid Tumor ◽  
Rna Synthesis ◽  
Rna Polymerase I ◽  
Solid Tumor Growth ◽  
Polymerase I

scholarly journals Structure and function of ribosomal RNA gene chromatin

2008 ◽  
Vol 36 (4) ◽  
pp. 619-624 ◽  
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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