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Ribosome Biogenesis in “War and Peace of the Cell”-2nd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 6887

Special Issue Editor

Special Issue Information

Dear Colleagues,

We are pleased to announce a second volume of the special issue on "Ribosome Biogenesis in “War and Peace of the Cell”".
The volume will be published in the International Journal of Molecular Sciences - IJMS (https://www.mdpi.com/journal/ijms/, ISSN 1422-0067, IF 4.183), and it is now open to receive submissions of full research articles and comprehensive review papers for peer-review and possible publication.

Intense investigations by numerous groups have identified a set of canonical pathways for the biogenesis of the ribosomal subunits in all three biological kingdoms. However, these pathways must be flexible to adapt ribosome biogenesis to organismal development and to stress stemming from environmental changes, mutations, and stochastic variations in the availability of ribosome components.
The goal of this special volume is to generate a rich collection of research and review papers on ribosomal formation following both canonical and modified pathways, switches between pathways, and the regulation of the rate of ribosome formation.
Below is a list of anticipated keywords and phrases, but do not feel limited by this list:
•    changes to the ribosome assembly pathway and kinetics in response to growth conditions, cell signaling, cell differentiation, and mutations
•    “specialized” ribosomes with non-canonical composition and function
•    surveillance of ribosome biogenesis
•    inactivation and degradation of mature ribosomes
•    interactions of ribosome biogenesis with other processes in the nucleus, nucleolus and cytoplasm of eukaryotic cells
•    coordination of other cellular processes, such as cell division, with the ribosome assembly process
•    deviations from the canonical model of the economy of ribosome biogenesis and cell growth (Warner 1999; Schaechter et al 1958).
•    Transport of ribosome components and particles
•    Human disease states linked to ribosome biogenesis

Prof. Dr. Lasse Lindahl
Guest Editor

Manuscript Submission Information

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Keywords

  • ribosome biogenesis
  • regulation of ribosome accumulation
  • cell division
  • ribosome surveillance
  • cell signaling
  • ribosome function
  • ribosome variants
  • ribosome stability cell economy
  • nucleolar functions
  • ribosome trafficking

Published Papers (3 papers)

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Research

21 pages, 3524 KiB  
Article
The Terminal Extensions of Dbp7 Influence Growth and 60S Ribosomal Subunit Biogenesis in Saccharomyces cerevisiae
by Julia Contreras, Óscar Ruiz-Blanco, Carine Dominique, Odile Humbert, Yves Henry, Anthony K. Henras, Jesús de la Cruz and Eduardo Villalobo
Int. J. Mol. Sci. 2023, 24(4), 3460; https://doi.org/10.3390/ijms24043460 - 9 Feb 2023
Viewed by 1535
Abstract
Ribosome synthesis is a complex process that involves a large set of protein trans-acting factors, among them DEx(D/H)-box helicases. These are enzymes that carry out remodelling activities onto RNAs by hydrolysing ATP. The nucleolar DEGD-box protein Dbp7 is required for the biogenesis [...] Read more.
Ribosome synthesis is a complex process that involves a large set of protein trans-acting factors, among them DEx(D/H)-box helicases. These are enzymes that carry out remodelling activities onto RNAs by hydrolysing ATP. The nucleolar DEGD-box protein Dbp7 is required for the biogenesis of large 60S ribosomal subunits. Recently, we have shown that Dbp7 is an RNA helicase that regulates the dynamic base-pairing between the snR190 small nucleolar RNA and the precursors of the ribosomal RNA within early pre-60S ribosomal particles. As the rest of DEx(D/H)-box proteins, Dbp7 has a modular organization formed by a helicase core region, which contains conserved motifs, and variable, non-conserved N- and C-terminal extensions. The role of these extensions remains unknown. Herein, we show that the N-terminal domain of Dbp7 is necessary for efficient nuclear import of the protein. Indeed, a basic bipartite nuclear localization signal (NLS) could be identified in its N-terminal domain. Removal of this putative NLS impairs, but does not abolish, Dbp7 nuclear import. Both N- and C-terminal domains are required for normal growth and 60S ribosomal subunit synthesis. Furthermore, we have studied the role of these domains in the association of Dbp7 with pre-ribosomal particles. Altogether, our results show that the N- and C-terminal domains of Dbp7 are important for the optimal function of this protein during ribosome biogenesis. Full article
(This article belongs to the Special Issue Ribosome Biogenesis in “War and Peace of the Cell”-2nd Edition)
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13 pages, 2543 KiB  
Article
9-Aminoacridine Inhibits Ribosome Biogenesis by Targeting Both Transcription and Processing of Ribosomal RNA
by Leonid Anikin and Dimitri G. Pestov
Int. J. Mol. Sci. 2022, 23(3), 1260; https://doi.org/10.3390/ijms23031260 - 23 Jan 2022
Cited by 7 | Viewed by 2421
Abstract
Aminoacridines, used for decades as antiseptic and antiparasitic agents, are prospective candidates for therapeutic repurposing and new drug development. Although the mechanisms behind their biological effects are not fully elucidated, they are most often attributed to the acridines’ ability to intercalate into DNA. [...] Read more.
Aminoacridines, used for decades as antiseptic and antiparasitic agents, are prospective candidates for therapeutic repurposing and new drug development. Although the mechanisms behind their biological effects are not fully elucidated, they are most often attributed to the acridines’ ability to intercalate into DNA. Here, we characterized the effects of 9-aminoacridine (9AA) on pre-rRNA metabolism in cultured mammalian cells. Our results demonstrate that 9AA inhibits both transcription of the ribosomal RNA precursors (pre-rRNA) and processing of the already synthesized pre-rRNAs, thereby rapidly abolishing ribosome biogenesis. Using a fluorescent intercalator displacement assay, we further show that 9AA can bind to RNA in vitro, which likely contributes to its ability to inhibit post-transcriptional steps in pre-rRNA maturation. These findings extend the arsenal of small-molecule compounds that can be used to block ribosome biogenesis in mammalian cells and have implications for the pharmacological development of new ribosome biogenesis inhibitors. Full article
(This article belongs to the Special Issue Ribosome Biogenesis in “War and Peace of the Cell”-2nd Edition)
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16 pages, 3386 KiB  
Article
Deficiency of the Ribosomal Protein uL5 Leads to Significant Rearrangements of the Transcriptional and Translational Landscapes in Mammalian Cells
by Elena S. Babaylova, Alexander V. Gopanenko, Alexey E. Tupikin, Marsel R. Kabilov, Alexey A. Malygin and Galina G. Karpova
Int. J. Mol. Sci. 2021, 22(24), 13485; https://doi.org/10.3390/ijms222413485 - 15 Dec 2021
Cited by 4 | Viewed by 2122
Abstract
Protein uL5 (formerly called L11) is an integral component of the large (60S) subunit of the human ribosome, and its deficiency in cells leads to the impaired biogenesis of 60S subunits. Using RNA interference, we reduced the level of uL5 in HEK293T cells [...] Read more.
Protein uL5 (formerly called L11) is an integral component of the large (60S) subunit of the human ribosome, and its deficiency in cells leads to the impaired biogenesis of 60S subunits. Using RNA interference, we reduced the level of uL5 in HEK293T cells by three times, which caused an almost proportional decrease in the content of the fraction corresponding to 80S ribosomes, without a noticeable diminution in the level of polysomes. By RNA sequencing of uL5-deficient and control cell samples, which were those of total mRNA and mRNA from the polysome fraction, we identified hundreds of differentially expressed genes (DEGs) at the transcriptome and translatome levels and revealed dozens of genes with altered translational efficiency (GATEs). Transcriptionally up-regulated DEGs were mainly associated with rRNA processing, pre-mRNA splicing, translation and DNA repair, while down-regulated DEGs were genes of membrane proteins; the type of regulation depended on the GC content in the 3′ untranslated regions of DEG mRNAs. The belonging of GATEs to up-regulated and down-regulated ones was determined by the coding sequence length of their mRNAs. Our findings suggest that the effects observed in uL5-deficient cells result from an insufficiency of translationally active ribosomes caused by a deficiency of 60S subunits. Full article
(This article belongs to the Special Issue Ribosome Biogenesis in “War and Peace of the Cell”-2nd Edition)
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