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The Evolving Ribosome Concept
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The Evolving Ribosome Concept

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

Deadline for manuscript submissions: closed (28 April 2024) | Viewed by 915

Special Issue Editor

Prof. Dr. Lasse Lindahl

E-Mail Website
Guest Editor
Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA
Interests: ribosome formation and function; RNA processing; protein-RNA complexes
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Ribosomes have traditionally been considered a homologous population, i.e., ribosomes are distributed evenly throughout the cytoplasm and all have the same structure and functional capabilities. In recent years, several observations suggest that this model needs revision. Emerging evidence suggests that ribosomes can be “specialized” with different compositions and functions: Some species contain paralogous ribosomal protein genes encoding (slightly) different sequences and have different intron-exon structures; rRNA can be differentially cleaved and both rRNA and ribosomal proteins can be decorated differentially with modifying groups; and protein translation may be distributed unevenly in the cell.

This special volume aims to generate a collection of papers that sheds light on the concept of specialized ribosomes and their potential importance for cell function, growth, and environmental adaptation. I invite the submission of original research papers, reviews, and theoretical considerations that contribute to the understanding of the evolving model of ribosomes and their translational properties.

Prof. Dr. Lasse Lindahl
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • specialised ribosomes
  • ribosome heterogeneity
  • differential rRNA modification
  • ribosomal protein paralog genes
  • variation ribosome composition

Published Papers (2 papers)

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19 pages, 1471 KiB  
Article
TGF-β2 Induces Ribosome Activity, Alters Ribosome Composition and Inhibits IRES-Mediated Translation in Chondrocytes
by Guus G. H. van den Akker, Alzbeta Chabronova, Bas A. C. Housmans, Laura van der Vloet, Don A. M. Surtel, Andy Cremers, Virginie Marchand, Yuri Motorin, Marjolein M. J. Caron, Mandy J. Peffers and Tim. J. M. Welting
Int. J. Mol. Sci. 2024, 25(9), 5031; https://doi.org/10.3390/ijms25095031 (registering DOI) - 05 May 2024
Viewed by 90
Abstract
Alterations in cell fate are often attributed to (epigenetic) regulation of gene expression. An emerging paradigm focuses on specialized ribosomes within a cell. However, little evidence exists for the dynamic regulation of ribosome composition and function. Here, we stimulated a chondrocytic cell line [...] Read more.
Alterations in cell fate are often attributed to (epigenetic) regulation of gene expression. An emerging paradigm focuses on specialized ribosomes within a cell. However, little evidence exists for the dynamic regulation of ribosome composition and function. Here, we stimulated a chondrocytic cell line with transforming growth factor beta (TGF-β2) and mapped changes in ribosome function, composition and ribosomal RNA (rRNA) epitranscriptomics. 35S Met/Cys incorporation was used to evaluate ribosome activity. Dual luciferase reporter assays were used to assess ribosomal modus. Ribosomal RNA expression and processing were determined by RT-qPCR, while RiboMethSeq and HydraPsiSeq were used to determine rRNA modification profiles. Label-free protein quantification of total cell lysates, isolated ribosomes and secreted proteins was done by LC-MS/MS. A three-day TGF-β2 stimulation induced total protein synthesis in SW1353 chondrocytic cells and human articular chondrocytes. Specifically, TGF-β2 induced cap-mediated protein synthesis, while IRES-mediated translation was not (P53 IRES) or little affected (CrPv IGR and HCV IRES). Three rRNA post-transcriptional modifications (PTMs) were affected by TGF-β2 stimulation (18S-Gm1447 downregulated, 18S-ψ1177 and 28S-ψ4598 upregulated). Proteomic analysis of isolated ribosomes revealed increased interaction with eIF2 and tRNA ligases and decreased association of eIF4A3 and heterogeneous nuclear ribonucleoprotein (HNRNP)s. In addition, thirteen core ribosomal proteins were more present in ribosomes from TGF-β2 stimulated cells, albeit with a modest fold change. A prolonged stimulation of chondrocytic cells with TGF-β2 induced ribosome activity and changed the mode of translation. These functional changes could be coupled to alterations in accessory proteins in the ribosomal proteome. Full article
(This article belongs to the Special Issue The Evolving Ribosome Concept)

Other

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8 pages, 572 KiB  
Hypothesis
The Ribosome Hypothesis: Decoding Mood Disorder Complexity
by Vandana Sharma, Karthik Swaminathan and Rammohan Shukla
Int. J. Mol. Sci. 2024, 25(5), 2815; https://doi.org/10.3390/ijms25052815 - 29 Feb 2024
Viewed by 519
Abstract
Several types of mood disorders lie along a continuum, with nebulous boundaries between them. Understanding the mechanisms that contribute to mood disorder complexity is critical for effective treatment. However, present treatments are largely centered around neurotransmission and receptor-based hypotheses, which, given the high [...] Read more.
Several types of mood disorders lie along a continuum, with nebulous boundaries between them. Understanding the mechanisms that contribute to mood disorder complexity is critical for effective treatment. However, present treatments are largely centered around neurotransmission and receptor-based hypotheses, which, given the high instance of treatment resistance, fail to adequately explain the complexities of mood disorders. In this opinion piece, based on our recent results, we propose a ribosome hypothesis of mood disorders. We suggest that any hypothesis seeking to explain the diverse nature of mood disorders must incorporate infrastructure diversity that results in a wide range of effects. Ribosomes, with their mobility across neurites and complex composition, have the potential to become specialized during stress; thus, ribosome diversity and dysregulation are well suited to explaining mood disorder complexity. Here, we first establish a framework connecting ribosomes to the current state of knowledge associated with mood disorders. Then, we describe the potential mechanisms through which ribosomes could homeostatically regulate systems to manifest diverse mood disorder phenotypes and discuss approaches for substantiating the ribosome hypothesis. Investigating these mechanisms as therapeutic targets holds promise for transdiagnostic avenues targeting mood disorders. Full article
(This article belongs to the Special Issue The Evolving Ribosome Concept)
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