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State-of-the-Art Molecular Biology in France
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State-of-the-Art Molecular Biology in France

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 (20 March 2024) | Viewed by 4427

Special Issue Editor

Dr. Youri Timsit

E-Mail Website1 Website2
Guest Editor
Mediterranean Institute of Oceanography UM 110, Aix-Marseille Université, CNRS, IRD, Campus de Luminy, 13288 Marseille, France
Interests: structural biology; DNA; ribosome; ribosomal proteins; chromatin folding; structural transitions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Like a highly resilient ecosystem, molecular biology research in France is masterfully resisting and still managing to produce exciting results in a very worrying financial and ideological context: the credits allocated to research are in free fall, and a 'Darwinian and unequal' research programme dictated by the CNRS presidency has recently provoked the indignation of a large part of the French scientific community. This Special Issue of IJMS is an opportunity to publish original results obtained by French teams in a context where the aphorism "publish or perish" is more relevant than ever. We encourage the submission of manuscripts that provide novel insights, new ideas and concepts that contribute to significant advances in the molecular biology. Topics include but are not limited to:

  • Biological activities at the molecular level;
  • Biological processes of cell functions and maintenance;
  • Molecular processes of cell division, senescence, and cell death;
  • Biomolecule interactions and cell-to-cell communication;
  • DNA and RNA biosynthesis, metabolism, interactions, and functions;
  • Protein biosynthesis, degradation, and functions;
  • Molecular mechanisms and models of disease;
  • Molecular processes of cell and organelle dynamics;
  • Gene functions, genetics, and genomics;
  • Signaling networks and system biology;
  • Protein structure and function;
  • Molecular mechanisms of reproduction and differentiation;
  • Molecular mechanisms of drugs and small molecules;
  • Molecular and medical bioinformatics;
  • Molecular methodologies and imaging techniques;
  • Marine molecular ecology and metagenomics.

Dr. Youri Timsit
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.

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Published Papers (2 papers)

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31 pages, 12407 KiB  
Article
Protein Fold Usages in Ribosomes: Another Glance to the Past
by Inzhu Tanoz and Youri Timsit
Int. J. Mol. Sci. 2024, 25(16), 8806; https://doi.org/10.3390/ijms25168806 - 13 Aug 2024
Cited by 2 | Viewed by 1247
Abstract
The analysis of protein fold usage, similar to codon usage, offers profound insights into the evolution of biological systems and the origins of modern proteomes. While previous studies have examined fold distribution in modern genomes, our study focuses on the comparative distribution and [...] Read more.
The analysis of protein fold usage, similar to codon usage, offers profound insights into the evolution of biological systems and the origins of modern proteomes. While previous studies have examined fold distribution in modern genomes, our study focuses on the comparative distribution and usage of protein folds in ribosomes across bacteria, archaea, and eukaryotes. We identify the prevalence of certain ‘super-ribosome folds,’ such as the OB fold in bacteria and the SH3 domain in archaea and eukaryotes. The observed protein fold distribution in the ribosomes announces the future power-law distribution where only a few folds are highly prevalent, and most are rare. Additionally, we highlight the presence of three copies of proto-Rossmann folds in ribosomes across all kingdoms, showing its ancient and fundamental role in ribosomal structure and function. Our study also explores early mechanisms of molecular convergence, where different protein folds bind equivalent ribosomal RNA structures in ribosomes across different kingdoms. This comparative analysis enhances our understanding of ribosomal evolution, particularly the distinct evolutionary paths of the large and small subunits, and underscores the complex interplay between RNA and protein components in the transition from the RNA world to modern cellular life. Transcending the concept of folds also makes it possible to group a large number of ribosomal proteins into five categories of urfolds or metafolds, which could attest to their ancestral character and common origins. This work also demonstrates that the gradual acquisition of extensions by simple but ordered folds constitutes an inexorable evolutionary mechanism. This observation supports the idea that simple but structured ribosomal proteins preceded the development of their disordered extensions. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Biology in France)
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26 pages, 3694 KiB  
Article
Specific Circular RNA Signature of Endothelial Cells: Potential Implications in Vascular Pathophysiology
by Leïla Halidou Diallo, Jérôme Mariette, Nathalie Laugero, Christian Touriol, Florent Morfoisse, Anne-Catherine Prats, Barbara Garmy-Susini and Eric Lacazette
Int. J. Mol. Sci. 2024, 25(1), 680; https://doi.org/10.3390/ijms25010680 - 4 Jan 2024
Cited by 3 | Viewed by 2303
Abstract
Circular RNAs (circRNAs) are a recently characterized family of gene transcripts forming a covalently closed loop of single-stranded RNA. The extent of their potential for fine-tuning gene expression is still being discovered. Several studies have implicated certain circular RNAs in pathophysiological processes within [...] Read more.
Circular RNAs (circRNAs) are a recently characterized family of gene transcripts forming a covalently closed loop of single-stranded RNA. The extent of their potential for fine-tuning gene expression is still being discovered. Several studies have implicated certain circular RNAs in pathophysiological processes within vascular endothelial cells and cancer cells independently. However, to date, no comparative study of circular RNA expression in different types of endothelial cells has been performed and analysed through the lens of their central role in vascular physiology and pathology. In this work, we analysed publicly available and original RNA sequencing datasets from arterial, veinous, and lymphatic endothelial cells to identify common and distinct circRNA expression profiles. We identified 4713 distinct circRNAs in the compared endothelial cell types, 95% of which originated from exons. Interestingly, the results show that the expression profile of circular RNAs is much more specific to each cell type than linear RNAs, and therefore appears to be more suitable for distinguishing between them. As a result, we have discovered a specific circRNA signature for each given endothelial cell type. Furthermore, we identified a specific endothelial cell circRNA signature that is composed four circRNAs: circCARD6, circPLXNA2, circCASC15 and circEPHB4. These circular RNAs are produced by genes that are related to endothelial cell migration pathways and cancer progression. More detailed studies of their functions could lead to a better understanding of the mechanisms involved in physiological and pathological (lymph)angiogenesis and might open new ways to tackle tumour spread through the vascular system. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Biology in France)
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