Share This Special Issue

Special Issue Editor

Dr. Dmitri Graifer

E-Mail Website
Guest Editor

Leading Scientific Researcher, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
Interests: structure of the eukaryotic ribosome; regulation of translation in eukaryotes; eukaryotic ribosomal proteins: functions within the ribosome and extra-ribosomalfunctions; transport of ribosomal proteins by exosomes

Special Issue Information

Dear Colleagues,

The ribosome consists of two subunits, with each containing several dozens of ribosomal proteins (RPs). Most of them are critically important constituents of the subunits and contribute to their structures’ ability to carry out translations; some RPs directly participate in the formation of ribosomal functional sites. Deciphering the structures of translational ribosomal complexes at a near-atomic resolution using X-ray crystallography and cryo-electron microscopy revealed details of the arrangement of the functional sites and provided ideas regarding interactions between the RPs and translation participants (mRNA, tRNAs and translation factors). However, the contribution of particular RP regions, which have been suggested to contact ribosomal ligands, to the work of the ribosomal machinery (especially the eukaryotic one) has become clear only recently, following investigations into the effects that mutations in these regions have on the translational properties of the ribosomes. Many eukaryotic RPs have non-canonical functions that often have no direct relation to protein synthesis (“extra-ribosomal” funtions). The knowledge of the functional assignments of RPs and their particular regions is important for understanding the molecular mechanisms of translation; it is also considerably relevant to biomedicine, since numerous data have revealed various links between disturbances in translation and/or extra-ribosomal functions of RPs and particular diseases.

Dr. Dmitri Graifer
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

ribosomal proteins
particular regions of ribosomal proteins
translation and its regulation
roles of particular ribosomal proteins’ regions in translation
roles of particular ribosomal proteins’ regions in extra-ribosomal functions
mutations in ribosomal proteins and human diseases

Published Papers (2 papers)

Download All Papers

Research

Jump to: Review

19 pages, 5964 KiB

Open AccessArticle

The Biological Action and Structural Characterization of Eryngitin 3 and 4, Ribotoxin-like Proteins from Pleurotus eryngii Fruiting Bodies

by Sara Ragucci, Nicola Landi, Lucía Citores, Rosario Iglesias, Rosita Russo, Angela Clemente, Michele Saviano, Paolo Vincenzo Pedone, Angela Chambery, José Miguel Ferreras and Antimo Di Maro

Int. J. Mol. Sci. 2023, 24(19), 14435; https://doi.org/10.3390/ijms241914435 - 22 Sep 2023

Viewed by 977

Abstract

Ribotoxin-like proteins (RL-Ps) are specific ribonucleases found in mushrooms that are able to cleave a single phosphodiester bond located in the sarcin–ricin loop (SRL) of the large rRNA. The cleaved SRL interacts differently with some ribosomal proteins (P-stalk). This action blocks protein synthesis because the damaged ribosomes are unable to interact with elongation factors. Here, the amino acid sequences of eryngitin 3 and 4, RL-Ps isolated from Pleurotus eryngii fruiting bodies, were determined to (i) obtain structural information on this specific ribonuclease family from edible mushrooms and (ii) explore the structural determinants which justify their different biological and antipathogenic activities. Indeed, eryngitin 3 exhibited higher toxicity with respect to eryngitin 4 against tumoral cell lines and model fungi. Structurally, eryngitin 3 and 4 consist of 132 amino acids, most of them identical and exhibiting a single free cysteinyl residue. The amino acidic differences between the two toxins are (i) an additional phenylalanyl residue at the N-terminus of eryngitin 3, not retrieved in eryngitin 4, and (ii) an additional arginyl residue at the C-terminus of eryngitin 4, not retrieved in eryngitin 3. The 3D models of eryngitins show slight differences at the N- and C-terminal regions. In particular, the positive electrostatic surface at the C-terminal of eryngitin 4 is due to the additional arginyl residue not retrieved in eryngitin 3. This additional positive charge could interfere with the binding to the SRL (substrate) or with some ribosomal proteins (P-stalk structure) during substrate recognition. Full article

(This article belongs to the Special Issue Structure and Function of Ribosomal Proteins 2024)

► Show Figures

Figure 1

Review

Jump to: Research

18 pages, 3266 KiB

Open AccessReview

Two “Edges” in Our Knowledge on the Functions of Ribosomal Proteins: The Revealed Contributions of Their Regions to Translation Mechanisms and the Issues of Their Extracellular Transport by Exosomes

by Anastasia Ochkasova, Grigory Arbuzov, Alexey Malygin and Dmitri Graifer

Int. J. Mol. Sci. 2023, 24(14), 11458; https://doi.org/10.3390/ijms241411458 - 14 Jul 2023

Viewed by 1163

Abstract

Ribosomal proteins (RPs), the constituents of the ribosome, belong to the most abundant proteins in the cell. A highly coordinated network of interactions implicating RPs and ribosomal RNAs (rRNAs) forms the functionally competent structure of the ribosome, enabling it to perform translation, the synthesis of polypeptide chain on the messenger RNA (mRNA) template. Several RPs contact ribosomal ligands, namely, those with transfer RNAs (tRNAs), mRNA or translation factors in the course of translation, and the contribution of a number of these particular contacts to the translation process has recently been established. Many ribosomal proteins also have various extra-ribosomal functions unrelated to translation. The least-understood and -discussed functions of RPs are those related to their participation in the intercellular communication via extracellular vesicles including exosomes, etc., which often carry RPs as passengers. Recently reported data show that such a kind of communication can reprogram a receptor cell and change its phenotype, which is associated with cancer progression and metastasis. Here, we review the state-of-art ideas on the implications of specific amino acid residues of RPs in the particular stages of the translation process in higher eukaryotes and currently available data on the transport of RPs by extracellular vesicles and its biological effects. Full article

(This article belongs to the Special Issue Structure and Function of Ribosomal Proteins 2024)

► Show Figures