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Microorganisms
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Analysis of Bacterial Ribosomes and Interacting Factors
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Analysis of Bacterial Ribosomes and Interacting Factors

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Molecular Microbiology and Immunology".

Deadline for manuscript submissions: closed (30 November 2021) | Viewed by 19109

Special Issue Editor

Dr. José Marques Andrade

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Guest Editor
Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
Interests: bacterial ribosomes; RNA biology; RNA processing and stability; RNA-binding proteins; RNases; small noncoding RNAs

Special Issue Information

Dear Colleagues,

Ribosomes are a natural wonder, a macromolecular machine responsible for protein synthesis in all living organisms. Bacterial ribosomes are composed of two asymmetric subunits that differ in their composition: the 30S small subunit is made up of one rRNA molecule (16S rRNA), while the 50S large subunit holds two rRNA molecules (5S and 23S rRNAs), and together with numerous ribosomal proteins, these associate to form the functionally active 70S ribosome. It is clear that ribosomal RNA and ribosomal proteins are the main components of this ribonucleoprotein complex. However, for correct in vivo assembly and function, ribosomes interact with other classes of RNA (such as mRNAs, tRNAs, and ncRNAs) and many nonribosomal proteins (including RNA chaperones, protein chaperones, elongation factors, and RNases). Indeed, mRNA sequences or tRNA availability, as examples, are known to affect ribosome activity. Ribosome-bound small ncRNAs are also capable of regulating gene expression, as has been shown with tRNA-derived fragments. Moreover, in addition to ribosomal proteins, there is a large list of nonribosomal proteins that act as auxiliary assembly factors and assist ribosome biogenesis.

In this Special Issue, we are interested in highlighting different regulatory mechanisms that affect the ribosome’s assembly and/or its activity across different microorganisms. These include the maturation, folding, stability and function of ribosome-interacting RNAs and proteins. Overall, we aim to address the multiple facets of ribosome biogenesis and its interacting partners in the control of the efficiency and fidelity of translation.

Dr. José Marques Andrade
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. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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

  • bacterial ribosomes
  • rRNA
  • mRNA
  • tRNA
  • ncRNA
  • ribosome biogenesis
  • ribosomal proteins
  • nonribosomal proteins
  • translation
  • quality control

Published Papers (6 papers)

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Review

21 pages, 3069 KiB  
Review
Protein Assistants of Small Ribosomal Subunit Biogenesis in Bacteria
by Elena Maksimova, Olesya Kravchenko, Alexey Korepanov and Elena Stolboushkina
Microorganisms 2022, 10(4), 747; https://doi.org/10.3390/microorganisms10040747 - 30 Mar 2022
Cited by 8 | Viewed by 2984
Abstract
Ribosome biogenesis is a fundamental and multistage process. The basic steps of ribosome assembly are the transcription, processing, folding, and modification of rRNA; the translation, folding, and modification of r-proteins; and consecutive binding of ribosomal proteins to rRNAs. Ribosome maturation is facilitated by [...] Read more.
Ribosome biogenesis is a fundamental and multistage process. The basic steps of ribosome assembly are the transcription, processing, folding, and modification of rRNA; the translation, folding, and modification of r-proteins; and consecutive binding of ribosomal proteins to rRNAs. Ribosome maturation is facilitated by biogenesis factors that include a broad spectrum of proteins: GTPases, RNA helicases, endonucleases, modification enzymes, molecular chaperones, etc. The ribosome assembly factors assist proper rRNA folding and protein–RNA interactions and may sense the checkpoints during the assembly to ensure correct order of this process. Inactivation of these factors is accompanied by severe growth phenotypes and accumulation of immature ribosomal subunits containing unprocessed rRNA, which reduces overall translation efficiency and causes translational errors. In this review, we focus on the structural and biochemical analysis of the 30S ribosomal subunit assembly factors RbfA, YjeQ (RsgA), Era, KsgA (RsmA), RimJ, RimM, RimP, and Hfq, which take part in the decoding-center folding. Full article
(This article belongs to the Special Issue Analysis of Bacterial Ribosomes and Interacting Factors)
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14 pages, 2055 KiB  
Review
Bacterial Ribosome Rescue Systems
by Daisuke Kurita and Hyouta Himeno
Microorganisms 2022, 10(2), 372; https://doi.org/10.3390/microorganisms10020372 - 05 Feb 2022
Cited by 4 | Viewed by 2087
Abstract
To maintain proteostasis, the cell employs multiple ribosome rescue systems to relieve the stalled ribosome on problematic mRNA. One example of problematic mRNA is non-stop mRNA that lacks an in-frame stop codon produced by endonucleolytic cleavage or transcription error. In Escherichia coli, [...] Read more.
To maintain proteostasis, the cell employs multiple ribosome rescue systems to relieve the stalled ribosome on problematic mRNA. One example of problematic mRNA is non-stop mRNA that lacks an in-frame stop codon produced by endonucleolytic cleavage or transcription error. In Escherichia coli, there are at least three ribosome rescue systems that deal with the ribosome stalled on non-stop mRNA. According to one estimation, 2–4% of translation is the target of ribosome rescue systems even under normal growth conditions. In the present review, we discuss the recent findings of ribosome rescue systems in bacteria. Full article
(This article belongs to the Special Issue Analysis of Bacterial Ribosomes and Interacting Factors)
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11 pages, 1372 KiB  
Review
Ribosomal Hibernation-Associated Factors in Escherichia coli
by Yasushi Maki and Hideji Yoshida
Microorganisms 2022, 10(1), 33; https://doi.org/10.3390/microorganisms10010033 - 24 Dec 2021
Cited by 5 | Viewed by 3995
Abstract
Bacteria convert active 70S ribosomes to inactive 100S ribosomes to survive under various stress conditions. This state, in which the ribosome loses its translational activity, is known as ribosomal hibernation. In gammaproteobacteria such as Escherichia coli, ribosome modulation factor and hibernation-promoting factor [...] Read more.
Bacteria convert active 70S ribosomes to inactive 100S ribosomes to survive under various stress conditions. This state, in which the ribosome loses its translational activity, is known as ribosomal hibernation. In gammaproteobacteria such as Escherichia coli, ribosome modulation factor and hibernation-promoting factor are involved in forming 100S ribosomes. The expression of ribosome modulation factor is regulated by (p)ppGpp (which is induced by amino acid starvation), cAMP-CRP (which is stimulated by reduced metabolic energy), and transcription factors involved in biofilm formation. This indicates that the formation of 100S ribosomes is an important strategy for bacterial survival under various stress conditions. In recent years, the structures of 100S ribosomes from various bacteria have been reported, enhancing our understanding of the 100S ribosome. Here, we present previous findings on the 100S ribosome and related proteins and describe the stress-response pathways involved in ribosomal hibernation. Full article
(This article belongs to the Special Issue Analysis of Bacterial Ribosomes and Interacting Factors)
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16 pages, 2115 KiB  
Review
The Role of the Universally Conserved ATPase YchF/Ola1 in Translation Regulation during Cellular Stress
by Victoria Landwehr, Martin Milanov, Jiang Hong and Hans-Georg Koch
Microorganisms 2022, 10(1), 14; https://doi.org/10.3390/microorganisms10010014 - 23 Dec 2021
Cited by 3 | Viewed by 3009
Abstract
The ability to respond to metabolic or environmental changes is an essential feature in all cells and involves both transcriptional and translational regulators that adjust the metabolic activity to fluctuating conditions. While transcriptional regulation has been studied in detail, the important role of [...] Read more.
The ability to respond to metabolic or environmental changes is an essential feature in all cells and involves both transcriptional and translational regulators that adjust the metabolic activity to fluctuating conditions. While transcriptional regulation has been studied in detail, the important role of the ribosome as an additional player in regulating gene expression is only beginning to emerge. Ribosome-interacting proteins are central to this translational regulation and include universally conserved ribosome interacting proteins, such as the ATPase YchF (Ola1 in eukaryotes). In both eukaryotes and bacteria, the cellular concentrations of YchF/Ola1 determine the ability to cope with different stress conditions and are linked to several pathologies in humans. The available data indicate that YchF/Ola1 regulates the stress response via controlling non-canonical translation initiation and via protein degradation. Although the molecular mechanisms appear to be different between bacteria and eukaryotes, increased non-canonical translation initiation is a common consequence of YchF/Ola1 regulated translational control in E. coli and H. sapiens. In this review, we summarize recent insights into the role of the universally conserved ATPase YchF/Ola1 in adapting translation to unfavourable conditions. Full article
(This article belongs to the Special Issue Analysis of Bacterial Ribosomes and Interacting Factors)
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13 pages, 2361 KiB  
Review
Trans-Translation Is an Appealing Target for the Development of New Antimicrobial Compounds
by Rodrigo Campos-Silva, Gaetano D’Urso, Olivier Delalande, Emmanuel Giudice, Alexandre José Macedo and Reynald Gillet
Microorganisms 2022, 10(1), 3; https://doi.org/10.3390/microorganisms10010003 - 21 Dec 2021
Cited by 6 | Viewed by 3258
Abstract
Because of the ever-increasing multidrug resistance in microorganisms, it is crucial that we find and develop new antibiotics, especially molecules with different targets and mechanisms of action than those of the antibiotics in use today. Translation is a fundamental process that uses a [...] Read more.
Because of the ever-increasing multidrug resistance in microorganisms, it is crucial that we find and develop new antibiotics, especially molecules with different targets and mechanisms of action than those of the antibiotics in use today. Translation is a fundamental process that uses a large portion of the cell’s energy, and the ribosome is already the target of more than half of the antibiotics in clinical use. However, this process is highly regulated, and its quality control machinery is actively studied as a possible target for new inhibitors. In bacteria, ribosomal stalling is a frequent event that jeopardizes bacterial wellness, and the most severe form occurs when ribosomes stall at the 3′-end of mRNA molecules devoid of a stop codon. Trans-translation is the principal and most sophisticated quality control mechanism for solving this problem, which would otherwise result in inefficient or even toxic protein synthesis. It is based on the complex made by tmRNA and SmpB, and because trans-translation is absent in eukaryotes, but necessary for bacterial fitness or survival, it is an exciting and realistic target for new antibiotics. Here, we describe the current and future prospects for developing what we hope will be a novel generation of trans-translation inhibitors. Full article
(This article belongs to the Special Issue Analysis of Bacterial Ribosomes and Interacting Factors)
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20 pages, 2664 KiB  
Review
RNase III, Ribosome Biogenesis and Beyond
by Maxence Lejars, Asaki Kobayashi and Eliane Hajnsdorf
Microorganisms 2021, 9(12), 2608; https://doi.org/10.3390/microorganisms9122608 - 17 Dec 2021
Cited by 2 | Viewed by 3021
Abstract
The ribosome is the universal catalyst for protein synthesis. Despite extensive studies, the diversity of structures and functions of this ribonucleoprotein is yet to be fully understood. Deciphering the biogenesis of the ribosome in a step-by-step manner revealed that this complexity is achieved [...] Read more.
The ribosome is the universal catalyst for protein synthesis. Despite extensive studies, the diversity of structures and functions of this ribonucleoprotein is yet to be fully understood. Deciphering the biogenesis of the ribosome in a step-by-step manner revealed that this complexity is achieved through a plethora of effectors involved in the maturation and assembly of ribosomal RNAs and proteins. Conserved from bacteria to eukaryotes, double-stranded specific RNase III enzymes play a large role in the regulation of gene expression and the processing of ribosomal RNAs. In this review, we describe the canonical role of RNase III in the biogenesis of the ribosome comparing conserved and unique features from bacteria to eukaryotes. Furthermore, we report additional roles in ribosome biogenesis re-enforcing the importance of RNase III. Full article
(This article belongs to the Special Issue Analysis of Bacterial Ribosomes and Interacting Factors)
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