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Bacterial Ribosomal Proteins: Evolution, Structure, Functions, Regulation

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

Deadline for manuscript submissions: closed (30 November 2023) | Viewed by 7653

Special Issue Editor


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Guest Editor
Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
Interests: bacterial gene expression; transcription regulation; translation regulation; ribosomal proteins; autogenous control; RNA–protein interactions

Special Issue Information

Dear Colleagues,

Ribosomal proteins are abundant and highly conserved cellular proteins that play an essential role in ribosome biogenesis and protein synthesis in all domains of life. In bacteria, they govern rRNA folding during ribosome assembly and provide communication between functional centers of a ribosome, such as the peptidyl transfer center, the tRNA binding sites, and the peptide exit tunnel. Although highly conserved, ribosomal proteins in different species possess structural diversity and may acquire new activities, which help the ribosome to adapt to the changes in lifestyle or environments where bacteria face new challenges. Ribosomes are the main target for numerous drugs, and mutations in ribosomal proteins may confer resistance to various antibiotics, which highlights the importance of thorough studies of individual proteins and their role in ribosome functions. In addition to their primary role in a cell as integral components of protein synthesis machinery, many ribosomal proteins have functions beyond the ribosome (the phenomenon known as moonlighting), acting either as individual regulatory proteins or in complexes with other cellular components.

The main goal of this Special Issue is to provide an overview of the recent advances in studies concerning the phylogeny and evolution of bacterial ribosomal proteins, their structural diversity, and specific activities both within and beyond the ribosome in different bacterial species, as well as the impact of mutations on these activities, diverse molecular mechanisms of regulation of ribosomal protein synthesis in living cells, the formation of functional complexes with other cellular components. I believe that this Special Issue will uncover many intriguing aspects of the ribosomal proteins, and thus will be useful for a broad group of readers interested in modern molecular microbiology.

Dr. Irina V Boni
Guest Editor

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Keywords

  • bacterial ribosomal proteins
  • phylogenie
  • evolution
  • structure
  • functions
  • control mechanisms
  • extraribosomal activities
  • mutations

Published Papers (5 papers)

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Research

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12 pages, 17730 KiB  
Article
The P-Site Loop of the Universally Conserved Bacterial Ribosomal Protein L5 Is Required for Maintaining Both Translation Rate and Fidelity
by Mikhail G. Bubunenko and Alexey P. Korepanov
Int. J. Mol. Sci. 2023, 24(18), 14285; https://doi.org/10.3390/ijms241814285 - 19 Sep 2023
Viewed by 749
Abstract
The bacterial ribosomal 5S rRNA-binding protein L5 is universally conserved (uL5). It contains the so-called P-site loop (PSL), which contacts the P-site tRNA in the ribosome. Certain PSL mutations in yeast are lethal, suggesting that the loop plays an important role in translation. [...] Read more.
The bacterial ribosomal 5S rRNA-binding protein L5 is universally conserved (uL5). It contains the so-called P-site loop (PSL), which contacts the P-site tRNA in the ribosome. Certain PSL mutations in yeast are lethal, suggesting that the loop plays an important role in translation. In this work, for the first time, a viable Escherichia coli strain was obtained with the deletion of the major part of the PSL (residues 73–80) of the uL5 protein. The deletion conferred cold sensitivity and drastically reduced the growth rate and overall protein synthesizing capacity of the mutant. Translation rate is decreased in mutant cells as compared to the control. At the same time, the deletion causes increased levels of −1 frameshifting and readthrough of all three stop codons. In general, the results show that the PSL of the uL5 is required for maintaining both the accuracy and rate of protein synthesis in vivo. Full article
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11 pages, 3679 KiB  
Article
Ribosome Protein Composition Mediates Translation during the Escherichia coli Stationary Phase
by Kaspar Reier, Aivar Liiv and Jaanus Remme
Int. J. Mol. Sci. 2023, 24(4), 3128; https://doi.org/10.3390/ijms24043128 - 04 Feb 2023
Cited by 3 | Viewed by 1559
Abstract
Bacterial ribosomes contain over 50 ribosome core proteins (r-proteins). Tens of non-ribosomal proteins bind to ribosomes to promote various steps of translation or suppress protein synthesis during ribosome hibernation. This study sets out to determine how translation activity is regulated during the prolonged [...] Read more.
Bacterial ribosomes contain over 50 ribosome core proteins (r-proteins). Tens of non-ribosomal proteins bind to ribosomes to promote various steps of translation or suppress protein synthesis during ribosome hibernation. This study sets out to determine how translation activity is regulated during the prolonged stationary phase. Here, we report the protein composition of ribosomes during the stationary phase. According to quantitative mass-spectrometry analysis, ribosome core proteins bL31B and bL36B are present during the late log and first days of the stationary phase and are replaced by corresponding A paralogs later in the prolonged stationary phase. Ribosome hibernation factors Rmf, Hpf, RaiA, and Sra are bound to the ribosomes during the onset and a few first days of the stationary phase when translation is strongly suppressed. In the prolonged stationary phase, a decrease in ribosome concentration is accompanied by an increase in translation and association of translation factors with simultaneous dissociation of ribosome hibernating factors. The dynamics of ribosome-associated proteins partially explain the changes in translation activity during the stationary phase. Full article
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15 pages, 7010 KiB  
Article
Yet Another Similarity between Mitochondrial and Bacterial Ribosomal Small Subunit Biogenesis Obtained by Structural Characterization of RbfA from S. aureus
by Aydar G. Bikmullin, Bulat Fatkhullin, Artem Stetsenko, Azat Gabdulkhakov, Natalia Garaeva, Liliia Nurullina, Evelina Klochkova, Alexander Golubev, Iskander Khusainov, Natalie Trachtmann, Dmitriy Blokhin, Albert Guskov, Shamil Validov, Konstantin Usachev and Marat Yusupov
Int. J. Mol. Sci. 2023, 24(3), 2118; https://doi.org/10.3390/ijms24032118 - 20 Jan 2023
Cited by 2 | Viewed by 1913
Abstract
Ribosome biogenesis is a complex and highly accurate conservative process of ribosomal subunit maturation followed by association. Subunit maturation comprises sequential stages of ribosomal RNA and proteins’ folding, modification and binding, with the involvement of numerous RNAses, helicases, GTPases, chaperones, RNA, protein-modifying enzymes, [...] Read more.
Ribosome biogenesis is a complex and highly accurate conservative process of ribosomal subunit maturation followed by association. Subunit maturation comprises sequential stages of ribosomal RNA and proteins’ folding, modification and binding, with the involvement of numerous RNAses, helicases, GTPases, chaperones, RNA, protein-modifying enzymes, and assembly factors. One such assembly factor involved in bacterial 30S subunit maturation is ribosomal binding factor A (RbfA). In this study, we present the crystal (determined at 2.2 Å resolution) and NMR structures of RbfA as well as the 2.9 Å resolution cryo-EM reconstruction of the 30S–RbfA complex from Staphylococcus aureus (S. aureus). Additionally, we show that the manner of RbfA action on the small ribosomal subunit during its maturation is shared between bacteria and mitochondria. The obtained results clarify the function of RbfA in the 30S maturation process and its role in ribosome functioning in general. Furthermore, given that S. aureus is a serious human pathogen, this study provides an additional prospect to develop antimicrobials targeting bacterial pathogens. Full article
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Review

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34 pages, 2250 KiB  
Review
Extraribosomal Functions of Bacterial Ribosomal Proteins—An Update, 2023
by Leonid V. Aseev, Ludmila S. Koledinskaya and Irina V. Boni
Int. J. Mol. Sci. 2024, 25(5), 2957; https://doi.org/10.3390/ijms25052957 - 03 Mar 2024
Viewed by 1160
Abstract
Ribosomal proteins (r-proteins) are abundant, highly conserved, and multifaceted cellular proteins in all domains of life. Most r-proteins have RNA-binding properties and can form protein–protein contacts. Bacterial r-proteins govern the co-transcriptional rRNA folding during ribosome assembly and participate in the formation of the [...] Read more.
Ribosomal proteins (r-proteins) are abundant, highly conserved, and multifaceted cellular proteins in all domains of life. Most r-proteins have RNA-binding properties and can form protein–protein contacts. Bacterial r-proteins govern the co-transcriptional rRNA folding during ribosome assembly and participate in the formation of the ribosome functional sites, such as the mRNA-binding site, tRNA-binding sites, the peptidyl transferase center, and the protein exit tunnel. In addition to their primary role in a cell as integral components of the protein synthesis machinery, many r-proteins can function beyond the ribosome (the phenomenon known as moonlighting), acting either as individual regulatory proteins or in complexes with various cellular components. The extraribosomal activities of r-proteins have been studied over the decades. In the past decade, our understanding of r-protein functions has advanced significantly due to intensive studies on ribosomes and gene expression mechanisms not only in model bacteria like Escherichia coli or Bacillus subtilis but also in little-explored bacterial species from various phyla. The aim of this review is to update information on the multiple functions of r-proteins in bacteria. Full article
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15 pages, 3169 KiB  
Review
The Discovery of Ribosomal Protein bL31 from Escherichia coli: A Long Story Revisited
by Akira Wada, Masami Ueta and Chieko Wada
Int. J. Mol. Sci. 2023, 24(4), 3445; https://doi.org/10.3390/ijms24043445 - 08 Feb 2023
Viewed by 1336
Abstract
Ribosomal protein bL31 in Escherichia coli was initially detected as a short form (62 amino acids) using Kaltschmidt and Wittmann’s two-dimensional polyacrylamide gel electrophoresis (2D PAGE), but the intact form (70 amino acids) was subsequently identified by means of Wada’s improved radical-free and [...] Read more.
Ribosomal protein bL31 in Escherichia coli was initially detected as a short form (62 amino acids) using Kaltschmidt and Wittmann’s two-dimensional polyacrylamide gel electrophoresis (2D PAGE), but the intact form (70 amino acids) was subsequently identified by means of Wada’s improved radical-free and highly reducing (RFHR) 2D PAGE, which was consistent with the analysis of its encoding gene rpmE. Ribosomes routinely prepared from the K12 wild-type strain contained both forms of bL31. ΔompT cells, which lack protease 7, only contained intact bL31, suggesting that protease 7 cleaves intact bL31 and generates short bL31 during ribosome preparation from wild-type cells. Intact bL31 was required for subunit association, and its eight cleaved C-terminal amino acids contributed to this function. 70S ribosomes protected bL31 from cleavage by protease 7, but free 50S did not. In vitro translation was assayed using three systems. The translational activities of wild-type and ΔrpmE ribosomes were 20% and 40% lower than those of ΔompT ribosomes, which contained one copy of intact bL31. The deletion of bL31 reduces cell growth. A structural analysis predicted that bL31 spans the 30S and 50S subunits, consistent with its functions in 70S association and translation. It is important to re-analyze in vitro translation with ribosomes containing only intact bL31. Full article
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