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Progress and Expansion of Ribosome Research
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Progress and Expansion of Ribosome Research

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

Deadline for manuscript submissions: closed (20 August 2023) | Viewed by 6682

Special Issue Editor

Dr. Chie Takemoto

E-Mail Website
Guest Editor
Protein Functional and Structural Biology Team, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
Interests: structure and function of the ribosome; tRNA; protein synthesis; RNA-protein interaction; X-ray crystallographic study; cryo-EM structural analysis

Special Issue Information

Dear Colleagues,

Ribosome is the machinery responsible for one of the fundamental biological activities, protein synthesis, and research to elucidate its function and structure has progressed along with the development of new technologies and drugs. In addition, the study of ribosome biosynthesis itself consists of so many processes from gene replication and transcription to protein synthesis and folding, that elucidating these processes is equivalent to unraveling the regulation of cellular functions. Recently, new aspects of ribosomes concerning to human diseases and cellular functions, including various RNAs and nuclei, begin to emerge through advanced approaches in genetics, biochemistry, cell biology, and structural biology, as well as new techniques such as single molecule measurement and observation. As an international networking venue, this special issue welcomes submissions of papers that present the latest results, findings, and innovations broadly related to ribosome research.

Dr. Chie Takemoto
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.

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Keywords

  • ribosome biogenesis, ribosomal protein, rRNA, nucleus: rDNA, transcription, RNA processing/modification, assembly factor
  • protein synthesis, protein folding/localization/modification, quality control: ribozyme, tRNA, mRNA, translational factor, chaperone, ubiquitination
  • ribosomopathy, metabolism: antibiotics, drug, cell cycle, phosphorylation, nuclease, protease
  • molecular mechanism, structural analysis, structural dynamics: ribosome profiling, single-molecule analysis, NMR, cryoEM, AFM, X-ray crystallography

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Published Papers (3 papers)

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Research

16 pages, 2362 KiB  
Article
Genetic Code Expansion and a Photo-Cross-Linking Reaction Facilitate Ribosome Display Selections for Identifying a Wide Range of Affinity Peptides
by Takuto Furuhashi, Kensaku Sakamoto and Akira Wada
Int. J. Mol. Sci. 2023, 24(21), 15661; https://doi.org/10.3390/ijms242115661 - 27 Oct 2023
Cited by 1 | Viewed by 1509
Abstract
Cell-free molecular display techniques have been utilized to select various affinity peptides from peptide libraries. However, conventional techniques have difficulties associated with the translational termination through in-frame UAG stop codons and the amplification of non-specific peptides, which hinders the desirable selection of low-affinity [...] Read more.
Cell-free molecular display techniques have been utilized to select various affinity peptides from peptide libraries. However, conventional techniques have difficulties associated with the translational termination through in-frame UAG stop codons and the amplification of non-specific peptides, which hinders the desirable selection of low-affinity peptides. To overcome these problems, we established a scheme for ribosome display selection of peptide epitopes bound to monoclonal antibodies and then applied genetic code expansion with synthetic X-tRNAUAG reprogramming of the UAG codons (X = Tyr, Trp, or p-benzoyl-l-phenylalanine (pBzo-Phe)) to the scheme. Based on the assessment of the efficiency of in vitro translation with X-tRNAUAG, we carried out ribosome display selection with genetic code expansion using Trp-tRNAUAG, and we verified that affinity peptides could be identified efficiently regardless of the presence of UAG codons in the peptide coding sequences. Additionally, after evaluating the photo-cross-linking reactions of pBzo-Phe-incorporated peptides, we performed ribosome display selection of low-affinity peptides in combination with genetic code expansion using pBzo-Phe-tRNAUAG and photo-irradiation. The results demonstrated that sub-micromolar low-affinity peptide epitopes could be identified through the formation of photo-induced covalent bonds with monoclonal antibodies. Thus, the developed ribosome display techniques could contribute to the promotion of diverse peptide-based research. Full article
(This article belongs to the Special Issue Progress and Expansion of Ribosome Research)
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19 pages, 6191 KiB  
Article
Crystal Structure of Pyrrolysyl-tRNA Synthetase from a Methanogenic Archaeon ISO4-G1 and Its Structure-Based Engineering for Highly-Productive Cell-Free Genetic Code Expansion with Non-Canonical Amino Acids
by Tatsuo Yanagisawa, Eiko Seki, Hiroaki Tanabe, Yoshifumi Fujii, Kensaku Sakamoto and Shigeyuki Yokoyama
Int. J. Mol. Sci. 2023, 24(7), 6256; https://doi.org/10.3390/ijms24076256 - 26 Mar 2023
Cited by 2 | Viewed by 2754
Abstract
Pairs of pyrrolysyl-tRNA synthetase (PylRS) and tRNAPyl from Methanosarcina mazei and Methanosarcina barkeri are widely used for site-specific incorporations of non-canonical amino acids into proteins (genetic code expansion). Previously, we achieved full productivity of cell-free protein synthesis for bulky non-canonical amino acids, [...] Read more.
Pairs of pyrrolysyl-tRNA synthetase (PylRS) and tRNAPyl from Methanosarcina mazei and Methanosarcina barkeri are widely used for site-specific incorporations of non-canonical amino acids into proteins (genetic code expansion). Previously, we achieved full productivity of cell-free protein synthesis for bulky non-canonical amino acids, including Nε-((((E)-cyclooct-2-en-1-yl)oxy)carbonyl)-L-lysine (TCO*Lys), by using Methanomethylophilus alvus PylRS with structure-based mutations in and around the amino acid binding pocket (first-layer and second-layer mutations, respectively). Recently, the PylRS·tRNAPyl pair from a methanogenic archaeon ISO4-G1 was used for genetic code expansion. In the present study, we determined the crystal structure of the methanogenic archaeon ISO4-G1 PylRS (ISO4-G1 PylRS) and compared it with those of structure-known PylRSs. Based on the ISO4-G1 PylRS structure, we attempted the site-specific incorporation of Nε-(p-ethynylbenzyloxycarbonyl)-L-lysine (pEtZLys) into proteins, but it was much less efficient than that of TCO*Lys with M. alvus PylRS mutants. Thus, the first-layer mutations (Y125A and M128L) of ISO4-G1 PylRS, with no additional second-layer mutations, increased the protein productivity with pEtZLys up to 57 ± 8% of that with TCO*Lys at high enzyme concentrations in the cell-free protein synthesis. Full article
(This article belongs to the Special Issue Progress and Expansion of Ribosome Research)
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11 pages, 1909 KiB  
Article
Mutation at the Site of Hydroxylation in the Ribosomal Protein uL15 (RPL27a) Causes Specific Changes in the Repertoire of mRNAs Translated in Mammalian Cells
by Elizaveta A. Zolotenkova, Alexander V. Gopanenko, Alexey E. Tupikin, Marsel R. Kabilov and Alexey A. Malygin
Int. J. Mol. Sci. 2023, 24(7), 6173; https://doi.org/10.3390/ijms24076173 - 24 Mar 2023
Cited by 2 | Viewed by 1732
Abstract
Ribosomal protein uL15 (RPL27a) carries a specific modification, hydroxylation, at the His39 residue, which neighbors the CCA terminus of the E-site-bound tRNA at the mammalian ribosome. Under hypoxia, the level of hydroxylation of this protein decreases. We transiently transfected HEK293T cells with constructs [...] Read more.
Ribosomal protein uL15 (RPL27a) carries a specific modification, hydroxylation, at the His39 residue, which neighbors the CCA terminus of the E-site-bound tRNA at the mammalian ribosome. Under hypoxia, the level of hydroxylation of this protein decreases. We transiently transfected HEK293T cells with constructs expressing wild-type uL15 or mutated uL15 (His39Ala) incapable of hydroxylation, and demonstrated that ribosomes containing both proteins are competent in translation. By applying RNA-seq to the total cellular and polysome-associated mRNAs, we identified differentially expressed genes (DEGs) in cells containing exogenous uL15 or its mutant form. Analyzing mRNA features of up- and down-regulated DEGs, we found an increase in the level of more abundant mRNAs and shorter CDSs in cells with uL15 mutant for both translated and total cellular mRNAs. The level of longer and rarer mRNAs, on the contrary, decreased. Our data show how ribosome heterogeneity can change the composition of the translatome and transcriptome, depending on the properties of the translated mRNAs. Full article
(This article belongs to the Special Issue Progress and Expansion of Ribosome Research)
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