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Transfer RNA Modification
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Transfer RNA Modification

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Epigenomics".

Deadline for manuscript submissions: closed (15 January 2024) | Viewed by 5118

Special Issue Editor

Dr. Chie Tomikawa

E-Mail Website
Guest Editor
Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama, Ehime 790-8577, Japan
Interests: tRNA modification network; tRNA transport

Special Issue Information

Dear Colleagues, 

To date, over 150 types of RNA modifications have been identified in various RNA molecules, 80% of which have been found in transfer RNA (tRNA). The primary function of tRNA modifications is to regulate precise protein synthesis by contributing to the stabilization of tRNA’s L-shaped structure, prolongation of tRNA’s half-life, binding of correct amino acids to tRNA, and inhibition of misreading. In particular, modified nucleosides in anticodons act to enhance, alter, or suppress codon–anticodon pairing. Modified nucleosides are also key in tRNA transport, tRNA processing, and tRNA quality control. Moreover, the effects of tRNA modification on diseases are also becoming clearer. Although many tRNA modifications are common across biological species, some types of tRNA modifications are not. tRNA modification enzymes are also thought to have existed since the beginning of life. Thus, the study of the enzymatic mechanisms and structures of tRNA modification enzymes is extremely important in considering the molecular evolution of life. Regarding the detection of modified nucleosides in tRNA, starting with classical TLC-based detection and mass spectrometry analysis, nanopore sequencing has finally made it possible to determine tRNA sequences containing modified nucleosides. In order to understand tRNA modifications broadly and deeply, I hope that this Special Issue brings together research from various perspectives.

Dr. Chie Tomikawa
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. Genes 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 2600 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

  • tRNA modification network
  • diseases linked with tRNA modifications
  • quality control of tRNA
  • chemical synthesis of tRNA
  • structure of tRNA modification enzymes
  • evolution of tRNA modification enzymes
  • tRNA transport
  • splicing and processing
  • tRNA sequencing methods

Published Papers (3 papers)

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Research

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15 pages, 1602 KiB  
Article
yaaJ, the tRNA-Specific Adenosine Deaminase, Is Dispensable in Bacillus subtilis
by Akiko Soma, Atsushi Kubota, Daisuke Tomoe, Yoshiho Ikeuchi, Fujio Kawamura, Hijiri Arimoto, Yuh Shiwa, Yu Kanesaki, Hideaki Nanamiya, Hirofumi Yoshikawa, Tsutomu Suzuki and Yasuhiko Sekine
Genes 2023, 14(8), 1515; https://doi.org/10.3390/genes14081515 - 25 Jul 2023
Viewed by 1382
Abstract
Post-transcriptional modifications of tRNA are crucial for their core function. The inosine (I; 6-deaminated adenosine) at the first position in the anticodon of tRNAArg(ICG) modulates the decoding capability and is generally considered essential for reading CGU, CGC, and CGA codons in [...] Read more.
Post-transcriptional modifications of tRNA are crucial for their core function. The inosine (I; 6-deaminated adenosine) at the first position in the anticodon of tRNAArg(ICG) modulates the decoding capability and is generally considered essential for reading CGU, CGC, and CGA codons in eubacteria. We report here that the Bacillus subtilis yaaJ gene encodes tRNA-specific adenosine deaminase and is non-essential for viability. A β−galactosidase reporter assay revealed that the translational activity of CGN codons was not impaired in the yaaJ-deletion mutant. Furthermore, tRNAArg(CCG) responsible for decoding the CGG codon was dispensable, even in the presence or absence of yaaJ. These results strongly suggest that tRNAArg with either the anticodon ICG or ACG has an intrinsic ability to recognize all four CGN codons, providing a fundamental concept of non-canonical wobbling mediated by adenosine and inosine nucleotides in the anticodon. This is the first example of the four-way wobbling by inosine nucleotide in bacterial cells. On the other hand, the absence of inosine modification induced +1 frameshifting, especially at the CGA codon. Additionally, the yaaJ deletion affected growth and competency. Therefore, the inosine modification is beneficial for translational fidelity and proper growth-phase control, and that is why yaaJ has been actually conserved in B. subtilis. Full article
(This article belongs to the Special Issue Transfer RNA Modification)
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Review

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21 pages, 667 KiB  
Review
Beyond the Anticodon: tRNA Core Modifications and Their Impact on Structure, Translation and Stress Adaptation
by Marcel-Joseph Yared, Agathe Marcelot and Pierre Barraud
Genes 2024, 15(3), 374; https://doi.org/10.3390/genes15030374 - 19 Mar 2024
Viewed by 1225
Abstract
Transfer RNAs (tRNAs) are heavily decorated with post-transcriptional chemical modifications. Approximately 100 different modifications have been identified in tRNAs, and each tRNA typically contains 5–15 modifications that are incorporated at specific sites along the tRNA sequence. These modifications may be classified into two [...] Read more.
Transfer RNAs (tRNAs) are heavily decorated with post-transcriptional chemical modifications. Approximately 100 different modifications have been identified in tRNAs, and each tRNA typically contains 5–15 modifications that are incorporated at specific sites along the tRNA sequence. These modifications may be classified into two groups according to their position in the three-dimensional tRNA structure, i.e., modifications in the tRNA core and modifications in the anticodon-loop (ACL) region. Since many modified nucleotides in the tRNA core are involved in the formation of tertiary interactions implicated in tRNA folding, these modifications are key to tRNA stability and resistance to RNA decay pathways. In comparison to the extensively studied ACL modifications, tRNA core modifications have generally received less attention, although they have been shown to play important roles beyond tRNA stability. Here, we review and place in perspective selected data on tRNA core modifications. We present their impact on tRNA structure and stability and report how these changes manifest themselves at the functional level in translation, fitness and stress adaptation. Full article
(This article belongs to the Special Issue Transfer RNA Modification)
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23 pages, 2251 KiB  
Review
Transfer RNA Modification Enzymes with a Thiouridine Synthetase, Methyltransferase and Pseudouridine Synthase (THUMP) Domain and the Nucleosides They Produce in tRNA
by Hiroyuki Hori
Genes 2023, 14(2), 382; https://doi.org/10.3390/genes14020382 - 31 Jan 2023
Cited by 3 | Viewed by 1972
Abstract
The existence of the thiouridine synthetase, methyltransferase and pseudouridine synthase (THUMP) domain was originally predicted by a bioinformatic study. Since the prediction of the THUMP domain more than two decades ago, many tRNA modification enzymes containing the THUMP domain have been identified. According [...] Read more.
The existence of the thiouridine synthetase, methyltransferase and pseudouridine synthase (THUMP) domain was originally predicted by a bioinformatic study. Since the prediction of the THUMP domain more than two decades ago, many tRNA modification enzymes containing the THUMP domain have been identified. According to their enzymatic activity, THUMP-related tRNA modification enzymes can be classified into five types, namely 4-thiouridine synthetase, deaminase, methyltransferase, a partner protein of acetyltransferase and pseudouridine synthase. In this review, I focus on the functions and structures of these tRNA modification enzymes and the modified nucleosides they produce. Biochemical, biophysical and structural studies of tRNA 4-thiouridine synthetase, tRNA methyltransferases and tRNA deaminase have established the concept that the THUMP domain captures the 3′-end of RNA (in the case of tRNA, the CCA-terminus). However, in some cases, this concept is not simply applicable given the modification patterns observed in tRNA. Furthermore, THUMP-related proteins are involved in the maturation of other RNAs as well as tRNA. Moreover, the modified nucleosides, which are produced by the THUMP-related tRNA modification enzymes, are involved in numerous biological phenomena, and the defects of genes for human THUMP-related proteins are implicated in genetic diseases. In this review, these biological phenomena are also introduced. Full article
(This article belongs to the Special Issue Transfer RNA Modification)
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