Review
Biochemistry & Molecular Biology
Olivier Finet, Carlo Yague-Sanz, Florian Marchand, Damien Hermand
Summary: The universal dihydrouridine (D) mark, generated by the Dus family of enzymes, has unique structural characteristics and potential biological significance. Recent studies have shown that D is not only present in tRNAs but also in mRNAs, highlighting its critical physiological relevance.
Article
Biochemistry & Molecular Biology
Murielle Lombard, Colbie J. Reed, Ludovic Pecqueur, Bruno Faivre, Sabrine Toubdji, Claudia Sudol, Damien Bregeon, Valerie De Crecy-Lagard, Djemel Hamdane
Summary: Dihydrouridine (D) is a modified base found in tRNAs and recently detected in eukaryotic mRNAs, which plays a significant role in the conformational plasticity of RNA molecules. The study on the structure-function relationships of eukaryotic Dus proteins has been limited, but the study combining phylogenetic analysis and molecular modeling provides insights into the evolutionary molecular basis of D biosynthesis by these enzymes.
Article
Biochemistry & Molecular Biology
Olivier Finet, Carlo Yague-Sanz, Lara Katharina Kruger, Phong Tran, Valerie Migeot, Max Louski, Alicia Nevers, Mathieu Rougemaille, Jingjing Sun, Felix G. M. Ernst, Ludivine Wacheul, Maxime Wery, Antonin Morillon, Peter Dedon, Denis L. J. Lafontaine, Damien Hermand
Summary: This study reveals the importance of RNA modifications in gene expression control, and develops a new integrated pipeline to detect modifications in a transcriptome-wide manner. The researchers identify a novel RNA modification and demonstrate its biological function in mRNA of fission yeast. They also find that the modification is evolutionarily conserved in human cells.
Article
Multidisciplinary Sciences
Jiazhi Li, Longfei Wang, Quentin Hahn, Radoslaw P. Nowak, Thibault Viennet, Esteban A. Orellana, Shourya S. Roy Burman, Hong Yue, Moritz Hunkeler, Pietro Fontana, Hao Wu, Haribabu Arthanari, Eric S. Fischer, Richard I. Gregory
Summary: Chemical modifications of RNA play a crucial role in various biological processes. N-7-methylguanosine (m(7)G) is essential for the integrity and stability of a large group of tRNAs. The METTL1-WDR4 complex acts as a methyltransferase that modifies G46 in specific tRNAs, and its dysregulation is implicated in tumorigenesis. However, the mechanism of tRNA substrate recognition and regulation of METTL1-WDR4 remains unknown.
Review
Biology
Jing Li, Wen-Yu Zhu, Wen-Qing Yang, Cai-Tao Li, Ru-Juan Liu
Summary: Chemical modifications of RNA molecules greatly increase their complexity and utility, with tRNAs being the most heavily modified and crucial for protein synthesis. Defects in tRNA modifications can lead to human diseases. Over 100 types of modifications have been found in tRNAs, with varying frequencies on different tRNAs. The occurrence of tRNA modifications is responsive to environmental changes, and there are numerous interactions among different sites and modifications.
SCIENCE CHINA-LIFE SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Hao Li, Han Dong, Beisi Xu, Qing-Ping Xiong, Cai-Tao Li, Wen-Qing Yang, Jing Li, Zhi-Xuan Huang, Qi-Yu Zeng, En-Duo Wang, Ru-Juan Liu
Summary: The previously uncharacterized tRNA-modifying enzyme hTrmt13 is found to regulate transcription in a dual mechanism, catalyzing tRNA 2'-O-methylation in the cytoplasm for translation regulation and binding DNA as a transcriptional co-activator in the nucleus for promoting cell migration. These dual functions are mutually exclusive and the expression of hTrmt13 is correlated with poor prognosis in cancer patients. This discovery provides a new perspective for epitranscriptomic regulation.
Article
Multidisciplinary Sciences
Ryota Yamagami, Jacob P. Sieg, Sarah M. Assmann, Philip C. Bevilacqua
Summary: RNA structure is crucial for cellular events, and the study of tRNA structure is challenging. The tRNA structure-seq workflow accurately determines the in vivo secondary structure of tRNA and provides insights into tRNA abundance and natural modifications.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Hovik Panosyan, Franziska R. Traube, Caterina Brandmayr, Mirko Wagner, Thomas Carell
Summary: The study analyzed the tRNA modification profiles of thermophilic aerobic bacilli strains to identify variations in phylogeny. The modified tRNA bases were found to be genus-specific and could be used to distinguish between obligate and moderate thermophilic bacilli. The presence of certain modifications, such as Gm and ms(2)i(6)A, was more pronounced in obligate thermophilic species.
Article
Genetics & Heredity
Yasemin Yoluc, Erik van de Logt, Stefanie Kellner-Kaiser
Summary: RNA modifications in response to stress in the model organism S. cerevisiae are dynamic and affected by factors such as stress exposure. In yeast, stress exposure leads to stalled transcription of tRNA and rRNA, with most modification profile changes linked to alterations on pre-existing RNAs. Additionally, stress exposure results in rapid loss of methylation damages in all RNAs studied.
Article
Biochemistry & Molecular Biology
Gyuhyeok Cho, Jangmin Lee, Jungwook Kim
Summary: The uridine at the 34th position of tRNA can be modified to affect decoding properties during translation. MnmC enzyme in bacteria like Escherichia coli converts cmnm(5)(s(2))U to mnm(5)(s(2))U, while MnmM enzyme in Bacillus subtilis converts nm(5)(s(2))U to mnm(5)(s(2))U.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Wei Wang, Yi Yang, Huanping Guo, Ming-Han Li, Xiao-Qing Chen, Xin-Yu Wei, Yu Chen, Hany M. M. Elsheikha, Xiao-Xuan Zhang
Summary: Using liquid chromatography-tandem mass spectrometry, we identified RNA modifications in three strains of Toxoplasma gondii and compared the diversity and patterns of modifications between different strains. We found significant differences in the modified nucleotides in tRNA and sncRNA, which were correlated with the expression of virulence proteins. These findings provide new insights into the diversity of RNA modifications in T. gondii and their potential role in virulence.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Andrew Behrens, Geraldine Rodschinka, Danny D. Nedialkova
Summary: The study overcame the challenges in measuring cellular tRNA abundance by using modification-induced misincorporation tRNA sequencing (mim-tRNAseq) method, accurately capturing tRNA abundance and modification status in cells. The research revealed significant heterogeneity of tRNA isodecoder pools among diverse human cell lines and surprising interdependence of modifications at distinct sites within the same tRNA transcript.
Review
Biochemistry & Molecular Biology
Richard Giege, Gilbert Eriani
Summary: tRNAs play a crucial role in ribosome-dependent protein synthesis and their accuracy relies on specific identity elements within tRNA molecules. Although the understanding of these identity elements has expanded, the increasing number of reported functional differences has caused confusion. Furthermore, other processes involving tRNAs have been discovered, revealing multiple novel identities on the same tRNA molecule. This review highlights the mechanistic and evolutionary aspects of tRNA and tRNA-like identities, as well as new methods for identifying multiple identities on a single tRNA.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Zhirou Li, Jinge Mao, Daiyun Huang, Bowen Song, Jia Meng
Summary: 5-methyluridine (m5U) is a crucial base on RNA molecules influencing cancer development and immune diseases. The RNADSN neural network model shows superior performance in predicting mRNA m5U sites, even without experimental data.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Bruno Faivre, Murielle Lombard, Soufyan Fakroun, Chau-Duy-Tam Vo, Catherine Goyenvalle, Vincent Guerineau, Ludovic Pecqueur, Marc Fontecave, Valerie De Crecy-Lagard, Damien Bregeon, Djemel Hamdane
Summary: Dihydrouridine (D) is a conserved tRNA-modified base in all kingdoms of life, synthesized by conserved dihydrouridine synthases (Dus). Characterization of a unique DusB gene in Mollicutes revealed its ability to simultaneously modify U17 to D17 and synthesize D20/D20a, exhibiting unprecedented multisite specificity.
Article
Biochemistry & Molecular Biology
Ai Kazayama, Ryota Yamagami, Takashi Yokogawa, Hiroyuki Hori
JOURNAL OF BIOCHEMISTRY
(2015)
Article
Cell Biology
Ryota Yamagami, Chie Tomikawa, Naoki Shigi, Ai Kazayama, Shin-ichi Asai, Hiroyuki Takuma, Akira Hirata, Dominique Fourmy, Haruichi Asahara, Kimitsuna Watanabe, Satoko Yoshizawa, Hiroyuki Hori
Article
Cell Biology
Misa Nakashima, Ryota Yamagami, Chie Tomikawa, Yuki Ochi, Toshiyuki Moriya, Haruichi Asahara, Dominique Fourmy, Satoko Yoshizawa, Tairo Oshima, Hiroyuki Hori
Article
Biochemistry & Molecular Biology
Ryota Yamagami, Ryota Miyake, Ayaka Fukumoto, Misa Nakashima, Hiroyuki Hori
JOURNAL OF BIOCHEMISTRY
(2018)
Article
Multidisciplinary Sciences
Ryota Yamagami, Jamie L. Bingaman, Erica A. Frankel, Philip C. Bevilacqua
NATURE COMMUNICATIONS
(2018)
Article
Biochemistry & Molecular Biology
Ryota Yamagami, Mohammad Kayedkhordeh, David H. Mathews, Philip C. Bevilacqua
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
Ryota Yamagami, Ruochuan Huang, Philip C. Beyilacqua
Article
Multidisciplinary Sciences
Kathleen A. Leamy, Ryota Yamagami, Neela H. Yennawar, Philip C. Bevilacqua
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Biochemistry & Molecular Biology
Ryota Yamagami, Jacob P. Sieg, Philip C. Bevilacqua
Summary: RNA regulates various cellular events and relies on magnesium ions to fold into complex structures. Recent studies show that weakly chelated magnesium ions can enhance RNA function, indicating the importance of considering chelated magnesium in future RNA and protein research.
Article
Biochemistry & Molecular Biology
Yu Nishida, Shiho Ohmori, Risa Kakizono, Kunpei Kawai, Miyu Namba, Kazuki Okada, Ryota Yamagami, Akira Hirata, Hiroyuki Hori
Summary: The Saccharomyces cerevisiae Trm11-Trm112 complex methylates the 2-amino group of guanosine at position 10 in tRNA, and this study investigates the elements required for methylation. The results show that precursor tRNA, tRNA with a special structure, and tRNA lacking the CCA terminus or regular-size variable region are not substrates for Trm11-Trm112. Additionally, the G10-C25 base pair is necessary for methylation, and Trm11-Trm112 also recognizes the anticodon-loop. The study provides insights into the m(2)G10 modification pattern of S. cerevisiae class I tRNAs and identifies Trm11-Trm112 binding sites.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Ryota Yamagami, Jacob P. Sieg, Sarah M. Assmann, Philip C. Bevilacqua
Summary: RNA structure is crucial for cellular events, and the study of tRNA structure is challenging. The tRNA structure-seq workflow accurately determines the in vivo secondary structure of tRNA and provides insights into tRNA abundance and natural modifications.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Ryota Yamagami, Hiroyuki Hori
Summary: Transfer RNAs undergo diverse posttranscriptional modifications to regulate cellular events. Recent RNA-seq techniques provide insights into tRNA features. This study adapts a tRNA-sequencing technique to analyze tRNA modifications and gain mechanistic insights into enzyme-substrate recognition.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Yuzuru Sugio, Ryota Yamagami, Naoki Shigi, Hiroyuki Hori
Summary: The modified nucleoside s(4)U is found in tRNA from bacteria and archaea and has been used as a biotechnological tool for RNA analysis. In this study, a sensitive and selective system for the detection of s(4)U was developed using biotin-coupled MTSEA biotin-XX. The system can analyze multiple samples in a short time span and can also be used to visualize newly transcribed tRNAs.
Review
Microbiology
Hiroyuki Hori, Takuya Kawamura, Takako Awai, Anna Ochi, Ryota Yamagami, Chie Tomikawa, Akira Hirata