Article
Biotechnology & Applied Microbiology
Morghan C. Lucas, Leszek P. Pryszcz, Rebeca Medina, Ivan Milenkovic, Noelia Camacho, Virginie Marchand, Yuri Motorin, Lluis Ribas de Pouplana, Eva Maria Novoa
Summary: Nano-tRNAseq is a nanopore-based method that allows for simultaneous quantification of tRNA abundance and chemical modifications, providing a new tool for studying tRNA. Re-processing of raw nanopore current intensity signals leads to more accurate tRNA abundance information. Nano-tRNAseq can reveal changes in tRNA populations in response to oxidative stress.
NATURE BIOTECHNOLOGY
(2023)
Article
Microbiology
Maxime Fages-Lartaud, Martin Frank Hohmann-Marriott
Summary: The compact translation machinery of chloroplasts makes them a promising platform for biotechnological innovation. In this study, we synthesize all available information on tRNA modifications in chloroplasts and assess translation efficiency for each modified anticodon-codon pair. We also analyze the enzymes associated with tRNA modifications and aminoacylation in Chlamydomonas reinhardtii chloroplasts. This work provides a comprehensive analysis of codon and anticodon interactions in chloroplasts and their implications for translation efficiency.
Article
Multidisciplinary Sciences
Sophie Martin, Kevin C. Allan, Otis Pinkard, Thomas Sweet, Paul J. Tesar, Jeff Coller
Summary: Mutations in tRNA processing factors can result in myelin disorders, particularly in oligodendrocytes. This study investigates the differences in tRNA modifications and mRNA decay between differentiated oligodendrocytes and precursor cells. The findings suggest that tRNA biology may play a crucial role in oligodendrocyte function, and disruptions in tRNA metabolism can contribute to leukodystrophies and white matter disease.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Liang Cui, Seetharamsing Balamkundu, Chuan-Fa Liu, Hong Ye, Jacob Hourihan, Astrid Rausch, Christopher Hauss, Emelie Nilsson, Matthias Hoetzinger, Karin Holmfeldt, Weijia Zhang, Laura Martinez-Alvarez, Xu Peng, Denise Tremblay, Sylvain Moinau, Natalie Solonenko, Matthew B. Sullivan, Yan-Jiun Lee, Andrew Mulholland, Peter R. Weigele, Valerie de Crecy-Lagard, Peter C. Dedon, Geoffrey Hutinet
Summary: Bacteriophages and bacteria constantly evolve new molecular tools in their arms race, and this study identifies various modifications of 7-deazaguanines and their related enzymes.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Huanping Guo, Lin Xia, Wei Wang, Wei Xu, Xipeng Shen, Xiao Wu, Tong He, Xuelin Jiang, Yinying Xu, Pan Zhao, Dongmei Tan, Xi Zhang, Yunfang Zhang
Summary: This study explores the tissue-specific distribution pattern of RNA modifications in mouse tissues under hypobaric hypoxia exposure. The abundance of RNA modifications is found to be tissue-specific and responsive to hypoxia exposure. Dysregulation of tRNA modifications under hypoxia attenuates cell proliferation rate and affects overall protein synthesis.
Article
Multidisciplinary Sciences
Roni Rak, Michal Polonsky, Inbal Eizenberg-Magar, Yufeng Mo, Yuriko Sakaguchi, Orel Mizrahi, Aharon Nachshon, Shlomit Reich-Zeliger, Noam Stern-Ginossar, Orna Dahan, Tsutomu Suzuki, Nir Friedman, Yitzhak Pilpel
Summary: The study revealed dynamic changes in tRNA and mRNA pools during T cell proliferation and differentiation. Reduction in specific tRNA modifications may lead to ribosomal frameshifting during T cell proliferation, potentially facilitating viral infection.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Cell Biology
Tsutomu Suzuki
Summary: tRNAs undergo heavy post-transcriptional modifications, which play crucial roles in accurate codon recognition and reading frame maintenance during protein synthesis. Recent studies have shown that tRNA modifications can be dynamically altered in response to cellular and environmental stresses, and deficiencies in tRNA modification can lead to mitochondrial diseases, neurological disorders, and cancer.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Valerie de Crecy-Lagard, Marshall Jaroch
Summary: Modified nucleotides in tRNA play a critical role in bacterial physiology, although their importance in translational regulation was previously overlooked. Recent breakthroughs in identifying tRNA modification genes and improving analytical tools have shed light on the key role of tRNA modifications in bacterial regulation. Through their decoding functions in translation and their link to metabolism, tRNA modifications are emerging as important components of the bacterial regulatory toolbox.
TRENDS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Christopher D. Katanski, Christopher P. Watkins, Wen Zhang, Matthew Reyer, Samuel Miller, Tao Pan
Summary: Queuosine (Q) is a tRNA modification that plays important roles in translation efficiency and fidelity. By using a method called periodate-treatment, Q modification in RNA samples can be analyzed at single base resolution. This method also enables the detection of other modifications. This method, called PAQS-seq, is widely applicable in studying the roles of Q and other modifications in mammalian and microbial tRNAs.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biochemistry & Molecular Biology
Weifang Cui, Deze Zhao, Junjie Jiang, Faqing Tang, Chunfang Zhang, Chaojun Duan
Summary: tRNA is a highly conserved and abundant RNA species that plays a crucial role in protein translation. tRNA molecules undergo post-transcriptional modifications by tRNA modifying enzymes. With the rapid development of high-throughput sequencing technology, various types of tRNA modifications have been discovered in different research fields. In this review, we discuss the biological functions of tRNA modifications, including tRNA stability, protein translation, cell cycle regulation, oxidative stress response, and immunity. We also explore the implications of tRNA modifications in human diseases. Additionally, we review emerging techniques for the detection and characterization of tRNA modifications.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Lu Wang, Shuibin Lin
Summary: tRNAs are crucial regulators in mRNA translation by recognizing mRNA codons and bridging amino acids. These modified tRNAs form complex secondary structures that facilitate codon recognition and mRNA translation. Recent studies have highlighted the regulatory roles of tRNA modifications in mRNA translation networks, which are closely associated with developmental diseases and cancer progression.
JOURNAL OF GENETICS AND GENOMICS
(2023)
Article
Biochemistry & Molecular Biology
Hua Huang, Huan Li, Ruining Pan, Sijia Wang, Xinhui Liu
Summary: The discovery of m6A has led to increasing interest in RNA epitranscriptomics. tRNAs play a crucial role in cellular function and their abnormal modifications can lead to diseases. Changes in tRNA modifications are associated with human cancers, including pancreatic cancer, suggesting potential therapeutic targets.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2021)
Review
Cell Biology
Ye Wang, En-Wei Tao, Juan Tan, Qin-Yan Gao, Ying-Xuan Chen, Jing-Yuan Fang
Summary: Transfer RNA (tRNA) plays a crucial role in translation and its heavily modified status greatly impacts its function. This review focuses on six different tRNA modifications and discusses their roles and mechanisms in tumorigenesis and tumor progression, providing insights into their clinical potential as biomarkers and therapeutic targets.
TRENDS IN CELL BIOLOGY
(2023)
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
Biotechnology & Applied Microbiology
Ian C. C. Nova, Justas Ritmejeris, Henry Brinkerhoff, Theo J. R. Koenig, Jens H. H. Gundlach, Cees Dekker
Summary: Drawing peptides through a nanopore allows for the detection of individual phosphorylation sites; Current methods cannot measure single molecules or differentiate between closely spaced phosphorylation sites; We can detect cancer-associated post-translational modifications at the single-molecule level by controlling the peptide's movement through a nanopore; With individual reads of single molecules, we can discriminate peptide sequences with one or two closely spaced phosphates with 95% accuracy.
NATURE BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Leticia Pollo-Oliveira, Roland Klassen, Nick Davis, Akif Ciftci, Jo Marie Bacusmo, Maria Martinelli, Michael S. DeMott, Thomas J. Begley, Peter C. Dedon, Raffael Schaffrath, Valerie de Crecy-Lagard
Article
Biochemistry & Molecular Biology
Pascal Sirand-Pugnet, Damien Bregeon, Laure Beven, Catherine Goyenvalle, Alain Blanchard, Simon Rose, Henri Grosjean, Stephen Douthwaite, Djemel Hamdane, Valerie De Crecy-Lagard
Article
Biochemistry & Molecular Biology
Janani Prahlad, Yifeng Yuan, Jiusheng Lin, Chou-Wei Chang, Dirk Iwata-Reuyl, Yilun Liu, Valerie de Crecy-Lagard, Mark A. Wilson
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Ecology
Tatyana Zamkovaya, Jamie S. Foster, Valerie de Crecy-Lagard, Ana Conesa
Summary: Microbial dark matter, consisting of unknown microbes, plays essential ecological roles and occupies top hubs within their communities. Excluding unknown taxa results in a reduction in network centrality measures, highlighting the importance of these unknown organisms.
Article
Biochemistry & Molecular Biology
Monika Simoliuniene, Emilija Zukauskiene, Lidija Truncaite, Liang Cui, Geoffrey Hutinet, Darius Kazlauskas, Algirdas Kaupinis, Martynas Skapas, Valerie de Crecy-Lagard, Peter C. Dedon, Mindaugas Valius, Rolandas Meskys, Eugenijus Simoliunas
Summary: A novel siphovirus, MED16, was isolated and characterized, revealing 73 ORFs with 26 encoding unique proteins. Phylogenetic analysis placed MED16 in a new genus with siphovirus morphology. The study provides new insights into Pantoea-infecting viruses and diversity of DNA modifications in bacteriophages.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Colbie J. Reed, Geoffrey Hutinet, Valerie de Crecy-Lagard
Summary: Members of the DUF34 family, also known as the NIF3 protein superfamily, have been widely annotated as GTP cyclohydrolase I type 2, but new research suggests they may serve as metal ion insertases, chaperones, or metallocofactor maturases. This diverse molecular function could explain their involvement in pathways such as cell differentiation, metal ion homeostasis, pathogen virulence, redox, and universal stress responses.
Article
Biochemistry & Molecular Biology
Qiang Li, Remi Zallot, Brian S. MacTavish, Alvaro Montoya, Daniel J. Payan, You Hu, John A. Gerlt, Alexander Angerhofer, Valerie De Crecy-Lagard, Steven D. Bruner
Summary: This study reveals the final step of queuosine biosynthesis and demonstrates new diversity in the chemistry of iron/sulfur-dependent enzymes, providing novel insights into the mechanism of these widely conserved tRNA modifications.
Article
Biochemistry & Molecular Biology
Damien Bregeon, Ludovic Pecqueur, Sabrine Toubdji, Claudia Sudol, Murielle Lombard, Marc Fontecave, Valerie de Crecy-Lagard, Yuri Motorin, Mark Helm, Djemel Hamdane
Summary: Recent studies have revealed that RNA molecules undergo post-transcriptional modifications, including dihydrouridine modifications that were originally believed to be specific to tRNA. These modifications have been found not only in tRNA but also in mRNA, and they play important roles in meiotic chromosome segregation, protein translation rates, and cell proliferation. Dihydrouridine modifications are introduced by dihydrouridine synthases.
ACS CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Shr-Hau Hung, Gregory Elliott, Thakku R. Ramkumar, Lyubomyr Burtnyak, Callum J. McGrenaghan, Sana Alkuzweny, Samia Quaiyum, Dirk Iwata-Reuyl, Xiaobei Pan, Brian D. Green, Vincent P. Kelly, Valerie De Crecy-Lagard, Manal A. Swairjo
Summary: Eukaryotic life relies on bacteria for the biosynthesis and supply of vitamins and micronutrients, including the micronutrient queuosine. The hydrolase enzyme QNG1 plays a crucial role in releasing queuine from queuosine-5'-monophosphate, which is essential for various physiological processes associated with queuine deficiency, such as metabolism, proliferation, differentiation, and cancer progression.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Genetics & Heredity
Remi Denise, Jill Babor, John A. Gerlt, Valerie de Crecy-Lagard
Summary: Using a comparative genomic approach, the synthesis and salvage pathways of PLP were predicted in 5840 bacterial and archaeal species. It was found that many organisms lack key genes involved in PLP synthesis pathways, and further research is needed to identify potential transporters. This work provides a starting point for modeling the exchanges of B6 vitamers, predicting sensitivity to drugs targeting PLP synthesis enzymes, and addressing gaps in knowledge.
MICROBIAL GENOMICS
(2023)
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
Microbiology
Jill Babor, Angela Tramonti, Caterina Nardella, Adam Deutschbauer, Roberto Contestabile, Valerie de Crecy-Legard
Summary: Through exploring different conditions affecting PLP metabolism in E. coli K12, we discovered that 4dPN cannot be used as a source of vitamin B6 and exhibits toxicity in various conditions where B6 vitamin homeostasis is disrupted. The toxicity of 4dPN is likely due to the inhibition of PLP-dependent enzyme activity by 4'-deoxypyridoxine phosphate and interference with pyridoxine uptake. These toxic effects are dependent on the phosphorylation of 4dPN by pyridoxal kinase.
Article
Biochemistry & Molecular Biology
Samanthi Herath Gedara, Evan Wood, Andrew Gustafson, Cui Liang, Shr-Hau Hung, Joshua Savage, Phuc Phan, Amit Luthra, Valerie de Crecy-Lagard, Peter Dedon, Manal A. Swairjo, Dirk Iwata-Reuyl
Summary: This study reports the discovery of modified nucleosides in DNA and their association with the bacterial queuosine tRNA modification pathway and the dpd gene cluster. The roles and structures of each protein involved in this pathway are elucidated through in vitro reconstitution and X-ray crystallography. Unexpected activities in DpdA and DpdB are identified, including ATPase activity in DpdB and catalytically essential residues in DpdA. Additionally, the independent function of DpdC in DNA modification is demonstrated.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Liang Cui, Seetharamsing Balamkundu, Chuan-Fa Liu, Hong Ye, Jacob Hourihan, Astrid Rausch, Christopher Hauss, Emelie Nilsson, Matthias Hoetzinger, Karin Holmfeldt, Weijia Zhang, Laura Martinez-Alvarez, Xu Peng, Denise Tremblay, Sylvain Moinau, Natalie Solonenko, Matthew B. Sullivan, Yan-Jiun Lee, Andrew Mulholland, Peter R. Weigele, Valerie de Crecy-Lagard, Peter C. Dedon, Geoffrey Hutinet
Summary: Bacteriophages and bacteria constantly evolve new molecular tools in their arms race, and this study identifies various modifications of 7-deazaguanines and their related enzymes.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Mathematical & Computational Biology
Valerie de Crecy-Lagard, Rocio Amorin de Hegedus, Cecilia Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan J. Bridge, Stephen K. Burley, Stacey Cleveland, Lucy J. Colwell, Ana Conesa, Christian Dallago, Antoine Danchin, Anita de Waard, Adam Deutschbauer, Raquel Dias, Yousong Ding, Gang Fang, Iddo Friedberg, John Gerlt, Joshua Goldford, Mark Gorelik, Benjamin M. Gyori, Christopher Henry, Geoffrey Hutinet, Marshall Jaroch, Peter D. Karp, Liudmyla Kondratova, Zhiyong Lu, Aron Marchler-Bauer, Maria-Jesus Martin, Claire McWhite, Gaurav D. Moghe, Paul Monaghan, Anne Morgat, Christopher J. Mungall, Darren A. Natale, William C. Nelson, Sean O'Donoghue, Christine Orengo, Katherine H. O'Toole, Predrag Radivojac, Colbie Reed, Richard J. Roberts, Dmitri Rodionov, Irina A. Rodionova, Jeffrey D. Rudolf, Lana Saleh, Gloria Sheynkman, Francoise Thibaud-Nissen, Paul D. Thomas, Peter Uetz, David Vallenet, Erica Watson Carter, Peter R. Weigele, Valerie Wood, Elisha M. Wood-Charlson, Jin Xu
Summary: In the past 25 years, biology has entered the genomic era and has become a science of 'big data'. However, accurate functional annotations of the proteins encoded by sequenced genomes are lacking, with only about half of the predicted proteins having accurate annotations. This gap in knowledge hampers the progress of biological research. To address this issue, a brainstorming meeting funded by the National Science Foundation was held in February 2022, bringing together data scientists, biocurators, computational biologists, and experimentalists to comprehensively assess the current state of functional annotations of protein families and propose solutions to move forward.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2022)
