51
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Zhang Y, Wang C. Demethyltransferase AlkBH1 substrate diversity and relationship to human diseases. Mol Biol Rep 2021; 48:4747-4756. [PMID: 34046849 DOI: 10.1007/s11033-021-06421-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/17/2021] [Indexed: 12/22/2022]
Abstract
AlkBH1 is a member of the AlkB superfamily which are kinds of Fe (II) and α-ketoglutarate (α-KG)-dependent dioxygenases. At present, only demethyltransferases FTO and AlkBH5 have relatively clear substrate studies among these members, the types and mechanisms of substrates catalysis of other members are not clear, especially the demethyltransferase AlkBH1. AlkBH1, as a demethylase, has important functions of reversing DNA methylation and repairing DNA damage. And it has become a promising target for the treatment of many cancers, the regulation of neurological and genetic related diseases. Many scholars have made important discoveries in the diversity of AlkBH1 substrates, but there is no comprehensive summary, which affects the design inhibitor target of AlkBH1. Herein, We are absorbed in the latest progress in the study of AlkBH1 substrate diversity and its relationship with human diseases. Besides, we also discuss future research directions and suggest other studies to reveal the specific catalytic effect of AlkBH1 on cancer substrates.
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Affiliation(s)
- Ying Zhang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, China
| | - Caiyan Wang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006, Guangdong, China.
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52
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Graille M. Division of labor in epitranscriptomics: What have we learnt from the structures of eukaryotic and viral multimeric RNA methyltransferases? WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1673. [PMID: 34044474 DOI: 10.1002/wrna.1673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 02/06/2023]
Abstract
The translation of an mRNA template into the corresponding protein is a highly complex and regulated choreography performed by ribosomes, tRNAs, and translation factors. Most RNAs involved in this process are decorated by multiple chemical modifications (known as epitranscriptomic marks) contributing to the efficiency, the fidelity, and the regulation of the mRNA translation process. Many of these epitranscriptomic marks are written by holoenzymes made of a catalytic subunit associated with an activating subunit. These holoenzymes play critical roles in cell development. Indeed, several mutations being identified in the genes encoding for those proteins are linked to human pathologies such as cancers and intellectual disorders for instance. This review describes the structural and functional properties of RNA methyltransferase holoenzymes, which when mutated often result in brain development pathologies. It illustrates how structurally different activating subunits contribute to the catalytic activity of these holoenzymes through common mechanistic trends that most likely apply to other classes of holoenzymes. This article is categorized under: RNA Processing > RNA Editing and Modification RNA Processing > Capping and 5' End Modifications.
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Affiliation(s)
- Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole Polytechnique, IP Paris, Palaiseau Cedex, France
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53
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Chao Y, Li HB, Zhou J. Multiple Functions of RNA Methylation in T Cells: A Review. Front Immunol 2021; 12:627455. [PMID: 33912158 PMCID: PMC8071866 DOI: 10.3389/fimmu.2021.627455] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/22/2021] [Indexed: 01/10/2023] Open
Abstract
RNA modification represents one of the most ubiquitous mechanisms of epigenetic regulation and plays an essential role in modulating cell proliferation, differentiation, fate determination, and other biological activities. At present, over 170 types of RNA modification have been discovered in messenger RNA (mRNA) and noncoding RNA (ncRNA). RNA methylation, as an abundant and widely studied epigenetic modification, is crucial for regulating various physiological or pathological states, especially immune responses. Considering the biological significance of T cells as a defense against viral infection and tumor challenge, in this review, we will summarize recent findings of how RNA methylation regulates T cell homeostasis and function, discuss the open questions in this rapidly expanding field of RNA modification, and provide the theoretical basis and potential therapeutic strategies involving targeting of RNA methylation to orchestrate beneficial T cell immune responses.
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Affiliation(s)
- Yinong Chao
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine - Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hua-Bing Li
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine - Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Zhou
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Jiao Tong University School of Medicine - Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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54
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Alriquet M, Calloni G, Martínez-Limón A, Delli Ponti R, Hanspach G, Hengesbach M, Tartaglia GG, Vabulas RM. The protective role of m1A during stress-induced granulation. J Mol Cell Biol 2021; 12:870-880. [PMID: 32462207 PMCID: PMC7883823 DOI: 10.1093/jmcb/mjaa023] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 05/21/2020] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional methylation of N6-adenine and N1-adenine can affect transcriptome turnover and translation. Furthermore, the regulatory function of N6-methyladenine (m6A) during heat shock has been uncovered, including the enhancement of the phase separation potential of RNAs. In response to acute stress, e.g. heat shock, the orderly sequestration of mRNAs in stress granules (SGs) is considered important to protect transcripts from the irreversible aggregation. Until recently, the role of N1-methyladenine (m1A) on mRNAs during acute stress response remains largely unknown. Here we show that the methyltransferase complex TRMT6/61A, which generates the m1A tag, is involved in transcriptome protection during heat shock. Our bioinformatics analysis indicates that occurrence of the m1A motif is increased in mRNAs known to be enriched in SGs. Accordingly, the m1A-generating methyltransferase TRMT6/61A accumulated in SGs and mass spectrometry confirmed enrichment of m1A in the SG RNAs. The insertion of a single methylation motif in the untranslated region of a reporter RNA leads to more efficient recovery of protein synthesis from that transcript after the return to normal temperature. Our results demonstrate far-reaching functional consequences of a minimal RNA modification on N1-adenine during acute proteostasis stress.
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Affiliation(s)
- Marion Alriquet
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Giulia Calloni
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Adrían Martínez-Limón
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Riccardo Delli Ponti
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Gerd Hanspach
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Gian G. Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- Department of Biology ‘Charles Darwin’, Sapienza University of Rome, 00185 Rome, Italy
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, 16163 Genoa, Italy
| | - R. Martin Vabulas
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
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55
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Yan TM, Pan Y, Yu ML, Hu K, Cao KY, Jiang ZH. Full-Range Profiling of tRNA Modifications Using LC-MS/MS at Single-Base Resolution through a Site-Specific Cleavage Strategy. Anal Chem 2021; 93:1423-1432. [PMID: 33382261 DOI: 10.1021/acs.analchem.0c03307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Transfer RNAs (tRNAs) are the most heavily modified RNA species. Liquid chromatography coupled with mass spectrometry (LC-MS/MS) is a powerful tool for characterizing tRNA modifications, which involves pretreating tRNAs with base-specific ribonucleases to produce smaller oligonucleotides amenable to MS. However, the quality and quantity of products from base-specific digestions are severely impacted by the base composition of tRNAs. This often leads to a loss of sequence information. Here, we report a method for the full-range profiling of tRNA modifications at single-base resolution by combining site-specific RNase H digestion with the LC-MS/MS and RNA-seq techniques. The key steps were designed to generate high-quality products of optimal lengths and ionization properties. A linear correlation between collision energies and the m/z of oligonucleotides significantly improved the information content of collision-induced dissociation (CID) spectra. False positives were eliminated by up to 95% using novel inclusion criteria for collecting a census of modifications. This method is illustrated by the mapping of mouse mitochondrial tRNAHis(GUG) and tRNAVal(UAC), which were hitherto not investigated. The identities and locations of the five species of modifications on these tRNAs were fully characterized. This approach is universally applicable to any tRNA species and provides an experimentally realizable pathway to the de novo sequencing of post-transcriptionally modified tRNAs with high sequence coverage.
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Affiliation(s)
- Tong-Meng Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Yu Pan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Meng-Lan Yu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Kua Hu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Kai-Yue Cao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Zhi-Hong Jiang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
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56
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Post-Transcriptional Modifications of Conserved Nucleotides in the T-Loop of tRNA: A Tale of Functional Convergent Evolution. Genes (Basel) 2021; 12:genes12020140. [PMID: 33499018 PMCID: PMC7912444 DOI: 10.3390/genes12020140] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/30/2022] Open
Abstract
The high conservation of nucleotides of the T-loop, including their chemical identity, are hallmarks of tRNAs from organisms belonging to the three Domains of Life. These structural characteristics allow the T-loop to adopt a peculiar intraloop conformation able to interact specifically with other conserved residues of the D-loop, which ultimately folds the mature tRNA in a unique functional canonical L-shaped architecture. Paradoxically, despite the high conservation of modified nucleotides in the T-loop, enzymes catalyzing their formation depend mostly on the considered organism, attesting for an independent but convergent evolution of the post-transcriptional modification processes. The driving force behind this is the preservation of a native conformation of the tRNA elbow that underlies the various interactions of tRNA molecules with different cellular components.
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57
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Tian S, Lai J, Yu T, Li Q, Chen Q. Regulation of Gene Expression Associated With the N6-Methyladenosine (m6A) Enzyme System and Its Significance in Cancer. Front Oncol 2021; 10:623634. [PMID: 33552994 PMCID: PMC7859513 DOI: 10.3389/fonc.2020.623634] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/04/2020] [Indexed: 01/19/2023] Open
Abstract
N6-methyladenosine (m6A), an important RNA modification, is a reversible behavior catalyzed by methyltransferase complexes (m6A "writers"), demethylated transferases (m6A "erasers"), and binding proteins (m6A "readers"). It plays a vital regulatory role in biological functions, involving in a variety of physiological and pathological processes. The level of m6A will affect the RNA metabolism including the degradation of mRNA, and processing or translation of the modified RNA. Its abnormal changes will lead to disrupting the regulation of gene expression and promoting the occurrence of aberrant cell behavior. The abnormal expression of m6A enzyme system can be a crucial impact disturbing the abundance of m6A, thus affecting the expression of oncogenes or tumor suppressor genes in various types of cancer. In this review, we elucidate the special role of m6A "writers", "erasers", and "readers" in normal physiology, and how their altered expression affects the cell metabolism and promotes the occurrence of tumors. We also discuss the potential to target these enzymes for cancer diagnosis, prognosis, and the development of new therapies.
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Affiliation(s)
- Shuoran Tian
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Junzhong Lai
- The Cancer Center, Union Hospital, Fujian Medical University, Fuzhou, China
| | - Tingting Yu
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Qiumei Li
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
| | - Qi Chen
- Fujian Key Laboratory of Innate Immune Biology, Biomedical Research Center of South China, College of Life Science, Fujian Normal University, Fuzhou, China
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58
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Li J, Zhang C, Yuan X, Cao Y. Molecular Characteristics of N1-Methyladenosine Regulators and Their Correlation with Overall Cancer Survival. DNA Cell Biol 2021; 40:513-522. [PMID: 33416433 DOI: 10.1089/dna.2020.6214] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
N1-methyladenosine (m1A) is a prevalent RNA modification widely affecting RNA structural stability, folding, and interactions with proteins. Recently, there have been increasing reports on the roles of m1A regulators in tumors. However, their mechanisms and clinical relevance remain unclear. This study systematically evaluates the epigenetic characteristics and clinical relevance of m1A regulators using bioinformatic methods. Our results show widespread gene expression changes for m1A regulators, which are related to the activation and inhibition of carcinogenic pathways and overall patient survival. Collectively, this investigation provides new insights into assessing tumor prognosis and targeted therapy.
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Affiliation(s)
- Juan Li
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China.,Department of Infectious Diseases and The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Chunting Zhang
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China.,Department of Infectious Diseases and The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Xin Yuan
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China.,Department of Infectious Diseases and The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Yuan Cao
- Department of Gynaecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
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59
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Shima H, Igarashi K. N 1-methyladenosine (m1A) RNA modification: the key to ribosome control. J Biochem 2021; 167:535-539. [PMID: 32129871 DOI: 10.1093/jb/mvaa026] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 02/20/2020] [Indexed: 11/14/2022] Open
Abstract
RNA displays diverse functions in living cells. The presence of various chemical modifications of RNA mediated by enzymes is one of the factors that impart such functional diversity to RNA. Among more than 100 types of RNA modification, N1-methyladenosine (m1A) is found mainly in tRNA and rRNA of many living organisms and is known to be deeply implicated in the topology or function of the two classes of RNA. In this commentary article, we would like to deal with the functional significance of m1A in RNA, and also to describe one methyltransferase installing m1A in a large subunit rRNA, whose orthologue in Caenorhabditis elegans was discovered recently and was reported in this journal.
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Affiliation(s)
- Hiroki Shima
- Department of Biochemistry, Tohoku University Graduate School of Medicine.,Regulatory Epigenome, Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, Miyagi 980-8575, Japan
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine.,Regulatory Epigenome, Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai, Miyagi 980-8575, Japan
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60
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Xiang S, Ma Y, Shen J, Zhao Y, Wu X, Li M, Yang X, Kaboli PJ, Du F, Ji H, Zheng Y, Li X, Li J, Wen Q, Xiao Z. m 5C RNA Methylation Primarily Affects the ErbB and PI3K-Akt Signaling Pathways in Gastrointestinal Cancer. Front Mol Biosci 2020; 7:599340. [PMID: 33365328 PMCID: PMC7750483 DOI: 10.3389/fmolb.2020.599340] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/28/2020] [Indexed: 12/22/2022] Open
Abstract
5-Methylcytosine (m5C) is a kind of methylation modification that occurs in both DNA and RNA and is present in the highly abundant tRNA and rRNA. It has an important impact on various human diseases including cancer. The function of m5C is modulated by regulatory proteins, including methyltransferases (writers) and special binding proteins (readers). This study aims at comprehensive study of the m5C RNA methylation-related genes and the main pathways under m5C RNA methylation in gastrointestinal (GI) cancer. Our result showed that the expression of m5C writers and reader was mostly up-regulated in GI cancer. The NSUN2 gene has the highest proportion of mutations found in GI cancer. Importantly, in liver cancer, higher expression of almost all m5C regulators was significantly associated with lower patient survival rate. In addition, the expression level of m5C-related genes is significantly different at various pathological stages. Finally, we have found through bioinformatics analysis that m5C regulatory proteins are closely related to the ErbB/PI3K–Akt signaling pathway and GSK3B was an important target for m5C regulators. Besides, the compound termed streptozotocin may be a key candidate drug targeting on GSK3B for molecular targeted therapy in GI cancer.
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Affiliation(s)
- Shixin Xiang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Yongshun Ma
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Xiao Yang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Parham Jabbarzadeh Kaboli
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Huijiao Ji
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Yuan Zheng
- Neijiang Health and Health Vocational College, Neijiang, China
| | - Xiang Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Jing Li
- Department of Oncology and Hematology, Hospital (T.C.M.) Affiliated to Southwest Medical University, Luzhou, China
| | - Qinglian Wen
- Department of Oncology, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
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61
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Scheitl CPM, Ghaem Maghami M, Lenz AK, Höbartner C. Site-specific RNA methylation by a methyltransferase ribozyme. Nature 2020; 587:663-667. [PMID: 33116304 PMCID: PMC7116789 DOI: 10.1038/s41586-020-2854-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 07/27/2020] [Indexed: 12/21/2022]
Abstract
Nearly all classes of coding and non-coding RNA undergo post-transcriptional modification, including RNA methylation. Methylated nucleotides are among the evolutionarily most-conserved features of transfer (t)RNA and ribosomal (r)RNA1,2. Many contemporary methyltransferases use the universal cofactor S-adenosylmethionine (SAM) as a methyl-group donor. SAM and other nucleotide-derived cofactors are considered to be evolutionary leftovers from an RNA world, in which ribozymes may have catalysed essential metabolic reactions beyond self-replication3. Chemically diverse ribozymes seem to have been lost in nature, but may be reconstructed in the laboratory by in vitro selection. Here we report a methyltransferase ribozyme that catalyses the site-specific installation of 1-methyladenosine in a substrate RNA, using O6-methylguanine as a small-molecule cofactor. The ribozyme shows a broad RNA-sequence scope, as exemplified by site-specific adenosine methylation in various RNAs. This finding provides fundamental insights into the catalytic abilities of RNA, serves a synthetic tool to install 1-methyladenosine in RNA and may pave the way to in vitro evolution of other methyltransferase and demethylase ribozymes.
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Affiliation(s)
- Carolin P M Scheitl
- Institut für Organische Chemie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Mohammad Ghaem Maghami
- Institut für Organische Chemie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Ann-Kathrin Lenz
- Institut für Organische Chemie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Claudia Höbartner
- Institut für Organische Chemie, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
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62
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RNA methylations in human cancers. Semin Cancer Biol 2020; 75:97-115. [DOI: 10.1016/j.semcancer.2020.11.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/23/2020] [Accepted: 11/08/2020] [Indexed: 12/24/2022]
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63
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Huong TT, Ngoc LNT, Kang H. Functional Characterization of a Putative RNA Demethylase ALKBH6 in Arabidopsis Growth and Abiotic Stress Responses. Int J Mol Sci 2020; 21:ijms21186707. [PMID: 32933187 PMCID: PMC7555452 DOI: 10.3390/ijms21186707] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/11/2020] [Accepted: 09/11/2020] [Indexed: 12/15/2022] Open
Abstract
RNA methylation and demethylation, which is mediated by RNA methyltransferases (referred to as “writers”) and demethylases (referred to as “erasers”), respectively, are emerging as a key regulatory process in plant development and stress responses. Although several studies have shown that AlkB homolog (ALKBH) proteins are potential RNA demethylases, the function of most ALKBHs is yet to be determined. The Arabidopsis thaliana genome contains thirteen genes encoding ALKBH proteins, the functions of which are largely unknown. In this study, we characterized the function of a potential eraser protein, ALKBH6 (At4g20350), during seed germination and seedling growth in Arabidopsis under abiotic stresses. The seeds of T-DNA insertion alkbh6 knockdown mutants germinated faster than the wild-type seeds under cold, salt, or abscisic acid (ABA) treatment conditions but not under dehydration stress conditions. Although no differences in seedling and root growth were observed between the alkbh6 mutant and wild-type under normal conditions, the alkbh6 mutant showed a much lower survival rate than the wild-type under salt, drought, or heat stress. Cotyledon greening of the alkbh6 mutants was much higher than that of the wild-type upon ABA application. Moreover, the transcript levels of ABA signaling-related genes, including ABI3 and ABI4, were down-regulated in the alkbh6 mutant compared to wild-type plants. Importantly, the ALKBH6 protein had an ability to bind to both m6A-labeled and m5C-labeled RNAs. Collectively, these results indicate that the potential eraser ALKBH6 plays important roles in seed germination, seedling growth, and survival of Arabidopsis under abiotic stresses.
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Affiliation(s)
- Trinh Thi Huong
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea; (T.T.H.); (L.N.T.N.)
- The Western Highlands Agriculture and Forestry Science Institute, Buon Ma Thuot, DakLak 63000, Vietnam
| | - Le Nguyen Tieu Ngoc
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea; (T.T.H.); (L.N.T.N.)
- Faculty of Forestry Agriculture, Tay Nguyen University, Buon Ma Thuot, DakLak 63000, Vietnam
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea; (T.T.H.); (L.N.T.N.)
- Correspondence: ; Tel.: +82-(62)-530-2181
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64
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Rashad S, Han X, Sato K, Mishima E, Abe T, Tominaga T, Niizuma K. The stress specific impact of ALKBH1 on tRNA cleavage and tiRNA generation. RNA Biol 2020; 17:1092-1103. [PMID: 32521209 PMCID: PMC7549645 DOI: 10.1080/15476286.2020.1779492] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/19/2020] [Accepted: 05/23/2020] [Indexed: 10/24/2022] Open
Abstract
tiRNAs are small non-coding RNAs produced when tRNA is cleaved under stress. tRNA methylation modifications has emerged in recent years as important regulators for tRNA structural stability and sensitivity to cleavage and tiRNA generation during stress, however, the specificity and higher regulation of such a process is not fully understood. Alkbh1 is a m1A demethylase that leads to destabilization of tRNA and enhanced tRNA cleavage. We examined the impact of Alkbh1 targeting via gene knockdown or overexpression on B35 rat neuroblastoma cell line fate following stresses and on tRNA cleavage. We show that Alkbh1 impact on cell fate and tRNA cleavage is a stress specific process that is impacted by the demethylating capacity of the cellular stress in question. We also show that not all tRNAs are cleaved equally following Alkbh1 manipulation and stress, and that Alkbh1 KD fails to rescue tRNAs from cleavage following demethylating stresses. These findings shed a light on the specificity and higher regulation of tRNA cleavage and should act as a guide for future work exploring the utility of Alkbh1 as a therapeutic target for cancers or ischaemic insult.
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Affiliation(s)
- Sherif Rashad
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Xiaobo Han
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kanako Sato
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Eikan Mishima
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takaaki Abe
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Clinical Biology and Hormonal Regulation, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Medical Science, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan
| | - Teiji Tominaga
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kuniyasu Niizuma
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
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65
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Atdjian C, Coelho D, Iannazzo L, Ethève-Quelquejeu M, Braud E. Synthesis of Triazole-Linked SAM-Adenosine Conjugates: Functionalization of Adenosine at N-1 or N-6 Position without Protecting Groups. Molecules 2020; 25:molecules25143241. [PMID: 32708658 PMCID: PMC7397255 DOI: 10.3390/molecules25143241] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/06/2020] [Accepted: 07/10/2020] [Indexed: 12/17/2022] Open
Abstract
More than 150 RNA chemical modifications have been identified to date. Among them, methylation of adenosine at the N-6 position (m6A) is crucial for RNA metabolism, stability and other important biological events. In particular, this is the most abundant mark found in mRNA in mammalian cells. The presence of a methyl group at the N-1 position of adenosine (m1A) is mostly found in ncRNA and mRNA and is mainly responsible for stability and translation fidelity. These modifications are installed by m6A and m1A RNA methyltransferases (RNA MTases), respectively. In human, deregulation of m6A RNA MTases activity is associated with many diseases including cancer. To date, the molecular mechanism involved in the methyl transfer, in particular substrate recognition, remains unclear. We report the synthesis of new SAM-adenosine conjugates containing a triazole linker branched at the N-1 or N-6 position of adenosine. Our methodology does not require protecting groups for the functionalization of adenosine at these two positions. The molecules described here were designed as potential bisubstrate analogues for m6A and m1A RNA MTases that could be further employed for structural studies. This is the first report of compounds mimicking the transition state of the methylation reaction catalyzed by m1A RNA MTases.
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66
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Mathlin J, Le Pera L, Colombo T. A Census and Categorization Method of Epitranscriptomic Marks. Int J Mol Sci 2020; 21:ijms21134684. [PMID: 32630140 PMCID: PMC7370119 DOI: 10.3390/ijms21134684] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 12/21/2022] Open
Abstract
In the past few years, thorough investigation of chemical modifications operated in the cells on ribonucleic acid (RNA) molecules is gaining momentum. This new field of research has been dubbed “epitranscriptomics”, in analogy to best-known epigenomics, to stress the potential of ensembles of RNA modifications to constitute a post-transcriptional regulatory layer of gene expression orchestrated by writer, reader, and eraser RNA-binding proteins (RBPs). In fact, epitranscriptomics aims at identifying and characterizing all functionally relevant changes involving both non-substitutional chemical modifications and editing events made to the transcriptome. Indeed, several types of RNA modifications that impact gene expression have been reported so far in different species of cellular RNAs, including ribosomal RNAs, transfer RNAs, small nuclear RNAs, messenger RNAs, and long non-coding RNAs. Supporting functional relevance of this largely unknown regulatory mechanism, several human diseases have been associated directly to RNA modifications or to RBPs that may play as effectors of epitranscriptomic marks. However, an exhaustive epitranscriptome’s characterization, aimed to systematically classify all RNA modifications and clarify rules, actors, and outcomes of this promising regulatory code, is currently not available, mainly hampered by lack of suitable detecting technologies. This is an unfortunate limitation that, thanks to an unprecedented pace of technological advancements especially in the sequencing technology field, is likely to be overcome soon. Here, we review the current knowledge on epitranscriptomic marks and propose a categorization method based on the reference ribonucleotide and its rounds of modifications (“stages”) until reaching the given modified form. We believe that this classification scheme can be useful to coherently organize the expanding number of discovered RNA modifications.
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Affiliation(s)
- Julia Mathlin
- Department of Life Sciences and Medicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
- Correspondence: (J.M.); (L.L.P.); Tel.: +39-06-4991-0556 (L.L.P.)
| | - Loredana Le Pera
- CNR-Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), 70126 Bari, Italy
- CNR-Institute of Molecular Biology and Pathology (IBPM), 00185 Rome, Italy;
- Correspondence: (J.M.); (L.L.P.); Tel.: +39-06-4991-0556 (L.L.P.)
| | - Teresa Colombo
- CNR-Institute of Molecular Biology and Pathology (IBPM), 00185 Rome, Italy;
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67
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Ma X, Si F, Liu X, Luan W. PRMdb: A Repository of Predicted RNA Modifications in Plants. PLANT & CELL PHYSIOLOGY 2020; 61:1213-1222. [PMID: 32542382 DOI: 10.1093/pcp/pcaa042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/28/2020] [Indexed: 06/11/2023]
Abstract
Evidence is mounting that RNA modifications play essential roles in posttranscriptional regulation of gene expression. So far, over 150 RNA modifications catalyzed by distinct enzymes have been documented. In plants, genome-wide identification of RNA modifications is largely limited to the model species Arabidopsis thaliana, while lacking in diverse non-model plants. Here, we present PRMdb, a plant RNA modification database, based on the analysis of thousands of RNA-seq, degradome-seq and small RNA-seq data from a wide range of plant species using the well-documented tool HAMR (high-throughput analysis of modified ribonucleotide). PRMdb provides a user-friendly interface that enables easy browsing and searching of the tRNA and mRNA modification data. We show that PRMdb collects high-confidence RNA modifications including novel RNA modification sites that can be validated by genomic PCR and reverse transcription PCR. In summary, PRMdb provides a valuable web resource for deciphering the epitranscriptomes in diverse plant species and will facilitate functional studies of RNA modifications in plants. RPMdb is available via http://www.biosequencing.cn/PRMdb/.
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Affiliation(s)
- Xuan Ma
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin 300387, China
| | - Fuyan Si
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaonan Liu
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin 300387, China
| | - Weijiang Luan
- College of Life Sciences, Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin 300387, China
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68
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Tang J, Jia P, Xin P, Chu J, Shi DQ, Yang WC. The Arabidopsis TRM61/TRM6 complex is a bona fide tRNA N1-methyladenosine methyltransferase. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3024-3036. [PMID: 32095811 PMCID: PMC7475180 DOI: 10.1093/jxb/eraa100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/24/2020] [Indexed: 05/04/2023]
Abstract
tRNA molecules, which contain the most abundant post-transcriptional modifications, are crucial for proper gene expression and protein biosynthesis. Methylation at N1 of adenosine 58 (A58) is critical for maintaining the stability of initiator methionyl-tRNA (tRNAiMet) in bacterial, archaeal, and eukaryotic tRNAs. However, although research has been conducted in yeast and mammals, it remains unclear how A58 in plant tRNAs is modified and involved in development. In this study, we identify the nucleus-localized complex AtTRM61/AtTRM6 in Arabidopsis as tRNA m1A58 methyltransferase. Deficiency or a lack of either AtTRM61 or AtTRM6 leads to embryo arrest and seed abortion. The tRNA m1A level decreases in conditionally complemented Attrm61/LEC1pro::AtTRM61 plants and this is accompanied by reduced levels of tRNAiMet, indicating the importance of the tRNA m1A modification for tRNAiMet stability. Taken together, our results demonstrate that tRNA m1A58 modification is necessary for tRNAiMet stability and is required for embryo development in Arabidopsis.
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Affiliation(s)
- Jun Tang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- The University of Chinese Academy of Sciences, Beijing, China
| | - Pengfei Jia
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Peiyong Xin
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- The University of Chinese Academy of Sciences, Beijing, China
| | - Dong-Qiao Shi
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- The University of Chinese Academy of Sciences, Beijing, China
| | - Wei-Cai Yang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- The University of Chinese Academy of Sciences, Beijing, China
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69
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McCown PJ, Ruszkowska A, Kunkler CN, Breger K, Hulewicz JP, Wang MC, Springer NA, Brown JA. Naturally occurring modified ribonucleosides. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1595. [PMID: 32301288 PMCID: PMC7694415 DOI: 10.1002/wrna.1595] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/18/2022]
Abstract
The chemical identity of RNA molecules beyond the four standard ribonucleosides has fascinated scientists since pseudouridine was characterized as the “fifth” ribonucleotide in 1951. Since then, the ever‐increasing number and complexity of modified ribonucleosides have been found in viruses and throughout all three domains of life. Such modifications can be as simple as methylations, hydroxylations, or thiolations, complex as ring closures, glycosylations, acylations, or aminoacylations, or unusual as the incorporation of selenium. While initially found in transfer and ribosomal RNAs, modifications also exist in messenger RNAs and noncoding RNAs. Modifications have profound cellular outcomes at various levels, such as altering RNA structure or being essential for cell survival or organism viability. The aberrant presence or absence of RNA modifications can lead to human disease, ranging from cancer to various metabolic and developmental illnesses such as Hoyeraal–Hreidarsson syndrome, Bowen–Conradi syndrome, or Williams–Beuren syndrome. In this review article, we summarize the characterization of all 143 currently known modified ribonucleosides by describing their taxonomic distributions, the enzymes that generate the modifications, and any implications in cellular processes, RNA structure, and disease. We also highlight areas of active research, such as specific RNAs that contain a particular type of modification as well as methodologies used to identify novel RNA modifications. This article is categorized under:RNA Processing > RNA Editing and Modification
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Affiliation(s)
- Phillip J McCown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Agnieszka Ruszkowska
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Charlotte N Kunkler
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Kurtis Breger
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jacob P Hulewicz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Matthew C Wang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Noah A Springer
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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70
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Gao C, Wang Y. mRNA Metabolism in Cardiac Development and Disease: Life After Transcription. Physiol Rev 2020; 100:673-694. [PMID: 31751167 PMCID: PMC7327233 DOI: 10.1152/physrev.00007.2019] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 09/06/2019] [Accepted: 10/30/2019] [Indexed: 02/06/2023] Open
Abstract
The central dogma of molecular biology illustrates the importance of mRNAs as critical mediators between genetic information encoded at the DNA level and proteomes/metabolomes that determine the diverse functional outcome at the cellular and organ levels. Although the total number of protein-producing (coding) genes in the mammalian genome is ~20,000, it is evident that the intricate processes of cardiac development and the highly regulated physiological regulation in the normal heart, as well as the complex manifestation of pathological remodeling in a diseased heart, would require a much higher degree of complexity at the transcriptome level and beyond. Indeed, in addition to an extensive regulatory scheme implemented at the level of transcription, the complexity of transcript processing following transcription is dramatically increased. RNA processing includes post-transcriptional modification, alternative splicing, editing and transportation, ribosomal loading, and degradation. While transcriptional control of cardiac genes has been a major focus of investigation in recent decades, a great deal of progress has recently been made in our understanding of how post-transcriptional regulation of mRNA contributes to transcriptome complexity. In this review, we highlight some of the key molecular processes and major players in RNA maturation and post-transcriptional regulation. In addition, we provide an update to the recent progress made in the discovery of RNA processing regulators implicated in cardiac development and disease. While post-transcriptional modulation is a complex and challenging problem to study, recent technological advancements are paving the way for a new era of exciting discoveries and potential clinical translation in the context of cardiac biology and heart disease.
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Affiliation(s)
- Chen Gao
- Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
| | - Yibin Wang
- Departments of Anesthesiology, Medicine, and Physiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California
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71
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Erber L, Hoffmann A, Fallmann J, Betat H, Stadler PF, Mörl M. LOTTE-seq (Long hairpin oligonucleotide based tRNA high-throughput sequencing): specific selection of tRNAs with 3'-CCA end for high-throughput sequencing. RNA Biol 2020; 17:23-32. [PMID: 31486704 PMCID: PMC6948972 DOI: 10.1080/15476286.2019.1664250] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/29/2019] [Accepted: 08/31/2019] [Indexed: 02/07/2023] Open
Abstract
Transfer RNAs belong to the most abundant type of ribonucleic acid in the cell, and detailed investigations revealed correlations between alterations in the tRNA pool composition and certain diseases like breast cancer. However, currently available methods do not sample the entire tRNA pool or lack specificity for tRNAs. A specific disadvantage of such methods is that only full-length tRNAs are analysed, while tRNA fragments or incomplete cDNAs due to RT stops at modified nucleosides are lost. Another drawback in certain approaches is that the tRNA fraction has to be isolated and separated from high molecular weight RNA, resulting in considerable labour costs and loss of material. Based on a hairpin-shaped adapter oligonucleotide selective for tRNA transcripts, we developed a highly specific protocol for efficient and comprehensive high-throughput analysis of tRNAs that combines the benefits of existing methods and eliminates their disadvantages. Due to a 3'-TGG overhang, the adapter is specifically ligated to the tRNA 3'-CCA end. Reverse transcription prior to the ligation of a second adapter allows to include prematurely terminated cDNA products, increasing the number of tRNA reads. This strategy renders this approach a powerful and universal tool to analyse the tRNA pool of cells and organisms under different conditions in health and disease.
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Affiliation(s)
- Lieselotte Erber
- Institute for Biochemistry, Leipzig University, Leipzig, Germany
| | - Anne Hoffmann
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
| | - Heike Betat
- Institute for Biochemistry, Leipzig University, Leipzig, Germany
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
- Facultad de Ciencias, Universidad Nacional de Colombia, Sede Botoga, Colombia
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
- Department of Theoretical Chemistry of the University of Vienna, Vienna, Austria
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Leipzig, Germany
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72
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Abstract
Over the past decades, tRNA was found to be a rich hub of RNA modifications such as 1-methyladenosine and 5-methycytosine modifications and others, holding more than half of all modifications occurring in RNA molecules. Moreover, tRNA was discovered to be a source of various small noncoding RNA species, such as the stress induced angiogenin cleaved tRNA halves (tiRNA) or the miRNA like tRNA derived fragments. tRNA cleavage under stress was fist discovered in bacteria and later was found to be conserved across different species, including mammals. Under cellular stress conditions, tRNA undergoes conformational changes and angiogenin cleaves it into 3' and 5' halves. 5'tiRNA halves were shown to repress protein translations. tRNA cleavage is thought of to be a cytoprotective mechanism by which cells evade apoptosis, however some data hints to the opposite; that tiRNA are cytotoxic or at least related to apoptosis initiation. tRNA cleavage also was shown to be affected by tRNA modifications via different enzymes in the cytosol and mitochondria. In this review, we will highlight the biology of tRNA cleavage, show the evidence of it being cytoprotective or a marker of cell death and shed a light on its role in disease models and human diseases as well as possible future directions in this field of RNA research.
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Affiliation(s)
- Sherif Rashad
- Department of Neurosurgery; Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kuniyasu Niizuma
- Department of Neurosurgery; Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine; Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
| | - Teiji Tominaga
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
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73
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Chen L, Wang P, Bahal R, Manautou JE, Zhong XB. Ontogenic mRNA expression of RNA modification writers, erasers, and readers in mouse liver. PLoS One 2019; 14:e0227102. [PMID: 31891622 PMCID: PMC6938302 DOI: 10.1371/journal.pone.0227102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/12/2019] [Indexed: 01/09/2023] Open
Abstract
RNA modifications are recently emerged epigenetic modifications. These diverse RNA modifications have been shown to regulate multiple biological processes, including development. RNA modifications are dynamically controlled by the “writers, erasers, and readers”, where RNA modifying proteins are able to add, remove, and recognize specific chemical modification groups on RNAs. However, little is known about the ontogenic expression of these RNA modifying proteins in various organs, such as liver. In the present study, the hepatic mRNA expression of selected RNA modifying proteins involve in m6A, m1A, m5C, hm5C, m7G, and Ψ modifications was analyzed using the RNA-seq technique. Liver samples were collected from male C57BL/6 mice at several ages from prenatal through neonatal, infant, child to young adult. Results showed that most of the RNA modifying proteins were highly expressed in prenatal mouse liver with a dramatic drop at birth. After birth, most of the RNA modifying proteins showed a downregulation trend during liver maturation. Moreover, the RNA modifying proteins that belong to the same enzyme family were expressed at different abundances at the same ages in mouse liver. In conclusion, this study unveils that the mRNA expression of RNA modifying proteins follows specific ontogenic expression patterns in mice liver during maturation. These data indicated that the changes in expression of RNA modifying proteins might have a potential role to regulate gene expression in liver through alteration of RNA modification status.
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Affiliation(s)
- Liming Chen
- Department of Pharmaceutic Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, United States of America
| | - Pei Wang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Raman Bahal
- Department of Pharmaceutic Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, United States of America
| | - José E. Manautou
- Department of Pharmaceutic Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, United States of America
| | - Xiao-bo Zhong
- Department of Pharmaceutic Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, United States of America
- * E-mail:
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74
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Dégut C, Roovers M, Barraud P, Brachet F, Feller A, Larue V, Al Refaii A, Caillet J, Droogmans L, Tisné C. Structural characterization of B. subtilis m1A22 tRNA methyltransferase TrmK: insights into tRNA recognition. Nucleic Acids Res 2019; 47:4736-4750. [PMID: 30931478 PMCID: PMC6511850 DOI: 10.1093/nar/gkz230] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/04/2019] [Accepted: 03/26/2019] [Indexed: 12/21/2022] Open
Abstract
1-Methyladenosine (m1A) is a modified nucleoside found at positions 9, 14, 22 and 58 of tRNAs, which arises from the transfer of a methyl group onto the N1-atom of adenosine. The yqfN gene of Bacillus subtilis encodes the methyltransferase TrmK (BsTrmK) responsible for the formation of m1A22 in tRNA. Here, we show that BsTrmK displays a broad substrate specificity, and methylates seven out of eight tRNA isoacceptor families of B. subtilis bearing an A22. In addition to a non-Watson–Crick base-pair between the target A22 and a purine at position 13, the formation of m1A22 by BsTrmK requires a full-length tRNA with intact tRNA elbow and anticodon stem. We solved the crystal structure of BsTrmK showing an N-terminal catalytic domain harbouring the typical Rossmann-like fold of Class-I methyltransferases and a C-terminal coiled-coil domain. We used NMR chemical shift mapping to drive the docking of BstRNASer to BsTrmK in complex with its methyl-donor cofactor S-adenosyl-L-methionine (SAM). In this model, validated by methyltransferase activity assays on BsTrmK mutants, both domains of BsTrmK participate in tRNA binding. BsTrmK recognises tRNA with very few structural changes in both partner, the non-Watson–Crick R13–A22 base-pair positioning the A22 N1-atom close to the SAM methyl group.
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Affiliation(s)
- Clément Dégut
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Sorbonne Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France
| | | | - Pierre Barraud
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Sorbonne Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France.,Laboratoire d'Expression génétique microbienne, CNRS, Univ. Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Franck Brachet
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Sorbonne Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France
| | - André Feller
- Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Valéry Larue
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Sorbonne Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France
| | - Abdalla Al Refaii
- Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Joël Caillet
- Laboratoire d'Expression génétique microbienne, CNRS, Univ. Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Louis Droogmans
- Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), 6041 Gosselies, Belgium
| | - Carine Tisné
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Sorbonne Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France.,Laboratoire d'Expression génétique microbienne, CNRS, Univ. Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
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75
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Leonardi A, Evke S, Lee M, Melendez JA, Begley TJ. Epitranscriptomic systems regulate the translation of reactive oxygen species detoxifying and disease linked selenoproteins. Free Radic Biol Med 2019; 143:573-593. [PMID: 31476365 PMCID: PMC7650020 DOI: 10.1016/j.freeradbiomed.2019.08.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 02/07/2023]
Abstract
Here we highlight the role of epitranscriptomic systems in post-transcriptional regulation, with a specific focus on RNA modifying writers required for the incorporation of the 21st amino acid selenocysteine during translation, and the pathologies linked to epitranscriptomic and selenoprotein defects. Epitranscriptomic marks in the form of enzyme-catalyzed modifications to RNA have been shown to be important signals regulating translation, with defects linked to altered development, intellectual impairment, and cancer. Modifications to rRNA, mRNA and tRNA can affect their structure and function, while the levels of these dynamic tRNA-specific epitranscriptomic marks are stress-regulated to control translation. The tRNA for selenocysteine contains five distinct epitranscriptomic marks and the ALKBH8 writer for the wobble uridine (U) has been shown to be vital for the translation of the glutathione peroxidase (GPX) and thioredoxin reductase (TRXR) family of selenoproteins. The reactive oxygen species (ROS) detoxifying selenocysteine containing proteins are a prime examples of how specialized translation can be regulated by specific tRNA modifications working in conjunction with distinct codon usage patterns, RNA binding proteins and specific 3' untranslated region (UTR) signals. We highlight the important role of selenoproteins in detoxifying ROS and provide details on how epitranscriptomic marks and selenoproteins can play key roles in and maintaining mitochondrial function and preventing disease.
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Affiliation(s)
- Andrea Leonardi
- Colleges of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY, USA
| | - Sara Evke
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA
| | - May Lee
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA
| | - J Andres Melendez
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA.
| | - Thomas J Begley
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA; RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
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76
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Chen Z, Qi M, Shen B, Luo G, Wu Y, Li J, Lu Z, Zheng Z, Dai Q, Wang H. Transfer RNA demethylase ALKBH3 promotes cancer progression via induction of tRNA-derived small RNAs. Nucleic Acids Res 2019; 47:2533-2545. [PMID: 30541109 PMCID: PMC6411830 DOI: 10.1093/nar/gky1250] [Citation(s) in RCA: 198] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/16/2018] [Accepted: 12/03/2018] [Indexed: 12/11/2022] Open
Abstract
Transfer RNA is heavily modified and plays a central role in protein synthesis and cellular functions. Here we demonstrate that ALKBH3 is a 1-methyladenosine (m1A) and 3-methylcytidine (m3C) demethylase of tRNA. ALKBH3 can promote cancer cell proliferation, migration and invasion. In vivo study confirms the regulation effects of ALKBH3 on growth of tumor xenograft. The m1A demethylated tRNA is more sensitive to angiogenin (ANG) cleavage, followed by generating tRNA-derived small RNAs (tDRs) around the anticodon regions. tDRs are conserved among species, which strengthen the ribosome assembly and prevent apoptosis triggered by cytochrome c (Cyt c). Our discovery opens a potential and novel paradigm of tRNA demethylase, which regulates biological functions via generation of tDRs.
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Affiliation(s)
- Zhuojia Chen
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.,Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Meijie Qi
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Guanzheng Luo
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.,School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yingmin Wu
- Department of Microbial and Biochemical Pharmacy, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jiexin Li
- Department of Microbial and Biochemical Pharmacy, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhike Lu
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Zhong Zheng
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Qing Dai
- Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Hongsheng Wang
- Department of Microbial and Biochemical Pharmacy, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.,Department of Chemistry, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
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77
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Abstract
Ribonucleic acid (RNA) is involved in translation and transcription, which are the mechanisms in which cells express genes (Alberts et al., 2002). The three classes of RNA discussed are transfer RNA (tRNA), messenger RNA (mRNA), and ribosomal RNA (rRNA). mRNA is the transcript encoded from DNA, rRNA is associated with ribosomes, and tRNA is associated with amino acids and is used to read mRNA transcripts to make proteins (Lodish, Berk, Zipursky, et al., 2000). Interestingly, the function of tRNA, rRNA, and mRNA can be significantly altered by chemical modifications at the co-transcriptional and post-transcriptional levels, and there are over 171 of these modifications identified thus far (Boccaletto et al., 2018; Modomics-Modified bases, 2017). Several of these modifications are linked to diseases such as cancer, diabetes, and neurological disorders. In this review, we will introduce a few RNA modifications with biological functions and how dysregulation of these RNA modifications is linked to human disease.
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Affiliation(s)
- Amber Yanas
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
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78
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Dégut C, Schwarz V, Ponchon L, Barraud P, Micura R, Tisné C. Design of cross-linked RNA/protein complexes for structural studies. Biochimie 2019; 164:95-98. [DOI: 10.1016/j.biochi.2019.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/28/2019] [Indexed: 10/27/2022]
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79
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Barraud P, Tisné C. To be or not to be modified: Miscellaneous aspects influencing nucleotide modifications in tRNAs. IUBMB Life 2019; 71:1126-1140. [PMID: 30932315 PMCID: PMC6850298 DOI: 10.1002/iub.2041] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/10/2019] [Indexed: 12/12/2022]
Abstract
Transfer RNAs (tRNAs) are essential components of the cellular protein synthesis machineries, but are also implicated in many roles outside translation. To become functional, tRNAs, initially transcribed as longer precursor tRNAs, undergo a tightly controlled biogenesis process comprising the maturation of their extremities, removal of intronic sequences if present, addition of the 3'-CCA amino-acid accepting sequence, and aminoacylation. In addition, the most impressive feature of tRNA biogenesis consists in the incorporation of a large number of posttranscriptional chemical modifications along its sequence. The chemical nature of these modifications is highly diverse, with more than hundred different modifications identified in tRNAs to date. All functions of tRNAs in cells are controlled and modulated by modifications, making the understanding of the mechanisms that determine and influence nucleotide modifications in tRNAs an essential point in tRNA biology. This review describes the different aspects that determine whether a certain position in a tRNA molecule is modified or not. We describe how sequence and structural determinants, as well as the presence of prior modifications control modification processes. We also describe how environmental factors and cellular stresses influence the level and/or the nature of certain modifications introduced in tRNAs, and report situations where these dynamic modulations of tRNA modification levels are regulated by active demodification processes. © 2019 IUBMB Life, 71(8):1126-1140, 2019.
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Affiliation(s)
- Pierre Barraud
- Expression génétique microbienneInstitut de biologie physico‐chimique (IBPC), UMR 8261, CNRS, Université Paris DiderotParisFrance
| | - Carine Tisné
- Expression génétique microbienneInstitut de biologie physico‐chimique (IBPC), UMR 8261, CNRS, Université Paris DiderotParisFrance
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80
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Alriquet M, Martínez-Limón A, Hanspach G, Hengesbach M, Tartaglia GG, Calloni G, Vabulas RM. Assembly of Proteins by Free RNA during the Early Phase of Proteostasis Stress. J Proteome Res 2019; 18:2835-2847. [PMID: 31244213 DOI: 10.1021/acs.jproteome.9b00143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
At any stage of their lifecycle, mRNAs are coated by specialized proteins. One of few circumstances when free mRNA appears in the cytosol is the disassembly of polysomes during the stress-induced shutdown of protein synthesis. Using quantitative mass spectrometry, we sought to identify the free RNA-interacting cellular machinery in heat-shocked mammalian cells. Free RNA-associated proteins displayed higher disorder and larger size, which supports the role of multivalent interactions during the initial phase of the association with RNAs during stress. Structural features of the free RNA interactors defined them as a subset of RNA-binding proteins. The interaction between these assembled proteins in vivo required RNA. Reconstitution of the association process in vitro indicated a multimolecular basis for increased binding to RNA upon heat shock in the cytosol. Our study represents a step toward understanding how free RNA is processed in the cytosol during proteostasis stress.
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Affiliation(s)
- Marion Alriquet
- Buchmann Institute for Molecular Life Sciences , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany.,Institute of Biophysical Chemistry , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
| | - Adrían Martínez-Limón
- Buchmann Institute for Molecular Life Sciences , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany.,Institute of Biophysical Chemistry , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
| | - Gerd Hanspach
- Institute for Organic Chemistry and Chemical Biology , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
| | - Gian G Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology , Universitat Pompeu Fabra (UPF), Institucio Catalana de Recerca i Estudis Avançats (ICREA) , 08002 Barcelona , Spain
| | - Giulia Calloni
- Buchmann Institute for Molecular Life Sciences , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany.,Institute of Biophysical Chemistry , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
| | - R Martin Vabulas
- Buchmann Institute for Molecular Life Sciences , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany.,Institute of Biophysical Chemistry , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
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81
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LC/MS analysis and deep sequencing reveal the accurate RNA composition in the HIV-1 virion. Sci Rep 2019; 9:8697. [PMID: 31213632 PMCID: PMC6581912 DOI: 10.1038/s41598-019-45079-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/30/2019] [Indexed: 01/23/2023] Open
Abstract
The mechanism of action of various viruses has been the primary focus of many studies. Yet, the data on RNA modifications in any type of virus are scarce. Methods for the sensitive analysis of RNA modifications have been developed only recently and they have not been applied to viruses. In particular, the RNA composition of HIV-1 virions has never been determined with sufficiently exact methods. Here, we reveal that the RNA of HIV-1 virions contains surprisingly high amount of the 1-methyladenosine. We are the first to use a liquid chromatography-mass spectrometry analysis (LC/MS) of virion RNA, which we combined with m1A profiling and deep sequencing. We found that m1A was present in the tRNA, but not in the genomic HIV-1 RNA and the abundant 7SL RNA. We were able to calculate that an HIV-1 virion contains per 2 copies of genomic RNA and 14 copies of 7SL RNA also 770 copies of tRNA, which is approximately 10 times more than thus far expected. These new insights into the composition of the HIV-1 virion can help in future studies to identify the role of nonprimer tRNAs in retroviruses. Moreover, we present a promising new tool for studying the compositions of virions.
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82
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Oerum S, Catala M, Atdjian C, Brachet F, Ponchon L, Barraud P, Iannazzo L, Droogmans L, Braud E, Ethève-Quelquejeu M, Tisné C. Bisubstrate analogues as structural tools to investigate m 6A methyltransferase active sites. RNA Biol 2019; 16:798-808. [PMID: 30879411 PMCID: PMC6546350 DOI: 10.1080/15476286.2019.1589360] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/24/2019] [Accepted: 02/27/2019] [Indexed: 12/20/2022] Open
Abstract
RNA methyltransferases (MTases) catalyse the transfer of a methyl group to their RNA substrates using most-often S-adenosyl-L-methionine (SAM) as cofactor. Only few RNA-bound MTases structures are currently available due to the difficulties in crystallising RNA:protein complexes. The lack of complex structures results in poorly understood RNA recognition patterns and methylation reaction mechanisms. On the contrary, many cofactor-bound MTase structures are available, resulting in well-understood protein:cofactor recognition, that can guide the design of bisubstrate analogues that mimic the state at which both the substrate and the cofactor is bound. Such bisubstrate analogues were recently synthesized for proteins monomethylating the N6-atom of adenine (m6A). These proteins include, amongst others, RlmJ in E. coli and METLL3:METT14 and METTL16 in human. As a proof-of-concept, we here test the ability of the bisubstrate analogues to mimic the substrate:cofactor bound state during catalysis by studying their binding to RlmJ using differential scanning fluorimetry, isothermal titration calorimetry and X-ray crystallography. We find that the methylated adenine base binds in the correct pocket, and thus these analogues could potentially be used broadly to study the RNA recognition and catalytic mechanism of m6A MTases. Two bisubstrate analogues bind RlmJ with micro-molar affinity, and could serve as starting scaffolds for inhibitor design against m6A RNA MTases. The same analogues cause changes in the melting temperature of the m1A RNA MTase, TrmK, indicating non-selective protein:compound complex formation. Thus, optimization of these molecular scaffolds for m6A RNA MTase inhibition should aim to increase selectivity, as well as affinity.
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Affiliation(s)
- Stephanie Oerum
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
| | - Marjorie Catala
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
| | - Colette Atdjian
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Franck Brachet
- Institut de Biologie Physico-Chimique, IBPC, CNRS, Paris, France
| | - Luc Ponchon
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Paris, France
| | - Pierre Barraud
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Louis Droogmans
- Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), Gosselies, Belgium
| | - Emmanuelle Braud
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Carine Tisné
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
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83
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Deciphering the Epitranscriptomic Signatures in Cell Fate Determination and Development. Stem Cell Rev Rep 2019; 15:474-496. [DOI: 10.1007/s12015-019-09894-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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84
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The chemical diversity of RNA modifications. Biochem J 2019; 476:1227-1245. [PMID: 31028151 DOI: 10.1042/bcj20180445] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 02/25/2019] [Accepted: 02/26/2019] [Indexed: 12/16/2022]
Abstract
Nucleic acid modifications in DNA and RNA ubiquitously exist among all the three kingdoms of life. This trait significantly broadens the genome diversity and works as an important means of gene transcription regulation. Although mammalian systems have limited types of DNA modifications, over 150 different RNA modification types have been identified, with a wide variety of chemical diversities. Most modifications occur on transfer RNA and ribosomal RNA, however many of the modifications also occur on other types of RNA species including mammalian mRNA and small nuclear RNA, where they are essential for many biological roles, including developmental processes and stem cell differentiation. These post-transcriptional modifications are enzymatically installed and removed in a site-specific manner by writer and eraser proteins respectively, while reader proteins can interpret modifications and transduce the signal for downstream functions. Dysregulation of mRNA modifications manifests as disease states, including multiple types of human cancer. In this review, we will introduce the chemical features and biological functions of these modifications in the coding and non-coding RNA species.
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85
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Insights into Catalytic and tRNA Recognition Mechanism of the Dual-Specific tRNA Methyltransferase from Thermococcus kodakarensis. Genes (Basel) 2019; 10:genes10020100. [PMID: 30704107 PMCID: PMC6410153 DOI: 10.3390/genes10020100] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 01/30/2023] Open
Abstract
The tRNA methyltransferase Trm10, conserved throughout Eukarya and Archaea, catalyzes N1-methylation of purine residues at position 9 using S-adenosyl methionine as the methyl donor. The Trm10 family exhibits diverse target nucleotide specificity, with some homologs that are obligate m¹G₉ or m¹A₉-specific enzymes, while others are bifunctional enzymes catalyzing both m¹G₉ and m¹A₉. This variability is particularly intriguing given different chemical properties of the target N1 atom of guanine and adenine. Here we performed an extensive kinetic and mutational analysis of the m¹G₉ and m¹A₉-catalyzing Trm10 from Thermococcus kodakarensis to gain insight into the active site that facilitates this unique bifunctionality. These results suggest that the rate-determining step for catalysis likely involves a conformational change to correctly position the substrate tRNA in the active site. In this model, kinetic preferences for certain tRNA can be explained by variations in the overall stability of the folded substrate tRNA, consistent with tRNA-specific differences in metal ion dependence. Together, these results provide new insight into the substrate recognition, active site and catalytic mechanism of m¹G/m¹A catalyzing bifunctional enzymes.
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86
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Ostrakhovitch EA, Tabibzadeh S. Homocysteine and age-associated disorders. Ageing Res Rev 2019; 49:144-164. [PMID: 30391754 DOI: 10.1016/j.arr.2018.10.010] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 09/30/2018] [Accepted: 10/25/2018] [Indexed: 12/26/2022]
Abstract
There are numerous theories of aging, a process which still seems inevitable. Aging leads to cancer and multi-systemic disorders as well as chronic diseases. Decline in age- associated cellular functions leads to neurodegeneration and cognitive decline that affect the quality of life. Accumulation of damage, mutations, metabolic changes, failure in cellular energy production and clearance of altered proteins over the lifetime, and hyperhomocysteinemia, ultimately result in tissue degeneration. The decline in renal functions, nutritional deficiencies, deregulation of methionine cycle and deficiencies of homocysteine remethylation and transsulfuration cofactors cause elevation of homocysteine with advancing age. Abnormal accumulation of homocysteine is a risk factor of cardiovascular, neurodegenerative and chronic kidney disease. Moreover, approximately 50% of people, aged 65 years and older develop hypertension and are at a high risk of developing cardiovascular insufficiency and incurable neurodegenerative disorders. Increasing evidence suggests inverse relation between cognitive impairment, cerebrovascular and cardiovascular events and renal function. Oxidative stress, inactivation of nitric oxide synthase pathway and mitochondria dysfunction associated with impaired homocysteine metabolism lead to aging tissue degeneration. In this review, we examine impact of high homocysteine levels on changes observed with aging that contribute to development and progression of age associated diseases.
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Affiliation(s)
- E A Ostrakhovitch
- Frontiers in Bioscience Research Institute in Aging and Cancer, Irvine, CA, USA.
| | - S Tabibzadeh
- Frontiers in Bioscience Research Institute in Aging and Cancer, Irvine, CA, USA.
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87
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Hu J, Manduzio S, Kang H. Epitranscriptomic RNA Methylation in Plant Development and Abiotic Stress Responses. FRONTIERS IN PLANT SCIENCE 2019; 10:500. [PMID: 31110512 PMCID: PMC6499213 DOI: 10.3389/fpls.2019.00500] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 04/01/2019] [Indexed: 05/19/2023]
Abstract
Recent advances in methylated RNA immunoprecipitation followed by sequencing and mass spectrometry have revealed widespread chemical modifications on mRNAs. Methylation of RNA bases such as N 6-methyladenosine (m6A) and 5-methylcytidine (m5C) is the most prevalent mRNA modifications found in eukaryotes. In recent years, cellular factors introducing, interpreting, and deleting specific methylation marks on mRNAs, designated as "writers (methyltransferase)," "readers (RNA-binding protein)," and "erasers (demethylase)," respectively, have been identified in plants and animals. An emerging body of evidence shows that methylation on mRNAs affects diverse aspects of RNA metabolism, including stability, splicing, nucleus-to-cytoplasm export, alternative polyadenylation, and translation. Although our understanding for roles of writers, readers, and erasers in plants is far behind that for their animal counterparts, accumulating reports clearly demonstrate that these factors are essential for plant growth and abiotic stress responses. This review emphasizes the crucial roles of epitranscriptomic modifications of RNAs in new layer of gene expression regulation during the growth and response of plants to abiotic stresses.
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88
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Wei J, Liu F, Lu Z, Fei Q, Ai Y, He PC, Shi H, Cui X, Su R, Klungland A, Jia G, Chen J, He C. Differential m 6A, m 6A m, and m 1A Demethylation Mediated by FTO in the Cell Nucleus and Cytoplasm. Mol Cell 2018; 71:973-985.e5. [PMID: 30197295 PMCID: PMC6151148 DOI: 10.1016/j.molcel.2018.08.011] [Citation(s) in RCA: 476] [Impact Index Per Article: 79.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 06/03/2018] [Accepted: 08/02/2018] [Indexed: 10/28/2022]
Abstract
FTO, the first RNA demethylase discovered, mediates the demethylation of internal N6-methyladenosine (m6A) and N6, 2-O-dimethyladenosine (m6Am) at the +1 position from the 5' cap in mRNA. Here we demonstrate that the cellular distribution of FTO is distinct among different cell lines, affecting the access of FTO to different RNA substrates. We find that FTO binds multiple RNA species, including mRNA, snRNA, and tRNA, and can demethylate internal m6A and cap m6Am in mRNA, internal m6A in U6 RNA, internal and cap m6Am in snRNAs, and N1-methyladenosine (m1A) in tRNA. FTO-mediated demethylation has a greater effect on the transcript levels of mRNAs possessing internal m6A than the ones with cap m6Am in the tested cells. We also show that FTO can directly repress translation by catalyzing m1A tRNA demethylation. Collectively, FTO-mediated RNA demethylation occurs to m6A and m6Am in mRNA and snRNA as well as m1A in tRNA.
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Affiliation(s)
- Jiangbo Wei
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - Fange Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - Zhike Lu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, 18 Shilongshan Road, Hangzhou 310064, China
| | - Qili Fei
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - Yuxi Ai
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - P Cody He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - Hailing Shi
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - Xiaolong Cui
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA
| | - Rui Su
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Arne Klungland
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Norway Institute of Basic Medical Sciences, University of Oslo, PO Box 1018 Blindern, 0315 Oslo, Norway
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57 Street, Chicago, IL 60637, USA.
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89
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Kadumuri RV, Janga SC. Epitranscriptomic Code and Its Alterations in Human Disease. Trends Mol Med 2018; 24:886-903. [PMID: 30120023 DOI: 10.1016/j.molmed.2018.07.010] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 02/07/2023]
Abstract
Innovations in epitranscriptomics have resulted in the identification of more than 160 RNA modifications to date. These developments, together with the recent discovery of writers, readers, and erasers of modifications occurring across a wide range of RNAs and tissue types, have led to a surge in integrative approaches for transcriptome-wide mapping of modifications and protein-RNA interaction profiles of epitranscriptome players. RNA modification maps and crosstalk between them have begun to elucidate the role of modifications as signaling switches, entertaining the notion of an epitranscriptomic code as a driver of the post-transcriptional fate of RNA. Emerging single-molecule sequencing technologies and development of antibodies specific to various RNA modifications could enable charting of transcript-specific epitranscriptomic marks across cell types and their alterations in disease.
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Affiliation(s)
- Rajashekar Varma Kadumuri
- Department of BioHealth Informatics, School of Informatics and Computing, Walker Plaza Building, Indiana University-Purdue University Indianapolis, 719 Indiana Avenue, Suite 319, Indianapolis, IN 46202, USA
| | - Sarath Chandra Janga
- Department of BioHealth Informatics, School of Informatics and Computing, Walker Plaza Building, Indiana University-Purdue University Indianapolis, 719 Indiana Avenue, Suite 319, Indianapolis, IN 46202, USA; Department of Medical and Molecular Genetics, Medical Research and Library Building, Indiana University School of Medicine, 975 West Walnut Street, Indianapolis, IN 46202, USA; Centre for Computational Biology and Bioinformatics, 5021 Health Information and Translational Sciences, Indiana University School of Medicine, 410 West 10th Street, Indianapolis, IN 46202, USA.
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90
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N 1-methyladenosine methylome in messenger RNA and non-coding RNA. Curr Opin Chem Biol 2018; 45:179-186. [PMID: 30007213 DOI: 10.1016/j.cbpa.2018.06.017] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/08/2018] [Accepted: 06/14/2018] [Indexed: 11/24/2022]
Abstract
Chemical modifications to rRNA, tRNA and mRNA provide a new regulatory layer of gene expression, which is termed as the `epitranscriptome'. N1-methyladenosine (m1A), first characterized more than 50 years ago, is a well-known modification in rRNA and tRNA. m1A in these abundant non-coding RNAs plays important roles in maintaining their biological functions. Recent studies also reveal that m1A is present in both nuclear-encoded and mitochondrial-encoded mRNA and is dynamically regulated by environmental and developmental conditions; m1A is found in a subset of nuclear-encoded long non-coding RNAs as well. Finally, we also discuss the potential challenges of identifying m1A modification in the human transcriptome.
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91
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Morena F, Argentati C, Bazzucchi M, Emiliani C, Martino S. Above the Epitranscriptome: RNA Modifications and Stem Cell Identity. Genes (Basel) 2018; 9:E329. [PMID: 29958477 PMCID: PMC6070936 DOI: 10.3390/genes9070329] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/15/2018] [Accepted: 06/25/2018] [Indexed: 02/07/2023] Open
Abstract
Sequence databases and transcriptome-wide mapping have revealed different reversible and dynamic chemical modifications of the nitrogen bases of RNA molecules. Modifications occur in coding RNAs and noncoding-RNAs post-transcriptionally and they can influence the RNA structure, metabolism, and function. The result is the expansion of the variety of the transcriptome. In fact, depending on the type of modification, RNA molecules enter into a specific program exerting the role of the player or/and the target in biological and pathological processes. Many research groups are exploring the role of RNA modifications (alias epitranscriptome) in cell proliferation, survival, and in more specialized activities. More recently, the role of RNA modifications has been also explored in stem cell biology. Our understanding in this context is still in its infancy. Available evidence addresses the role of RNA modifications in self-renewal, commitment, and differentiation processes of stem cells. In this review, we will focus on five epitranscriptomic marks: N6-methyladenosine, N1-methyladenosine, 5-methylcytosine, Pseudouridine (Ψ) and Adenosine-to-Inosine editing. We will provide insights into the function and the distribution of these chemical modifications in coding RNAs and noncoding-RNAs. Mainly, we will emphasize the role of epitranscriptomic mechanisms in the biology of naïve, primed, embryonic, adult, and cancer stem cells.
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Affiliation(s)
- Francesco Morena
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06126 Perugia, Italy.
| | - Chiara Argentati
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06126 Perugia, Italy.
| | - Martina Bazzucchi
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06126 Perugia, Italy.
| | - Carla Emiliani
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06126 Perugia, Italy.
- CEMIN, Center of Excellence of Nanostructured Innovative Materials, University of Perugia, 06126 Perugia, Italy.
| | - Sabata Martino
- Department of Chemistry, Biology and Biotechnologies, University of Perugia, 06126 Perugia, Italy.
- CEMIN, Center of Excellence of Nanostructured Innovative Materials, University of Perugia, 06126 Perugia, Italy.
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92
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Oerum S, Roovers M, Rambo RP, Kopec J, Bailey HJ, Fitzpatrick F, Newman JA, Newman WG, Amberger A, Zschocke J, Droogmans L, Oppermann U, Yue WW. Structural insight into the human mitochondrial tRNA purine N1-methyltransferase and ribonuclease P complexes. J Biol Chem 2018; 293:12862-12876. [PMID: 29880640 PMCID: PMC6102140 DOI: 10.1074/jbc.ra117.001286] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/24/2018] [Indexed: 01/17/2023] Open
Abstract
Mitochondrial tRNAs are transcribed as long polycistronic transcripts of precursor tRNAs and undergo posttranscriptional modifications such as endonucleolytic processing and methylation required for their correct structure and function. Among them, 5'-end processing and purine 9 N1-methylation of mitochondrial tRNA are catalyzed by two proteinaceous complexes with overlapping subunit composition. The Mg2+-dependent RNase P complex for 5'-end cleavage comprises the methyltransferase domain-containing protein tRNA methyltransferase 10C, mitochondrial RNase P subunit (TRMT10C/MRPP1), short-chain oxidoreductase hydroxysteroid 17β-dehydrogenase 10 (HSD17B10/MRPP2), and metallonuclease KIAA0391/MRPP3. An MRPP1-MRPP2 subcomplex also catalyzes the formation of 1-methyladenosine/1-methylguanosine at position 9 using S-adenosyl-l-methionine as methyl donor. However, a lack of structural information has precluded insights into how these complexes methylate and process mitochondrial tRNA. Here, we used a combination of X-ray crystallography, interaction and activity assays, and small angle X-ray scattering (SAXS) to gain structural insight into the two tRNA modification complexes and their components. The MRPP1 N terminus is involved in tRNA binding and monomer-monomer self-interaction, whereas the C-terminal SPOUT fold contains key residues for S-adenosyl-l-methionine binding and N1-methylation. The entirety of MRPP1 interacts with MRPP2 to form the N1-methylation complex, whereas the MRPP1-MRPP2-MRPP3 RNase P complex only assembles in the presence of precursor tRNA. This study proposes low-resolution models of the MRPP1-MRPP2 and MRPP1-MRPP2-MRPP3 complexes that suggest the overall architecture, stoichiometry, and orientation of subunits and tRNA substrates.
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Affiliation(s)
- Stephanie Oerum
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | | | - Robert P Rambo
- Diamond Light Source, Harwell Science and Innovation Center, Didcot OX11 0QG, United Kingdom
| | - Jola Kopec
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Henry J Bailey
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Fiona Fitzpatrick
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Joseph A Newman
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - William G Newman
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, University of Manchester, Manchester, M13 9WL, United Kingdom
| | - Albert Amberger
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Johannes Zschocke
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Louis Droogmans
- Laboratoire de Microbiologie, Universite libre de Bruxelles, 1050 Belgium
| | - Udo Oppermann
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom; Botnar Research Centre, NIHR Oxford Biomedical Research Unit, Oxford OX3 7LD, United Kingdom.
| | - Wyatt W Yue
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, United Kingdom.
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93
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Engel M, Chen A. The emerging role of mRNA methylation in normal and pathological behavior. GENES BRAIN AND BEHAVIOR 2017; 17:e12428. [PMID: 29027751 DOI: 10.1111/gbb.12428] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 10/02/2017] [Accepted: 10/09/2017] [Indexed: 12/11/2022]
Abstract
Covalent RNA modifications were recently rediscovered as abundant RNA chemical tags. Similarly to DNA epigenetic modifications, they have been proposed as essential regulators of gene expression. Here we focus on 3 of the most abundant adenosine methylations: N6-methyladenosine (m6 A), N6,2'-O-dimethyladenosine (m6 Am) and N1-methyladenosine (m1 A). We review the potential role of these modifications on mature mRNA in regulating gene expression within the adult brain, nervous system function and normal and pathological behavior. Dynamic mRNA modifications, summarized as the epitranscriptome, regulate transcript maturation, translation and decay, and thus crucially determine gene expression beyond primary transcription regulation. However, the extent of this regulation in the healthy and maladapted adult brain is poorly understood. Analyzing this novel layer of gene expression control in addition to epigenetics and posttranslational regulation of proteins will be highly relevant for understanding the molecular underpinnings of behavior and psychiatric disorders.
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Affiliation(s)
- M Engel
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - A Chen
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany.,Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
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94
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Väre VYP, Eruysal ER, Narendran A, Sarachan KL, Agris PF. Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function. Biomolecules 2017; 7:E29. [PMID: 28300792 PMCID: PMC5372741 DOI: 10.3390/biom7010029] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/06/2017] [Accepted: 03/06/2017] [Indexed: 12/21/2022] Open
Abstract
RNAs are central to all gene expression through the control of protein synthesis. Four major nucleosides, adenosine, guanosine, cytidine and uridine, compose RNAs and provide sequence variation, but are limited in contributions to structural variation as well as distinct chemical properties. The ability of RNAs to play multiple roles in cellular metabolism is made possible by extensive variation in length, conformational dynamics, and the over 100 post-transcriptional modifications. There are several reviews of the biochemical pathways leading to RNA modification, but the physicochemical nature of modified nucleosides and how they facilitate RNA function is of keen interest, particularly with regard to the contributions of modified nucleosides. Transfer RNAs (tRNAs) are the most extensively modified RNAs. The diversity of modifications provide versatility to the chemical and structural environments. The added chemistry, conformation and dynamics of modified nucleosides occurring at the termini of stems in tRNA's cloverleaf secondary structure affect the global three-dimensional conformation, produce unique recognition determinants for macromolecules to recognize tRNAs, and affect the accurate and efficient decoding ability of tRNAs. This review will discuss the impact of specific chemical moieties on the structure, stability, electrochemical properties, and function of tRNAs.
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Affiliation(s)
- Ville Y P Väre
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Emily R Eruysal
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Amithi Narendran
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Kathryn L Sarachan
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Paul F Agris
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
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