1
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Guillen-Angel M, Roignant JY. Exploring pseudouridylation: dysregulation in disease and therapeutic potential. Curr Opin Genet Dev 2024; 87:102210. [PMID: 38833893 DOI: 10.1016/j.gde.2024.102210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/03/2024] [Accepted: 05/17/2024] [Indexed: 06/06/2024]
Abstract
Pseudouridine (Ψ), the most abundant RNA modification, plays a role in pre-mRNA splicing, RNA stability, protein translation efficiency, and cellular responses to environmental stress. Dysregulation of pseudouridylation is linked to human diseases. This review explores recent insights into the role of RNA pseudouridylation alterations in human disorders and the therapeutic potential of Ψ. We discuss the impact of the reduction of Ψ levels in ribosomal, messenger, and transfer RNA in RNA processing, protein translation, and consequently its role in neurodevelopmental diseases and cancer. Furthermore, we review the success of N1-methyl-Ψ messenger RNA vaccines against COVID-19 and the development of RNA-guided pseudouridylation enzymes for treating genetic diseases caused by premature stop codons.
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Affiliation(s)
- Maria Guillen-Angel
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jean-Yves Roignant
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland; Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany.
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2
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Shi D, Wang B, Li H, Lian Y, Ma Q, Liu T, Cao M, Ma Y, Shi L, Yuan W, Shi J, Chu Y. Pseudouridine synthase 1 regulates erythropoiesis via transfer RNAs pseudouridylation and cytoplasmic translation. iScience 2024; 27:109265. [PMID: 38450158 PMCID: PMC10915626 DOI: 10.1016/j.isci.2024.109265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 12/21/2023] [Accepted: 02/14/2024] [Indexed: 03/08/2024] Open
Abstract
Pseudouridylation plays a regulatory role in various physiological and pathological processes. A prime example is the mitochondrial myopathy, lactic acidosis, and sideroblastic anemia syndrome (MLASA), characterized by defective pseudouridylation resulting from genetic mutations in pseudouridine synthase 1 (PUS1). However, the roles and mechanisms of pseudouridylation in normal erythropoiesis and MLASA-related anemia remain elusive. We established a mouse model carrying a point mutation (R110W) in the enzymatic domain of PUS1, mimicking the common mutation in human MLASA. Pus1-mutant mice exhibited anemia at 4 weeks old. Impaired mitochondrial oxidative phosphorylation was also observed in mutant erythroblasts. Mechanistically, mutant erythroblasts showed defective pseudouridylation of targeted tRNAs, altered tRNA profiles, decreased translation efficiency of ribosomal protein genes, and reduced globin synthesis, culminating in ineffective erythropoiesis. Our study thus provided direct evidence that pseudouridylation participates in erythropoiesis in vivo. We demonstrated the critical role of pseudouridylation in regulating tRNA homeostasis, cytoplasmic translation, and erythropoiesis.
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Affiliation(s)
- Deyang Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
- Department of Hematology, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou, Henan 450003, China
| | - Bichen Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Haoyuan Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Yu Lian
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Qiuyi Ma
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Tong Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Mutian Cao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Yuanwu Ma
- Key Laboratory of Human Disease Comparative Medicine, National Health Commission of China (NHC), Institute of Laboratory Animal Science, Peking Union Medicine College, Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Lei Shi
- Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Haihe Laboratory of Cell Ecosystem, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Weiping Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Jun Shi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Yajing Chu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
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3
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Li Y, Liu Y, Zhang Y, Wu Y, Xing Z, Wang J, Fan GH. Discovery of a First-in-Class CD38 Inhibitor for the Treatment of Mitochondrial Myopathy. J Med Chem 2023; 66:12762-12775. [PMID: 37696000 DOI: 10.1021/acs.jmedchem.3c00391] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
CD38 is a crucial NADase in mammalian tissues that degrades NAD+ and thus regulates cellular NAD+ levels. Abnormal CD38 expression is linked to mitochondrial dysfunction under several pathological conditions. We present a novel CD38 inhibitor, compound 1, with high potency for CD38 (IC50 of 11 nM) and minimal activity against other targets. In a Pus1 knockout (Pus1-/-) mouse model of mitochondrial myopathy, compound 1 treatment rescued the decline in running endurance in a dose-dependent manner, associated with an elevated NAD+ level in muscle tissue, increased expression of Nrf2, which is known to promote mitochondrial biogenesis, and reduced lactate production. RNA sequencing data indicated that compound 1 has a great effect on mitochondrial function, metabolic processes, muscle contraction/development, and actin filament organization via regulating the expression of relevant genes. Compound 1 is a promising candidate for its excellent in vivo efficacy, favorable pharmacokinetics, and attractive safety profile.
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Affiliation(s)
- Yue Li
- Department of Medicinal Chemistry, Immunophage Biotech Co., Ltd, No. 10 Lv Zhou Huan Road, Shanghai 201112, P. R. China
| | - Yuanyuan Liu
- Department of Neurosciences, Immunophage Biotech Co., Ltd, No. 10 Lv Zhou Huan Road, Shanghai 201112, P. R. China
- Guangxi Key Laboratory of Regenerative Medicine, and Guangxi Key Laboratory of Brain Science, Department of Cell Biology and Genetics, School of Basic Medical Sciences, Guangxi Medical University, Nanning 530021, Guangxi , China
| | - Yong Zhang
- Department of Integrated Biological Platform Sciences, Immunophage Biotech Co., Ltd, No. 10 Lv Zhou Huan Road, Shanghai 201112, P. R. China
| | - Yong Wu
- Department of Medicinal Chemistry, Immunophage Biotech Co., Ltd, No. 10 Lv Zhou Huan Road, Shanghai 201112, P. R. China
| | - Zili Xing
- Department of Neurosciences, Immunophage Biotech Co., Ltd, No. 10 Lv Zhou Huan Road, Shanghai 201112, P. R. China
| | - JianFei Wang
- Executive Office, Immunophage Biotech Co., Ltd, No. 10 Lv Zhou Huan Road, Shanghai 201112, P. R. China
- Shanghai Laboratory Animal Research Center, Shanghai 200031, China
| | - Guo-Huang Fan
- Executive Office, Immunophage Biotech Co., Ltd, No. 10 Lv Zhou Huan Road, Shanghai 201112, P. R. China
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4
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Keszthelyi TM, Tory K. The importance of pseudouridylation: human disorders related to the fifth nucleoside. Biol Futur 2023:10.1007/s42977-023-00158-3. [PMID: 37000312 DOI: 10.1007/s42977-023-00158-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 03/09/2023] [Indexed: 04/01/2023]
Abstract
Pseudouridylation is one of the most abundant RNA modifications in eukaryotes, making pseudouridine known as the "fifth nucleoside." This highly conserved alteration affects all non-coding and coding RNA types. Its role and importance have been increasingly widely researched, especially considering that its absence or damage leads to serious hereditary diseases. Here, we summarize the human genetic disorders described to date that are related to the participants of the pseudouridylation process.
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Affiliation(s)
| | - Kálmán Tory
- Department of Pediatrics, Semmelweis University, Budapest, Hungary
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5
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Taurine Stimulates AMP-Activated Protein Kinase and Modulates the Skeletal Muscle Functions in Rats via the Induction of Intracellular Calcium Influx. Int J Mol Sci 2023; 24:ijms24044125. [PMID: 36835534 PMCID: PMC9962205 DOI: 10.3390/ijms24044125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/06/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Taurine (2-aminoethanesulfonic acid) is a free amino acid abundantly found in mammalian tissues. Taurine plays a role in the maintenance of skeletal muscle functions and is associated with exercise capacity. However, the mechanism underlying taurine function in skeletal muscles has not yet been elucidated. In this study, to investigate the mechanism of taurine function in the skeletal muscles, the effects of short-term administration of a relatively low dose of taurine on the skeletal muscles of Sprague-Dawley rats and the underlying mechanism of taurine function in cultured L6 myotubes were investigated. The results obtained in this study in rats and L6 cells indicate that taurine modulates the skeletal muscle function by stimulating the expression of genes and proteins associated with mitochondrial and respiratory metabolism through the activation of AMP-activated protein kinase via the calcium signaling pathway.
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6
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The role of post-transcriptional modifications during development. Biol Futur 2022:10.1007/s42977-022-00142-3. [PMID: 36481986 DOI: 10.1007/s42977-022-00142-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022]
Abstract
AbstractWhile the existence of post-transcriptional modifications of RNA nucleotides has been known for decades, in most RNA species the exact positions of these modifications and their physiological function have been elusive until recently. Technological advances, such as high-throughput next-generation sequencing (NGS) methods and nanopore-based mapping technologies, have made it possible to map the position of these modifications with single nucleotide accuracy, and genetic screens have uncovered the “writer”, “reader” and “eraser” proteins that help to install, interpret and remove such modifications, respectively. These discoveries led to intensive research programmes with the aim of uncovering the roles of these modifications during diverse biological processes. In this review, we assess novel discoveries related to the role of post-transcriptional modifications during animal development, highlighting how these discoveries can affect multiple aspects of development from fertilization to differentiation in many species.
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7
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Dogan SA, Giacchin G, Zito E, Viscomi C. Redox Signaling and Stress in Inherited Myopathies. Antioxid Redox Signal 2022; 37:301-323. [PMID: 35081731 DOI: 10.1089/ars.2021.0266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Significance: Reactive oxygen species (ROS) are highly reactive compounds that behave like a double-edged sword; they damage cellular structures and act as second messengers in signal transduction. Mitochondria and endoplasmic reticulum (ER) are interconnected organelles with a central role in ROS production, detoxification, and oxidative stress response. Skeletal muscle is the most abundant tissue in mammals and one of the most metabolically active ones and thus relies mainly on oxidative phosphorylation (OxPhos) to synthesize adenosine triphosphate. The impairment of OxPhos leads to myopathy and increased ROS production, thus affecting both redox poise and signaling. In addition, ROS enter the ER and trigger ER stress and its maladaptive response, which also lead to a myopathic phenotype with mitochondrial involvement. Here, we review the role of ROS signaling in myopathies due to either mitochondrial or ER dysfunction. Recent Advances: Relevant advances have been evolving over the last 10 years on the intricate ROS-dependent pathways that act as modifiers of the disease course in several myopathies. To this end, pathways related to mitochondrial biogenesis, satellite cell differentiation, and ER stress have been studied extensively in myopathies. Critical Issues: The analysis of the chemistry and the exact quantitation, as well as the localization of ROS, are still challenging due to the intrinsic labile nature of ROS and the technical limitations of their sensors. Future Directions: The mechanistic studies of the pathogenesis of mitochondrial and ER-related myopathies offer a unique possibility to discover novel ROS-dependent pathways. Antioxid. Redox Signal. 37, 301-323.
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Affiliation(s)
- Sukru Anil Dogan
- Department of Molecular Biology and Genetics, Center for Life Sciences and Technologies, Bogazici University, Istanbul, Turkey
| | - Giacomo Giacchin
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Ester Zito
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy.,Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Carlo Viscomi
- Department of Biomedical Sciences, University of Padova, Padova, Italy
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8
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Maruta H, Abe R, Yamashita H. Effect of Long-Term Supplementation with Acetic Acid on the Skeletal Muscle of Aging Sprague Dawley Rats. Int J Mol Sci 2022; 23:ijms23094691. [PMID: 35563082 PMCID: PMC9101554 DOI: 10.3390/ijms23094691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/14/2022] [Accepted: 04/21/2022] [Indexed: 12/10/2022] Open
Abstract
Mitochondrial function in skeletal muscle, which plays an essential role in oxidative capacity and physical activity, declines with aging. Acetic acid activates AMP-activated protein kinase (AMPK), which plays a key role in the regulation of whole-body energy by phosphorylating key metabolic enzymes in both biosynthetic and oxidative pathways and stimulates gene expression associated with slow-twitch fibers and mitochondria in skeletal muscle cells. In this study, we investigate whether long-term supplementation with acetic acid improves age-related changes in the skeletal muscle of aging rats in association with the activation of AMPK. Male Sprague Dawley (SD) rats were administered acetic acid orally from 37 to 56 weeks of age. Long-term supplementation with acetic acid decreased the expression of atrophy-related genes, such as atrogin-1, muscle RING-finger protein-1 (MuRF1), and transforming growth factor beta (TGF-β), activated AMPK, and affected the proliferation of mitochondria and type I fiber-related molecules in muscles. The findings suggest that acetic acid exhibits an anti-aging function in the skeletal muscles of aging rats.
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Affiliation(s)
- Hitomi Maruta
- Department of Nutritional Science, Faculty of Health and Welfare Science, Okayama Prefectural University, 111 Kuboki, Soja 719-1197, Okayama, Japan;
| | - Reina Abe
- Graduate School of Health and Welfare Science, Okayama Prefectural University, 111 Kuboki, Soja 719-1197, Okayama, Japan;
| | - Hiromi Yamashita
- Department of Nutritional Science, Faculty of Health and Welfare Science, Okayama Prefectural University, 111 Kuboki, Soja 719-1197, Okayama, Japan;
- Graduate School of Health and Welfare Science, Okayama Prefectural University, 111 Kuboki, Soja 719-1197, Okayama, Japan;
- Correspondence: ; Tel.: +81-866-94-2150
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9
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Chemical modifications to mRNA nucleobases impact translation elongation and termination. Biophys Chem 2022; 285:106780. [DOI: 10.1016/j.bpc.2022.106780] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/03/2022] [Accepted: 02/13/2022] [Indexed: 12/15/2022]
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10
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Noncoding RNAs-associated ceRNA networks involved in the amelioration of skeletal muscle aging after whey protein supplementation. J Nutr Biochem 2022; 104:108968. [DOI: 10.1016/j.jnutbio.2022.108968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 01/06/2022] [Accepted: 01/19/2022] [Indexed: 11/23/2022]
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11
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Lin TY, Mehta R, Glatt S. Pseudouridines in RNAs: switching atoms means shifting paradigms. FEBS Lett 2021; 595:2310-2322. [PMID: 34468991 PMCID: PMC9290505 DOI: 10.1002/1873-3468.14188] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/18/2021] [Accepted: 08/22/2021] [Indexed: 01/21/2023]
Abstract
The structure, stability, and function of various coding and noncoding RNAs are influenced by chemical modifications. Pseudouridine (Ψ) is one of the most abundant post‐transcriptional RNA base modifications and has been detected at individual positions in tRNAs, rRNAs, mRNAs, and snRNAs, which are referred to as Ψ‐sites. By allowing formation of additional bonds with neighboring atoms, Ψ strengthens RNA–RNA and RNA–protein interactions. Although many aspects of the underlying modification reactions remain unclear, the advent of new transcriptome‐wide methods to quantitatively detect Ψ‐sites has recently changed our perception of the functional roles and importance of Ψ. For instance, it is now clear that the occurrence of Ψs appears to be directly linked to the lifetime and the translation efficiency of a given mRNA molecule. Furthermore, the administration of Ψ‐containing RNAs reduces innate immune responses, which appears strikingly advantageous for the development of generations of mRNA‐based vaccines. In this review, we aim to comprehensively summarize recent discoveries that highlight the impact of Ψ on various types of RNAs and outline possible novel biomedical applications of Ψ.
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Affiliation(s)
- Ting-Yu Lin
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Rahul Mehta
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
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12
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Somepalli G, Sahoo S, Singh A, Hannenhalli S. Prioritizing and characterizing functionally relevant genes across human tissues. PLoS Comput Biol 2021; 17:e1009194. [PMID: 34270548 PMCID: PMC8284802 DOI: 10.1371/journal.pcbi.1009194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 06/17/2021] [Indexed: 11/29/2022] Open
Abstract
Knowledge of genes that are critical to a tissue's function remains difficult to ascertain and presents a major bottleneck toward a mechanistic understanding of genotype-phenotype links. Here, we present the first machine learning model-FUGUE-combining transcriptional and network features, to predict tissue-relevant genes across 30 human tissues. FUGUE achieves an average cross-validation auROC of 0.86 and auPRC of 0.50 (expected 0.09). In independent datasets, FUGUE accurately distinguishes tissue or cell type-specific genes, significantly outperforming the conventional metric based on tissue-specific expression alone. Comparison of tissue-relevant transcription factors across tissue recapitulate their developmental relationships. Interestingly, the tissue-relevant genes cluster on the genome within topologically associated domains and furthermore, are highly enriched for differentially expressed genes in the corresponding cancer type. We provide the prioritized gene lists in 30 human tissues and an open-source software to prioritize genes in a novel context given multi-sample transcriptomic data.
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Affiliation(s)
- Gowthami Somepalli
- Department of Computer Science, University of Maryland, College Park, Maryland, United States of America
| | - Sarthak Sahoo
- Undergraduate program, Indian Institute of Science, Bengaluru, India
| | - Arashdeep Singh
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sridhar Hannenhalli
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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13
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The expanding world of tRNA modifications and their disease relevance. Nat Rev Mol Cell Biol 2021; 22:375-392. [PMID: 33658722 DOI: 10.1038/s41580-021-00342-0] [Citation(s) in RCA: 263] [Impact Index Per Article: 87.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2021] [Indexed: 02/08/2023]
Abstract
Transfer RNA (tRNA) is an adapter molecule that links a specific codon in mRNA with its corresponding amino acid during protein synthesis. tRNAs are enzymatically modified post-transcriptionally. A wide variety of tRNA modifications are found in the tRNA anticodon, which are crucial for precise codon recognition and reading frame maintenance, thereby ensuring accurate and efficient protein synthesis. In addition, tRNA-body regions are also frequently modified and thus stabilized in the cell. Over the past two decades, 16 novel tRNA modifications were discovered in various organisms, and the chemical space of tRNA modification continues to expand. Recent studies have revealed that tRNA modifications can be dynamically altered in response to levels of cellular metabolites and environmental stresses. Importantly, we now understand that deficiencies in tRNA modification can have pathological consequences, which are termed 'RNA modopathies'. Dysregulation of tRNA modification is involved in mitochondrial diseases, neurological disorders and cancer.
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14
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Ma Y, Maruta H, Sun B, Wang C, Isono C, Yamashita H. Effects of long-term taurine supplementation on age-related changes in skeletal muscle function of Sprague-Dawley rats. Amino Acids 2021; 53:159-170. [PMID: 33398526 DOI: 10.1007/s00726-020-02934-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 12/19/2020] [Indexed: 12/16/2022]
Abstract
Taurine (2-aminoethanesulfonic acid) is a free amino acid found abundantly in mammalian tissues. Increasing evidence suggests that taurine plays a role in the maintenance of skeletal muscle function and increase of exercise capacity. Most energy drinks contain this amino acid; however, there is insufficient research on the effects of long-term, low-dose supplementation of taurine. In this study, we investigated the effects of long-term administration of taurine at low doses on aging in rodents. In Experiment 1, we examined age-related changes in aging Sprague-Dawley (SD) rats (32-92 weeks old) that O2 consumption and spontaneous activity decreased significantly with aging. In Experiment 2, we examined the effects of long-term (21-week) administration of taurine on healthy aging SD rats. SD rats were stabilized for 32-34 weeks and divided into three groups, administrated water (control), 0.5% taurine (25 mg/kg body weight (BW)/day), or 1% taurine (50 mg/kg BW/day) from age 34 to 56 weeks (5 days/week, 5 mL/kg BW). Our findings suggest that long-term administration of taurine at relatively low dose could attenuate the age-related decline in O2 consumption and spontaneous locomotor activity. Upon intestinal absorption, taurine might modulate age-related changes in respiratory metabolism and skeletal muscle function via peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α), succinate dehydrogenase (SDH), cytochrome c (Cycs), myocyte enhancer factor 2A (MEF2A), glucose transporter 4 (GLUT4), and myoglobin, which are regulated by the activation of AMP-activated protein kinase (AMPK). This article examines the mechanism underlying the effects of taurine on age-related changes, which may have potential clinical implications.
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Affiliation(s)
- Yun Ma
- Graduate School of Health and Welfare Science, Okayama Prefectural University, Soja, Okayama, 719-1197, Japan
| | - Hitomi Maruta
- Department of Nutritional Science, Okayama Prefectural University, Soja, Okayama, 719-1197, Japan
| | - Baojun Sun
- Graduate School of Health and Welfare Science, Okayama Prefectural University, Soja, Okayama, 719-1197, Japan
| | - Chengduo Wang
- Graduate School of Health and Welfare Science, Okayama Prefectural University, Soja, Okayama, 719-1197, Japan
| | - Chiaki Isono
- Graduate School of Health and Welfare Science, Okayama Prefectural University, Soja, Okayama, 719-1197, Japan
| | - Hiromi Yamashita
- Graduate School of Health and Welfare Science, Okayama Prefectural University, Soja, Okayama, 719-1197, Japan. .,Department of Nutritional Science, Okayama Prefectural University, Soja, Okayama, 719-1197, Japan.
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15
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Fakruddin M, Wei FY, Suzuki T, Asano K, Kaieda T, Omori A, Izumi R, Fujimura A, Kaitsuka T, Miyata K, Araki K, Oike Y, Scorrano L, Suzuki T, Tomizawa K. Defective Mitochondrial tRNA Taurine Modification Activates Global Proteostress and Leads to Mitochondrial Disease. Cell Rep 2019; 22:482-496. [PMID: 29320742 DOI: 10.1016/j.celrep.2017.12.051] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 10/30/2017] [Accepted: 12/14/2017] [Indexed: 12/14/2022] Open
Abstract
A subset of mitochondrial tRNAs (mt-tRNAs) contains taurine-derived modifications at 34U of the anticodon. Loss of taurine modification has been linked to the development of mitochondrial diseases, but the molecular mechanism is still unclear. Here, we showed that taurine modification is catalyzed by mitochondrial optimization 1 (Mto1) in mammals. Mto1 deficiency severely impaired mitochondrial translation and respiratory activity. Moreover, Mto1-deficient cells exhibited abnormal mitochondrial morphology owing to aberrant trafficking of nuclear DNA-encoded mitochondrial proteins, including Opa1. The mistargeted proteins were aggregated and misfolded in the cytoplasm, which induced cytotoxic unfolded protein response. Importantly, application of chemical chaperones successfully suppressed cytotoxicity by reducing protein misfolding and increasing functional mitochondrial proteins in Mto1-deficient cells and mice. Thus, our results demonstrate the essential role of taurine modification in mitochondrial translation and reveal an intrinsic protein homeostasis network between the mitochondria and cytosol, which has therapeutic potential for mitochondrial diseases.
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Affiliation(s)
- Md Fakruddin
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan; Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Kana Asano
- Department of Chemistry and Biotechnology, School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Takashi Kaieda
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Akiko Omori
- Department of Biology, University of Padova, Padova 35121, Italy
| | - Ryoma Izumi
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Atsushi Fujimura
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Taku Kaitsuka
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Keishi Miyata
- Department of Molecular Genetics, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Kimi Araki
- Institute of Resource Development and Analysis, Kumamoto University, Kumamoto 860-8556, Japan
| | - Yuichi Oike
- Department of Molecular Genetics, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Luca Scorrano
- Department of Biology, University of Padova, Padova 35121, Italy
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan.
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16
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Charging the code - tRNA modification complexes. Curr Opin Struct Biol 2019; 55:138-146. [PMID: 31102979 DOI: 10.1016/j.sbi.2019.03.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/08/2019] [Indexed: 02/06/2023]
Abstract
All types of cellular RNAs are post-transcriptionally modified, constituting the so called 'epitranscriptome'. In particular, tRNAs and their anticodon stem loops represent major modification hotspots. The attachment of small chemical groups at the heart of the ribosomal decoding machinery can directly affect translational rates, reading frame maintenance, co-translational folding dynamics and overall proteome stability. The variety of tRNA modification patterns is driven by the activity of specialized tRNA modifiers and large modification complexes. Notably, the absence or dysfunction of these cellular machines is correlated with several human pathophysiologies. In this review, we aim to highlight the most recent scientific progress and summarize currently available structural information of the most prominent eukaryotic tRNA modifiers.
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Ducamp S, Fleming MD. The molecular genetics of sideroblastic anemia. Blood 2019; 133:59-69. [PMID: 30401706 PMCID: PMC6318428 DOI: 10.1182/blood-2018-08-815951] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/21/2018] [Indexed: 01/19/2023] Open
Abstract
The sideroblastic anemias (SAs) are a group of inherited and acquired bone marrow disorders defined by pathological iron accumulation in the mitochondria of erythroid precursors. Like most hematological diseases, the molecular genetic basis of the SAs has ridden the wave of technology advancement. Within the last 30 years, with the advent of positional cloning, the human genome project, solid-state genotyping technologies, and next-generation sequencing have evolved to the point where more than two-thirds of congenital SA cases, and an even greater proportion of cases of acquired clonal disease, can be attributed to mutations in a specific gene or genes. This review focuses on an analysis of the genetics of these diseases and how understanding these defects may contribute to the design and implementation of rational therapies.
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Affiliation(s)
- Sarah Ducamp
- Department of Pathology, Boston Children's Hospital, Boston, MA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Boston, MA
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18
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The emerging impact of tRNA modifications in the brain and nervous system. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:412-428. [PMID: 30529455 DOI: 10.1016/j.bbagrm.2018.11.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/21/2018] [Accepted: 11/23/2018] [Indexed: 01/19/2023]
Abstract
A remarkable number of neurodevelopmental disorders have been linked to defects in tRNA modifications. These discoveries place tRNA modifications in the spotlight as critical modulators of gene expression pathways that are required for proper organismal growth and development. Here, we discuss the emerging molecular and cellular functions of the diverse tRNA modifications linked to cognitive and neurological disorders. In particular, we describe how the structure and location of a tRNA modification influences tRNA folding, stability, and function. We then highlight how modifications in tRNA can impact multiple aspects of protein translation that are instrumental for maintaining proper cellular proteostasis. Importantly, we describe how perturbations in tRNA modification lead to a spectrum of deleterious biological outcomes that can disturb neurodevelopment and neurological function. Finally, we summarize the biological themes shared by the different tRNA modifications linked to cognitive disorders and offer insight into the future questions that remain to decipher the role of tRNA modifications. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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19
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Cogliati S, Lorenzi I, Rigoni G, Caicci F, Soriano ME. Regulation of Mitochondrial Electron Transport Chain Assembly. J Mol Biol 2018; 430:4849-4873. [DOI: 10.1016/j.jmb.2018.09.016] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/20/2018] [Accepted: 09/25/2018] [Indexed: 12/26/2022]
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20
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Brissot P, Bernard DG, Brissot E, Loréal O, Troadec MB. Rare anemias due to genetic iron metabolism defects. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 777:52-63. [PMID: 30115430 DOI: 10.1016/j.mrrev.2018.06.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/05/2018] [Accepted: 06/21/2018] [Indexed: 01/19/2023]
Abstract
Anemia is defined by a deficiency of hemoglobin, an iron-rich protein that binds oxygen in the blood. It can be due to multiple causes, either acquired or genetic. Alterations of genes involved in iron metabolism may be responsible, usually at a young age, for rare forms of chronic and often severe congenital anemia. These diseases encompass a variety of sideroblastic anemias, characterized by the presence of ring sideroblasts in the bone marrow. Clinical expression of congenital sideroblastic anemia is either monosyndromic (restricted to hematological lineages) or polysyndromic (with systemic expression), depending on whether iron metabolism, and especially heme synthesis, is directly or indirectly affected. Beside sideroblastic anemias, a number of other anemias can develop due to mutations of key proteins acting either on cellular iron transport (such as the DMT1 transporter), plasma iron transport (transferrin), and iron recycling (ceruloplasmin). Contrasting with the aforementioned entities which involve compartmental, and sometimes, systemic iron excess, the iron refractory iron deficiency anemia (IRIDA) corresponds to a usually severe anemia with whole body iron deficiency related to chronic increase of plasma hepcidin, the systemic negative regulator of plasma iron. Once clinically suggested, these diseases are confirmed by genetic testing in specialized laboratories.
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Affiliation(s)
- Pierre Brissot
- INSERM, Univ Rennes, INRA, Institut NUMECAN (Nutrition, Metabolisms and Cancer), UMR_S 1241, F-35000 Rennes, France.
| | - Delphine G Bernard
- UMR 1078 "Génétique, Génomique Fonctionnelle et Biotechnologies", INSERM, Univ. Brest, EFS, IBSAM, Brest, France
| | - Eolia Brissot
- Sorbonne Universités, UPMC Univ. Paris 06, AP-HP, Centre de recherche Saint-Antoine, UMR-S938, Paris, France; Service d'Hématologie Clinique et de Thérapie Cellulaire, Hôpital Saint Antoine, APHP, Paris, France
| | - Olivier Loréal
- INSERM, Univ Rennes, INRA, Institut NUMECAN (Nutrition, Metabolisms and Cancer), UMR_S 1241, F-35000 Rennes, France
| | - Marie-Bérengère Troadec
- Univ. Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F- 35000 Rennes, France.
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21
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Fix DK, Hardee JP, Gao S, VanderVeen BN, Velázquez KT, Carson JA. Role of gp130 in basal and exercise-trained skeletal muscle mitochondrial quality control. J Appl Physiol (1985) 2018; 124:1456-1470. [PMID: 29389248 DOI: 10.1152/japplphysiol.01063.2017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The IL-6 cytokine family activates intracellular signaling pathways through glycoprotein-130 (gp130), and this signaling has established regulatory roles in muscle glucose metabolism and proteostasis. Although the IL-6 family has been implicated as myokines regulating the muscles' metabolic response to exercise, gp130's role in mitochondrial quality control involving fission, fusion, mitophagy, and biogenesis is not well understood. Therefore, we examined gp130's role in basal and exercise-trained muscle mitochondrial quality control. Muscles from C57BL/6, skeletal muscle-specific gp130 knockout (KO) mice, and C2C12 myotubes, were examined. KO did not alter treadmill run-to-fatigue or indices of mitochondrial content [cytochrome- c oxidase (COX) activity] or biogenesis (AMPK, peroxisome proliferator-activated receptor-γ coactivator-1α, mitochondrial transcription factor A, and COX IV). KO increased mitochondrial fission 1 protein (FIS-1) while suppressing mitofusin-1 (MFN-1), which was recapitulated in myotubes after gp130 knockdown. KO induced ubiquitin-binding protein p62, Parkin, and ubiquitin in isolated mitochondria from gastrocnemius muscles. Knockdown of gp130 in myotubes suppressed STAT3 and induced accumulation of microtubule-associated protein-1 light chain 3B (LC3)-II relative to LC3-I. Suppression of myotube STAT3 did not alter FIS-1 or MFN-1. Exercise training increased muscle gp130 and suppressed STAT3. KO did not alter the exercise-training induction of COX activity, biogenesis, FIS-1, or Beclin-1. KO increased MFN-1 and suppressed 4-hydroxynonenal after exercise training. These findings suggest a role for gp130 in the modulation of mitochondrial dynamics and autophagic processes. NEW & NOTEWORTHY Although the IL-6 family of cytokines has been implicated in the regulation of skeletal muscle protein turnover and metabolism, less is understood about its role in mitochondrial quality control. We examined the glycoprotein-130 receptor in the regulation of skeletal muscle mitochondria quality control in the basal and exercise-trained states. We report that the muscle glycoprotein-130 receptor modulates basal mitochondrial dynamics and autophagic processes and is not necessary for exercise-training mitochondrial adaptations to quality control.
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Affiliation(s)
- Dennis K Fix
- Integrative Muscle Biology Laboratory, Division of Applied Physiology, Department of Exercise Science, University of South Carolina , Columbia, South Carolina
| | - Justin P Hardee
- Integrative Muscle Biology Laboratory, Division of Applied Physiology, Department of Exercise Science, University of South Carolina , Columbia, South Carolina
| | - Song Gao
- Integrative Muscle Biology Laboratory, Division of Applied Physiology, Department of Exercise Science, University of South Carolina , Columbia, South Carolina
| | - Brandon N VanderVeen
- Integrative Muscle Biology Laboratory, Division of Applied Physiology, Department of Exercise Science, University of South Carolina , Columbia, South Carolina
| | - Kandy T Velázquez
- Integrative Muscle Biology Laboratory, Division of Applied Physiology, Department of Exercise Science, University of South Carolina , Columbia, South Carolina.,Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina , Columbia, South Carolina
| | - James A Carson
- Integrative Muscle Biology Laboratory, Division of Applied Physiology, Department of Exercise Science, University of South Carolina , Columbia, South Carolina.,Center for Colon Cancer Research, University of South Carolina , Columbia, South Carolina
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22
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Burn-induced muscle metabolic derangements and mitochondrial dysfunction are associated with activation of HIF-1α and mTORC1: Role of protein farnesylation. Sci Rep 2017; 7:6618. [PMID: 28747716 PMCID: PMC5529411 DOI: 10.1038/s41598-017-07011-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/21/2017] [Indexed: 12/28/2022] Open
Abstract
Metabolic derangements are a clinically significant complication of major trauma (e.g., burn injury) and include various aspects of metabolism, such as insulin resistance, muscle wasting, mitochondrial dysfunction and hyperlactatemia. Nonetheless, the molecular pathogenesis and the relation between these diverse metabolic alterations are poorly understood. We have previously shown that burn increases farnesyltransferase (FTase) expression and protein farnesylation and that FTase inhibitor (FTI) prevents burn-induced hyperlactatemia, insulin resistance, and increased proteolysis in mouse skeletal muscle. In this study, we found that burn injury activated mTORC1 and hypoxia-inducible factor (HIF)-1α, which paralleled dysfunction, morphological alterations (i.e., enlargement, partial loss of cristae structure) and impairment of respiratory supercomplex assembly of the mitochondria, and ER stress. FTI reversed or ameliorated all of these alterations in burned mice. These findings indicate that these burn-induced changes, which encompass various aspects of metabolism, may be linked to one another and require protein farnesylation. Our results provide evidence of involvement of the mTORC1-HIF-1α pathway in burn-induced metabolic derangements. Our study identifies protein farnesylation as a potential hub of the signaling network affecting multiple aspects of metabolic alterations after burn injury and as a novel potential molecular target to improve the clinical outcome of severely burned patients.
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23
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Deryusheva S, Gall JG. Dual nature of pseudouridylation in U2 snRNA: Pus1p-dependent and Pus1p-independent activities in yeasts and higher eukaryotes. RNA (NEW YORK, N.Y.) 2017; 23:1060-1067. [PMID: 28432181 PMCID: PMC5473140 DOI: 10.1261/rna.061226.117] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/18/2017] [Indexed: 05/05/2023]
Abstract
The pseudouridine at position 43 in vertebrate U2 snRNA is one of the most conserved post-transcriptional modifications of spliceosomal snRNAs; the equivalent position is pseudouridylated in U2 snRNAs in different phyla including fungi, insects, and worms. Pseudouridine synthase Pus1p acts alone on U2 snRNA to form this pseudouridine in yeast Saccharomyces cerevisiae and mouse. Furthermore, in S. cerevisiae, Pus1p is the only pseudouridine synthase for this position. Using an in vivo yeast cell system, we tested enzymatic activity of Pus1p from the fission yeast Schizosaccharomyces pombe, the worm Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and the frog Xenopus tropicalis We demonstrated that Pus1p from C. elegans has no enzymatic activity on U2 snRNA when expressed in yeast cells, whereas in similar experiments, position 44 in yeast U2 snRNA (equivalent to position 43 in vertebrates) is a genuine substrate for Pus1p from S. cerevisiae, S. pombe, Drosophila, Xenopus, and mouse. However, when we analyzed U2 snRNAs from Pus1 knockout mice and the pus1Δ S. pombe strain, we could not detect any changes in their modification patterns when compared to wild-type U2 snRNAs. In S. pombe, we found a novel box H/ACA RNA encoded downstream from the RPC10 gene and experimentally verified its guide RNA activity for positioning Ψ43 and Ψ44 in U2 snRNA. In vertebrates, we showed that SCARNA8 (also known as U92 scaRNA) is a guide for U2-Ψ43 in addition to its previously established targets U2-Ψ34/Ψ44.
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Affiliation(s)
- Svetlana Deryusheva
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
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24
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Rintala-Dempsey AC, Kothe U. Eukaryotic stand-alone pseudouridine synthases - RNA modifying enzymes and emerging regulators of gene expression? RNA Biol 2017; 14:1185-1196. [PMID: 28045575 PMCID: PMC5699540 DOI: 10.1080/15476286.2016.1276150] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
For a long time, eukaryotic stand-alone pseudouridine synthases (Pus enzymes) were neglected as non-essential enzymes adding seemingly simple modifications to tRNAs and small nuclear RNAs. Most studies were limited to the identification and initial characterization of the yeast Pus enzymes. However, recent transcriptome-wide mapping of pseudouridines in yeast and humans revealed pervasive modification of mRNAs and other non-coding RNAs by Pus enzymes which is dynamically regulated in response to cellular stress. Moreover, mutations in at least 2 genes encoding human Pus enzymes cause inherited diseases affecting muscle and brain function. Together, the recent findings suggest a broader-than-anticipated role of the Pus enzymes which are emerging as potential regulators of gene expression. In this review, we summarize the current knowledge on Pus enzymes, generate hypotheses regarding their cellular function and outline future areas of research of pseudouridine synthases.
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Affiliation(s)
- Anne C Rintala-Dempsey
- a Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry , University of Lethbridge , Lethbridge , AB , Canada
| | - Ute Kothe
- a Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry , University of Lethbridge , Lethbridge , AB , Canada
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25
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Wu Y, Wei FY, Kawarada L, Suzuki T, Araki K, Komohara Y, Fujimura A, Kaitsuka T, Takeya M, Oike Y, Suzuki T, Tomizawa K. Mtu1-Mediated Thiouridine Formation of Mitochondrial tRNAs Is Required for Mitochondrial Translation and Is Involved in Reversible Infantile Liver Injury. PLoS Genet 2016; 12:e1006355. [PMID: 27689697 PMCID: PMC5045200 DOI: 10.1371/journal.pgen.1006355] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/08/2016] [Indexed: 12/26/2022] Open
Abstract
Reversible infantile liver failure (RILF) is a unique heritable liver disease characterized by acute liver failure followed by spontaneous recovery at an early stage of life. Genetic mutations in MTU1 have been identified in RILF patients. MTU1 is a mitochondrial enzyme that catalyzes the 2-thiolation of 5-taurinomethyl-2-thiouridine (τm5s2U) found in the anticodon of a subset of mitochondrial tRNAs (mt-tRNAs). Although the genetic basis of RILF is clear, the molecular mechanism that drives the pathogenesis remains elusive. We here generated liver-specific knockout of Mtu1 (Mtu1LKO) mice, which exhibited symptoms of liver injury characterized by hepatic inflammation and elevated levels of plasma lactate and AST. Mechanistically, Mtu1 deficiency resulted in a loss of 2-thiolation in mt-tRNAs, which led to a marked impairment of mitochondrial translation. Consequently, Mtu1LKO mice exhibited severe disruption of mitochondrial membrane integrity and a broad decrease in respiratory complex activities in the hepatocytes. Interestingly, mitochondrial dysfunction induced signaling pathways related to mitochondrial proliferation and the suppression of oxidative stress. The present study demonstrates that Mtu1-dependent 2-thiolation of mt-tRNA is indispensable for mitochondrial translation and that Mtu1 deficiency is a primary cause of RILF. In addition, Mtu1 deficiency is associated with multiple cytoprotective pathways that might prevent catastrophic liver failure and assist in the recovery from liver injury. Mitochondrial transfer tRNA (mt-tRNA) contains a variety of chemical modifications that are introduced post-transcriptionally. Three mt-tRNAs for Lys, Gln and Glu contain 5-taurinomethyl-2-thiouridine (τm5s2U) in their anticodons. It is known that the loss of 2-thiolation of τm5s2U is strongly associated with the development of reversible infantile liver failure (RILF) because pathogenic mutations of RILF were found in the MTU1 gene, which encodes an enzyme responsible for the 2-thiolation of τm5s2U. However, the molecular mechanism underlying RILF pathogenesis associated with a lack of MTU1 remains elusive. To understand the physiological function of MTU1 and its association with liver failure, we generated liver-specific Mtu1-deficient (Mtu1LKO) mice. Mtu1 deficiency abolished 2-thiouridine formation in the three mt-tRNAs. Loss of the 2-thiouridine modification resulted in a marked impairment of mitochondrial translation and abnormal mitochondrial structure. Consequently, the Mtu1LKO mice exhibited liver injury, which resembles the symptoms of RILF patients. Furthermore, mitochondrial dysfunction in Mtu1LKO mice induced mitochondrial biogenesis and suppressed oxidative stress. These findings elucidate the cellular and physiological functions of Mtu1 and provide a mouse model for understanding RILF pathogenesis.
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Affiliation(s)
- Yong Wu
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi, Japan
| | - Layla Kawarada
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Kimi Araki
- Division of Developmental Genetics, Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Yoshihiro Komohara
- Department of Cell Pathology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Atsushi Fujimura
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Taku Kaitsuka
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Motohiro Takeya
- Department of Cell Pathology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yuichi Oike
- Department of Molecular Genetics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
- * E-mail:
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