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Zhang F, Ignatova VV, Ming GL, Song H. Advances in brain epitranscriptomics research and translational opportunities. Mol Psychiatry 2024; 29:449-463. [PMID: 38123727 PMCID: PMC11116067 DOI: 10.1038/s41380-023-02339-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/16/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
Various chemical modifications of all RNA transcripts, or epitranscriptomics, have emerged as crucial regulators of RNA metabolism, attracting significant interest from both basic and clinical researchers due to their diverse functions in biological processes and immense clinical potential as highlighted by the recent profound success of RNA modifications in improving COVID-19 mRNA vaccines. Rapid accumulation of evidence underscores the critical involvement of various RNA modifications in governing normal neural development and brain functions as well as pathogenesis of brain disorders. Here we provide an overview of RNA modifications and recent advancements in epitranscriptomic studies utilizing animal models to elucidate important roles of RNA modifications in regulating mammalian neurogenesis, gliogenesis, synaptic formation, and brain function. Moreover, we emphasize the pivotal involvement of RNA modifications and their regulators in the pathogenesis of various human brain disorders, encompassing neurodevelopmental disorders, brain tumors, psychiatric and neurodegenerative disorders. Furthermore, we discuss potential translational opportunities afforded by RNA modifications in combatting brain disorders, including their use as biomarkers, in the development of drugs or gene therapies targeting epitranscriptomic pathways, and in applications for mRNA-based vaccines and therapies. We also address current limitations and challenges hindering the widespread clinical application of epitranscriptomic research, along with the improvements necessary for future progress.
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Affiliation(s)
- Feng Zhang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Valentina V Ignatova
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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2
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Ueda S, Yagi M, Tomoda E, Matsumoto S, Ueyanagi Y, Do Y, Setoyama D, Matsushima Y, Nagao A, Suzuki T, Ide T, Mori Y, Oyama N, Kang D, Uchiumi T. Mitochondrial haplotype mutation alleviates respiratory defect of MELAS by restoring taurine modification in tRNA with 3243A > G mutation. Nucleic Acids Res 2023; 51:7480-7495. [PMID: 37439353 PMCID: PMC10415116 DOI: 10.1093/nar/gkad591] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 07/14/2023] Open
Abstract
The 3243A > G in mtDNA is a representative mutation in mitochondrial diseases. Mitochondrial protein synthesis is impaired due to decoding disorder caused by severe reduction of 5-taurinomethyluridine (τm5U) modification of the mutant mt-tRNALeu(UUR) bearing 3243A > G mutation. The 3243A > G heteroplasmy in peripheral blood reportedly decreases exponentially with age. Here, we found three cases with mild respiratory symptoms despite bearing high rate of 3243A > G mutation (>90%) in blood mtDNA. These patients had the 3290T > C haplotypic mutation in addition to 3243A > G pathogenic mutation in mt-tRNALeu(UUR) gene. We generated cybrid cells of these cases to examine the effects of the 3290T > C mutation on mitochondrial function and found that 3290T > C mutation improved mitochondrial translation, formation of respiratory chain complex, and oxygen consumption rate of pathogenic cells associated with 3243A > G mutation. We measured τm5U frequency of mt-tRNALeu(UUR) with 3243A > G mutation in the cybrids by a primer extension method assisted with chemical derivatization of τm5U, showing that hypomodification of τm5U was significantly restored by the 3290T > C haplotypic mutation. We concluded that the 3290T > C is a haplotypic mutation that suppresses respiratory deficiency of mitochondrial disease by restoring hypomodified τm5U in mt-tRNALeu(UUR) with 3243A > G mutation, implying a potential therapeutic measure for mitochondrial disease associated with pathogenic mutations in mt-tRNAs.
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Affiliation(s)
- Saori Ueda
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mikako Yagi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Ena Tomoda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Shinya Matsumoto
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yasushi Ueyanagi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yura Do
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Daiki Setoyama
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuichi Matsushima
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Japan
| | - Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tomomi Ide
- Department of Cardiovascular Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yusuke Mori
- Department of Internal Medicine Kitakyushu City Yahata Hospital, 2-6-2 Ogura, Yahatahigashi-ku, Kitakyushu 805-8534, Japan
| | - Noriko Oyama
- Department of Endocrinology and Metabolism, Fukuoka Children's Hospital, 5-1-1 Kashiiteriha, Higashi-ku, Fukuoka 813-0017, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takeshi Uchiumi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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3
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Xing S, Jiang S, Wang S, Lin P, Sun H, Peng H, Yang J, Kong H, Wang S, Bai Q, Qiu R, Dai W, Yuan J, Ma Y, Yu X, Yao Y, Su J. Association of mitochondrial DNA variation with high myopia in a Han Chinese population. Mol Genet Genomics 2023:10.1007/s00438-023-02036-y. [PMID: 37277661 PMCID: PMC10363046 DOI: 10.1007/s00438-023-02036-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/15/2023] [Indexed: 06/07/2023]
Abstract
High myopia (HM), which is characterized by oxidative stress, is one of the leading causes of visual impairment and blindness across the world. Family and population genetic studies have uncovered nuclear-genome variants in proteins functioned in the mitochondria. However, whether mitochondrial DNA mutations are involved in HM remains unexplored. Here, we performed the first large-scale whole-mitochondrial genome study in 9613 HM cases and 9606 control subjects of Han Chinese ancestry for identifying HM-associated mitochondrial variants. The single-variant association analysis identified nine novel genetic variants associated with HM reaching the entire mitochondrial wide significance level, including rs370378529 in ND2 with an odds ratio (OR) of 5.25. Interestingly, eight out of nine variants were predominantly located in related sub-haplogroups, i.e. m.5261G > A in B4b1c, m.12280A > G in G2a4, m.7912G > A in D4a3b, m.94G > A in D4e1, m.14857 T > C in D4e3, m.14280A > G in D5a2, m.16272A > G in G2a4, m.8718A > G in M71 and F1a3, indicating that the sub-haplogroup background can increase the susceptible risk for high myopia. The polygenic risk score analysis of the target and validation cohorts indicated a high accuracy for predicting HM with mtDNA variants (AUC = 0.641). Cumulatively, our findings highlight the critical roles of mitochondrial variants in untangling the genetic etiology of HM.
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Affiliation(s)
- Shilai Xing
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Siyi Jiang
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Siyu Wang
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Peng Lin
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Haojun Sun
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Hui Peng
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jiaying Yang
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Hengte Kong
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Sheng Wang
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Qingshi Bai
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Ruowen Qiu
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Wei Dai
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, China
| | - Jian Yuan
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- National Clinical Research Center for Ocular Disease, Wenzhou, 325027, China
| | - Yunlong Ma
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- National Clinical Research Center for Ocular Disease, Wenzhou, 325027, China
| | - Xiaoguang Yu
- Institute of PSI Genomics, Wenzhou, 325024, China
| | - Yinghao Yao
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, 325101, Zhejiang, China.
| | - Jianzhong Su
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, China.
- National Clinical Research Center for Ocular Disease, Wenzhou, 325027, China.
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, 325101, Zhejiang, China.
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4
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Suzuki T, Yashiro Y, Kikuchi I, Ishigami Y, Saito H, Matsuzawa I, Okada S, Mito M, Iwasaki S, Ma D, Zhao X, Asano K, Lin H, Kirino Y, Sakaguchi Y, Suzuki T. Complete chemical structures of human mitochondrial tRNAs. Nat Commun 2020; 11:4269. [PMID: 32859890 PMCID: PMC7455718 DOI: 10.1038/s41467-020-18068-6] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/27/2020] [Indexed: 11/09/2022] Open
Abstract
Mitochondria generate most cellular energy via oxidative phosphorylation. Twenty-two species of mitochondrial (mt-)tRNAs encoded in mtDNA translate essential subunits of the respiratory chain complexes. mt-tRNAs contain post-transcriptional modifications introduced by nuclear-encoded tRNA-modifying enzymes. They are required for deciphering genetic code accurately, as well as stabilizing tRNA. Loss of tRNA modifications frequently results in severe pathological consequences. Here, we perform a comprehensive analysis of post-transcriptional modifications of all human mt-tRNAs, including 14 previously-uncharacterized species. In total, we find 18 kinds of RNA modifications at 137 positions (8.7% in 1575 nucleobases) in 22 species of human mt-tRNAs. An up-to-date list of 34 genes responsible for mt-tRNA modifications are provided. We identify two genes required for queuosine (Q) formation in mt-tRNAs. Our results provide insight into the molecular mechanisms underlying the decoding system and could help to elucidate the molecular pathogenesis of human mitochondrial diseases caused by aberrant tRNA modifications.
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Affiliation(s)
- Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yuka Yashiro
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Ittoku Kikuchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yuma Ishigami
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Hironori Saito
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Ikuya Matsuzawa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Shunpei Okada
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
- Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba, 278-0022, Japan
| | - Mari Mito
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shintaro Iwasaki
- RNA System Biochemistry Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Ding Ma
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Xuewei Zhao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kana Asano
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Huan Lin
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 570228, Haikou, Hainan, P.R. China
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, 113-8656, Japan.
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5
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Toompuu M, Tuomela T, Laine P, Paulin L, Dufour E, Jacobs HT. Polyadenylation and degradation of structurally abnormal mitochondrial tRNAs in human cells. Nucleic Acids Res 2019. [PMID: 29518244 PMCID: PMC6007314 DOI: 10.1093/nar/gky159] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
RNA 3' polyadenylation is known to serve diverse purposes in biology, in particular, regulating mRNA stability and translation. Here we determined that, upon exposure to high levels of the intercalating agent ethidium bromide (EtBr), greater than those required to suppress mitochondrial transcription, mitochondrial tRNAs in human cells became polyadenylated. Relaxation of the inducing stress led to rapid turnover of the polyadenylated tRNAs. The extent, kinetics and duration of tRNA polyadenylation were EtBr dose-dependent, with mitochondrial tRNAs differentially sensitive to the stress. RNA interference and inhibitor studies indicated that ongoing mitochondrial ATP synthesis, plus the mitochondrial poly(A) polymerase and SUV3 helicase were required for tRNA polyadenylation, while polynucleotide phosphorylase counteracted the process and was needed, along with SUV3, for degradation of the polyadenylated tRNAs. Doxycycline treatment inhibited both tRNA polyadenylation and turnover, suggesting a possible involvement of the mitoribosome, although other translational inhibitors had only minor effects. The dysfunctional tRNALeu(UUR) bearing the pathological A3243G mutation was constitutively polyadenylated at a low level, but this was markedly enhanced after doxycycline treatment. We propose that polyadenylation of structurally and functionally abnormal mitochondrial tRNAs entrains their PNPase/SUV3-mediated destruction, and that this pathway could play an important role in mitochondrial diseases associated with tRNA mutations.
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Affiliation(s)
- Marina Toompuu
- Faculty of Medicine and Life Sciences, BioMediTech Institute and Tampere University Hospital, FI-33014 University of Tampere, Finland
| | - Tea Tuomela
- Faculty of Medicine and Life Sciences, BioMediTech Institute and Tampere University Hospital, FI-33014 University of Tampere, Finland
| | - Pia Laine
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Eric Dufour
- Faculty of Medicine and Life Sciences, BioMediTech Institute and Tampere University Hospital, FI-33014 University of Tampere, Finland
| | - Howard T Jacobs
- Faculty of Medicine and Life Sciences, BioMediTech Institute and Tampere University Hospital, FI-33014 University of Tampere, Finland.,Institute of Biotechnology, FI-00014 University of Helsinki, Finland
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Santos M, Fidalgo A, Varanda AS, Oliveira C, Santos MAS. tRNA Deregulation and Its Consequences in Cancer. Trends Mol Med 2019; 25:853-865. [PMID: 31248782 DOI: 10.1016/j.molmed.2019.05.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/24/2019] [Accepted: 05/28/2019] [Indexed: 02/06/2023]
Abstract
The expression of transfer RNAs (tRNAs) is deregulated in cancer cells but the mechanisms and functional meaning of such deregulation are poorly understood. The proteome of cancer cells is not fully encoded by their transcriptome, however, the contribution of mRNA translation to such diversity remains to be elucidated. We review data supporting the hypothesis that tRNA expression deregulation and translational error rate is an important contributor to proteome diversity and cell population heterogeneity, genome instability, and drug resistance in tumors. This hypothesis is aligned with recent data in various model organisms, showing unanticipated adaptive roles of translational errors (adaptive mistranslation), expression control of specific gene subsets by tRNAs, and proteome diversification by elevation of translational error rates in tumors.
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Affiliation(s)
- Mafalda Santos
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal; Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal; Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Ana Fidalgo
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - A Sofia Varanda
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal; Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal; Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal
| | - Carla Oliveira
- Expression Regulation in Cancer, Instituto de Investigação e Inovação em Saúde, University of Porto, Portugal; Institute of Molecular Pathology and Immunology University of Porto (IPATIMUP), Porto, Portugal; Department of Pathology, Medical Faculty of Porto, Porto, Portugal.
| | - Manuel A S Santos
- Department of Medical Sciences and Institute of Biomedicine - iBiMED, University of Aveiro, Aveiro, Portugal.
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7
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Wang D, Ning C, Xiang H, Zheng X, Kong M, Yin T, Liu J, Zhao X. Polymorphism of mitochondrial tRNA genes associated with the number of pigs born alive. J Anim Sci Biotechnol 2018; 9:86. [PMID: 30534375 PMCID: PMC6260895 DOI: 10.1186/s40104-018-0299-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/17/2018] [Indexed: 11/13/2022] Open
Abstract
Background Mutations in mitochondrial tRNA genes have been widely reported association with human reproductions. It is also important to explore the effect on the number of piglets born alive (NBA). Here, 1017 sows were used to investigate the association between polymorphisms in mitochondrial tRNA genes and NBA. Results In total, 16 mutations were found in mitochondrial tRNA genes, of which 13 mutations were significantly associated with NBA (P < 0.05). The reproductions of mutant carriers were significantly greater than that of wild carriers by 0.989 piglets born alive/sow farrowing. To test whether the mutations altered the structure of mitochondrial tRNAs, the secondary and tertiary structures were predicted. In result, C2255T changed the secondary structure of tRNA-Val by elongating the T stem and shrinking the T loop, and C2255T and G2259A in the tRNA-Val gene, C6217T and T6219C in the tRNA-Ala gene, and T15283C in the tRNA-Glu gene altered the tertiary structure of their tRNAs, respectively by changing the folding form of the T arm, and C16487T in the tRNA-Thr gene changed the tertiary structure of mitochondrial tRNA-Thr by influencing the folding form of the acceptor arm. Conclusions Results highlight the effect of mitochondrial tRNA genes on the number of piglets born alive, and suggest that polymorphic sites of the tRNA genes be genetic markers for selection of pig reproduction. Electronic supplementary material The online version of this article (10.1186/s40104-018-0299-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dan Wang
- 1National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Chao Ning
- 1National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Hai Xiang
- 2School of Life Science and Engineering, Foshan University, Foshan, 528225 China
| | - Xianrui Zheng
- 1National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Minghua Kong
- 1National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Tao Yin
- 1National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Jianfeng Liu
- 1National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Xingbo Zhao
- 1National Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
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8
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Abstract
BACKGROUND Given the etiologic heterogeneity of disease classification using clinical phenomenology, we employed contemporary criteria to classify variants associated with myoclonic epilepsy with ragged-red fibers (MERRF) syndrome and to assess the strength of evidence of gene-disease associations. Standardized approaches are used to clarify the definition of MERRF, which is essential for patient diagnosis, patient classification, and clinical trial design. METHODS Systematic literature and database search with application of standardized assessment of gene-disease relationships using modified Smith criteria and of variants reported to be associated with MERRF using modified Yarham criteria. RESULTS Review of available evidence supports a gene-disease association for two MT-tRNAs and for POLG. Using modified Smith criteria, definitive evidence of a MERRF gene-disease association is identified for MT-TK. Strong gene-disease evidence is present for MT-TL1 and POLG. Functional assays that directly associate variants with oxidative phosphorylation impairment were critical to mtDNA variant classification. In silico analysis was of limited utility to the assessment of individual MT-tRNA variants. With the use of contemporary classification criteria, several mtDNA variants previously reported as pathogenic or possibly pathogenic are reclassified as neutral variants. CONCLUSIONS MERRF is primarily an MT-TK disease, with pathogenic variants in this gene accounting for ~90% of MERRF patients. Although MERRF is phenotypically and genotypically heterogeneous, myoclonic epilepsy is the clinical feature that distinguishes MERRF from other categories of mitochondrial disorders. Given its low frequency in mitochondrial disorders, myoclonic epilepsy is not explained simply by an impairment of cellular energetics. Although MERRF phenocopies can occur in other genes, additional data are needed to establish a MERRF disease-gene association. This approach to MERRF emphasizes standardized classification rather than clinical phenomenology, thus improving patient diagnosis and clinical trial design.
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9
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Chen D, Li F, Yang Q, Tian M, Zhang Z, Zhang Q, Chen Y, Guan MX. The defective expression of gtpbp3 related to tRNA modification alters the mitochondrial function and development of zebrafish. Int J Biochem Cell Biol 2016; 77:1-9. [PMID: 27184967 DOI: 10.1016/j.biocel.2016.05.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 05/02/2016] [Accepted: 05/12/2016] [Indexed: 01/13/2023]
Abstract
Human mitochondrial DNA (mtDNA) mutations have been associated with a wide spectrum of clinical abnormalities. However, nuclear modifier gene(s) modulate the phenotypic expression of pathogenic mtDNA mutations. In our previous investigation, we identified the human GTPBP3 related to mitochondrial tRNA modification, acting as a modifier to influence of deafness-associated mtDNA mutation. Mutations in GTPBP3 have been found to be associated with other human diseases. However, the pathophysiology of GTPBP3-associated disorders is still not fully understood. Here, we reported the generation and characterization of Gtpbp3 depletion zebrafish model using antisense morpholinos. Zebrafish gtpbp3 has three isoforms localized at mitochondria. Zebrafish gtpbp3 is expressed at various embryonic stages and in multiple tissues. In particular, the gtpbp3 was expressed more abundantly in adult zebrafish ovary and testis. The expression of zebrafish gtpbp3 can functionally restore the growth defects caused by the mss1/gtpbp3 mutation in yeast. A marked decrease of mitochondrial ATP generation accompanied by increased levels of apoptosis and reactive oxygen species were observed in gtpbp3 knockdown zebrafish embryos. The Gtpbp3 morphants exhibited defective in embryonic development including bleeding, melenin, oedema and curved tails within 5days post fertilization, as compared with uninjected controls. The co-injection of wild type gtpbp3 mRNA partially rescued these defects in Gtpbp3 morphants. These data suggest that zebrafish Gtpbp3 is a structural and functional homolog of human and yeast GTPBP3. The mitochondrial dysfunction caused by defective Gtpbp3 may alter the embryonic development in the zebrafish. In addition, this zebrafish model of mitochondrial disease may provide unique opportunities for studying defective tRNA modification, mitochondrial biogenesis, and pathophysiology of mitochondrial disorders.
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Affiliation(s)
- Danni Chen
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Feng Li
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qingxian Yang
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Miao Tian
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Zengming Zhang
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qinghai Zhang
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ye Chen
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Min-Xin Guan
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310058, China; Joining Institute of Genetics and Genomic Medicine between Zhejiang University and University of Toronto, Zhejiang University, Hangzhou, Zhejiang, China.
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10
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Armengod ME, Meseguer S, Villarroya M, Prado S, Moukadiri I, Ruiz-Partida R, Garzón MJ, Navarro-González C, Martínez-Zamora A. Modification of the wobble uridine in bacterial and mitochondrial tRNAs reading NNA/NNG triplets of 2-codon boxes. RNA Biol 2015; 11:1495-507. [PMID: 25607529 DOI: 10.4161/15476286.2014.992269] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Posttranscriptional modification of the uridine located at the wobble position (U34) of tRNAs is crucial for optimization of translation. Defects in the U34 modification of mitochondrial-tRNAs are associated with a group of rare diseases collectively characterized by the impairment of the oxidative phosphorylation system. Retrograde signaling pathways from mitochondria to nucleus are involved in the pathophysiology of these diseases. These pathways may be triggered by not only the disturbance of the mitochondrial (mt) translation caused by hypomodification of tRNAs, but also as a result of nonconventional roles of mt-tRNAs and mt-tRNA-modifying enzymes. The evolutionary conservation of these enzymes supports their importance for cell and organismal functions. Interestingly, bacterial and eukaryotic cells respond to stress by altering the expression or activity of these tRNA-modifying enzymes, which leads to changes in the modification status of tRNAs. This review summarizes recent findings about these enzymes and sets them within the previous data context.
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Affiliation(s)
- M Eugenia Armengod
- a Laboratory of RNA Modification and Mitochondrial Diseases ; Centro de Investigación Príncipe Felipe ; Valencia , Spain
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11
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Powell C, Kopajtich R, D’Souza AR, Rorbach J, Kremer L, Husain R, Dallabona C, Donnini C, Alston C, Griffin H, Pyle A, Chinnery P, Strom T, Meitinger T, Rodenburg R, Schottmann G, Schuelke M, Romain N, Haller R, Ferrero I, Haack T, Taylor R, Prokisch H, Minczuk M. TRMT5 Mutations Cause a Defect in Post-transcriptional Modification of Mitochondrial tRNA Associated with Multiple Respiratory-Chain Deficiencies. Am J Hum Genet 2015; 97:319-28. [PMID: 26189817 PMCID: PMC4573257 DOI: 10.1016/j.ajhg.2015.06.011] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/16/2015] [Indexed: 10/29/2022] Open
Abstract
Deficiencies in respiratory-chain complexes lead to a variety of clinical phenotypes resulting from inadequate energy production by the mitochondrial oxidative phosphorylation system. Defective expression of mtDNA-encoded genes, caused by mutations in either the mitochondrial or nuclear genome, represents a rapidly growing group of human disorders. By whole-exome sequencing, we identified two unrelated individuals carrying compound heterozygous variants in TRMT5 (tRNA methyltransferase 5). TRMT5 encodes a mitochondrial protein with strong homology to members of the class I-like methyltransferase superfamily. Both affected individuals presented with lactic acidosis and evidence of multiple mitochondrial respiratory-chain-complex deficiencies in skeletal muscle, although the clinical presentation of the two affected subjects was remarkably different; one presented in childhood with failure to thrive and hypertrophic cardiomyopathy, and the other was an adult with a life-long history of exercise intolerance. Mutations in TRMT5 were associated with the hypomodification of a guanosine residue at position 37 (G37) of mitochondrial tRNA; this hypomodification was particularly prominent in skeletal muscle. Deficiency of the G37 modification was also detected in human cells subjected to TRMT5 RNAi. The pathogenicity of the detected variants was further confirmed in a heterologous yeast model and by the rescue of the molecular phenotype after re-expression of wild-type TRMT5 cDNA in cells derived from the affected individuals. Our study highlights the importance of post-transcriptional modification of mitochondrial tRNAs for faithful mitochondrial function.
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12
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Tischner C, Hofer A, Wulff V, Stepek J, Dumitru I, Becker L, Haack T, Kremer L, Datta AN, Sperl W, Floss T, Wurst W, Chrzanowska-Lightowlers Z, De Angelis MH, Klopstock T, Prokisch H, Wenz T. MTO1 mediates tissue specificity of OXPHOS defects via tRNA modification and translation optimization, which can be bypassed by dietary intervention. Hum Mol Genet 2015; 24:2247-66. [PMID: 25552653 PMCID: PMC4380071 DOI: 10.1093/hmg/ddu743] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 12/12/2014] [Accepted: 12/22/2014] [Indexed: 11/15/2022] Open
Abstract
Mitochondrial diseases often exhibit tissue-specific pathologies, but this phenomenon is poorly understood. Here we present regulation of mitochondrial translation by the Mitochondrial Translation Optimization Factor 1, MTO1, as a novel player in this scenario. We demonstrate that MTO1 mediates tRNA modification and controls mitochondrial translation rate in a highly tissue-specific manner associated with tissue-specific OXPHOS defects. Activation of mitochondrial proteases, aberrant translation products, as well as defects in OXPHOS complex assembly observed in MTO1 deficient mice further imply that MTO1 impacts translation fidelity. In our mouse model, MTO1-related OXPHOS deficiency can be bypassed by feeding a ketogenic diet. This therapeutic intervention is independent of the MTO1-mediated tRNA modification and involves balancing of mitochondrial and cellular secondary stress responses. Our results thereby establish mammalian MTO1 as a novel factor in the tissue-specific regulation of OXPHOS and fine tuning of mitochondrial translation accuracy.
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Affiliation(s)
- Christin Tischner
- Institute for Genetics and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zülpicher Str. 47A, Cologne 50674, Germany
| | - Annette Hofer
- Institute for Genetics and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zülpicher Str. 47A, Cologne 50674, Germany
| | - Veronika Wulff
- Institute for Genetics and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zülpicher Str. 47A, Cologne 50674, Germany
| | - Joanna Stepek
- Institute for Genetics and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zülpicher Str. 47A, Cologne 50674, Germany
| | - Iulia Dumitru
- Institute for Genetics and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zülpicher Str. 47A, Cologne 50674, Germany
| | - Lore Becker
- Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-University, Munich 80336, Germany, German Mouse Clinic, Institute of Experimental Genetics
| | - Tobias Haack
- Institute of Human Genetics, German Network for Mitochondrial Disorders (mitoNET), Germany
| | - Laura Kremer
- Institute of Human Genetics, German Network for Mitochondrial Disorders (mitoNET), Germany
| | - Alexandre N Datta
- Division of Neuropediatrics and Developmental Medicine, University Children's Hospital Basel (UKBB), University of Basel, Basel 4031, Switzerland
| | - Wolfgang Sperl
- German Network for Mitochondrial Disorders (mitoNET), Germany, Department of Pediatrics, Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Thomas Floss
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environment and Health (GmbH), Neuherberg 85764, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environment and Health (GmbH), Neuherberg 85764, Germany, Technical University Munich, Helmholtz Zentrum München, Neuherberg 85764, Germany, DZNE-German Center for Neurodegenerative Diseases, Munich, Germany, Max Planck Institute of Psychiatry, Munich 80804, Germany, German Center for Vertigo and Balance Disorders, Munich, Germany
| | - Zofia Chrzanowska-Lightowlers
- The Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, The Medical School, Newcastle upon Tyne NE2 4HH, UK
| | - Martin Hrabe De Angelis
- German Mouse Clinic, Institute of Experimental Genetics, German Center for Vertigo and Balance Disorders, Munich, Germany, Center of Life and Food Sciences Weihenstephan, Technische Universitat München, Freising 85350, Germany, German Center for Diabetes Research (DZD), Neuherberg 85764, Germany and Technische Universität München, Freising-Weihenstephan 85354, Germany
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-University, Munich 80336, Germany, German Mouse Clinic, Institute of Experimental Genetics, German Network for Mitochondrial Disorders (mitoNET), Germany, DZNE-German Center for Neurodegenerative Diseases, Munich, Germany, German Center for Vertigo and Balance Disorders, Munich, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environment and Health (GmbH), Neuherberg 85764, Germany
| | - Tina Wenz
- Institute for Genetics and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Zülpicher Str. 47A, Cologne 50674, Germany, German Network for Mitochondrial Disorders (mitoNET), Germany,
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13
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Powell CA, Nicholls TJ, Minczuk M. Nuclear-encoded factors involved in post-transcriptional processing and modification of mitochondrial tRNAs in human disease. Front Genet 2015; 6:79. [PMID: 25806043 PMCID: PMC4354410 DOI: 10.3389/fgene.2015.00079] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/16/2015] [Indexed: 11/29/2022] Open
Abstract
The human mitochondrial genome (mtDNA) encodes 22 tRNAs (mt-tRNAs) that are necessary for the intraorganellar translation of the 13 mtDNA-encoded subunits of the mitochondrial respiratory chain complexes. Maturation of mt-tRNAs involves 5′ and 3′ nucleolytic excision from precursor RNAs, as well as extensive post-transcriptional modifications. Recent data suggest that over 7% of all mt-tRNA residues in mammals undergo post-transcriptional modification, with over 30 different modified mt-tRNA positions so far described. These processing and modification steps are necessary for proper mt-tRNA function, and are performed by dedicated, nuclear-encoded enzymes. Recent growing evidence suggests that mutations in these nuclear genes (nDNA), leading to incorrect maturation of mt-tRNAs, are a cause of human mitochondrial disease. Furthermore, mtDNA mutations in mt-tRNA genes, which may also affect mt-tRNA function, processing, and modification, are also frequently associated with human disease. In theory, all pathogenic mt-tRNA variants should be expected to affect only a single process, which is mitochondrial translation, albeit to various extents. However, the clinical manifestations of mitochondrial disorders linked to mutations in mt-tRNAs are extremely heterogeneous, ranging from defects of a single tissue to complex multisystem disorders. This review focuses on the current knowledge of nDNA coding for proteins involved in mt-tRNA maturation that have been linked to human mitochondrial pathologies. We further discuss the possibility that tissue specific regulation of mt-tRNA modifying enzymes could play an important role in the clinical heterogeneity observed for mitochondrial diseases caused by mutations in mt-tRNA genes.
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Affiliation(s)
- Christopher A Powell
- Mitochondrial Genetics, Mitochondrial Biology Unit, Medical Research Council, Cambridge, UK
| | - Thomas J Nicholls
- Mitochondrial Genetics, Mitochondrial Biology Unit, Medical Research Council, Cambridge, UK
| | - Michal Minczuk
- Mitochondrial Genetics, Mitochondrial Biology Unit, Medical Research Council, Cambridge, UK
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14
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Salinas-Giegé T, Giegé R, Giegé P. tRNA biology in mitochondria. Int J Mol Sci 2015; 16:4518-59. [PMID: 25734984 PMCID: PMC4394434 DOI: 10.3390/ijms16034518] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/23/2015] [Accepted: 01/29/2015] [Indexed: 01/23/2023] Open
Abstract
Mitochondria are the powerhouses of eukaryotic cells. They are considered as semi-autonomous because they have retained genomes inherited from their prokaryotic ancestor and host fully functional gene expression machineries. These organelles have attracted considerable attention because they combine bacterial-like traits with novel features that evolved in the host cell. Among them, mitochondria use many specific pathways to obtain complete and functional sets of tRNAs as required for translation. In some instances, tRNA genes have been partially or entirely transferred to the nucleus and mitochondria require precise import systems to attain their pool of tRNAs. Still, tRNA genes have also often been maintained in mitochondria. Their genetic arrangement is more diverse than previously envisaged. The expression and maturation of mitochondrial tRNAs often use specific enzymes that evolved during eukaryote history. For instance many mitochondria use a eukaryote-specific RNase P enzyme devoid of RNA. The structure itself of mitochondrial encoded tRNAs is also very diverse, as e.g., in Metazoan, where tRNAs often show non canonical or truncated structures. As a result, the translational machinery in mitochondria evolved adapted strategies to accommodate the peculiarities of these tRNAs, in particular simplified identity rules for their aminoacylation. Here, we review the specific features of tRNA biology in mitochondria from model species representing the major eukaryotic groups, with an emphasis on recent research on tRNA import, maturation and aminoacylation.
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Affiliation(s)
- Thalia Salinas-Giegé
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg Cedex, France.
| | - Richard Giegé
- Institut de Biologie Moléculaire et Cellulaire, CNRS and Université de Strasbourg, 15 rue René Descartes, F-67084 Strasbourg Cedex, France.
| | - Philippe Giegé
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg Cedex, France.
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15
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Meseguer S, Martínez-Zamora A, García-Arumí E, Andreu AL, Armengod ME. The ROS-sensitive microRNA-9/9* controls the expression of mitochondrial tRNA-modifying enzymes and is involved in the molecular mechanism of MELAS syndrome. Hum Mol Genet 2014; 24:167-84. [PMID: 25149473 DOI: 10.1093/hmg/ddu427] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Mitochondrial dysfunction activates mitochondria-to-nucleus signaling pathways whose components are mostly unknown. Identification of these components is important to understand the molecular mechanisms underlying mitochondrial diseases and to discover putative therapeutic targets. MELAS syndrome is a rare neurodegenerative disease caused by mutations in mitochondrial (mt) DNA affecting mt-tRNA(Leu(UUR)). Patient and cybrid cells exhibit elevated oxidative stress. Moreover, mutant mt-tRNAs(Leu(UUR)) lack the taurine-containing modification normally present at the wobble uridine (U34) of wild-type mt-tRNA(Leu(UUR)), which is considered an etiology of MELAS. However, the molecular mechanism is still unclear. We found that MELAS cybrids exhibit a significant decrease in the steady-state levels of several mt-tRNA-modification enzymes, which is not due to transcriptional regulation. We demonstrated that oxidative stress mediates an NFkB-dependent induction of microRNA-9/9*, which acts as a post-transcriptional negative regulator of the mt-tRNA-modification enzymes GTPBP3, MTO1 and TRMU. Down-regulation of these enzymes by microRNA-9/9* affects the U34 modification status of non-mutant tRNAs and contributes to the MELAS phenotype. Anti-microRNA-9 treatments of MELAS cybrids reverse the phenotype, whereas miR-9 transfection of wild-type cells mimics the effects of siRNA-mediated down-regulation of GTPBP3, MTO1 and TRMU. Our data represent the first evidence that an mt-DNA disease can directly affect microRNA expression. Moreover, we demonstrate that the modification status of mt-tRNAs is dynamic and that cells respond to stress by modulating the expression of mt-tRNA-modifying enzymes. microRNA-9/9* is a crucial player in mitochondria-to-nucleus signaling as it regulates expression of nuclear genes in response to changes in the functional state of mitochondria.
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Affiliation(s)
- Salvador Meseguer
- Laboratory of RNA Modification and Mitochondrial Diseases, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain
| | - Ana Martínez-Zamora
- Laboratory of RNA Modification and Mitochondrial Diseases, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain
| | - Elena García-Arumí
- Hospital Universitari Vall d'Hebron, Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona 08035, Spain Biomedical Research Networking Centre for Rare Diseases (CIBERER) (node U701), Barcelona, Spain and
| | - Antonio L Andreu
- Hospital Universitari Vall d'Hebron, Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona 08035, Spain Biomedical Research Networking Centre for Rare Diseases (CIBERER) (node U701), Barcelona, Spain and
| | - M-Eugenia Armengod
- Laboratory of RNA Modification and Mitochondrial Diseases, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain CIBERER (node U721), Valencia, Spain
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16
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Torres AG, Batlle E, Ribas de Pouplana L. Role of tRNA modifications in human diseases. Trends Mol Med 2014; 20:306-14. [PMID: 24581449 DOI: 10.1016/j.molmed.2014.01.008] [Citation(s) in RCA: 298] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 01/17/2014] [Accepted: 01/23/2014] [Indexed: 12/22/2022]
Abstract
Transfer RNAs (tRNAs) are key for efficient and accurate protein translation. To be fully active, tRNAs need to be heavily modified post-transcriptionally. Growing evidence indicates that tRNA modifications and the enzymes catalyzing such modifications may play important roles in complex human pathologies. Here, we have compiled current knowledge that directly link tRNA modifications to human diseases such as cancer, type 2 diabetes (T2D), neurological disorders, and mitochondrial-linked disorders. The molecular mechanisms behind these connections remain, for the most part, unknown. As we progress towards the understanding of the roles played by hypomodified tRNAs in human disease, novel areas of therapeutic intervention may be discovered.
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Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB), Parc Cientific de Barcelona, 08028 Catalunya, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB), Parc Cientific de Barcelona, 08028 Catalunya, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08010 Catalunya, Spain
| | - Lluis Ribas de Pouplana
- Institute for Research in Biomedicine (IRB), Parc Cientific de Barcelona, 08028 Catalunya, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08010 Catalunya, Spain.
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17
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Sarin LP, Leidel SA. Modify or die?--RNA modification defects in metazoans. RNA Biol 2014; 11:1555-67. [PMID: 25692999 PMCID: PMC4615230 DOI: 10.4161/15476286.2014.992279] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 11/06/2014] [Accepted: 11/10/2014] [Indexed: 12/21/2022] Open
Abstract
Chemical RNA modifications are present in all kingdoms of life and many of these post-transcriptional modifications are conserved throughout evolution. However, most of the research has been performed on single cell organisms, whereas little is known about how RNA modifications contribute to the development of metazoans. In recent years, the identification of RNA modification genes in genome wide association studies (GWAS) has sparked new interest in previously neglected genes. In this review, we summarize recent findings that connect RNA modification defects and phenotypes in higher eukaryotes. Furthermore, we discuss the implications of aberrant tRNA modification in various human diseases including metabolic defects, mitochondrial dysfunctions, neurological disorders, and cancer. As the molecular mechanisms of these diseases are being elucidated, we will gain first insights into the functions of RNA modifications in higher eukaryotes and finally understand their roles during development.
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MESH Headings
- Amyotrophic Lateral Sclerosis/genetics
- Amyotrophic Lateral Sclerosis/metabolism
- Amyotrophic Lateral Sclerosis/pathology
- Animals
- Dysautonomia, Familial/genetics
- Dysautonomia, Familial/metabolism
- Dysautonomia, Familial/pathology
- Epilepsy, Rolandic/genetics
- Epilepsy, Rolandic/metabolism
- Epilepsy, Rolandic/pathology
- Genome-Wide Association Study
- Humans
- Intellectual Disability/genetics
- Intellectual Disability/metabolism
- Intellectual Disability/pathology
- Mutation
- Neoplasms/genetics
- Neoplasms/metabolism
- Neoplasms/pathology
- Nucleic Acid Conformation
- Phenotype
- RNA/genetics
- RNA/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Mitochondrial
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- tRNA Methyltransferases/genetics
- tRNA Methyltransferases/metabolism
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Affiliation(s)
- L Peter Sarin
- Max Planck Institute for Molecular Biomedicine; Münster, Germany
| | - Sebastian A Leidel
- Max Planck Institute for Molecular Biomedicine; Münster, Germany
- Faculty of Medicine; University of Münster; Münster, Germany
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18
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Zheng J, Sha-sha G, Xiao-wen T, Yi Z, Min-xin G. Human Mitochondrial tRNA Mutations in Maternally Inherited Deafness. J Otol 2013. [DOI: 10.1016/s1672-2930(13)50006-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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19
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Jing Z, Yan–chun J, Min–Xin G. Mitochondrial tRNA mutations associated with deafness. J Otol 2012. [DOI: 10.1016/s1672-2930(12)50009-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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20
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Koga Y, Povalko N, Nishioka J, Katayama K, Yatsuga S, Matsuishi T. Molecular pathology of MELAS and l-arginine effects. Biochim Biophys Acta Gen Subj 2012; 1820:608-14. [DOI: 10.1016/j.bbagen.2011.09.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Revised: 07/07/2011] [Accepted: 09/07/2011] [Indexed: 11/30/2022]
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21
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Zheng J, Ji Y, Guan MX. Mitochondrial tRNA mutations associated with deafness. Mitochondrion 2012; 12:406-13. [PMID: 22538251 DOI: 10.1016/j.mito.2012.04.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 03/15/2012] [Accepted: 04/09/2012] [Indexed: 10/28/2022]
Abstract
Mitochondrial tRNA mutations are one of the important causes of both syndromic and non-syndromic deafness. Of those, syndromic deafness-associated tRNA mutations such as tRNA(Leu(UUR)) 3243A>G are often present in heteroplasmy, while non-syndromic deafness-associated tRNA mutations including tRNA(Ser(UCN)) 7445A>G often occur in homplasmy or in high levels of heteroplasmy. These tRNA mutations are the primary mutations leading to hearing loss. However, other tRNA mutations such as tRNA(Thr) 15927G>A and tRNA(Ser(UCN)) 7444G>A may act in synergy with the primary mitochondrial DNA mutations, modulating the phenotypic manifestation of the primary mitochondrial DNA mutations. Theses tRNA mutations cause structural and functional alteration. A failure in tRNA metabolism caused by these tRNA mutations impaired mitochondrial translation and respiration, thereby causing mitochondrial dysfunctions responsible for deafness. These data offer valuable information for the early diagnosis, management and treatment of maternally inherited deafness.
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Affiliation(s)
- Jing Zheng
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical College, Wenzhou, Zhejiang, China
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22
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Suzuki T, Nagao A, Suzuki T. Human Mitochondrial tRNAs: Biogenesis, Function, Structural Aspects, and Diseases. Annu Rev Genet 2011; 45:299-329. [DOI: 10.1146/annurev-genet-110410-132531] [Citation(s) in RCA: 413] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Mitochondria are eukaryotic organelles that generate most of the energy in the cell by oxidative phosphorylation (OXPHOS). Each mitochondrion contains multiple copies of a closed circular double-stranded DNA genome (mtDNA). Human (mammalian) mtDNA encodes 13 essential subunits of the inner membrane complex responsible for OXPHOS. These mRNAs are translated by the mitochondrial protein synthesis machinery, which uses the 22 species of mitochondrial tRNAs (mt tRNAs) encoded by mtDNA. The unique structural features of mt tRNAs distinguish them from cytoplasmic tRNAs bearing the canonical cloverleaf structure. The genes encoding mt tRNAs are highly susceptible to point mutations, which are a primary cause of mitochondrial dysfunction and are associated with a wide range of pathologies. A large number of nuclear factors involved in the biogenesis and function of mt tRNAs have been identified and characterized, including processing endonucleases, tRNA-modifying enzymes, and aminoacyl-tRNA synthetases. These nuclear factors are also targets of pathogenic mutations linked to various diseases, indicating the functional importance of mt tRNAs for mitochondrial activity.
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Affiliation(s)
| | - Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
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Clinical and cellular consequences of the mutation m.12300G>A in the mitochondrial tRNA(Leu(CUN)) gene. Mitochondrion 2011; 12:288-93. [PMID: 22094595 DOI: 10.1016/j.mito.2011.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 10/27/2011] [Accepted: 10/28/2011] [Indexed: 11/22/2022]
Abstract
We report, for the first time, a patient with an overlap MERRF-NARP syndrome who carries the mutation m.12300G>A in the mitochondrial tRNA(Leu(CUN)) gene. The mutation was heteroplamic and more abundant in her muscle and fibroblast than in blood from her oligosymptomatic mother. Single muscle fiber analysis revealed that the proportion of mutant mtDNA in ragged red fibers was higher than that in normal fibers. Combined defects of mitochondrial respiratory chain complexes were detected in muscle, fibroblasts and transmitochondrial hybrid cells. Significant reduction of total ATP and mitochondrial membrane potential and an increased production of reactive oxygen species were observed.
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Suzuki T, Nagao A, Suzuki T. Human mitochondrial diseases caused by lack of taurine modification in mitochondrial tRNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:376-86. [PMID: 21957023 DOI: 10.1002/wrna.65] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mitochondrial DNA mutations that cause mitochondrial dysfunction are responsible for a wide spectrum of human diseases, referred to as mitochondrial diseases. Pathogenic point mutations are found frequently in genes encoding mitochondrial (mt) tRNAs, indicating that impaired functioning of mutant mt tRNAs is the primary cause of mitochondrial dysfunction. Our previous studies revealed the absence of posttranscriptional taurine modification at the anticodon wobble uridine in mutant mt tRNAs isolated from cells derived from patients with two major classes of mitochondrial diseases, MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes) and MERRF (myoclonus epilepsy associated with ragged red fibers). Defective taurine modification of the mutant mt tRNAs results in a deficiency in protein synthesis as the cognate codons of the mutant mt tRNA cannot be decoded. These findings represent the first evidence of a molecular pathogenesis caused by an RNA modification disorder.
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Affiliation(s)
- Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan.
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Yarham JW, Elson JL, Blakely EL, McFarland R, Taylor RW. Mitochondrial tRNA mutations and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 1:304-24. [DOI: 10.1002/wrna.27] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- John W. Yarham
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Joanna L. Elson
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Emma L. Blakely
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Robert McFarland
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Robert W. Taylor
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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Characterization of human GTPBP3, a GTP-binding protein involved in mitochondrial tRNA modification. Mol Cell Biol 2008; 28:7514-31. [PMID: 18852288 DOI: 10.1128/mcb.00946-08] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human GTPBP3 is an evolutionarily conserved, multidomain protein involved in mitochondrial tRNA modification. Characterization of its biochemical properties and the phenotype conferred by GTPBP3 inactivation is crucial to understanding the role of this protein in tRNA maturation and its effects on mitochondrial respiration. We show that the two most abundant GTPBP3 isoforms exhibit moderate affinity for guanine nucleotides like their bacterial homologue, MnmE, although they hydrolyze GTP at a 100-fold lower rate. This suggests that regulation of the GTPase activity, essential for the tRNA modification function of MnmE, is different in GTPBP3. In fact, potassium-induced dimerization of the G domain leads to stimulation of the GTPase activity in MnmE but not in GTPBP3. The GTPBP3 N-terminal domain mediates a potassium-independent dimerization, which appears as an evolutionarily conserved property of the protein family, probably related to the construction of the binding site for the one-carbon-unit donor in the modification reaction. Partial inactivation of GTPBP3 by small interfering RNA reduces oxygen consumption, ATP production, and mitochondrial protein synthesis, while the degradation of these proteins slightly increases. It also results in mitochondria with defective membrane potential and increased superoxide levels. These phenotypic traits suggest that GTPBP3 defects contribute to the pathogenesis of some oxidative phosphorylation diseases.
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Finsterer J. Genetic, pathogenetic, and phenotypic implications of the mitochondrial A3243G tRNALeu(UUR) mutation. Acta Neurol Scand 2007; 116:1-14. [PMID: 17587249 DOI: 10.1111/j.1600-0404.2007.00836.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Mitochondrial disorders are frequently caused by mutations in mitochondrial genes and usually present as multisystem disease. One of the most frequent mitochondrial mutations is the A3,243G transition in the tRNALeu(UUR) gene. The phenotypic expression of the mutation is variable and comprises syndromic or non-syndromic mitochondrial disorders. Among the syndromic manifestations the mitochondrial encephalopathy, lactacidosis, and stroke-like episode (MELAS) syndrome is the most frequent. In single cases the A3,243G mutation may be associated with maternally inherited diabetes and deafness syndrome, myoclonic epilepsy and ragged-red fibers (MERRF) syndrome, MELAS/MERRF overlap syndrome, maternally inherited Leigh syndrome, chronic external ophthalmoplegia, or Kearns-Sayre syndrome. The wide phenotypic variability of the mutation is explained by the peculiarities of the mitochondrial DNA, such as heteroplasmy and mitotic segregation, resulting in different mutation loads in different tissues and family members. Moreover, there is some evidence that additional mtDNA sequence variations (polymorphisms, haplotypes) influence the phenotype of the A3,243G mutation. This review aims to give an overview on the actual knowledge about the genetic, pathogenetic, and phenotypic implications of the A3,243G mtDNA mutation.
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Affiliation(s)
- J Finsterer
- Krankenanstalt Rudolfstiftung, Vienna, Austria.
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Durham SE, Samuels DC, Cree LM, Chinnery PF. Normal levels of wild-type mitochondrial DNA maintain cytochrome c oxidase activity for two pathogenic mitochondrial DNA mutations but not for m.3243A-->G. Am J Hum Genet 2007; 81:189-95. [PMID: 17564976 PMCID: PMC1950909 DOI: 10.1086/518901] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Accepted: 04/17/2007] [Indexed: 12/29/2022] Open
Abstract
Mitochondrial DNA (mtDNA) mutations are a common cause of human disease and accumulate as part of normal ageing and in common neurodegenerative disorders. Cells express a biochemical defect only when the proportion of mutated mtDNA exceeds a critical threshold, but it is not clear whether the actual cause of this defect is a loss of wild-type mtDNA, an excess of mutated mtDNA, or a combination of the two. Here, we show that segments of human skeletal muscle fibers harboring two pathogenic mtDNA mutations retain normal cytochrome c oxidase (COX) activity by maintaining a minimum amount of wild-type mtDNA. For these mutations, direct measurements of mutated and wild-type mtDNA molecules within the same skeletal muscle fiber are consistent with the "maintenance of wild type" hypothesis, which predicts that there is nonselective proliferation of mutated and wild-type mtDNA in response to the molecular defect. However, for the m.3243A-->G mutation, a superabundance of wild-type mtDNA was found in many muscle-fiber sections with negligible COX activity, indicating that the pathogenic mechanism for this particular mutation involves interference with the function of the wild-type mtDNA or wild-type gene products.
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Affiliation(s)
- Steve E Durham
- Mitochondrial Research Group, Newcastle University, Newcastle, UK
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