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Kopajtich R, Nicholls TJ, Rorbach J, Metodiev MD, Freisinger P, Mandel H, Vanlander A, Ghezzi D, Carrozzo R, Taylor RW, Marquard K, Murayama K, Wieland T, Schwarzmayr T, Mayr JA, Pearce SF, Powell CA, Saada A, Ohtake A, Invernizzi F, Lamantea E, Sommerville EW, Pyle A, Chinnery PF, Crushell E, Okazaki Y, Kohda M, Kishita Y, Tokuzawa Y, Assouline Z, Rio M, Feillet F, Mousson de Camaret B, Chretien D, Munnich A, Menten B, Sante T, Smet J, Régal L, Lorber A, Khoury A, Zeviani M, Strom TM, Meitinger T, Bertini ES, Van Coster R, Klopstock T, Rötig A, Haack TB, Minczuk M, Prokisch H. Mutations in GTPBP3 cause a mitochondrial translation defect associated with hypertrophic cardiomyopathy, lactic acidosis, and encephalopathy. Am J Hum Genet 2014; 95:708-20. [PMID: 25434004 PMCID: PMC4259976 DOI: 10.1016/j.ajhg.2014.10.017] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 10/29/2014] [Indexed: 11/22/2022] Open
Abstract
Respiratory chain deficiencies exhibit a wide variety of clinical phenotypes resulting from defective mitochondrial energy production through oxidative phosphorylation. These defects can be caused by either mutations in the mtDNA or mutations in nuclear genes coding for mitochondrial proteins. The underlying pathomechanisms can affect numerous pathways involved in mitochondrial physiology. By whole-exome and candidate gene sequencing, we identified 11 individuals from 9 families carrying compound heterozygous or homozygous mutations in GTPBP3, encoding the mitochondrial GTP-binding protein 3. Affected individuals from eight out of nine families presented with combined respiratory chain complex deficiencies in skeletal muscle. Mutations in GTPBP3 are associated with a severe mitochondrial translation defect, consistent with the predicted function of the protein in catalyzing the formation of 5-taurinomethyluridine (τm(5)U) in the anticodon wobble position of five mitochondrial tRNAs. All case subjects presented with lactic acidosis and nine developed hypertrophic cardiomyopathy. In contrast to individuals with mutations in MTO1, the protein product of which is predicted to participate in the generation of the same modification, most individuals with GTPBP3 mutations developed neurological symptoms and MRI involvement of thalamus, putamen, and brainstem resembling Leigh syndrome. Our study of a mitochondrial translation disorder points toward the importance of posttranscriptional modification of mitochondrial tRNAs for proper mitochondrial function.
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Affiliation(s)
- Robert Kopajtich
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | | | - Joanna Rorbach
- MRC Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, UK
| | - Metodi D Metodiev
- INSERM U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, 75015 Paris, France
| | - Peter Freisinger
- Department of Pediatrics, Klinikum Reutlingen, 72764 Reutlingen, Germany
| | - Hanna Mandel
- Metabolic Unit, Children's Hospital, Ramban Health Care Campus, 31096 Haifa, Israel
| | - Arnaud Vanlander
- Department of Pediatric Neurology and Metabolism, University Hospital Ghent, 9000 Ghent, Belgium
| | - Daniele Ghezzi
- Unit of Molecular Neurogenetics, Fondazione IRCCS (Istituto di Ricovero e Cura a CarattereScientifico) Istituto Neurologico "Carlo Besta," 20126 Milan, Italy
| | - Rosalba Carrozzo
- Unità di Malattie Neuromuscolari e Neurodegenerative, Laboratorio di Medicina Molecolare, Dipartimento di Neuroscienze, IRCCS Ospedale Pediatrico Bambino Gesù, 00165 Roma, Italy
| | - Robert W Taylor
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Klaus Marquard
- Department of Neuropediatrics, Klinikum Stuttgart, 70176 Stuttgart, Germany
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Chiba 266-0007, Japan
| | - Thomas Wieland
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
| | - Thomas Schwarzmayr
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
| | - Johannes A Mayr
- Department of Pediatrics, Paracelsus Medical University Salzburg, 5020 Salzburg, Austria
| | - Sarah F Pearce
- MRC Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, UK
| | | | - Ann Saada
- Monique and Jacques Roboh Department of Genetic Research and the Department of Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, 91120 Jerusalem, Israel
| | - Akira Ohtake
- Department of Pediatrics, Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan
| | - Federica Invernizzi
- Unit of Molecular Neurogenetics, Fondazione IRCCS (Istituto di Ricovero e Cura a CarattereScientifico) Istituto Neurologico "Carlo Besta," 20126 Milan, Italy
| | - Eleonora Lamantea
- Unit of Molecular Neurogenetics, Fondazione IRCCS (Istituto di Ricovero e Cura a CarattereScientifico) Istituto Neurologico "Carlo Besta," 20126 Milan, Italy
| | - Ewen W Sommerville
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Angela Pyle
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Patrick F Chinnery
- Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Ellen Crushell
- Metabolic Paediatrician, National Centre for Inherited Metabolic Disorders, Temple Street Children's University Hospital, Dublin 1, Ireland
| | - Yasushi Okazaki
- Department of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Saitama 350-1241, Japan; Department of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Saitama 350-1241, Japan
| | - Masakazu Kohda
- Department of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Saitama 350-1241, Japan
| | - Yoshihito Kishita
- Department of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Saitama 350-1241, Japan
| | - Yoshimi Tokuzawa
- Department of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Saitama 350-1241, Japan
| | - Zahra Assouline
- Departments of Pediatrics and Genetics, Hôpital Necker-Enfants Malades, 75015 Paris, France
| | - Marlène Rio
- Departments of Pediatrics and Genetics, Hôpital Necker-Enfants Malades, 75015 Paris, France
| | - François Feillet
- Service de médecine infantile, Hôpitald'Enfants de Brabois, CHU de Nancy, 54511 Vandoeuvre-les Nancy, France
| | | | - Dominique Chretien
- INSERM U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, 75015 Paris, France
| | - Arnold Munnich
- INSERM U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, 75015 Paris, France; Departments of Pediatrics and Genetics, Hôpital Necker-Enfants Malades, 75015 Paris, France
| | - Björn Menten
- Center for Medical Genetics, Ghent University, Ghent University Hospital, 9000 Ghent, Belgium
| | - Tom Sante
- Center for Medical Genetics, Ghent University, Ghent University Hospital, 9000 Ghent, Belgium
| | - Joél Smet
- Department of Pediatric Neurology and Metabolism, University Hospital Ghent, 9000 Ghent, Belgium
| | - Luc Régal
- Department of Pediatrics, Metabolic Center, University Hospital Leuven, 3000 Leuven, Belgium
| | - Abraham Lorber
- Department of Pediatric Cardiology, Ramban Medical Center, 31096 Haifa, Israel
| | - Asaad Khoury
- Department of Pediatric Cardiology, Ramban Medical Center, 31096 Haifa, Israel
| | - Massimo Zeviani
- MRC Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, UK; Unit of Molecular Neurogenetics, Fondazione IRCCS (Istituto di Ricovero e Cura a CarattereScientifico) Istituto Neurologico "Carlo Besta," 20126 Milan, Italy
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; DZHK (German Centre for Cardiovascular Research), partner site Munich, 81675 Munich, Germany; Munich Heart Alliance, 80802 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany
| | - Enrico S Bertini
- Unità di Malattie Neuromuscolari e Neurodegenerative, Laboratorio di Medicina Molecolare, Dipartimento di Neuroscienze, IRCCS Ospedale Pediatrico Bambino Gesù, 00165 Roma, Italy
| | - Rudy Van Coster
- Department of Pediatric Neurology and Metabolism, University Hospital Ghent, 9000 Ghent, Belgium
| | - Thomas Klopstock
- Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany; German Research Center for Neurodegenerative Diseases (DZNE), 80336 Munich, Germany; Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-University, 80336 Munich, Germany
| | - Agnès Rötig
- INSERM U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, 75015 Paris, France
| | - Tobias B Haack
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, UK.
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany.
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102
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Li MJ, Wang J. Current trend of annotating single nucleotide variation in humans--A case study on SNVrap. Methods 2014; 79-80:32-40. [PMID: 25308971 DOI: 10.1016/j.ymeth.2014.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 09/25/2014] [Accepted: 10/02/2014] [Indexed: 12/16/2022] Open
Abstract
As high throughput methods, such as whole genome genotyping arrays, whole exome sequencing (WES) and whole genome sequencing (WGS), have detected huge amounts of genetic variants associated with human diseases, function annotation of these variants is an indispensable step in understanding disease etiology. Large-scale functional genomics projects, such as The ENCODE Project and Roadmap Epigenomics Project, provide genome-wide profiling of functional elements across different human cell types and tissues. With the urgent demands for identification of disease-causal variants, comprehensive and easy-to-use annotation tool is highly in demand. Here we review and discuss current progress and trend of the variant annotation field. Furthermore, we introduce a comprehensive web portal for annotating human genetic variants. We use gene-based features and the latest functional genomics datasets to annotate single nucleotide variation (SNVs) in human, at whole genome scale. We further apply several function prediction algorithms to annotate SNVs that might affect different biological processes, including transcriptional gene regulation, alternative splicing, post-transcriptional regulation, translation and post-translational modifications. The SNVrap web portal is freely available at http://jjwanglab.org/snvrap.
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Affiliation(s)
- Mulin Jun Li
- Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, China
| | - Junwen Wang
- Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China; Shenzhen Institute of Research and Innovation, The University of Hong Kong, Shenzhen, China.
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103
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Brooks AP, Li Voon Chong JSW. Observations on age at diagnosis of type 1 diabetes and family history in a small population: the Winchester cohort. PRACTICAL DIABETES 2014. [DOI: 10.1002/pdi.1897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- AP Brooks
- Specialist Diabetes Service; Hampshire Hospitals NHS Foundation Trust at Royal Hampshire County Hospital; Winchester UK
| | - JSW Li Voon Chong
- Specialist Diabetes Service; Hampshire Hospitals NHS Foundation Trust at Royal Hampshire County Hospital; Winchester UK
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104
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Lehmann D, Schubert K, Joshi PR, Baty K, Blakely EL, Zierz S, Taylor RW, Deschauer M. A novel m.7539C>T point mutation in the mt-tRNA(Asp) gene associated with multisystemic mitochondrial disease. Neuromuscul Disord 2014; 25:81-4. [PMID: 25447692 PMCID: PMC4317191 DOI: 10.1016/j.nmd.2014.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 09/03/2014] [Accepted: 09/17/2014] [Indexed: 11/18/2022]
Abstract
Mitochondrial transfer RNA (mt-tRNA) mutations are the commonest sub-type of mitochondrial (mtDNA) mutations associated with human disease. We report a patient with multisytemic disease characterised by myopathy, spinal ataxia, sensorineural hearing loss, cataract and cognitive impairment in whom a novel m.7539C>T mt-tRNA(Asp) transition was identified. Muscle biopsy revealed extensive histopathological findings including cytochrome c oxidase (COX)-deficient fibres. Pyrosequencing confirmed mtDNA heteroplasmy for the mutation whilst single muscle fibre segregation studies revealed statistically significant higher mutation loads in COX-deficient fibres than in COX-positive fibres. Absence from control databases, hierarchical mt-tRNA mutation segregation within tissues, and occurrence at conserved sequence positions, further confirm this novel mt-tRNA mutation to be pathogenic. To date only three mt-tRNA(Asp) gene mutations have been described with clear evidence of pathogenicity. The novel m.7539C>T mt-tRNA(Asp) gene mutation extends the spectrum of pathogenic mutations in this gene, further supporting the notion that mt-tRNA(Asp) gene mutations are associated with multisystemic disease presentations.
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Affiliation(s)
- Diana Lehmann
- Department of Neurology, University of Halle-Wittenberg, Ernst-Grube-Str. 40, Halle/Saale 06097, Germany
| | - Kathrin Schubert
- Department of Neurology, University of Halle-Wittenberg, Ernst-Grube-Str. 40, Halle/Saale 06097, Germany
| | - Pushpa R Joshi
- Department of Neurology, University of Halle-Wittenberg, Ernst-Grube-Str. 40, Halle/Saale 06097, Germany
| | - Karen Baty
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - Emma L Blakely
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - Stephan Zierz
- Department of Neurology, University of Halle-Wittenberg, Ernst-Grube-Str. 40, Halle/Saale 06097, Germany
| | - Robert W Taylor
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - Marcus Deschauer
- Department of Neurology, University of Halle-Wittenberg, Ernst-Grube-Str. 40, Halle/Saale 06097, Germany.
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105
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Guy MP, Young DL, Payea MJ, Zhang X, Kon Y, Dean KM, Grayhack EJ, Mathews DH, Fields S, Phizicky EM. Identification of the determinants of tRNA function and susceptibility to rapid tRNA decay by high-throughput in vivo analysis. Genes Dev 2014; 28:1721-32. [PMID: 25085423 PMCID: PMC4117946 DOI: 10.1101/gad.245936.114] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In order to comprehensively define the effects of sequence variation on tRNA function, Guy et al. developed a high-throughput in vivo screen to quantify the activity of the nonsense suppressor SUP4oc of Saccharomyces cerevisiae. SUP4oc tolerated numerous sequence variations, accommodated slippage in tertiary and secondary interactions, and exhibited genetic interactions that suggest an alternative functional tRNA conformation. Mutations that sensitized SUP4oc to rapid tRNA decay were found to be located throughout the sequence. This shows that the integrity of the entire tRNA molecule is under surveillance by cellular quality control machinery. Sequence variation in tRNA genes influences the structure, modification, and stability of tRNA; affects translation fidelity; impacts the activity of numerous isodecoders in metazoans; and leads to human diseases. To comprehensively define the effects of sequence variation on tRNA function, we developed a high-throughput in vivo screen to quantify the activity of a model tRNA, the nonsense suppressor SUP4oc of Saccharomyces cerevisiae. Using a highly sensitive fluorescent reporter gene with an ochre mutation, fluorescence-activated cell sorting of a library of SUP4oc mutant yeast strains, and deep sequencing, we scored 25,491 variants. Unexpectedly, SUP4oc tolerates numerous sequence variations, accommodates slippage in tertiary and secondary interactions, and exhibits genetic interactions that suggest an alternative functional tRNA conformation. Furthermore, we used this methodology to define tRNA variants subject to rapid tRNA decay (RTD). Even though RTD normally degrades tRNAs with exposed 5′ ends, mutations that sensitize SUP4oc to RTD were found to be located throughout the sequence, including the anti-codon stem. Thus, the integrity of the entire tRNA molecule is under surveillance by cellular quality control machinery. This approach to assess activity at high throughput is widely applicable to many problems in tRNA biology.
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Affiliation(s)
- Michael P Guy
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, USA 14642
| | | | - Matthew J Payea
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, USA 14642
| | - Xiaoju Zhang
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, USA 14642
| | - Yoshiko Kon
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, USA 14642
| | - Kimberly M Dean
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, USA 14642
| | - Elizabeth J Grayhack
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, USA 14642
| | - David H Mathews
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, USA 14642
| | - Stanley Fields
- Department of Genome Sciences, Department of Medicine, Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA 98195
| | - Eric M Phizicky
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York, USA 14642;
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106
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Jiang Z, Yu J, Xia B, Zhuo G. Mitochondrial tRNAThr 15891C>G mutation was not associated with Leber's hereditary optic neuropathy in Han Chinese patients. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1564-6. [PMID: 25186221 DOI: 10.3109/19401736.2014.953137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mutations in mitochondrial DNA (mtDNA) were the most important causes of Leber's hereditary optic neuropathy (LHON). To date, approximately 25 LHON-associated mtDNA mutations have been identified in various ethnic populations. Three primary mutations, the 3460G > A, 11778G > A and 14484T > C, in genes encoding the subunits of respiratory chain complex I, were the most common LHON-associated mtDNA mutations. Moreover, secondary mutations in mt-tRNA genes have been reported increasingly to be associated with LHON, simply due to the high mutation rates of mt-tRNAs. There is a lack of functional analysis and a poor genetic evaluation of a certain mt-tRNA mutation, which failed to meet the classic pathogenicity scoring system. As a result, how to classify a pathogenic mutation in mt-tRNA gene became important for both geneticist and clinician to diagnosis the LHON or the suspicious of LHON. In this study, we reassessed the role of a point mutation in mt-tRNA(Thr) gene which had been reported to be a mutation associated with LHON, the pathogenicity of this mutation has been discussed in this context.
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Affiliation(s)
- Zhaochang Jiang
- a Department of Pathology , Second affiliated hospital of Zhejiang University , Hangzhou , China
| | - Jinfang Yu
- b Department of Cardiology , Xiaoshan First People's Hospital , Hangzhou , China
| | - Bohou Xia
- c Department of Pharmacy , Hunan University of Traditional Chinese Medicine , Changsha , China , and
| | - Guangchao Zhuo
- d Central Laboratory , Hangzhou First People's Hospital , Hangzhou , China
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107
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Abstract
Understanding regulation of mitochondrial DNA (mtDNA) expression is of considerable interest given that mitochondrial dysfunction is important in human pathology and aging. Similar to the situation in bacteria, there is no compartmentalization between transcription and translation in mitochondria; hence, both processes are likely to have a direct molecular crosstalk. Accumulating evidence suggests that there are important mechanisms for regulation of mammalian mtDNA expression at the posttranscriptional level. Regulation of mRNA maturation, mRNA stability, translational coordination, ribosomal biogenesis, and translation itself all form the basis for controlling oxidative phosphorylation capacity. Consequently, a wide variety of inherited human mitochondrial diseases are caused by mutations of nuclear genes regulating various aspects of mitochondrial translation. Furthermore, mutations of mtDNA, associated with human disease and aging, often affect tRNA genes critical for mitochondrial translation. Recent advances in molecular understanding of mitochondrial translation regulation will most likely provide novel avenues for modulating mitochondrial function for treating human disease.
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Affiliation(s)
- B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; Röntgen-Ångström-Cluster, Karolinska Institutet Outstation, Centre for Structural Systems Biology, DESY Campus, 22603 Hamburg, Germany; European Molecular Biology Laboratory, Hamburg Unit, 22603 Hamburg, Germany.
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 509 31 Cologne, Germany; Department of Laboratory Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden.
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108
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Mitochondrial tRNA cleavage by tRNA-targeting ribonuclease causes mitochondrial dysfunction observed in mitochondrial disease. Biochem Biophys Res Commun 2014; 451:131-6. [PMID: 25065742 DOI: 10.1016/j.bbrc.2014.07.084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 07/17/2014] [Indexed: 11/21/2022]
Abstract
Mitochondrial DNA (mtDNA) is a genome possessed by mitochondria. Since reactive oxygen species (ROS) are generated during aerobic respiration in mitochondria, mtDNA is commonly exposed to the risk of DNA damage. Mitochondrial disease is caused by mitochondrial dysfunction, and mutations or deletions on mitochondrial tRNA (mt tRNA) genes are often observed in mtDNA of patients with the disease. Hence, the correlation between mt tRNA activity and mitochondrial dysfunction has been assessed. Then, cybrid cells, which are constructed by the fusion of an enucleated cell harboring altered mtDNA with a ρ(0) cell, have long been used for the analysis due to difficulty in mtDNA manipulation. Here, we propose a new method that involves mt tRNA cleavage by a bacterial tRNA-specific ribonuclease. The ribonuclease tagged with a mitochondrial-targeting sequence (MTS) was successfully translocated to the mitochondrial matrix. Additionally, mt tRNA cleavage, which resulted in the decrease of cytochrome c oxidase (COX) activity, was observed.
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109
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Jackson CB, Neuwirth C, Hahn D, Nuoffer JM, Frank S, Gallati S, Schaller A. Novel mitochondrial tRNA(Ile) m.4282A>G gene mutation leads to chronic progressive external ophthalmoplegia plus phenotype. Br J Ophthalmol 2014; 98:1453-9. [PMID: 25034047 DOI: 10.1136/bjophthalmol-2014-305300] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND/AIM To investigate the underlying pathomechanism in a 33-year-old female Caucasian patient presenting with chronic progressive external ophthalmoplegia (CPEO) plus symptoms. METHODS Histochemical analysis of skeletal muscle and biochemical measurements of individual oxidative phosphorylation (OXPHOS) complexes. Genetic analysis of mitochondrial DNA in various tissues with subsequent investigation of single muscle fibres for correlation of mutational load. RESULTS The patient's skeletal muscle showed 20% of cytochrome c oxidase-negative fibres and 8% ragged-red fibres. Genetic analysis of the mitochondrial DNA revealed a novel point mutation in the mitochondrial tRNA(Ile) (MTTI) gene at position m.4282G>A. The heteroplasmy was determined in blood, buccal cells and muscle by restriction fragment length polymorphism (RFLP) combined with a last fluorescent cycle. The total mutational load was 38% in skeletal muscle, but was not detectable in blood or buccal cells of the patient. The phenotype segregated with the mutational load as determined by analysis of single cytochrome c oxidase-negative/positive fibres by laser capture microdissection and subsequent LFC-RFLP. CONCLUSIONS We describe a novel MTTI transition mutation at nucleotide position m.4282G>A associated with a CPEO plus phenotype. The novel variant at position m.4282G>A disrupts the middle bond of the D-stem of the tRNA(Ile) and is highly conserved. The conservation and phenotype-genotype segregation strongly suggest pathogenicity and is in good agreement with the MTTI gene being frequently associated with CPEO. This novel variant broadens the spectrum of MTTI mutations causing CPEO.
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Affiliation(s)
- Christopher B Jackson
- Division of Human Genetics, Departments of Pediatrics and Clinical Research, Inselspital, University of Berne, Berne, Switzerland Institute of Clinical Chemistry, Inselspital, University of Berne, Berne, Switzerland Graduate School for Cellular and Biomedical Sciences, University of Berne, Berne, Switzerland
| | - Christoph Neuwirth
- Neuromuscular Diseases Centre, Cantonal Hospital St.Gallen, St.Gallen, Switzerland
| | - Dagmar Hahn
- Institute of Clinical Chemistry, Inselspital, University of Berne, Berne, Switzerland
| | - J-M Nuoffer
- Institute of Clinical Chemistry, Inselspital, University of Berne, Berne, Switzerland
| | - Stephan Frank
- Division of Neuropathology, Institute of Pathology, Basle University Hospital, Basle, Switzerland
| | - Sabina Gallati
- Division of Human Genetics, Departments of Pediatrics and Clinical Research, Inselspital, University of Berne, Berne, Switzerland
| | - André Schaller
- Division of Human Genetics, Departments of Pediatrics and Clinical Research, Inselspital, University of Berne, Berne, Switzerland
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110
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Mitochondrial DNA polymorphisms associated with longevity in the Turkish population. Mitochondrion 2014; 17:7-13. [DOI: 10.1016/j.mito.2014.04.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/16/2014] [Accepted: 04/21/2014] [Indexed: 01/21/2023]
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111
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Wang Y, Dong P, Li L, Li X, Wang H, Yang X, Wang S, Li Z, Shang X. The mitochondrial tRNA(Met) 4454T > C variant may not be associated with essential hypertension in Han Chinese population. MITOCHONDRIAL DNA 2014; 25:124-125. [PMID: 23627313 DOI: 10.3109/19401736.2013.786705] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Affiliation(s)
- Yanyu Wang
- The First Affiliated Hospital, Henan University of Science and Technology , Henan , P.R. China and
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Wei L, Gao W, Ma Y, Cao Q, Zhang X. Is mitochondrial tRNACysG5821A a deleterious mutation? ACTA ACUST UNITED AC 2014; 26:202-4. [DOI: 10.3109/19401736.2014.892107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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113
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Blakely EL, Yarham JW, Alston CL, Craig K, Poulton J, Brierley C, Park SM, Dean A, Xuereb JH, Anderson KN, Compston A, Allen C, Sharif S, Enevoldson P, Wilson M, Hammans SR, Turnbull DM, McFarland R, Taylor RW. Pathogenic mitochondrial tRNA point mutations: nine novel mutations affirm their importance as a cause of mitochondrial disease. Hum Mutat 2014; 34:1260-8. [PMID: 23696415 PMCID: PMC3884772 DOI: 10.1002/humu.22358] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/10/2013] [Indexed: 11/26/2022]
Abstract
Mutations in the mitochondrial genome, and in particular the mt-tRNAs, are an important cause of human disease. Accurate classification of the pathogenicity of novel variants is vital to allow accurate genetic counseling for patients and their families. The use of weighted criteria based on functional studies—outlined in a validated pathogenicity scoring system—is therefore invaluable in determining whether novel or rare mt-tRNA variants are pathogenic. Here, we describe the identification of nine novel mt-tRNA variants in nine families, in which the probands presented with a diverse range of clinical phenotypes including mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes, isolated progressive external ophthalmoplegia, epilepsy, deafness and diabetes. Each of the variants identified (m.4289T>C, MT-TI; m.5541C>T, MT-TW; m.5690A>G, MT-TN; m.7451A>T, MT-TS1; m.7554G>A, MT-TD; m.8304G>A, MT-TK; m.12206C>T, MT-TH; m.12317T>C, MT-TL2; m.16023G>A, MT-TP) was present in a different tRNA, with evidence in support of pathogenicity, and where possible, details of mutation transmission documented. Through the application of the pathogenicity scoring system, we have classified six of these variants as “definitely pathogenic” mutations (m.5541C>T, m.5690A>G, m.7451A>T, m.12206C>T, m.12317T>C, and m.16023G>A), whereas the remaining three currently lack sufficient evidence and are therefore classed as ‘possibly pathogenic’ (m.4289T>C, m.7554G>A, and m.8304G>A).
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Affiliation(s)
- Emma L Blakely
- Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, UK
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114
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Pathological Mutations of the Mitochondrial Human Genome: the Instrumental Role of the Yeast S. cerevisiae. Diseases 2014. [DOI: 10.3390/diseases2010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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115
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Govindaraj P, Khan NA, Rani B, Rani DS, Selvaraj P, Jyothi V, Bahl A, Narasimhan C, Rakshak D, Premkumar K, Khullar M, Thangaraj K. Mitochondrial DNA variations associated with hypertrophic cardiomyopathy. Mitochondrion 2013; 16:65-72. [PMID: 24215792 DOI: 10.1016/j.mito.2013.10.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 10/17/2013] [Accepted: 10/29/2013] [Indexed: 01/11/2023]
Abstract
Hypertrophic cardiomyopathy (HCM) is a primary disorder, characterized by unexplained hypertrophy of the left ventricle that frequently involved in the inter-ventricular septum. Mitochondrial DNA (mtDNA) mutations and haplogroups have been found to be associated with several diseases. Therefore, in the present study, we have sequenced the complete mtDNA of 114 clinically well-characterized HCM patients to look for the role of mtDNA variations and haplogroups in HCM phenotype among Indian patients. Complete mtDNA analysis revealed 28 novel variations, 25 disease-associated and 50 private mutations. We found 13 (11.40%) HCM patients having novel non-synonymous and/or MT-tRNA variations, of which two (m.4797C>M and m.8728T>Y) were in heteroplasmic condition. In silico prediction showed that a few mutations are pathogenic, which may affect the energy production in the heart. Unlike some of the other studies, we did not find association of mitochondrial haplogroup with HCM.
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Affiliation(s)
- Periyasamy Govindaraj
- Department of Biomedical Science, School of Basic Medical Sciences, Bharathidasan University, Tiruchirappalli, India
| | | | - Bindu Rani
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Deepa Selvi Rani
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | | | - Ajay Bahl
- Department of Cardiology, PGIMER, Chandigarh, India
| | | | | | - Kumpati Premkumar
- Department of Biomedical Science, School of Basic Medical Sciences, Bharathidasan University, Tiruchirappalli, India
| | - Madhu Khullar
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
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116
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Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J. RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs. Hum Mutat 2013; 34:546-56. [PMID: 23315997 PMCID: PMC3708107 DOI: 10.1002/humu.22273] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 12/18/2012] [Indexed: 02/05/2023]
Abstract
Structural characteristics are essential for the functioning of many noncoding RNAs and cis-regulatory elements of mRNAs. SNPs may disrupt these structures, interfere with their molecular function, and hence cause a phenotypic effect. RNA folding algorithms can provide detailed insights into structural effects of SNPs. The global measures employed so far suffer from limited accuracy of folding programs on large RNAs and are computationally too demanding for genome-wide applications. Here, we present a strategy that focuses on the local regions of maximal structural change between mutant and wild-type. These local regions are approximated in a “screening mode” that is intended for genome-wide applications. Furthermore, localized regions are identified as those with maximal discrepancy. The mutation effects are quantified in terms of empirical P values. To this end, the RNAsnp software uses extensive precomputed tables of the distribution of SNP effects as function of length and GC content. RNAsnp thus achieves both a noise reduction and speed-up of several orders of magnitude over shuffling-based approaches. On a data set comprising 501 SNPs associated with human-inherited diseases, we predict 54 to have significant local structural effect in the untranslated region of mRNAs. RNAsnp is available at http://rth.dk/resources/rnasnp.
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117
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Serre V, Rozanska A, Beinat M, Chretien D, Boddaert N, Munnich A, Rötig A, Chrzanowska-Lightowlers ZM. Mutations in mitochondrial ribosomal protein MRPL12 leads to growth retardation, neurological deterioration and mitochondrial translation deficiency. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1832:1304-12. [PMID: 23603806 PMCID: PMC3787750 DOI: 10.1016/j.bbadis.2013.04.014] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 03/25/2013] [Accepted: 04/10/2013] [Indexed: 12/11/2022]
Abstract
Multiple respiratory chain deficiencies represent a common cause of mitochondrial diseases and are associated with a wide range of clinical symptoms. We report a subject, born to consanguineous parents, with growth retardation and neurological deterioration. Multiple respiratory chain deficiency was found in muscle and fibroblasts of the subject as well as abnormal assembly of complexes I and IV. A microsatellite genotyping of the family members detected only one region of homozygosity on chromosome 17q24.2-q25.3 in which we focused our attention to genes involved in mitochondrial translation. We sequenced MRPL12, encoding the mitochondrial ribosomal protein L12 and identified a c.542C>T transition in exon 5 changing a highly conserved alanine into a valine (p.Ala181Val). This mutation resulted in a decreased steady-state level of MRPL12 protein, with altered integration into the large ribosomal subunit. Moreover, an overall mitochondrial translation defect was observed in the subject's fibroblasts with a significant reduction of synthesis of COXI, COXII and COXIII subunits. Modeling of MRPL12 shows Ala181 positioned in a helix potentially involved in an interface of interaction suggesting that the p.Ala181Val change might be predicted to alter interactions with the elongation factors. These results contrast with the eubacterial orthologues of human MRPL12, where L7/L12 proteins do not appear to have a selective effect on translation. Therefore, analysis of the mutated version found in the subject presented here suggests that the mammalian protein does not function in an entirely analogous manner to the eubacterial L7/L12 equivalent.
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Affiliation(s)
- Valérie Serre
- Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine and INSERM U781, Hôpital Necker-Enfants Malades, 149 rue de Sèvres, 75015 Paris, France
| | - Agata Rozanska
- Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Marine Beinat
- Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine and INSERM U781, Hôpital Necker-Enfants Malades, 149 rue de Sèvres, 75015 Paris, France
| | - Dominique Chretien
- Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine and INSERM U781, Hôpital Necker-Enfants Malades, 149 rue de Sèvres, 75015 Paris, France
| | - Nathalie Boddaert
- Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine and INSERM U781, Hôpital Necker-Enfants Malades, 149 rue de Sèvres, 75015 Paris, France
| | - Arnold Munnich
- Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine and INSERM U781, Hôpital Necker-Enfants Malades, 149 rue de Sèvres, 75015 Paris, France
| | - Agnès Rötig
- Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine and INSERM U781, Hôpital Necker-Enfants Malades, 149 rue de Sèvres, 75015 Paris, France
- Department of Pediatrics, Hôpital Necker-Enfants-Malades, 149 rue de Sèvres, 75015 Paris, France
| | - Zofia M. Chrzanowska-Lightowlers
- Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom
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118
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Zhou L, Wang H, Wei J, Wang Y, Wang Y. No association between mitochondrial tRNA(Val) T1658C mutation and chronic progressive external ophthalmoplegia (CPEO). ACTA ACUST UNITED AC 2013; 25:385-6. [PMID: 23815321 DOI: 10.3109/19401736.2013.803097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mutations in mitochondrial tRNA genes are one of the most important causes of mitochondrial diseases. Recently, a novel mt-tRNA(Val) T1658C mutation has been reported to be associated with chronic progressive external ophthalmoplegia (CPEO). To test this association, we performed a phylogenetic analysis of T1658C mutation, moreover, we used the bioinformatic tool to predict the thermodynamic change of tRNA(Val) with and without this mutation. Surprisingly, T1658C mutation was not evolutionary conserved and had little effect on tRNA(Val) folding. These data indicated that T1658C mutation should still be categorized as a polymorphism.
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Affiliation(s)
- Lijun Zhou
- First affiliated Hospital of Henan University of Science and Technology , Luoyang , People's Republic of China and
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119
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HDAC inhibitors attenuate the development of hypersensitivity in models of neuropathic pain. Pain 2013; 154:1668-1679. [PMID: 23693161 PMCID: PMC3763368 DOI: 10.1016/j.pain.2013.05.021] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 04/23/2013] [Accepted: 05/03/2013] [Indexed: 12/20/2022]
Abstract
Histone deacetylase inhibitors (HDACIs) interfere with the epigenetic process of histone acetylation and are known to have analgesic properties in models of chronic inflammatory pain. The aim of this study was to determine whether these compounds could also affect neuropathic pain. Different class I HDACIs were delivered intrathecally into rat spinal cord in models of traumatic nerve injury and antiretroviral drug–induced peripheral neuropathy (stavudine, d4T). Mechanical and thermal hypersensitivity was attenuated by 40% to 50% as a result of HDACI treatment, but only if started before any insult. The drugs globally increased histone acetylation in the spinal cord, but appeared to have no measurable effects in relevant dorsal root ganglia in this treatment paradigm, suggesting that any potential mechanism should be sought in the central nervous system. Microarray analysis of dorsal cord RNA revealed the signature of the specific compound used (MS-275) and suggested that its main effect was mediated through HDAC1. Taken together, these data support a role for histone acetylation in the emergence of neuropathic pain.
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120
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Early-onset cataracts, spastic paraparesis, and ataxia caused by a novel mitochondrial tRNAGlu (MT-TE) gene mutation causing severe complex I deficiency: a clinical, molecular, and neuropathologic study. J Neuropathol Exp Neurol 2013; 72:164-75. [PMID: 23334599 DOI: 10.1097/nen.0b013e31828129c5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Mitochondrial respiratory chain disease is associated with a spectrum of clinical presentations and considerable genetic heterogeneity. Here we report molecular genetic and neuropathologic findings from an adult with an unusual manifestation of mitochondrial DNA disease. Clinical features included early-onset cataracts, ataxia, and progressive paraparesis, with sequencing revealing the presence of a novel de novo m.14685G>A mitochondrial tRNA(Glu) (MT-TE) gene mutation. Muscle biopsy showed that 13% and 34% of muscle fibers lacked cytochrome c oxidase activity and complex I subunit expression, respectively. Biochemical studies confirmed a marked decrease in complex I activity. Neuropathologic investigation revealed a large cystic lesion affecting the left putamen, caudate nucleus, and internal capsule, with evidence of marked microvacuolation, neuron loss, perivascular lacunae, and blood vessel mineralization. The internal capsule showed focal axonal loss, whereas brainstem and spinal cord showed descending anterograde degeneration in medullary pyramids and corticospinal tracts. In agreement with muscle biopsy findings, reduced complex I immunoreactivity was detected in the remaining neuronal populations, particularly in the basal ganglia and cerebellum, correlating with the neurologic dysfunction exhibited by the patient. This study emphasizes the importance of molecular genetic and postmortem neuropathologic analyses for furthering our understanding of underlying mechanisms of mitochondrial disorders.
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121
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Yao P, Fox PL. Aminoacyl-tRNA synthetases in medicine and disease. EMBO Mol Med 2013; 5:332-43. [PMID: 23427196 PMCID: PMC3598075 DOI: 10.1002/emmm.201100626] [Citation(s) in RCA: 215] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 11/30/2012] [Accepted: 01/15/2013] [Indexed: 12/12/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) are essential and ubiquitous 'house-keeping' enzymes responsible for charging amino acids to their cognate tRNAs and providing the substrates for global protein synthesis. Recent studies have revealed a role of multiple ARSs in pathology, and their potential use as pharmacological targets and therapeutic reagents. The ongoing discovery of genetic mutations in human ARSs is increasing exponentially and can be considered an important determinant of disease etiology. Several chemical compounds target bacterial, fungal and human ARSs as antibiotics or disease-targeting medicines. Remarkably, ongoing exploration of noncanonical functions of ARSs has shown important contributions to control of angiogenesis, inflammation, tumourigenesis and other important physiopathological processes. Here, we summarize the roles of ARSs in human diseases and medicine, focusing on the most recent and exciting discoveries.
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Affiliation(s)
- Peng Yao
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
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122
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Schwenzer H, Zoll J, Florentz C, Sissler M. Pathogenic implications of human mitochondrial aminoacyl-tRNA synthetases. Top Curr Chem (Cham) 2013; 344:247-92. [PMID: 23824528 DOI: 10.1007/128_2013_457] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Mitochondria are considered as the powerhouse of eukaryotic cells. They host several central metabolic processes fueling the oxidative phosphorylation pathway (OXPHOS) that produces ATP from its precursors ADP and inorganic phosphate Pi (PPi). The respiratory chain complexes responsible for the OXPHOS pathway are formed from complementary sets of protein subunits encoded by the nuclear genome and the mitochondrial genome, respectively. The expression of the mitochondrial genome requires a specific and fully active translation machinery from which aminoacyl-tRNA synthetases (aaRSs) are key actors. Whilst the macromolecules involved in mammalian mitochondrial translation have been under investigation for many years, there has been an explosion of interest in human mitochondrial aaRSs (mt-aaRSs) since the discovery of a large (and growing) number of mutations in these genes that are linked to a variety of neurodegenerative disorders. Herein we will review the present knowledge on mt-aaRSs in terms of their biogenesis, their connection to mitochondrial respiration, i.e., the respiratory chain (RC) complexes, and to the mitochondrial translation machinery. The pathology-related mutations detected so far are described, with special attention given to their impact on mt-aaRSs biogenesis, functioning, and/or subsequent activities. The collected data to date shed light on the diverse routes that are linking primary molecular possible impact of a mutation to its phenotypic expression. It is envisioned that a variety of mechanisms, inside and outside the translation machinery, would play a role on the heterogeneous manifestations of mitochondrial disorders.
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Affiliation(s)
- Hagen Schwenzer
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, IBMC, 15 rue René Descartes, 67084, Strasbourg Cedex, France,
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123
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Yarham JW, Blakely EL, Alston CL, Roberts ME, Ealing J, Pal P, Turnbull DM, McFarland R, Taylor RW. The m.3291T>C mt-tRNA(Leu(UUR)) mutation is definitely pathogenic and causes multisystem mitochondrial disease. J Neurol Sci 2012; 325:165-9. [PMID: 23273904 PMCID: PMC3560033 DOI: 10.1016/j.jns.2012.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/03/2012] [Accepted: 12/05/2012] [Indexed: 12/02/2022]
Abstract
Mitochondrial tRNA point mutations are important causes of human disease, and have been associated with a diverse range of clinical phenotypes. Definitively proving the pathogenicity of any given mt-tRNA mutation requires combined molecular, genetic and functional studies. Subsequent evaluation of the mutation using a pathogenicity scoring system is often very helpful in concluding whether or not the mutation is causing disease. Despite several independent reports linking the m.3291T>C mutation to disease in humans, albeit in association with several different phenotypes, its pathogenicity remains controversial. A lack of conclusive functional evidence and an over-emphasis on the poor evolutionary conservation of the affected nucleotide have contributed to this controversy. Here we describe an adult patient who presented with deafness and lipomas and evidence of mitochondrial abnormalities in his muscle biopsy, who harbours the m.3291T > C mutation, providing conclusive evidence of pathogenicity through analysis of mutation segregation with cytochrome c oxidase (COX) deficiency in single muscle fibres, underlining the importance of performing functional studies when assessing pathogenicity.
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Affiliation(s)
- John W Yarham
- Wellcome Trust Centre for Mitochondrial Research, Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, United Kingdom
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124
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Non-syndromic Hearing Impairment in a Hungarian Family with the m.7510T>C Mutation of Mitochondrial tRNA(Ser(UCN)) and Review of Published Cases. JIMD Rep 2012; 9:105-111. [PMID: 23430555 DOI: 10.1007/8904_2012_187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 09/19/2012] [Accepted: 09/24/2012] [Indexed: 04/06/2023] Open
Abstract
The m.7510T>C mitochondrial DNA (mtDNA) mutation is a tRNA(Ser(UCN)) alteration leading to matrilineal isolated hearing impairment. The current paper reviews the available reports on the m.7510T>C mtDNA mutation, with special attention to phenotypic variations and haplogroup background. A Hungarian family, the fourth family reported in the literature, is presented, in which analysis of three generations with bilateral isolated hearing loss revealed the m.7510T>C tRNA(Ser(UCN)) mutation in homoplasmic form in the affected members. Haplogroup analysis verified an unnamed subgroup of mitochondrial haplogroup H. Previously reported Spanish and North American Caucasian families belong to different subgroups of haplogroup H. Analyzing our biobank of Hungarian patients with sensorineural hearing loss, we did not detect this mutation in any other patient, nor was it found in Caucasian haplogroup H control samples. Comparing the cases reported so far, there is interfamilial variablity in the age of onset, accompanying symptoms, and haplogroup background. Our case adds further genetic evidence for the pathogenicity of the m.7510T>C mutation and underlines the need to include full mtDNA sequencing in the screening for unexplained hearing loss.
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125
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Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease. Nat Rev Neurosci 2012; 13:528-41. [PMID: 22814587 DOI: 10.1038/nrn3234] [Citation(s) in RCA: 420] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Novel classes of small and long non-coding RNAs (ncRNAs) are being characterized at a rapid pace, driven by recent paradigm shifts in our understanding of genomic architecture, regulation and transcriptional output, as well as by innovations in sequencing technologies and computational and systems biology. These ncRNAs can interact with DNA, RNA and protein molecules; engage in diverse structural, functional and regulatory activities; and have roles in nuclear organization and transcriptional, post-transcriptional and epigenetic processes. This expanding inventory of ncRNAs is implicated in mediating a broad spectrum of processes including brain evolution, development, synaptic plasticity and disease pathogenesis.
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126
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Yarham JW, McFarland R, Taylor RW, Elson JL. A proposed consensus panel of organisms for determining evolutionary conservation of mt-tRNA point mutations. Mitochondrion 2012; 12:533-8. [PMID: 22781547 PMCID: PMC3510436 DOI: 10.1016/j.mito.2012.06.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 04/19/2012] [Accepted: 06/28/2012] [Indexed: 11/23/2022]
Abstract
Assigning pathogenicity to mt-tRNA variants requires multiple strands of evidence. Evolutionary conservation is often considered mandatory, but lack of a standard panel of organisms to assess conservation complicates comparison between reports and undermines the value of conservation-based evidence. We demonstrate that intra-species MTT sequence variation is sufficiently low for sequence data from a single organism to adequately represent a species. On this basis, we propose a standardised panel of organisms for conservation assessment and describe integration of this conservation panel into a pathogenicity scoring system designed to assess mt-tRNA variation associated with mitochondrial disease.
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Affiliation(s)
- John W Yarham
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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127
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Abstract
According to a recent report by Sunami et al., a maternally inherited Japanese family with variable phenotypes including mitochondrial myopathy, recurrent headache, and myoclonus and epilepsy had been described to be associated with mitochondrial tRNA(Leu(UUR)) 3291T>C mutation. In order to verify this association, we reanalyzed the clinical and molecular datasets obtained from Sunami's work; in addition, a phylogenetic approach was employed to evaluate the conservation index of this mutation among different species. We further utilized RNA Fold Web Server to predict the minimum free energy (MFE) of tRNA(Leu(UUR)) gene with and without this mutation. Most strikingly, a low level of conservation was found regarding 3291T>C mutation and a slight change in MFE had been observed between the wild type and the mutant. Our negative results gave no support for an active role for this mutation on the clinical expression of mitochondrial disorders.
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Affiliation(s)
- Yu Ding
- Central Laboratory, Hangzhou First People's Hospital, Hangzhou, People's Republic of China
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128
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Affiliation(s)
- Werner J H Koopman
- Department of Biochemistry, Nijmegen Center for Molecular Life Sciences, Nijmegen, The Netherlands
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129
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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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130
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Yarham JW, Al-Dosary M, Blakely EL, Alston CL, Taylor RW, Elson JL, McFarland R. A comparative analysis approach to determining the pathogenicity of mitochondrial tRNA mutations. Hum Mutat 2011; 32:1319-25. [PMID: 21882289 DOI: 10.1002/humu.21575] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 07/07/2011] [Indexed: 01/24/2023]
Abstract
Distinguishing pathogenic from polymorphic changes poses significant problems for geneticists and despite 30 years of postgenomic experience this remains the case in mitochondrial genetics. Base substitutions in mitochondrial tRNA (mt-tRNA) genes are particularly difficult, but important, because they are common causes of pathology and associated with high rates of transmission. Providing accurate genetic advice to patients and their families is of paramount importance in disease prevention, and brings into sharp focus the factors used to distinguish pathogenic from polymorphic variants. We have reevaluated our pathogenicity scoring system for mt-tRNA mutations following a considerable increase in the number reported since the system was devised in 2004. This allowed us to address notable issues including the underestimation of "definitely pathogenic" mutations resulting from insufficient data collection. We illustrate the robustness of our revised scoring system using novel pathogenic and previously reported polymorphic changes and conclude that while clear evidence from single-fiber and/or trans-mitochondrial cybrid studies remains the gold standard for assigning pathogenicity, our scoring system is valuable for deciding which mt-tRNA mutations to investigate further using these labor-intensive techniques.
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Affiliation(s)
- John W Yarham
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, UK
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