51
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Szabóová D, Hapala I, Sulo P. The complete mitochondrial DNA sequence from Kazachstania sinensis reveals a general +1C frameshift mechanism in CTGY codons. FEMS Yeast Res 2018. [PMID: 29528462 DOI: 10.1093/femsyr/foy028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The complete mitochondrial DNA (mtDNA) sequence from Kazachstania sinensis was analysed and compared to mtDNA from related yeasts. It contained the same set of genes; however, it only contained 23 tRNAs, as the trnR2 gene was absent. Most of the 12 introns within cox1, cob and rnl genes were inserted in the same sites as in other yeasts; however, two introns in rnl were in unusual positions. Traits such as gene order and GC cluster number were more related to Saccharomyces than to the other Kazachstania or linked clades. The most exceptional feature was the +1 frameshift in cox3, atp6 and cob open reading frames that was also found in other Kazachstania, Nakaseomyces delphensis and Candida glabrata. Comparison of DNA and protein sequences revealed the universal sites of +1C frameshifts were either CTGT or CTGC sequences. Moreover, an A→G substitution was found at position 37 in the anticodon stem loop tRNA gene for cysteine in all species with frameshifts but not in other sibling yeasts. This substitution allowed strong Watson-Crick base-pairing between an unmodified G (ACG) and the skipped C in the CTGY, leading to this quadruplet being read as cysteine.
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Affiliation(s)
- Dana Szabóová
- Department of Biochemistry, Comenius University, Faculty of Natural Sciences, Ilkovicova ulica 6, Bratislava 84215, Slovakia
| | - Ivan Hapala
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences SAS, Dúbravská 9, Bratislava 840 05, Slovakia
| | - Pavol Sulo
- Department of Biochemistry, Comenius University, Faculty of Natural Sciences, Ilkovicova ulica 6, Bratislava 84215, Slovakia
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52
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Gödiker J, Grüneberg M, DuChesne I, Reunert J, Rust S, Westermann C, Wada Y, Classen G, Langhans CD, Schlingmann KP, Rodenburg RJ, Pohlmann R, Marquardt T. QIL1-dependent assembly of MICOS complex-lethal mutation in C19ORF70 resulting in liver disease and severe neurological retardation. J Hum Genet 2018; 63:707-716. [PMID: 29618761 DOI: 10.1038/s10038-018-0442-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/27/2018] [Accepted: 02/27/2018] [Indexed: 01/29/2023]
Abstract
Seven subunits of the mitochondrial contact site and cristae junction (CJ) organizing system (MICOS) in humans have been recently described in function and structure. QIL1 (also named MIC13) is a small complex that is crucial for the maintenance and assembling of MICOS. A novel mutation of an essential splice site in the C19orf70 gene encoding QIL1 induces severe mitochondrial encephalopathy, hepatopathy and lactate acidosis consistent with psychomotor retardation. In addition, bilateral kidney stones were observed. Disassembly of MICOS complex subunits displays lack of MIC10-MIC26-MIC27-QIL1 subcomplex, resulting in aberrant cristae structure and a loss of cristae junctions and contact sites. In liver and muscle tissue, the activity of the respiratory chain complexes (OXPHOS) was severely impaired. Defects in MICOS complex do not only affect mitochondrial architecture, but also mitochondrial fusion, metabolic signalling, lipid trafficking and cellular electric homeostasis.
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Affiliation(s)
- J Gödiker
- Department of General Paediatrics, Metabolic Diseases, University Children's Hospital Muenster, Albert-Schweitzer-Campus 1, Gebäude A1, 48149, Muenster, Germany
| | - M Grüneberg
- Department of General Paediatrics, Metabolic Diseases, University Children's Hospital Muenster, Albert-Schweitzer-Campus 1, Gebäude A1, 48149, Muenster, Germany
| | - I DuChesne
- Department of General Paediatrics, Metabolic Diseases, University Children's Hospital Muenster, Albert-Schweitzer-Campus 1, Gebäude A1, 48149, Muenster, Germany
| | - J Reunert
- Department of General Paediatrics, Metabolic Diseases, University Children's Hospital Muenster, Albert-Schweitzer-Campus 1, Gebäude A1, 48149, Muenster, Germany
| | - S Rust
- Department of General Paediatrics, Metabolic Diseases, University Children's Hospital Muenster, Albert-Schweitzer-Campus 1, Gebäude A1, 48149, Muenster, Germany
| | - C Westermann
- Gerhard-Domagk-Institute of Pathology, University Hospital Muenster, Domagkstraße 17, 48149, Muenster, Germany
| | - Y Wada
- Osaka Medical Center and Research Institute for Maternal and Child Health, 840 Murodo-cho, Izumi, Osaka, 594-1101, Japan
| | - G Classen
- Department of General Paediatrics, Evangelisches Klinikum Bethel, Grenzweg 10, 33617, Bielefeld, Germany
| | - C D Langhans
- Division of Neuropediatrics and Paediatric Metabolic Medicine, University Children's Hospital Heidelberg, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - K P Schlingmann
- Department of General Paediatrics, University Children's Hospital, Waldeyerstr. 22, 48149, Muenster, Germany
| | - R J Rodenburg
- Department of Paediatrics, Radboud Center for Mitochondrial Medicine, 830 Translational Metabolic Laboratory, Radboud UMC, Nijmegen, The Netherlands
| | - R Pohlmann
- Institute of Physiological Chemistry and Pathobiochemistry, University of Muenster, Waldeyerstraße 15, 48149, Muenster, Germany
| | - T Marquardt
- Department of General Paediatrics, Metabolic Diseases, University Children's Hospital Muenster, Albert-Schweitzer-Campus 1, Gebäude A1, 48149, Muenster, Germany.
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53
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Pan T. Modifications and functional genomics of human transfer RNA. Cell Res 2018; 28:395-404. [PMID: 29463900 PMCID: PMC5939049 DOI: 10.1038/s41422-018-0013-y] [Citation(s) in RCA: 208] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/27/2017] [Indexed: 11/18/2022] Open
Abstract
Transfer RNA (tRNA) is present at tens of millions of transcripts in a human cell and is the most abundant RNA in moles among all cellular RNAs. tRNA is also the most extensively modified RNA with, on an average, 13 modifications per molecule. The primary function of tRNA as the adaptor of amino acids and the genetic code in protein synthesis is well known. tRNA modifications play multi-faceted roles in decoding and other cellular processes. The abundance, modification, and aminoacylation (charging) levels of tRNAs contribute to mRNA decoding in ways that reflect the cell type and its environment; however, how these factors work together to maximize translation efficiency remains to be understood. tRNAs also interact with many proteins not involved in translation and this may coordinate translation activity and other processes in the cell. This review focuses on the modifications and the functional genomics of human tRNA and discusses future perspectives on the explorations of human tRNA biology.
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Affiliation(s)
- Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.
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54
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Abstract
Globally, diabetes is the leading cause of chronic kidney disease and end-stage renal disease, which are major risk factors for cardiovascular disease and death. Despite this burden, the factors that precipitate the development and progression of diabetic kidney disease (DKD) remain to be fully elucidated. Mitochondrial dysfunction is associated with kidney disease in nondiabetic contexts, and increasing evidence suggests that dysfunctional renal mitochondria are pathological mediators of DKD. These complex organelles have a broad range of functions, including the generation of ATP. The kidneys are mitochondrially rich, highly metabolic organs that require vast amounts of ATP for their normal function. The delivery of metabolic substrates for ATP production, such as fatty acids and oxygen, is altered by diabetes. Changes in metabolic fuel sources in diabetes to meet ATP demands result in increased oxygen consumption, which contributes to renal hypoxia. Inherited factors including mutations in genes that impact mitochondrial function and/or substrate delivery may also be important risk factors for DKD. Hence, we postulate that the diabetic milieu and inherited factors that underlie abnormalities in mitochondrial function synergistically drive the development and progression of DKD.
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Affiliation(s)
- Josephine M Forbes
- Glycation and Diabetes Group, Mater Research Institute, The University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia.,Mater Clinical School, School of Medicine, The University of Queensland, St Lucia, Queensland, Australia.,Departments of Medicine and Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - David R Thorburn
- Departments of Medicine and Paediatrics, The University of Melbourne, Parkville, Victoria, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
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55
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O'Byrne JJ, Tarailo-Graovac M, Ghani A, Champion M, Deshpande C, Dursun A, Ozgul RK, Freisinger P, Garber I, Haack TB, Horvath R, Barić I, Husain RA, Kluijtmans LAJ, Kotzaeridou U, Morris AA, Ross CJ, Santra S, Smeitink J, Tarnopolsky M, Wortmann SB, Mayr JA, Brunner-Krainz M, Prokisch H, Wasserman WW, Wevers RA, Engelke UF, Rodenburg RJ, Ting TW, McFarland R, Taylor RW, Salvarinova R, van Karnebeek CDM. The genotypic and phenotypic spectrum of MTO1 deficiency. Mol Genet Metab 2018; 123:28-42. [PMID: 29331171 PMCID: PMC5780301 DOI: 10.1016/j.ymgme.2017.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/11/2017] [Accepted: 11/11/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND Mitochondrial diseases, a group of multi-systemic disorders often characterized by tissue-specific phenotypes, are usually progressive and fatal disorders resulting from defects in oxidative phosphorylation. MTO1 (Mitochondrial tRNA Translation Optimization 1), an evolutionarily conserved protein expressed in high-energy demand tissues has been linked to human early-onset combined oxidative phosphorylation deficiency associated with hypertrophic cardiomyopathy, often referred to as combined oxidative phosphorylation deficiency-10 (COXPD10). MATERIAL AND METHODS Thirty five cases of MTO1 deficiency were identified and reviewed through international collaboration. The cases of two female siblings, who presented at 1 and 2years of life with seizures, global developmental delay, hypotonia, elevated lactate and complex I and IV deficiency on muscle biopsy but without cardiomyopathy, are presented in detail. RESULTS For the description of phenotypic features, the denominator varies as the literature was insufficient to allow for complete ascertainment of all data for the 35 cases. An extensive review of all known MTO1 deficiency cases revealed the most common features at presentation to be lactic acidosis (LA) (21/34; 62% cases) and hypertrophic cardiomyopathy (15/34; 44% cases). Eventually lactic acidosis and hypertrophic cardiomyopathy are described in 35/35 (100%) and 27/34 (79%) of patients with MTO1 deficiency, respectively; with global developmental delay/intellectual disability present in 28/29 (97%), feeding difficulties in 17/35 (49%), failure to thrive in 12/35 (34%), seizures in 12/35 (34%), optic atrophy in 11/21 (52%) and ataxia in 7/34 (21%). There are 19 different pathogenic MTO1 variants identified in these 35 cases: one splice-site, 3 frameshift and 15 missense variants. None have bi-allelic variants that completely inactivate MTO1; however, patients where one variant is truncating (i.e. frameshift) while the second one is a missense appear to have a more severe, even fatal, phenotype. These data suggest that complete loss of MTO1 is not viable. A ketogenic diet may have exerted a favourable effect on seizures in 2/5 patients. CONCLUSION MTO1 deficiency is lethal in some but not all cases, and a genotype-phenotype relation is suggested. Aside from lactic acidosis and cardiomyopathy, developmental delay and other phenotypic features affecting multiple organ systems are often present in these patients, suggesting a broader spectrum than hitherto reported. The diagnosis should be suspected on clinical features and the presence of markers of mitochondrial dysfunction in body fluids, especially low residual complex I, III and IV activity in muscle. Molecular confirmation is required and targeted genomic testing may be the most efficient approach. Although subjective clinical improvement was observed in a small number of patients on therapies such as ketogenic diet and dichloroacetate, no evidence-based effective therapy exists.
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Affiliation(s)
- James J O'Byrne
- Division of Biochemical Diseases, Department of Pediatrics, BC Children's Hospital, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada
| | - Maja Tarailo-Graovac
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada; BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada; Institute of Physiology and Biochemistry, Faculty of Biology, The University of Belgrade, Belgrade, Serbia
| | - Aisha Ghani
- Division of Biochemical Diseases, Department of Pediatrics, BC Children's Hospital, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada
| | - Michael Champion
- Department of Inherited Metabolic Disease, Guy's and St Thomas' NHS Foundation Trusts, Evelina London Children's Hospital, London, UK
| | - Charu Deshpande
- Clinical Genetics Unit, Guys and St Thomas' NHS Foundation Trust, London, UK
| | - Ali Dursun
- Hacettepe University, Faculty of Medicine, Institute of Child Health, Department of Pediatric Metabolism, Ankara, Turkey
| | - Riza K Ozgul
- Hacettepe University, Faculty of Medicine, Institute of Child Health, Department of Pediatric Metabolism, Ankara, Turkey
| | - Peter Freisinger
- Department of Pediatrics, Klinikum Reutlingen, Reutlingen, Germany
| | - Ian Garber
- BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada
| | - Tobias B Haack
- Institute of Human Genetics, Technische Universität München, Munich, Germany; Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Rita Horvath
- John Walton Muscular Dystrophy Research Centre, Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Ivo Barić
- University Hospital Center Zagreb & School of Medicine, University of Zagreb, Croatia
| | - Ralf A Husain
- Centre for Inborn Metabolic Disorders, Department of Neuropediatrics, Jena University Hospital, Jena, Germany
| | - Leo A J Kluijtmans
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Urania Kotzaeridou
- Department of General Pediatrics, Division of Neuropediatrics and Metabolic Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Andrew A Morris
- Willink Biochemical Genetics Unit, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Colin J Ross
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Saikat Santra
- Department of Clinical Inherited Metabolic Disorders, Birmingham Children's Hospital, Steelhouse Lane, Birmingham, UK
| | - Jan Smeitink
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mark Tarnopolsky
- Department of Pediatrics, Division of Neuromuscular and Neurometabolic Diseases, McMaster University Medical Centre, Hamilton, ON, Canada
| | - Saskia B Wortmann
- Institute of Human Genetics, Technische Universität München, Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum Munich, Neuherberg, Germany; Department of Pediatrics, Salzburger Landeskliniken (SALK), Paracelsus Medical University (PMU), Salzburg, Austria
| | - Johannes A Mayr
- Department of Pediatrics, Salzburger Landeskliniken (SALK), Paracelsus Medical University (PMU), Salzburg, Austria
| | | | - Holger Prokisch
- Institute of Human Genetics, Technische Universität München, Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada; BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Ron A Wevers
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Udo F Engelke
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Richard J Rodenburg
- Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Teck Wah Ting
- Genetics Service, Department of Pediatrics, KK Women's and Children's Hospital, Singapore
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Ramona Salvarinova
- Division of Biochemical Diseases, Department of Pediatrics, BC Children's Hospital, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada; BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada; Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Clara D M van Karnebeek
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada; BC Children's Hospital Research Institute, University of British Columbia, Vancouver, Canada; Departments of Pediatrics and Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands.
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56
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Panneman DM, Smeitink JA, Rodenburg RJ. Mining for mitochondrial mechanisms: Linking known syndromes to mitochondrial function. Clin Genet 2017; 93:943-951. [PMID: 28686290 DOI: 10.1111/cge.13094] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/30/2017] [Accepted: 07/03/2017] [Indexed: 12/28/2022]
Abstract
Mitochondrial disorders (MDs) are caused by defects in 1 or multiple complexes of the oxidative phosphorylation (OXPHOS) machinery. MDs are associated with a broad range of clinical signs and symptoms, and have considerable clinical overlap with other neuromuscular syndromes. This overlap might be due to involvement of mitochondrial pathways in some of these non-mitochondrial syndromes. Here, we give an overview of around 25 non-mitochondrial syndromes, diagnosed in patients who were initially suspected to have a MD on the basis of clinical and biochemical parameters. In addition, we highlight the mitochondrial connections of 6 of these non-mitochondrial syndromes (eg, Rett syndrome and Dravet syndrome) diagnosed in multiple patients. Further research to unravel the interplay between these genes and mitochondria may help to increase knowledge on these syndromes. Additionally, it may open new avenues for research on pathways interacting with mitochondrial function in order to find new targets for therapeutics to treat MDs. The data presented in this review underline the importance of careful assessment of clinical, genetic, and biochemical data in all patients suspected of a neuromuscular syndrome, and highlights the importance of the role of clinical geneticists, physicians, and clinical biochemists in recognizing the possible mitochondrial connection of non-mitochondrial syndromes.
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Affiliation(s)
- D M Panneman
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - J A Smeitink
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - R J Rodenburg
- Department of Pediatrics, Radboud Center for Mitochondrial Medicine, Radboud University Medical Centre, Nijmegen, the Netherlands
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57
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Zhou M, Xue L, Chen Y, Li H, He Q, Wang B, Meng F, Wang M, Guan MX. A hypertension-associated mitochondrial DNA mutation introduces an m 1G37 modification into tRNA Met, altering its structure and function. J Biol Chem 2017; 293:1425-1438. [PMID: 29222331 DOI: 10.1074/jbc.ra117.000317] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/13/2017] [Indexed: 12/20/2022] Open
Abstract
Defective nucleotide modifications of mitochondrial tRNAs have been associated with several human diseases, but their pathophysiology remains poorly understood. In this report, we investigated the pathogenic molecular mechanism underlying a hypertension-associated 4435A→G mutation in mitochondrial tRNAMet The m.4435A→G mutation affected a highly conserved adenosine at position 37, 3' adjacent to the tRNA's anticodon, which is important for the fidelity of codon recognition and stabilization. We hypothesized that the m.4435A→G mutation introduced an m1G37 modification of tRNAMet, altering its structure and function. Primer extension and methylation activity assays indeed confirmed that the m.4435A→G mutation created a tRNA methyltransferase 5 (TRMT5)-catalyzed m1G37 modification of tRNAMet We found that this mutation altered the tRNAMet structure, indicated by an increased melting temperature and electrophoretic mobility of the mutated tRNA compared with the wildtype molecule. We demonstrated that cybrid cell lines carrying the m.4435A→G mutation exhibited significantly decreased efficiency in aminoacylation and steady-state levels of tRNAMet, as compared with those of control cybrids. The aberrant tRNAMet metabolism resulted in variable decreases in mitochondrial DNA (mtDNA)-encoded polypeptides in the mutant cybrids. Furthermore, we found that the m.4435A→G mutation caused respiratory deficiency, markedly diminished mitochondrial ATP levels and membrane potential, and increased the production of reactive oxygen species in mutant cybrids. These results demonstrated that an aberrant m1G37 modification of mitochondrial tRNAMet affected the structure and function of its tRNA and consequently altered mitochondrial function. Our findings provide critical insights into the pathophysiology of maternally inherited hypertension, which is manifested by the deficient tRNA nucleotide modification.
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Affiliation(s)
- Mi Zhou
- From the Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China.,the Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China
| | - Ling Xue
- the Attardi Institute of Mitochondrial Biomedicine and
| | - Yaru Chen
- the Attardi Institute of Mitochondrial Biomedicine and
| | - Haiying Li
- the Department of Cardiology, the First Affiliated Hospital, Wenzhou Medical University, Wenzhou, 325035 Zhejiang, China
| | - Qiufen He
- the Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China
| | - Bibin Wang
- the Attardi Institute of Mitochondrial Biomedicine and
| | - Feilong Meng
- From the Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China.,the Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China
| | - Meng Wang
- From the Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China.,the Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China
| | - Min-Xin Guan
- From the Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China, .,the Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058 Zhejiang, China.,the Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, 310058 Zhejiang, China, and.,the Joining Institute of Genetics and Genomic Medicine between Zhejiang University and University of Toronto, Hangzhou, 310058 Zhejiang, China
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58
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Chen H, Sun M, Fan Z, Tong M, Chen G, Li D, Ye J, Yang Y, Zhu Y, Zhu J. Mitochondrial C4375T mutation might be a molecular risk factor in a maternal Chinese hypertensive family under haplotype C. Clin Exp Hypertens 2017; 40:518-523. [PMID: 29200319 DOI: 10.1080/10641963.2017.1403622] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Here, we reported a Han Chinese essential hypertensive pedigree based on clinical hereditary and molecular data. To know the molecular basis on this family, mitochondrial genome of one proband from the family was identified through direct sequencing analysis. The age of onset year and affected degree of patients are different in this family. And matrilineal family members carrying C4375T mutation and belong to Eastern Asian halopgroup C. Phylogenetic analysis shows 4375C is highly conservative in 17 species. It is suggested that these mutations might participate in the development of hypertension in this family. And halopgroup C might play a modifying role on the phenotype in this Chinese hypertensive family.
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Affiliation(s)
- Hong Chen
- a Intensive Care Unit , Ningbo First Hospital, Ningbo, China.,b Intensive Care Unit , Ningbo Hospital of Zhejiang University, Ningbo, China
| | - Min Sun
- a Intensive Care Unit , Ningbo First Hospital, Ningbo, China.,b Intensive Care Unit , Ningbo Hospital of Zhejiang University, Ningbo, China
| | - Zhen Fan
- a Intensive Care Unit , Ningbo First Hospital, Ningbo, China.,b Intensive Care Unit , Ningbo Hospital of Zhejiang University, Ningbo, China
| | - Maoqing Tong
- c Department of Cardiology , Ningbo First Hospital, Ningbo, China.,d Key Laboratory of Molecular Medicine , Ningbo First Hospital , Ningbo , Zhejiang P.R. China
| | - Guodong Chen
- a Intensive Care Unit , Ningbo First Hospital, Ningbo, China.,b Intensive Care Unit , Ningbo Hospital of Zhejiang University, Ningbo, China
| | - Danhui Li
- a Intensive Care Unit , Ningbo First Hospital, Ningbo, China.,b Intensive Care Unit , Ningbo Hospital of Zhejiang University, Ningbo, China
| | - Jihui Ye
- a Intensive Care Unit , Ningbo First Hospital, Ningbo, China.,b Intensive Care Unit , Ningbo Hospital of Zhejiang University, Ningbo, China
| | - Yumin Yang
- a Intensive Care Unit , Ningbo First Hospital, Ningbo, China.,b Intensive Care Unit , Ningbo Hospital of Zhejiang University, Ningbo, China
| | - Yongding Zhu
- a Intensive Care Unit , Ningbo First Hospital, Ningbo, China.,b Intensive Care Unit , Ningbo Hospital of Zhejiang University, Ningbo, China
| | - Jianhua Zhu
- a Intensive Care Unit , Ningbo First Hospital, Ningbo, China.,b Intensive Care Unit , Ningbo Hospital of Zhejiang University, Ningbo, China
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59
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Garone C, D’Souza AR, Dallabona C, Lodi T, Rebelo-Guiomar P, Rorbach J, Donati MA, Procopio E, Montomoli M, Guerrini R, Zeviani M, Calvo SE, Mootha VK, DiMauro S, Ferrero I, Minczuk M. Defective mitochondrial rRNA methyltransferase MRM2 causes MELAS-like clinical syndrome. Hum Mol Genet 2017; 26:4257-4266. [PMID: 28973171 PMCID: PMC5886288 DOI: 10.1093/hmg/ddx314] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 02/02/2023] Open
Abstract
Defects in nuclear-encoded proteins of the mitochondrial translation machinery cause early-onset and tissue-specific deficiency of one or more OXPHOS complexes. Here, we report a 7-year-old Italian boy with childhood-onset rapidly progressive encephalomyopathy and stroke-like episodes. Multiple OXPHOS defects and decreased mtDNA copy number (40%) were detected in muscle homogenate. Clinical features combined with low level of plasma citrulline were highly suggestive of mitochondrial encephalopathy, lactic acidosis and stroke-like episodes (MELAS) syndrome, however, the common m.3243 A > G mutation was excluded. Targeted exome sequencing of genes encoding the mitochondrial proteome identified a damaging mutation, c.567 G > A, affecting a highly conserved amino acid residue (p.Gly189Arg) of the MRM2 protein. MRM2 has never before been linked to a human disease and encodes an enzyme responsible for 2'-O-methyl modification at position U1369 in the human mitochondrial 16S rRNA. We generated a knockout yeast model for the orthologous gene that showed a defect in respiration and the reduction of the 2'-O-methyl modification at the equivalent position (U2791) in the yeast mitochondrial 21S rRNA. Complementation with the mrm2 allele carrying the equivalent yeast mutation failed to rescue the respiratory phenotype, which was instead completely rescued by expressing the wild-type allele. Our findings establish that defective MRM2 causes a MELAS-like phenotype, and suggests the genetic screening of the MRM2 gene in patients with a m.3243 A > G negative MELAS-like presentation.
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Affiliation(s)
- Caterina Garone
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
- Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA
| | - Aaron R D’Souza
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences and Environmental Sustainability - University of Parma, Parma 43121, Italy
| | - Tiziana Lodi
- Department of Chemistry, Life Sciences and Environmental Sustainability - University of Parma, Parma 43121, Italy
| | - Pedro Rebelo-Guiomar
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
- Graduate Program in Areas of Basic and Applied Biology (GABBA), University of Porto, 4099-002, Portugal
| | - Joanna Rorbach
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | | | - Elena Procopio
- Metabolic Unit, A. Meyer Children's Hospital, Florence 50139, Italy
| | - Martino Montomoli
- Pediatric Neurology Unit and Laboratories, “A. Meyer” Children's Hospital, University of Florence, 50139, Italy
| | - Renzo Guerrini
- Pediatric Neurology Unit and Laboratories, “A. Meyer” Children's Hospital, University of Florence, 50139, Italy
| | - Massimo Zeviani
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Sarah E Calvo
- Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, and Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Vamsi K Mootha
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, and Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Salvatore DiMauro
- Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA
| | - Ileana Ferrero
- Department of Chemistry, Life Sciences and Environmental Sustainability - University of Parma, Parma 43121, Italy
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
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60
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Tarnopolsky MA, Brady L, Tetreault M. TRMT5 mutations are associated with features of complex hereditary spastic paraparesis. Neurology 2017; 89:2210-2211. [PMID: 29021354 DOI: 10.1212/wnl.0000000000004657] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/23/2017] [Indexed: 11/15/2022] Open
Affiliation(s)
- Mark A Tarnopolsky
- From McMaster University (M.A.T., L.B.), Hamilton; and McGill University (M.T.), Montreal, Canada.
| | - Lauren Brady
- From McMaster University (M.A.T., L.B.), Hamilton; and McGill University (M.T.), Montreal, Canada
| | - Martine Tetreault
- From McMaster University (M.A.T., L.B.), Hamilton; and McGill University (M.T.), Montreal, Canada
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61
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Abstract
PURPOSE OF REVIEW Mitochondrial disorders are an increasingly recognized cause of heart dysfunction, with the primary manifestations being cardiomyopathy and conduction defects. This review focuses on the complex genetics of mitochondrial disease and recently discovered conditions that affect mitochondrial function. RECENT FINDINGS Next-generation sequencing techniques, especially whole-exome sequencing, have led to the discovery of a number of conditions that cause mitochondrial dysfunction and subsequent cardiac abnormalities. Nuclear DNA defects are the main cause of mitochondrial disease in children, with disease pathogenesis being related to either abnormalities in specific mitochondrial electron transport chain subunits or in proteins related to subunit or mitochondrial DNA maintenance, mitochondrial protein translation, lipid bilayer structure, or other aspects of mitochondrial function. SUMMARY Currently, symptomatic therapy using standard medications targeting relief of complications is the primary approach to treatment. There are no US Food and Drug Administration-approved therapies for the specific treatment of mitochondrial disease. However, on the basis of recent advances in understanding of the pathophysiology of these complex disorders, various novel approaches are either in clinical trials or in development.
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Affiliation(s)
- Gregory M Enns
- Department of Pediatrics, Stanford University, Stanford, California, USA
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62
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Bohnsack MT, Sloan KE. The mitochondrial epitranscriptome: the roles of RNA modifications in mitochondrial translation and human disease. Cell Mol Life Sci 2017; 75:241-260. [PMID: 28752201 PMCID: PMC5756263 DOI: 10.1007/s00018-017-2598-6] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 07/08/2017] [Accepted: 07/17/2017] [Indexed: 11/28/2022]
Abstract
Mitochondrial protein synthesis is essential for the production of components of the oxidative phosphorylation system. RNA modifications in the mammalian mitochondrial translation apparatus play key roles in facilitating mitochondrial gene expression as they enable decoding of the non-conventional genetic code by a minimal set of tRNAs, and efficient and accurate protein synthesis by the mitoribosome. Intriguingly, recent transcriptome-wide analyses have also revealed modifications in mitochondrial mRNAs, suggesting that the concept of dynamic regulation of gene expression by the modified RNAs (the “epitranscriptome”) extends to mitochondria. Furthermore, it has emerged that defects in RNA modification, arising from either mt-DNA mutations or mutations in nuclear-encoded mitochondrial modification enzymes, underlie multiple mitochondrial diseases. Concomitant advances in the identification of the mitochondrial RNA modification machinery and recent structural views of the mitochondrial translation apparatus now allow the molecular basis of such mitochondrial diseases to be understood on a mechanistic level.
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Affiliation(s)
- Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
- Göttingen Centre for Molecular Biosciences, University of Göttingen, Justus-von-Liebig-Weg 11, 37077, Göttingen, Germany.
| | - Katherine E Sloan
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
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63
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Pearce SF, Rorbach J, Haute LV, D’Souza AR, Rebelo-Guiomar P, Powell CA, Brierley I, Firth AE, Minczuk M. Maturation of selected human mitochondrial tRNAs requires deadenylation. eLife 2017; 6:e27596. [PMID: 28745585 PMCID: PMC5544427 DOI: 10.7554/elife.27596] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/21/2017] [Indexed: 02/02/2023] Open
Abstract
Human mitochondria contain a genome (mtDNA) that encodes essential subunits of the oxidative phosphorylation system. Expression of mtDNA entails multi-step maturation of precursor RNA. In other systems, the RNA life cycle involves surveillance mechanisms, however, the details of RNA quality control have not been extensively characterised in human mitochondria. Using a mitochondrial ribosome profiling and mitochondrial poly(A)-tail RNA sequencing (MPAT-Seq) assay, we identify the poly(A)-specific exoribonuclease PDE12 as a major factor for the quality control of mitochondrial non-coding RNAs. The lack of PDE12 results in a spurious polyadenylation of the 3' ends of the mitochondrial (mt-) rRNA and mt-tRNA. While the aberrant adenylation of 16S mt-rRNA did not affect the integrity of the mitoribosome, spurious poly(A) additions to mt-tRNA led to reduced levels of aminoacylated pool of certain mt-tRNAs and mitoribosome stalling at the corresponding codons. Therefore, our data uncover a new, deadenylation-dependent mtRNA maturation pathway in human mitochondria.
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Affiliation(s)
- Sarah F Pearce
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Joanna Rorbach
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Lindsey Van Haute
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Aaron R D’Souza
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Pedro Rebelo-Guiomar
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
- Graduate Program in Areas of Basic and Applied Biology, University of Porto, Porto, Portugal
| | - Christopher A Powell
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Ian Brierley
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Andrew E Firth
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
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64
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Thymidine kinase 2 and alanyl-tRNA synthetase 2 deficiencies cause lethal mitochondrial cardiomyopathy: case reports and review of the literature. Cardiol Young 2017; 27:936-944. [PMID: 27839525 DOI: 10.1017/s1047951116001876] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Cardiomyopathy is a common manifestation in neonates and infants with mitochondrial disorders. In this study, we report two cases manifesting with fatal mitochondrial hypertrophic cardiomyopathy, which include the third known patient with thymidine kinase 2 deficiency and the ninth patient with alanyl-tRNA synthetase 2 deficiency. The girl with thymidine kinase 2 deficiency had hypertrophic cardiomyopathy together with regression of gross motor development at the age of 13 months. Neurological symptoms and cardiac involvement progressed into severe myopathy, psychomotor arrest, and cardiorespiratory failure at the age of 22 months. The imaging methods and autoptic studies proved that she suffered from unique findings of leucoencephalopathy, severe, mainly cerebellar neuronal degeneration, and hepatic steatosis. The girl with alanyl-tRNA synthetase 2 deficiency presented with cardiac failure and underlying hypertrophic cardiomyopathy within 12 hours of life and subsequently died at 9 weeks of age. Muscle biopsy analyses demonstrated respiratory chain complex I and IV deficiencies, and histological evaluation revealed massive mitochondrial accumulation and cytochrome c oxidase-negative fibres in both cases. Exome sequencing in the first case revealed compound heterozygozity for one novel c.209T>C and one previously published c.416C>T mutation in the TK2 gene, whereas in the second case homozygozity for the previously described mutation c.1774C>T in the AARS2 gene was determined. The thymidine kinase 2 mutations resulted in severe mitochondrial DNA depletion (to 12% of controls) in the muscle. We present, for the first time, severe leucoencephalopathy and hepatic steatosis in a patient with thymidine kinase 2 deficiency and the finding of a ragged red fibre-like image in the muscle biopsy in a patient with alanyl-tRNA synthetase 2 deficiency.
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65
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Jung J, Kim LJ, Wang X, Wu Q, Sanvoranart T, Hubert CG, Prager BC, Wallace LC, Jin X, Mack SC, Rich JN. Nicotinamide metabolism regulates glioblastoma stem cell maintenance. JCI Insight 2017; 2:90019. [PMID: 28515364 DOI: 10.1172/jci.insight.90019] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 04/18/2017] [Indexed: 12/29/2022] Open
Abstract
Metabolic dysregulation promotes cancer growth through not only energy production, but also epigenetic reprogramming. Here, we report that a critical node in methyl donor metabolism, nicotinamide N-methyltransferase (NNMT), ranked among the most consistently overexpressed metabolism genes in glioblastoma relative to normal brain. NNMT was preferentially expressed by mesenchymal glioblastoma stem cells (GSCs). NNMT depletes S-adenosyl methionine (SAM), a methyl donor generated from methionine. GSCs contained lower levels of methionine, SAM, and nicotinamide, but they contained higher levels of oxidized nicotinamide adenine dinucleotide (NAD+) than differentiated tumor cells. In concordance with the poor prognosis associated with DNA hypomethylation in glioblastoma, depletion of methionine, a key upstream methyl group donor, shifted tumors toward a mesenchymal phenotype and accelerated tumor growth. Targeting NNMT expression reduced cellular proliferation, self-renewal, and in vivo tumor growth of mesenchymal GSCs. Supporting a mechanistic link between NNMT and DNA methylation, targeting NNMT reduced methyl donor availability, methionine levels, and unmethylated cytosine, with increased levels of DNA methyltransferases, DNMT1 and DNMT3A. Supporting the clinical significance of these findings, NNMT portended poor prognosis for glioblastoma patients. Collectively, our findings support NNMT as a GSC-specific therapeutic target in glioblastoma by disrupting oncogenic DNA hypomethylation.
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Affiliation(s)
- Jinkyu Jung
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Leo Jy Kim
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine.,Medical Scientist Training Program, School of Medicine.,Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Xiuxing Wang
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Qiulian Wu
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Tanwarat Sanvoranart
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Christopher G Hubert
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Briana C Prager
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine.,Medical Scientist Training Program, School of Medicine.,Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Lisa C Wallace
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Xun Jin
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Stephen C Mack
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jeremy N Rich
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine
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66
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Väre VYP, Eruysal ER, Narendran A, Sarachan KL, Agris PF. Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function. Biomolecules 2017; 7:E29. [PMID: 28300792 PMCID: PMC5372741 DOI: 10.3390/biom7010029] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/06/2017] [Accepted: 03/06/2017] [Indexed: 12/21/2022] Open
Abstract
RNAs are central to all gene expression through the control of protein synthesis. Four major nucleosides, adenosine, guanosine, cytidine and uridine, compose RNAs and provide sequence variation, but are limited in contributions to structural variation as well as distinct chemical properties. The ability of RNAs to play multiple roles in cellular metabolism is made possible by extensive variation in length, conformational dynamics, and the over 100 post-transcriptional modifications. There are several reviews of the biochemical pathways leading to RNA modification, but the physicochemical nature of modified nucleosides and how they facilitate RNA function is of keen interest, particularly with regard to the contributions of modified nucleosides. Transfer RNAs (tRNAs) are the most extensively modified RNAs. The diversity of modifications provide versatility to the chemical and structural environments. The added chemistry, conformation and dynamics of modified nucleosides occurring at the termini of stems in tRNA's cloverleaf secondary structure affect the global three-dimensional conformation, produce unique recognition determinants for macromolecules to recognize tRNAs, and affect the accurate and efficient decoding ability of tRNAs. This review will discuss the impact of specific chemical moieties on the structure, stability, electrochemical properties, and function of tRNAs.
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Affiliation(s)
- Ville Y P Väre
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Emily R Eruysal
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Amithi Narendran
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Kathryn L Sarachan
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Paul F Agris
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
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67
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Dealing with an Unconventional Genetic Code in Mitochondria: The Biogenesis and Pathogenic Defects of the 5-Formylcytosine Modification in Mitochondrial tRNA Met. Biomolecules 2017; 7:biom7010024. [PMID: 28257121 PMCID: PMC5372736 DOI: 10.3390/biom7010024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/24/2017] [Indexed: 01/13/2023] Open
Abstract
Human mitochondria contain their own genome, which uses an unconventional genetic code. In addition to the standard AUG methionine codon, the single mitochondrial tRNA Methionine (mt-tRNAMet) also recognises AUA during translation initiation and elongation. Post-transcriptional modifications of tRNAs are important for structure, stability, correct folding and aminoacylation as well as decoding. The unique 5-formylcytosine (f5C) modification of position 34 in mt-tRNAMet has been long postulated to be crucial for decoding of unconventional methionine codons and efficient mitochondrial translation. However, the enzymes responsible for the formation of mitochondrial f5C have been identified only recently. The first step of the f5C pathway consists of methylation of cytosine by NSUN3. This is followed by further oxidation by ABH1. Here, we review the role of f5C, the latest breakthroughs in our understanding of the biogenesis of this unique mitochondrial tRNA modification and its involvement in human disease.
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68
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Zaganelli S, Rebelo-Guiomar P, Maundrell K, Rozanska A, Pierredon S, Powell CA, Jourdain AA, Hulo N, Lightowlers RN, Chrzanowska-Lightowlers ZM, Minczuk M, Martinou JC. The Pseudouridine Synthase RPUSD4 Is an Essential Component of Mitochondrial RNA Granules. J Biol Chem 2017; 292:4519-4532. [PMID: 28082677 PMCID: PMC5377769 DOI: 10.1074/jbc.m116.771105] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/11/2017] [Indexed: 11/21/2022] Open
Abstract
Mitochondrial gene expression is a fundamental process that is largely dependent on nuclear-encoded proteins. Several steps of mitochondrial RNA processing and maturation, including RNA post-transcriptional modification, appear to be spatially organized into distinct foci, which we have previously termed mitochondrial RNA granules (MRGs). Although an increasing number of proteins have been localized to MRGs, a comprehensive analysis of the proteome of these structures is still lacking. Here, we have applied a microscopy-based approach that has allowed us to identify novel components of the MRG proteome. Among these, we have focused our attention on RPUSD4, an uncharacterized mitochondrial putative pseudouridine synthase. We show that RPUSD4 depletion leads to a severe reduction of the steady-state level of the 16S mitochondrial (mt) rRNA with defects in the biogenesis of the mitoribosome large subunit and consequently in mitochondrial translation. We report that RPUSD4 binds 16S mt-rRNA, mt-tRNAMet, and mt-tRNAPhe, and we demonstrate that it is responsible for pseudouridylation of the latter. These data provide new insights into the relevance of RNA pseudouridylation in mitochondrial gene expression.
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Affiliation(s)
- Sofia Zaganelli
- From the Department of Cell Biology, University of Geneva, 30 quai Ernest-Ansermet, 1211 Genève 4, Switzerland
| | - Pedro Rebelo-Guiomar
- Medical Research Council Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, United Kingdom.,Graduate Program in Areas of Basic and Applied Biology (GABBA), University of Porto, Porto 4200-135, Portugal
| | - Kinsey Maundrell
- From the Department of Cell Biology, University of Geneva, 30 quai Ernest-Ansermet, 1211 Genève 4, Switzerland
| | - Agata Rozanska
- Wellcome Trust Centre for Mitochondrial Research, Institute of Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom, and
| | - Sandra Pierredon
- From the Department of Cell Biology, University of Geneva, 30 quai Ernest-Ansermet, 1211 Genève 4, Switzerland
| | - Christopher A Powell
- Medical Research Council Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Alexis A Jourdain
- From the Department of Cell Biology, University of Geneva, 30 quai Ernest-Ansermet, 1211 Genève 4, Switzerland
| | - Nicolas Hulo
- Institute of Genetics and Genomics of Geneva, Université de Genève, 1211 Genève 4, Switzerland
| | - Robert N Lightowlers
- Wellcome Trust Centre for Mitochondrial Research, Institute of Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom, and
| | - Zofia M Chrzanowska-Lightowlers
- Wellcome Trust Centre for Mitochondrial Research, Institute of Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom, and
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Jean-Claude Martinou
- From the Department of Cell Biology, University of Geneva, 30 quai Ernest-Ansermet, 1211 Genève 4, Switzerland,
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69
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Human mitochondrial ribosomes can switch their structural RNA composition. Proc Natl Acad Sci U S A 2016; 113:12198-12201. [PMID: 27729525 DOI: 10.1073/pnas.1609338113] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The recent developments in cryo-EM have revolutionized our access to previously refractory structures. In particular, such studies of mammalian mitoribosomes have confirmed the absence of any 5S rRNA species and revealed the unexpected presence of a mitochondrially encoded tRNA (mt-tRNA) that usurps this position. Although the cryo-EM structures resolved the conundrum of whether mammalian mitoribosomes contain a 5S rRNA, they introduced a new dilemma: Why do human and porcine mitoribosomes integrate contrasting mt-tRNAs? Human mitoribosomes have been shown to integrate mt-tRNAVal compared with the porcine use of mt-tRNAPhe We have explored this observation further. Our studies examine whether a range of mt-tRNAs are used by different mammals, or whether the mt-tRNA selection is strictly limited to only these two species of the 22 tRNAs encoded by the mitochondrial genome (mtDNA); whether there is tissue-specific variation within a single organism; and what happens to the human mitoribosome when levels of the mt-tRNAVal are depleted. Our data demonstrate that only mt-tRNAVal or mt-tRNAPhe are found in the mitoribosomes of five different mammals, each mammal favors the same mt-tRNA in all tissue types, and strikingly, when steady-state levels of mt-tRNAVal are reduced, human mitoribosome biogenesis displays an adaptive response by switching to the incorporation of mt-tRNAPhe to generate translationally competent machinery.
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70
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Wedatilake Y, Niazi R, Fassone E, Powell CA, Pearce S, Plagnol V, Saldanha JW, Kleta R, Chong WK, Footitt E, Mills PB, Taanman JW, Minczuk M, Clayton PT, Rahman S. TRNT1 deficiency: clinical, biochemical and molecular genetic features. Orphanet J Rare Dis 2016; 11:90. [PMID: 27370603 PMCID: PMC4930608 DOI: 10.1186/s13023-016-0477-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/24/2016] [Indexed: 11/10/2022] Open
Abstract
Background TRNT1 (CCA-adding transfer RNA nucleotidyl transferase) enzyme deficiency is a new metabolic disease caused by defective post-transcriptional modification of mitochondrial and cytosolic transfer RNAs (tRNAs). Results We investigated four patients from two families with infantile-onset cyclical, aseptic febrile episodes with vomiting and diarrhoea, global electrolyte imbalance during these episodes, sideroblastic anaemia, B lymphocyte immunodeficiency, retinitis pigmentosa, hepatosplenomegaly, exocrine pancreatic insufficiency and renal tubulopathy. Other clinical features found in children include sensorineural deafness, cerebellar atrophy, brittle hair, partial villous atrophy and nephrocalcinosis. Whole exome sequencing and bioinformatic filtering were utilised to identify recessive compound heterozygous TRNT1 mutations (missense mutation c.668T>C, p.Ile223Thr and a novel splice mutation c.342+5G>T) segregating with disease in the first family. The second family was found to have a homozygous TRNT1 mutation (c.569G>T), p.Arg190Ile, (previously published). We found normal mitochondrial translation products using passage matched controls and functional perturbation of 3’ CCA addition to mitochondrial tRNAs (tRNACys, tRNALeuUUR and tRNAHis) in fibroblasts from two patients, demonstrating a pathomechanism affecting the CCA addition to mt-tRNAs. Acute management of these patients included transfusion for anaemia, fluid and electrolyte replacement and immunoglobulin therapy. We also describe three-year follow-up findings after treatment by bone marrow transplantation in one patient, with resolution of fever and reversal of the abnormal metabolic profile. Conclusions Our report highlights that TRNT1 mutations cause a spectrum of disease ranging from a childhood-onset complex disease with manifestations in most organs to an adult-onset isolated retinitis pigmentosa presentation. Systematic review of all TRNT1 cases and mutations reported to date revealed a distinctive phenotypic spectrum and metabolic and other investigative findings, which will facilitate rapid clinical recognition of future cases.
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Affiliation(s)
- Yehani Wedatilake
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - Rojeen Niazi
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - Elisa Fassone
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | | | | | | | - José W Saldanha
- Division of Mathematical Biology, National Institute for Medical Research, Mill Hill, London, UK
| | - Robert Kleta
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK.,UCL Genetics Institute, London, UK.,Division of Medicine, UCL, London, UK
| | - W Kling Chong
- Radiology Department, Great Ormond Street Hospital, London, UK
| | - Emma Footitt
- Metabolic medicine department, Great Ormond Street Hospital, London, UK
| | - Philippa B Mills
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - Jan-Willem Taanman
- Department of Clinical Neurosciences, UCL Institute of Neurology, London, UK
| | | | - Peter T Clayton
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - Shamima Rahman
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK. .,Mitochondrial Research Group, Genetics and Genomic Medicine Programme, UCL Institute of Child Health, 30, Guilford Street, London, WC1N 1EH, UK.
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71
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Metodiev M, Thompson K, Alston C, Morris A, He L, Assouline Z, Rio M, Bahi-Buisson N, Pyle A, Griffin H, Siira S, Filipovska A, Munnich A, Chinnery P, McFarland R, Rötig A, Taylor R. Recessive Mutations in TRMT10C Cause Defects in Mitochondrial RNA Processing and Multiple Respiratory Chain Deficiencies. Am J Hum Genet 2016; 98:993-1000. [PMID: 27132592 PMCID: PMC4863561 DOI: 10.1016/j.ajhg.2016.03.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/14/2016] [Indexed: 12/31/2022] Open
Abstract
Mitochondrial disorders are clinically and genetically diverse, with mutations in mitochondrial or nuclear genes able to cause defects in mitochondrial gene expression. Recently, mutations in several genes encoding factors involved in mt-tRNA processing have been identified to cause mitochondrial disease. Using whole-exome sequencing, we identified mutations in TRMT10C (encoding the mitochondrial RNase P protein 1 [MRPP1]) in two unrelated individuals who presented at birth with lactic acidosis, hypotonia, feeding difficulties, and deafness. Both individuals died at 5 months after respiratory failure. MRPP1, along with MRPP2 and MRPP3, form the mitochondrial ribonuclease P (mt-RNase P) complex that cleaves the 5′ ends of mt-tRNAs from polycistronic precursor transcripts. Additionally, a stable complex of MRPP1 and MRPP2 has m1R9 methyltransferase activity, which methylates mt-tRNAs at position 9 and is vital for folding mt-tRNAs into their correct tertiary structures. Analyses of fibroblasts from affected individuals harboring TRMT10C missense variants revealed decreased protein levels of MRPP1 and an increase in mt-RNA precursors indicative of impaired mt-RNA processing and defective mitochondrial protein synthesis. The pathogenicity of the detected variants—compound heterozygous c.542G>T (p.Arg181Leu) and c.814A>G (p.Thr272Ala) changes in subject 1 and a homozygous c.542G>T (p.Arg181Leu) variant in subject 2—was validated by the functional rescue of mt-RNA processing and mitochondrial protein synthesis defects after lentiviral transduction of wild-type TRMT10C. Our study suggests that these variants affect MRPP1 protein stability and mt-tRNA processing without affecting m1R9 methyltransferase activity, identifying mutations in TRMT10C as a cause of mitochondrial disease and highlighting the importance of RNA processing for correct mitochondrial function.
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