1
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Zhang F, Dang QCL, Vik SB. Human clinical mutations in mitochondrially encoded subunits of Complex I can be successfully modeled in E. coli. Mitochondrion 2022; 64:59-72. [PMID: 35306226 PMCID: PMC9035099 DOI: 10.1016/j.mito.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/21/2022] [Accepted: 03/15/2022] [Indexed: 11/28/2022]
Abstract
Respiratory Complex I is the site of a large fraction of the mutations that appear to cause mitochondrial disease. Seven of its subunits are mitochondrially encoded, and therefore, such mutants are particularly difficult to construct in cell-culture model systems. We have selected 13 human clinical mutations found in ND2, ND3, ND4, ND4L, ND5 and ND6 that are generally found at subunit interfaces, and not in critical residues. These mutations have been modeled in E. coli subunits of Complex I, nuoN, nuoA, nuoM, nuoK, nuoL, and nuoJ, respectively. All mutants were expressed from a plasmid encoding the entire nuo operon, and membrane vesicles were analyzed for deamino-NADH oxidase activity, and proton translocation activity. ND5 mutants were also analyzed using a time-delayed expression system, recently described by this lab. Other mutants were analyzed for the ability to associate in subcomplexes, after expression of subsets of the genes. For most mutants there was a positive correlation between those that were previously determined to be pathogenic, or likely to be pathogenic, and those that we found with compromised Complex I activity or subunit interactions in E. coli. In conclusion, this approach provides another way to explore the deleterious effects of human mitochondrial mutations, and it can contribute to molecular understanding of such mutations.
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Affiliation(s)
- Fang Zhang
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Quynh-Chi L Dang
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA
| | - Steven B Vik
- Department of Biological Sciences, Southern Methodist University, Dallas, TX 75275-0376, USA.
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2
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Subrahmanian N, Castonguay AD, Fatnes TA, Hamel PP. Chlamydomonas reinhardtii as a plant model system to study mitochondrial complex I dysfunction. PLANT DIRECT 2020; 4:e00200. [PMID: 32025618 PMCID: PMC6996877 DOI: 10.1002/pld3.200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/13/2019] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
Mitochondrial complex I, a proton-pumping NADH: ubiquinone oxidoreductase, is required for oxidative phosphorylation. However, the contribution of several human mutations to complex I deficiency is poorly understood. The unicellular alga Chlamydomonas reinhardtii was utilized to study complex I as, unlike in mammals, mutants with complete loss of the holoenzyme are viable. From a forward genetic screen for complex I-deficient insertional mutants, six mutants exhibiting complex I deficiency with assembly defects were isolated. Chlamydomonas mutants isolated from our screens, lacking the subunits NDUFV2 and NDUFB10, were used to reconstruct and analyze the effect of two human mutations in these subunit-encoding genes. The K209R substitution in NDUFV2, reported in Parkinson's disease patients, did not significantly affect the enzyme activity or assembly. The C107S substitution in the NDUFB10 subunit, reported in a case of fatal infantile cardiomyopathy, is part of a conserved C-(X)11-C motif. The cysteine substitutions, at either one or both positions, still allowed low levels of holoenzyme formation, indicating that this motif is crucial for complex I function but not strictly essential for assembly. We show that the algal mutants provide a simple and useful platform to delineate the consequences of patient mutations on complex I function.
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Affiliation(s)
- Nitya Subrahmanian
- Department of Molecular GeneticsThe Ohio State UniversityColumbusOHUSA
- Plant Cellular and Molecular Biology Graduate ProgramThe Ohio State UniversityColumbusOHUSA
| | - Andrew David Castonguay
- Department of Molecular GeneticsThe Ohio State UniversityColumbusOHUSA
- Molecular Genetics Graduate ProgramThe Ohio State UniversityColumbusOHUSA
| | - Thea Aspelund Fatnes
- Department of Molecular GeneticsThe Ohio State UniversityColumbusOHUSA
- Present address:
Fürst Medical LaboratoryOsloNorway
| | - Patrice Paul Hamel
- Department of Molecular GeneticsThe Ohio State UniversityColumbusOHUSA
- Department of Biological Chemistry and PharmacologyThe Ohio State UniversityColumbusOHUSA
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3
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Mani S, Rao SN, Kranthi Kumar M. Genetic heterogeneity of mitochondrial genome in thiamine deficient Leigh syndrome patients. J Neurol Sci 2019; 404:91-100. [DOI: 10.1016/j.jns.2019.07.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 10/26/2022]
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4
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Soldath P, Madsen KL, Buch AE, Duno M, Wibrand F, Vissing J. Pure exercise intolerance and ophthalmoplegia associated with the m.12,294G > A mutation in the MT-TL2 gene: a case report. BMC Musculoskelet Disord 2017; 18:419. [PMID: 29052516 PMCID: PMC5649050 DOI: 10.1186/s12891-017-1781-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 10/12/2017] [Indexed: 12/22/2022] Open
Abstract
Background Pure exercise intolerance associated with exclusive affection of skeletal muscle is a very rare phenotype of patients with mitochondrial myopathy. Moreover, the exercise intolerance in these rare patients is yet not well explored, as most of known cases have not been assessed by objective testing, but only by interview. We report a patient with a mitochondrial DNA (mtDNA) mutation that gives rise to an exclusive myopathy associated with exercise intolerance and ophthalmoplegia. We quantified the patient’s exercise intolerance through detailed exercise testing. Case presentation A 39-year-old man presented with exercise intolerance and chronic progressive external ophthalmoplegia. Sequencing of the entire mtDNA identified a m.12,294G > A mutation in the MT-TL2 gene. The mutation was heteroplasmic in skeletal muscle (75%) while undetectable in blood, urinary sediment, and buccal mucosa as well as in tissues from the patient’s mother. The mutation affected a highly conserved site in the anticodon stem of the mitochondrial transfer RNA Leucine (CUN) molecule and lead to a severe combined respiratory chain defect. Exercise physiological studies in the patient demonstrated a significantly reduced maximal oxygen uptake of 20.4 ml O2 × min−1 × kg−1 (about half of normal) as well as threefold elevated lactate/pyruvate ratios. Conclusion The findings of our study support that the m.12,294G > A mutation is pathogenic. Likely, the mutation arose sporadically in early embryogenesis after differentiation of the mesoderm into muscle progenitor cells, leading to a pure myopathic phenotype.
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Affiliation(s)
- Patrick Soldath
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Department of Neurology, Copenhagen Neuromuscular Center, Rigshospitalet, Copenhagen, Denmark.
| | - Karen Lindhardt Madsen
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Neurology, Copenhagen Neuromuscular Center, Rigshospitalet, Copenhagen, Denmark
| | - Astrid Emilie Buch
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Neurology, Copenhagen Neuromuscular Center, Rigshospitalet, Copenhagen, Denmark
| | - Morten Duno
- Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark
| | - Flemming Wibrand
- Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark
| | - John Vissing
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Neurology, Copenhagen Neuromuscular Center, Rigshospitalet, Copenhagen, Denmark
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5
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In silico analysis for predicting pathogenicity of five unclassified mitochondrial DNA mutations associated with mitochondrial cytopathies' phenotypes. Eur J Med Genet 2017; 60:172-177. [DOI: 10.1016/j.ejmg.2016.12.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 12/13/2016] [Accepted: 12/21/2016] [Indexed: 11/17/2022]
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6
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Xu B, Li X, Du M, Zhou C, Fang H, Lyu J, Yang Y. Novel mutation of ND4 gene identified by targeted next-generation sequencing in patient with Leigh syndrome. J Hum Genet 2016; 62:291-297. [PMID: 27761019 DOI: 10.1038/jhg.2016.127] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 09/14/2016] [Accepted: 09/14/2016] [Indexed: 01/21/2023]
Abstract
By using next-generation sequencing targeted to MitoExome including the entire mtDNA and exons of 1033 genes encoding the mitochondrial proteome, we described here a novel m.11240C>T mutation in the mitochondrial ND4 gene from a patient with Leigh syndrome. High mutant loads of m.11240C>T were detected in blood, urinary epithelium, oral mucosal epithelium cells, and skin fibroblasts of the patient. Decreased mitochondrial complex I activity was found in transmitochondrial cybrids containing the m.11240C>T mutation with biochemical analysis. Furthermore, functional investigations confirmed that mitochondria with the m.11240C>T variant exhibited lower adenosine triphosphate-related mitochondrial respiration. However, complex I assembly in mutant cybrids was not affected. While this mutation was located in the fourth hydrophobic trans-membrane region of ND4 gene, we suggested that mutation of m.11240C>T might impair the proton pumping channel of complex I but had little effect on the complex I assembly. In conclusion, we identified m.11240C>T as a novel mitochondrial disease-related mtDNA mutation.
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Affiliation(s)
- Bing Xu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Zhejiang, China
| | - Xiyuan Li
- Department of Pediatrics, Peking University First Hospital, Beijing, China.,Institute of Computing Technology, Chinese Academy of Science, Beijing, China
| | - Miaomiao Du
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Zhejiang, China
| | - Chao Zhou
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Zhejiang, China
| | - Hezhi Fang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Zhejiang, China
| | - Jianxin Lyu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Zhejiang, China
| | - Yanling Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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7
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Horga A, Pitceathly RDS, Blake JC, Woodward CE, Zapater P, Fratter C, Mudanohwo EE, Plant GT, Houlden H, Sweeney MG, Hanna MG, Reilly MM. Peripheral neuropathy predicts nuclear gene defect in patients with mitochondrial ophthalmoplegia. ACTA ACUST UNITED AC 2014; 137:3200-12. [PMID: 25281868 PMCID: PMC4240292 DOI: 10.1093/brain/awu279] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mitochondrial ophthalmoplegia is a genetically heterogeneous disorder. Horga et al. investigate whether peripheral neuropathy can predict the underlying genetic defect in patients with progressive external ophthalmoplegia. Results indicate that neuropathy is highly predictive of a nuclear DNA defect and that it is rarely associated with single mitochondrial DNA deletions. Progressive external ophthalmoplegia is a common clinical feature in mitochondrial disease caused by nuclear DNA defects and single, large-scale mitochondrial DNA deletions and is less frequently associated with point mutations of mitochondrial DNA. Peripheral neuropathy is also a frequent manifestation of mitochondrial disease, although its prevalence and characteristics varies considerably among the different syndromes and genetic aetiologies. Based on clinical observations, we systematically investigated whether the presence of peripheral neuropathy could predict the underlying genetic defect in patients with progressive external ophthalmoplegia. We analysed detailed demographic, clinical and neurophysiological data from 116 patients with genetically-defined mitochondrial disease and progressive external ophthalmoplegia. Seventy-eight patients (67%) had a single mitochondrial DNA deletion, 12 (10%) had a point mutation of mitochondrial DNA and 26 (22%) had mutations in either POLG, C10orf2 or RRM2B, or had multiple mitochondrial DNA deletions in muscle without an identified nuclear gene defect. Seventy-seven patients had neurophysiological studies; of these, 16 patients (21%) had a large-fibre peripheral neuropathy. The prevalence of peripheral neuropathy was significantly lower in patients with a single mitochondrial DNA deletion (2%) as compared to those with a point mutation of mitochondrial DNA or with a nuclear DNA defect (44% and 52%, respectively; P < 0.001). Univariate analyses revealed significant differences in the distribution of other clinical features between genotypes, including age at disease onset, gender, family history, progressive external ophthalmoplegia at clinical presentation, hearing loss, pigmentary retinopathy and extrapyramidal features. However, binomial logistic regression analysis identified peripheral neuropathy as the only independent predictor associated with a nuclear DNA defect (P = 0.002; odds ratio 8.43, 95% confidence interval 2.24–31.76). Multinomial logistic regression analysis identified peripheral neuropathy, family history and hearing loss as significant predictors of the genotype, and the same three variables showed the highest performance in genotype classification in a decision tree analysis. Of these variables, peripheral neuropathy had the highest specificity (91%), negative predictive value (83%) and positive likelihood ratio (5.87) for the diagnosis of a nuclear DNA defect. These results indicate that peripheral neuropathy is a rare finding in patients with single mitochondrial DNA deletions but that it is highly predictive of an underlying nuclear DNA defect. This observation may facilitate the development of diagnostic algorithms. We suggest that nuclear gene testing may enable a more rapid diagnosis and avoid muscle biopsy in patients with progressive external ophthalmoplegia and peripheral neuropathy.
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Affiliation(s)
- Alejandro Horga
- 1 MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Robert D S Pitceathly
- 1 MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Julian C Blake
- 2 Department of Clinical Neurophysiology, Norfolk and Norwich University Hospital, Norwich, NR4 7UY, UK
| | - Catherine E Woodward
- 3 Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Pedro Zapater
- 4 Clinical Pharmacology Section, Hospital General Universitario, Alicante, 03010, Spain
| | - Carl Fratter
- 5 Oxford Medical Genetics Laboratories, Oxford University Hospitals NHS Trust, Oxford, OX3 7LE, UK
| | - Ese E Mudanohwo
- 3 Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Gordon T Plant
- 6 National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Henry Houlden
- 1 MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Mary G Sweeney
- 3 Neurogenetics Unit, National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Michael G Hanna
- 1 MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - Mary M Reilly
- 1 MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
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8
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Hiniker A, Wong LJ, Berven S, Truong CK, Adesina AM, Margeta M. Axial mitochondrial myopathy in a patient with rapidly progressive adult-onset scoliosis. Acta Neuropathol Commun 2014; 2:137. [PMID: 25223649 PMCID: PMC4180433 DOI: 10.1186/s40478-014-0137-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 09/04/2014] [Indexed: 01/13/2023] Open
Abstract
Axial myopathy can be the underlying cause of rapidly progressive adult-onset scoliosis; however, the pathogenesis of this disorder remains poorly understood. Here we present a case of a 69-year old woman with a family history of scoliosis affecting both her mother and her son, who over 4 years developed rapidly progressive scoliosis. The patient had a history of stable scoliosis since adolescence that worsened significantly at age 65, leading to low back pain and radiculopathy. Paraspinal muscle biopsy showed morphologic evidence of a mitochondrial myopathy. Diagnostic deficiencies of electron transport chain enzymes were not detected using standard bioassays, but mitochondrial immunofluorescence demonstrated many muscle fibers totally or partially deficient for complexes I, III, IV-I, and IV-IV. Massively parallel sequencing of paraspinal muscle mtDNA detected multiple deletions as well as a 40.9% heteroplasmic novel m.12293G > A (MT-TL2) variant, which changes a G:C pairing to an A:C mispairing in the anticodon stem of tRNA LeuCUN. Interestingly, these mitochondrial abnormalities were not detected in the blood of either the patient or her son, suggesting that the patient’s rapidly progressive late onset scoliosis was due to the acquired paraspinal mitochondrial myopathy; the cause of non-progressive scoliosis in the other two family members currently remains unexplained. Notably, this case illustrates that isolated mitochondrial myopathy can underlie rapidly-progressive adult-onset scoliosis and should be considered in the differential diagnosis of the primary axial myopathy.
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9
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Larosa V, Coosemans N, Motte P, Bonnefoy N, Remacle C. Reconstruction of a human mitochondrial complex I mutation in the unicellular green alga Chlamydomonas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:759-768. [PMID: 22268373 DOI: 10.1111/j.1365-313x.2012.04912.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Defects in complex I (NADH:ubiquinone oxidoreductase (EC 1.6.5.3)) are the most frequent cause of human respiratory disorders. The pathogenicity of a given human mitochondrial mutation can be difficult to demonstrate because the mitochondrial genome harbors large numbers of polymorphic base changes that have no pathogenic significance. In addition, mitochondrial mutations are usually found in the heteroplasmic state, which may hide the biochemical effect of the mutation. We propose that the unicellular green alga Chlamydomonas could be used to study such mutations because (i) respiratory complex-deficient mutants are viable and mitochondrial mutations are found in the homoplasmic state, (ii) transformation of the mitochondrial genome is feasible, and (iii) Chlamydomonas complex I is similar to that of humans. To illustrate this proposal, we introduced a Leu157Pro substitution into the Chlamydomonas ND4 subunit of complex I in two recipient strains by biolistic transformation, demonstrating that site-directed mutagenesis of the Chlamydomonas mitochondrial genome is possible. This substitution did not lead to any respiratory enzyme defects when present in the heteroplasmic state in a patient with chronic progressive external ophthalmoplegia. When present in the homoplasmic state in the alga, the mutation does not prevent assembly of whole complex I (950 kDa) and the NADH dehydrogenase activity of the peripheral arm of the complex is mildly affected. However, the NADH:duroquinone oxidoreductase activity is strongly reduced, suggesting that the substitution could affect binding of ubiquinone to the membrane domain. The in vitro defects correlate with a decrease in dark respiration and growth rate in vivo.
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Affiliation(s)
- Véronique Larosa
- Genetics of Microorganisms, Department of Life Sciences, Institute of Botany, University of Liege, B-4000 Liege, Belgium
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10
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A novel mutation in the mitochondrial tRNAAla gene (m.5636T>C) in a patient with progressive external ophthalmoplegia. Mitochondrion 2011; 11:228-33. [DOI: 10.1016/j.mito.2010.08.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 07/21/2010] [Accepted: 08/20/2010] [Indexed: 11/23/2022]
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11
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Limongelli G, Rahman S, Pitceathly RD, Hanna MG, Elliott PM. Cardiac manifestations of mitochondrial disorders: reply. Eur J Heart Fail 2010. [DOI: 10.1093/eurjhf/hfq074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Shamima Rahman
- MRC Centre for Neuromuscular Diseases, Institute of Neurology and The National Hospital for Neurology and Neurosurgery Queen Square
- University College London London UK
| | - Robert D.S. Pitceathly
- MRC Centre for Neuromuscular Diseases, Institute of Neurology and The National Hospital for Neurology and Neurosurgery Queen Square
- University College London London UK
| | - Michael G. Hanna
- MRC Centre for Neuromuscular Diseases, Institute of Neurology and The National Hospital for Neurology and Neurosurgery Queen Square
- University College London London UK
| | - Perry M. Elliott
- The Heart Hospital University College London 16‐18 Westmoreland Street London W1G 8PH UK
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12
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Álvarez-Iglesias V, Mosquera-Miguel A, Cerezo M, Quintáns B, Zarrabeitia MT, Cuscó I, Lareu MV, García Ó, Pérez-Jurado L, Carracedo Á, Salas A. New population and phylogenetic features of the internal variation within mitochondrial DNA macro-haplogroup R0. PLoS One 2009; 4:e5112. [PMID: 19340307 PMCID: PMC2660437 DOI: 10.1371/journal.pone.0005112] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Accepted: 03/09/2009] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND R0 embraces the most common mitochondrial DNA (mtDNA) lineage in West Eurasia, namely, haplogroup H (approximately 40%). R0 sub-lineages are badly defined in the control region and therefore, the analysis of diagnostic coding region polymorphisms is needed in order to gain resolution in population and medical studies. METHODOLOGY/PRINCIPAL FINDINGS We sequenced the first hypervariable segment (HVS-I) of 518 individuals from different North Iberian regions. The mtDNAs belonging to R0 (approximately 57%) were further genotyped for a set of 71 coding region SNPs characterizing major and minor branches of R0. We found that the North Iberian Peninsula shows moderate levels of population stratification; for instance, haplogroup V reaches the highest frequency in Cantabria (north-central Iberia), but lower in Galicia (northwest Iberia) and Catalonia (northeast Iberia). When compared to other European and Middle East populations, haplogroups H1, H3 and H5a show frequency peaks in the Franco-Cantabrian region, declining from West towards the East and South Europe. In addition, we have characterized, by way of complete genome sequencing, a new autochthonous clade of haplogroup H in the Basque country, named H2a5. Its coalescence age, 15.6+/-8 thousand years ago (kya), dates to the period immediately after the Last Glacial Maximum (LGM). CONCLUSIONS/SIGNIFICANCE In contrast to other H lineages that experienced re-expansion outside the Franco-Cantabrian refuge after the LGM (e.g. H1 and H3), H2a5 most likely remained confined to this area till present days.
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Affiliation(s)
- Vanesa Álvarez-Iglesias
- Unidade de Xenética, Instituto de Medicina Legal and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Ana Mosquera-Miguel
- Unidade de Xenética, Instituto de Medicina Legal and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Maria Cerezo
- Unidade de Xenética, Instituto de Medicina Legal and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - Beatriz Quintáns
- Fundación Pública Galega de Medicina Xenómica (FPGMX), and Ciber de enfermedades raras (CIBERER), Hospital Clínico Universitario, Universidade de Santiago de Compostela, Galicia, Spain
| | | | - Ivon Cuscó
- Unidad de Genética, Universitat Pompeu Fabra, and U735 CIBER de enfermedades raras (CIBERER), Barcelona, Spain
| | - Maria Victoria Lareu
- Unidade de Xenética, Instituto de Medicina Legal and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | | | - Luis Pérez-Jurado
- Unidad de Genética, Universitat Pompeu Fabra, and U735 CIBER de enfermedades raras (CIBERER), Barcelona, Spain
- Programa de Medicina Molecular y Genética, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Ángel Carracedo
- Unidade de Xenética, Instituto de Medicina Legal and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
- Fundación Pública Galega de Medicina Xenómica (FPGMX), and Ciber de enfermedades raras (CIBERER), Hospital Clínico Universitario, Universidade de Santiago de Compostela, Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Medicina Legal and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
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13
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Cardaioli E, Da Pozzo P, Malfatti E, Gallus G, Rubegni A, Malandrini A, Gaudiano C, Guidi L, Serni G, Berti G, Dotti M, Federico A. Chronic progressive external ophthalmoplegia: A new heteroplasmic tRNALeu(CUN) mutation of mitochondrial DNA. J Neurol Sci 2008; 272:106-9. [DOI: 10.1016/j.jns.2008.05.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2007] [Revised: 05/05/2008] [Accepted: 05/08/2008] [Indexed: 11/26/2022]
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14
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Filosto M, Tonin P, Scarpelli M, Savio C, Greco F, Mancuso M, Vattemi G, Govoni V, Rizzuto N, Tupler R, Tomelleri G. Novel mitochondrial tRNA Leu(CUN) transition and D4Z4 partial deletion in a patient with a facioscapulohumeral phenotype. Neuromuscul Disord 2008; 18:204-9. [PMID: 18343111 DOI: 10.1016/j.nmd.2007.12.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Revised: 11/22/2007] [Accepted: 12/07/2007] [Indexed: 10/22/2022]
Abstract
Point mutations in mtDNA-encoded tRNA genes frequently cause isolated myopathies but rarely cause the facioscapulohumeral phenotype. We report on a patient affected with chronic progressive weakness of facioscapulohumeral/peroneal muscles whose muscle biopsy showed a mitochondrial myopathy. mtDNA direct sequencing and RFLP analysis revealed a heteroplasmic transition T12313C which disrupts a conserved site in the T Psi C stem of the tRNA(Leu(CUN)) gene and fulfills the accepted criteria of pathogenicity. A partial deletion of the nuclear DNA D4Z4 region with residual repeat sizes of 25 kb was also found in the patient and in her mother. This is the first reported case of mitochondrial myopathy/facioscapulohumeral muscular dystrophy (FSHD) "double trouble".
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Affiliation(s)
- Massimiliano Filosto
- Department of Neurological Sciences and Vision, Section of Clinical Neurology, University of Verona, Italy
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15
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Tzen CY, Mau BL, Hsu HJ. Analysis of disease-associated ND4 mutations: How do we know which mutation is pathogenic? Mitochondrion 2007; 7:151-6. [PMID: 17280878 DOI: 10.1016/j.mito.2006.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Accepted: 10/06/2006] [Indexed: 11/17/2022]
Abstract
It is not uncommon to identify more than one mtDNA replacement mutations in the specimens from patients. However, we usually do not know if the identified mtDNA mutation is pathogenic or not. Even functional assays are available to use, we would not know which mutation(s) is to be tested. To provide a rapid method for initial evaluation for the pathogenicity of the replacement mutation, we compared three evolutional analyses: primate conservation index (PCI), mammalian conservation index (MCI), and conservation index across a wide spectrum of species (CI). After analyzing 35 so-called diseases-associated replacement mutations of ND4, we found 8 pathogenic mutations, 15 nonpathogenic mutations, and 12 mutations of undetermined significance. The MCI classification appears to be the best one among the three systems. This study demonstrates that evolutional analysis can serve as a rapid evaluation for the pathogenicity of mtDNA replacement mutations.
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Affiliation(s)
- Chin-Yuan Tzen
- Department of Pathology, Mackay Memorial Hospital, Taipei, Taiwan.
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Cardaioli E, Da Pozzo P, Radi E, Dotti MT, Federico A. A novel heteroplasmic tRNALeu(CUN) mtDNA point mutation associated with chronic progressive external ophthalmoplegia. Biochem Biophys Res Commun 2005; 327:675-8. [PMID: 15649400 DOI: 10.1016/j.bbrc.2004.11.170] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2004] [Indexed: 10/26/2022]
Abstract
We have sequenced all mitochondrial tRNA genes from a patient with chronic progressive external ophthalmoplegia (CPEO) and mitochondrial myopathy, who had no detectable large mtDNA deletions. Direct sequencing failed to detect previously reported mutations and showed a heteroplasmic mutation at nucleotide 12,276 in the tRNA(Leu(CUN)) gene, in the dihydrouridine stem, which is highly conserved through the species during evolution. RFLP analyses confirmed that 18% of muscle mtDNA harbored the mutation, while it was absent from DNA of fibroblasts and lymphocytes of the proband and in 110 patients with other encephalomyopathies. To date, besides large and single nucleotide deletions, several point mutations on mitochondrial tRNA genes have been reported in CPEO patients, but only three were in the gene coding for tRNA(Leu(CUN)).
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Affiliation(s)
- Elena Cardaioli
- Department of Neurological and Behavioural Sciences, University of Siena, Italy
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Palanichamy MG, Sun C, Agrawal S, Bandelt HJ, Kong QP, Khan F, Wang CY, Chaudhuri TK, Palla V, Zhang YP. Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of South Asia. Am J Hum Genet 2004; 75:966-78. [PMID: 15467980 PMCID: PMC1182158 DOI: 10.1086/425871] [Citation(s) in RCA: 247] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2004] [Accepted: 09/08/2004] [Indexed: 11/03/2022] Open
Abstract
To resolve the phylogeny of the autochthonous mitochondrial DNA (mtDNA) haplogroups of India and determine the relationship between the Indian and western Eurasian mtDNA pools more precisely, a diverse subset of 75 macrohaplogroup N lineages was chosen for complete sequencing from a collection of >800 control-region sequences sampled across India. We identified five new autochthonous haplogroups (R7, R8, R30, R31, and N5) and fully characterized the autochthonous haplogroups (R5, R6, N1d, U2a, U2b, and U2c) that were previously described only by first hypervariable segment (HVS-I) sequencing and coding-region restriction-fragment-length polymorphism analysis. Our findings demonstrate that the Indian mtDNA pool, even when restricted to macrohaplogroup N, harbors at least as many deepest-branching lineages as the western Eurasian mtDNA pool. Moreover, the distribution of the earliest branches within haplogroups M, N, and R across Eurasia and Oceania provides additional evidence for a three-founder-mtDNA scenario and a single migration route out of Africa.
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Affiliation(s)
- Malliya gounder Palanichamy
- Laboratory for Conservation and Utilization of Bioresources, Yunnan University, and Laboratory of Cellular and Molecular Evolution and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Graduate School of the Chinese Academy of Sciences, Beijing; Department of Medical Genetics, Sanjay Gandhi Institute of Medical Sciences, Lucknow, India; Fachbereich Mathematik, Universität Hamburg, Hamburg; Department of Zoology, North Bengal University, Siliguri West Bengal, India; and Department of Anthropology, Sri Venkateswara University, Tirupati, India
| | - Chang Sun
- Laboratory for Conservation and Utilization of Bioresources, Yunnan University, and Laboratory of Cellular and Molecular Evolution and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Graduate School of the Chinese Academy of Sciences, Beijing; Department of Medical Genetics, Sanjay Gandhi Institute of Medical Sciences, Lucknow, India; Fachbereich Mathematik, Universität Hamburg, Hamburg; Department of Zoology, North Bengal University, Siliguri West Bengal, India; and Department of Anthropology, Sri Venkateswara University, Tirupati, India
| | - Suraksha Agrawal
- Laboratory for Conservation and Utilization of Bioresources, Yunnan University, and Laboratory of Cellular and Molecular Evolution and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Graduate School of the Chinese Academy of Sciences, Beijing; Department of Medical Genetics, Sanjay Gandhi Institute of Medical Sciences, Lucknow, India; Fachbereich Mathematik, Universität Hamburg, Hamburg; Department of Zoology, North Bengal University, Siliguri West Bengal, India; and Department of Anthropology, Sri Venkateswara University, Tirupati, India
| | - Hans-Jürgen Bandelt
- Laboratory for Conservation and Utilization of Bioresources, Yunnan University, and Laboratory of Cellular and Molecular Evolution and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Graduate School of the Chinese Academy of Sciences, Beijing; Department of Medical Genetics, Sanjay Gandhi Institute of Medical Sciences, Lucknow, India; Fachbereich Mathematik, Universität Hamburg, Hamburg; Department of Zoology, North Bengal University, Siliguri West Bengal, India; and Department of Anthropology, Sri Venkateswara University, Tirupati, India
| | - Qing-Peng Kong
- Laboratory for Conservation and Utilization of Bioresources, Yunnan University, and Laboratory of Cellular and Molecular Evolution and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Graduate School of the Chinese Academy of Sciences, Beijing; Department of Medical Genetics, Sanjay Gandhi Institute of Medical Sciences, Lucknow, India; Fachbereich Mathematik, Universität Hamburg, Hamburg; Department of Zoology, North Bengal University, Siliguri West Bengal, India; and Department of Anthropology, Sri Venkateswara University, Tirupati, India
| | - Faisal Khan
- Laboratory for Conservation and Utilization of Bioresources, Yunnan University, and Laboratory of Cellular and Molecular Evolution and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Graduate School of the Chinese Academy of Sciences, Beijing; Department of Medical Genetics, Sanjay Gandhi Institute of Medical Sciences, Lucknow, India; Fachbereich Mathematik, Universität Hamburg, Hamburg; Department of Zoology, North Bengal University, Siliguri West Bengal, India; and Department of Anthropology, Sri Venkateswara University, Tirupati, India
| | - Cheng-Ye Wang
- Laboratory for Conservation and Utilization of Bioresources, Yunnan University, and Laboratory of Cellular and Molecular Evolution and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Graduate School of the Chinese Academy of Sciences, Beijing; Department of Medical Genetics, Sanjay Gandhi Institute of Medical Sciences, Lucknow, India; Fachbereich Mathematik, Universität Hamburg, Hamburg; Department of Zoology, North Bengal University, Siliguri West Bengal, India; and Department of Anthropology, Sri Venkateswara University, Tirupati, India
| | - Tapas Kumar Chaudhuri
- Laboratory for Conservation and Utilization of Bioresources, Yunnan University, and Laboratory of Cellular and Molecular Evolution and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Graduate School of the Chinese Academy of Sciences, Beijing; Department of Medical Genetics, Sanjay Gandhi Institute of Medical Sciences, Lucknow, India; Fachbereich Mathematik, Universität Hamburg, Hamburg; Department of Zoology, North Bengal University, Siliguri West Bengal, India; and Department of Anthropology, Sri Venkateswara University, Tirupati, India
| | - Venkatramana Palla
- Laboratory for Conservation and Utilization of Bioresources, Yunnan University, and Laboratory of Cellular and Molecular Evolution and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Graduate School of the Chinese Academy of Sciences, Beijing; Department of Medical Genetics, Sanjay Gandhi Institute of Medical Sciences, Lucknow, India; Fachbereich Mathematik, Universität Hamburg, Hamburg; Department of Zoology, North Bengal University, Siliguri West Bengal, India; and Department of Anthropology, Sri Venkateswara University, Tirupati, India
| | - Ya-Ping Zhang
- Laboratory for Conservation and Utilization of Bioresources, Yunnan University, and Laboratory of Cellular and Molecular Evolution and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Graduate School of the Chinese Academy of Sciences, Beijing; Department of Medical Genetics, Sanjay Gandhi Institute of Medical Sciences, Lucknow, India; Fachbereich Mathematik, Universität Hamburg, Hamburg; Department of Zoology, North Bengal University, Siliguri West Bengal, India; and Department of Anthropology, Sri Venkateswara University, Tirupati, India
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