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Antolínez-Fernández Á, Esteban-Ramos P, Fernández-Moreno MÁ, Clemente P. Molecular pathways in mitochondrial disorders due to a defective mitochondrial protein synthesis. Front Cell Dev Biol 2024; 12:1410245. [PMID: 38855161 PMCID: PMC11157125 DOI: 10.3389/fcell.2024.1410245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/09/2024] [Indexed: 06/11/2024] Open
Abstract
Mitochondria play a central role in cellular metabolism producing the necessary ATP through oxidative phosphorylation. As a remnant of their prokaryotic past, mitochondria contain their own genome, which encodes 13 subunits of the oxidative phosphorylation system, as well as the tRNAs and rRNAs necessary for their translation in the organelle. Mitochondrial protein synthesis depends on the import of a vast array of nuclear-encoded proteins including the mitochondrial ribosome protein components, translation factors, aminoacyl-tRNA synthetases or assembly factors among others. Cryo-EM studies have improved our understanding of the composition of the mitochondrial ribosome and the factors required for mitochondrial protein synthesis and the advances in next-generation sequencing techniques have allowed for the identification of a growing number of genes involved in mitochondrial pathologies with a defective translation. These disorders are often multisystemic, affecting those tissues with a higher energy demand, and often present with neurodegenerative phenotypes. In this article, we review the known proteins required for mitochondrial translation, the disorders that derive from a defective mitochondrial protein synthesis and the animal models that have been established for their study.
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Affiliation(s)
- Álvaro Antolínez-Fernández
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paula Esteban-Ramos
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Miguel Ángel Fernández-Moreno
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paula Clemente
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
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2
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Bayona-Bafaluy MP, Iglesias E, López-Gallardo E, Emperador S, Pacheu-Grau D, Labarta L, Montoya J, Ruiz-Pesini E. Genetic aspects of the oxidative phosphorylation dysfunction in dilated cardiomyopathy. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 786:108334. [PMID: 33339579 DOI: 10.1016/j.mrrev.2020.108334] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 12/27/2022]
Abstract
Dilated cardiomyopathy is a frequent and extremely heterogeneous medical condition. Deficits in the oxidative phosphorylation system have been described in patients suffering from dilated cardiomyopathy. Hence, mutations in proteins related to this biochemical pathway could be etiological factors for some of these patients. Here, we review the clinical phenotypes of patients harboring pathological mutations in genes related to the oxidative phosphorylation system, either encoded in the mitochondrial or in the nuclear genome, presenting with dilated cardiomyopathy. In addition to the clinical heterogeneity of these patients, the large genetic heterogeneity has contributed to an improper allocation of pathogenicity for many candidate mutations. We suggest criteria to avoid incorrect assignment of pathogenicity to newly found mutations and discuss possible therapies targeting the oxidative phosphorylation function.
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Affiliation(s)
- M Pilar Bayona-Bafaluy
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza. C/ Miguel Servet, 177. 50013, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13., 50009, Zaragoza, Spain; Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain.
| | - Eldris Iglesias
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza. C/ Miguel Servet, 177. 50013, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13., 50009, Zaragoza, Spain.
| | - Ester López-Gallardo
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza. C/ Miguel Servet, 177. 50013, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13., 50009, Zaragoza, Spain; Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain.
| | - Sonia Emperador
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza. C/ Miguel Servet, 177. 50013, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13., 50009, Zaragoza, Spain; Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain.
| | - David Pacheu-Grau
- Department of Cellular Biochemistry, University Medical Center, Georg-August University,Humboldtalle, 23., 37073, Göttingen, Germany.
| | - Lorenzo Labarta
- Unidad de Cuidados Intensivos, Hospital San Jorge, Av. Martínez de Velasco, 36., 22004, Huesca, Spain.
| | - Julio Montoya
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza. C/ Miguel Servet, 177. 50013, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13., 50009, Zaragoza, Spain; Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain.
| | - Eduardo Ruiz-Pesini
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza. C/ Miguel Servet, 177. 50013, Zaragoza, Spain; Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13., 50009, Zaragoza, Spain; Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029, Madrid, Spain; Fundación ARAID, Av. de Ranillas, 1-D., 50018, Zaragoza, Spain.
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3
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Pacheu-Grau D, Wasilewski M, Oeljeklaus S, Gibhardt CS, Aich A, Chudenkova M, Dennerlein S, Deckers M, Bogeski I, Warscheid B, Chacinska A, Rehling P. COA6 Facilitates Cytochrome c Oxidase Biogenesis as Thiol-reductase for Copper Metallochaperones in Mitochondria. J Mol Biol 2020; 432:2067-2079. [PMID: 32061935 PMCID: PMC7254062 DOI: 10.1016/j.jmb.2020.01.036] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 12/15/2022]
Abstract
The mitochondrial cytochrome c oxidase, the terminal enzyme of the respiratory chain, contains heme and copper centers for electron transfer. The conserved COX2 subunit contains the CuA site, a binuclear copper center. The copper chaperones SCO1, SCO2, and COA6, are required for CuA center formation. Loss of function of these chaperones and the concomitant cytochrome c oxidase deficiency cause severe human disorders. Here we analyzed the molecular function of COA6 and the consequences of COA6 deficiency for mitochondria. Our analyses show that loss of COA6 causes combined complex I and complex IV deficiency and impacts membrane potential-driven protein transport across the inner membrane. We demonstrate that COA6 acts as a thiol-reductase to reduce disulfide bridges of critical cysteine residues in SCO1 and SCO2. Cysteines within the CX3CXNH domain of SCO2 mediate its interaction with COA6 but are dispensable for SCO2-SCO1 interaction. Our analyses define COA6 as thiol-reductase, which is essential for CuA biogenesis.
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Affiliation(s)
- David Pacheu-Grau
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany.
| | - Michał Wasilewski
- Laboratory of Mitochondrial Biogenesis, Centre of New Technologies, University of Warsaw, Warsaw, Poland; ReMedy International Research Agenda Unit, Centre of New Technologies, University of Warsaw, Poland
| | - Silke Oeljeklaus
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, D-79104 Freiburg, Germany
| | - Christine Silvia Gibhardt
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Abhishek Aich
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Margarita Chudenkova
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Markus Deckers
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Ivan Bogeski
- Molecular Physiology, Institute of Cardiovascular Physiology, University Medical Center, Georg-August-University, Göttingen, Germany
| | - Bettina Warscheid
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, D-79104 Freiburg, Germany
| | - Agnieszka Chacinska
- Laboratory of Mitochondrial Biogenesis, Centre of New Technologies, University of Warsaw, Warsaw, Poland; ReMedy International Research Agenda Unit, Centre of New Technologies, University of Warsaw, Poland
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany; Max-Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany.
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4
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Prajapati P, Dalwadi P, Gohel D, Singh K, Sripada L, Bhatelia K, Joshi B, Roy M, Wang WX, Springer JE, Singh R, Singh R. Enforced lysosomal biogenesis rescues erythromycin- and clindamycin-induced mitochondria-mediated cell death in human cells. Mol Cell Biochem 2019; 461:23-36. [PMID: 31309409 DOI: 10.1007/s11010-019-03585-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 07/04/2019] [Indexed: 12/23/2022]
Abstract
Antibiotics are the front-line treatment against many bacterial infectious diseases in human. The excessive and long-term use of antibiotics in human cause several side effects. It is important to understand the underlying molecular mechanisms of action of antibiotics in the host cell to avoid the side effects due to the prevalent uses. In the current study, we investigated the crosstalk between mitochondria and lysosomes in the presence of widely used antibiotics: erythromycin (ERM) and clindamycin (CLDM), which target the 50S subunit of bacterial ribosomes. We report here that both ERM and CLDM induced caspase activation and cell death in several different human cell lines. The activity of the mitochondrial respiratory chain was compromised in the presence of ERM and CLDM leading to bioenergetic crisis and generation of reactive oxygen species. Antibiotics treatment impaired autophagy flux and lysosome numbers, resulting in decreased removal of damaged mitochondria through mitophagy, hence accumulation of defective mitochondria. We further show that over-expression of transcription factor EB (TFEB) increased the lysosome number, restored mitochondrial function and rescued ERM- and CLDM-induced cell death. These studies indicate that antibiotics alter mitochondria and lysosome interactions leading to apoptotsis and may develop a novel approach for targeting inter-organelle crosstalk to limit deleterious antibiotic-induced side effects.
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Affiliation(s)
- Paresh Prajapati
- Department of Bio-Chemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Sayajigunj, Vadodara, Gujarat, 390002, India.,Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40536, USA.,Neuroscience, University of Kentucky, Lexington, KY, 40536, USA
| | - Pooja Dalwadi
- Department of Bio-Chemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Sayajigunj, Vadodara, Gujarat, 390002, India
| | - Dhruv Gohel
- Department of Bio-Chemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Sayajigunj, Vadodara, Gujarat, 390002, India
| | - Kritarth Singh
- Department of Bio-Chemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Sayajigunj, Vadodara, Gujarat, 390002, India
| | - Lakshmi Sripada
- Department of Bio-Chemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Sayajigunj, Vadodara, Gujarat, 390002, India
| | - Khyati Bhatelia
- Department of Bio-Chemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Sayajigunj, Vadodara, Gujarat, 390002, India
| | - Bhavana Joshi
- Department of Bio-Chemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Sayajigunj, Vadodara, Gujarat, 390002, India
| | - Milton Roy
- Department of Bio-Chemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Sayajigunj, Vadodara, Gujarat, 390002, India
| | - Wang-Xia Wang
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40536, USA.,Sanders Brown Center on Aging Center, University of Kentucky, Lexington, KY, 40536, USA.,Pathology & Laboratory Medicine, University of Kentucky, Lexington, KY, 40536, USA
| | - Joe E Springer
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40536, USA.,Neuroscience, University of Kentucky, Lexington, KY, 40536, USA
| | - Rochika Singh
- Department of Cell Biology, School of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Koba Institutional Area, Gandhinagar, Gujarat, 382007, India.
| | - Rajesh Singh
- Department of Bio-Chemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Sayajigunj, Vadodara, Gujarat, 390002, India.
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5
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Pacheu-Grau D, Callegari S, Emperador S, Thompson K, Aich A, Topol SE, Spencer EG, McFarland R, Ruiz-Pesini E, Torkamani A, Taylor RW, Montoya J, Rehling P. Mutations of the mitochondrial carrier translocase channel subunit TIM22 cause early-onset mitochondrial myopathy. Hum Mol Genet 2018; 27:4135-4144. [PMID: 30452684 PMCID: PMC6240735 DOI: 10.1093/hmg/ddy305] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/10/2018] [Accepted: 08/10/2018] [Indexed: 11/13/2022] Open
Abstract
Protein import into mitochondria is facilitated by translocases within the outer and the inner mitochondrial membranes that are dedicated to a highly specific subset of client proteins. The mitochondrial carrier translocase (TIM22 complex) inserts multispanning proteins, such as mitochondrial metabolite carriers and translocase subunits (TIM23, TIM17A/B and TIM22), into the inner mitochondrial membrane. Both types of substrates are essential for mitochondrial metabolic function and biogenesis. Here, we report on a subject, diagnosed at 1.5 years, with a neuromuscular presentation, comprising hypotonia, gastroesophageal reflux disease and persistently elevated serum and Cerebrospinal fluid lactate (CSF). Patient fibroblasts displayed reduced oxidative capacity and altered mitochondrial morphology. Using trans-mitochondrial cybrid cell lines, we excluded a candidate variant in mitochondrial DNA as causative of these effects. Whole-exome sequencing identified compound heterozygous variants in the TIM22 gene (NM_013337), resulting in premature truncation in one allele (p.Tyr25Ter) and a point mutation in a conserved residue (p.Val33Leu), within the intermembrane space region, of the TIM22 protein in the second allele. Although mRNA transcripts of TIM22 were elevated, biochemical analyses revealed lower levels of TIM22 protein and an even greater deficiency of TIM22 complex formation. In agreement with a defect in carrier translocase function, carrier protein amounts in the inner membrane were found to be reduced. This is the first report of pathogenic variants in the TIM22 pore-forming subunit of the carrier translocase affecting the biogenesis of inner mitochondrial membrane proteins critical for metabolite exchange.
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Affiliation(s)
- David Pacheu-Grau
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, D-37073, Germany
| | - Sylvie Callegari
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, D-37073, Germany
| | - Sonia Emperador
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza-CIBER de Enfermedades Raras (CIBERER)-Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, 50013, Spain
| | - Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Abhishek Aich
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, D-37073, Germany
| | - Sarah E Topol
- The Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Emily G Spencer
- The Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Eduardo Ruiz-Pesini
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza-CIBER de Enfermedades Raras (CIBERER)-Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, 50013, Spain
| | - Ali Torkamani
- The Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, United States
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Julio Montoya
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza-CIBER de Enfermedades Raras (CIBERER)-Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, 50013, Spain
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, D-37073, Germany
- Max-Planck Institute for Biophysical Chemistry, D-37077, Göttingen, Germany
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6
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Pacheu-Grau D, Rucktäschel R, Deckers M. Mitochondrial dysfunction and its role in tissue-specific cellular stress. Cell Stress 2018; 2:184-199. [PMID: 31225486 PMCID: PMC6551628 DOI: 10.15698/cst2018.07.147] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial bioenergetics require the coordination of two different and independent genomes. Mutations in either genome will affect mitochondrial functionality and produce different sources of cellular stress. Depending on the kind of defect and stress, different tissues and organs will be affected, leading to diverse pathological conditions. There is no curative therapy for mitochondrial diseases, nevertheless, there are strategies described that fight the various stress forms caused by the malfunctioning organelles. Here, we will revise the main kinds of stress generated by mutations in mitochondrial genes and outline several ways of fighting this stress.
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Affiliation(s)
- David Pacheu-Grau
- Department of Cellular Biochemistry, University Medical Center Göttingen, Germany
| | - Robert Rucktäschel
- Department of Cellular Biochemistry, University Medical Center Göttingen, Germany
| | - Markus Deckers
- Department of Cellular Biochemistry, University Medical Center Göttingen, Germany
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7
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Emperador S, Pacheu-Grau D, Bayona-Bafaluy MP, Garrido-Pérez N, Martín-Navarro A, López-Pérez MJ, Montoya J, Ruiz-Pesini E. An MRPS12 mutation modifies aminoglycoside sensitivity caused by 12S rRNA mutations. Front Genet 2015; 5:469. [PMID: 25642242 PMCID: PMC4294204 DOI: 10.3389/fgene.2014.00469] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 12/19/2014] [Indexed: 01/22/2023] Open
Abstract
Several homoplasmic pathologic mutations in mitochondrial DNA, such as those causing Leber hereditary optic neuropathy or non-syndromic hearing loss, show incomplete penetrance. Therefore, other elements must modify their pathogenicity. Discovery of these modifying factors is not an easy task because in multifactorial diseases conventional genetic approaches may not always be informative. Here, we have taken an evolutionary approach to unmask putative modifying factors for a particular homoplasmic pathologic mutation causing aminoglycoside-induced and non-syndromic hearing loss, the m.1494C>T transition in the mitochondrial DNA. The mutation is located in the decoding site of the mitochondrial ribosomal RNA. We first looked at mammalian species that had fixed the human pathologic mutation. These mutations are called compensated pathogenic deviations because an organism carrying one must also have another that suppresses the deleterious effect of the first. We found that species from the primate family Cercopithecidae (old world monkeys) harbor the m.1494T allele even if their auditory function is normal. In humans the m.1494T allele increases the susceptibility to aminoglycosides. However, in primary fibroblasts from a Cercopithecidae species, aminoglycosides do not impair cell growth, respiratory complex IV activity and quantity or the mitochondrial protein synthesis. Interestingly, this species also carries a fixed mutation in the mitochondrial ribosomal protein S12. We show that the expression of this variant in a human m.1494T cell line reduces its susceptibility to aminoglycosides. Because several mutations in this human protein have been described, they may possibly explain the absence of pathologic phenotype in some pedigree members with the most frequent pathologic mutations in mitochondrial ribosomal RNA.
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Affiliation(s)
- Sonia Emperador
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain ; Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza Zaragoza, Spain ; Centros de Investigación Biomédica en Red de Enfermedades Raras, Universidad de Zaragoza Zaragoza, Spain
| | - David Pacheu-Grau
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain
| | - M Pilar Bayona-Bafaluy
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain
| | - Nuria Garrido-Pérez
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain
| | - Antonio Martín-Navarro
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain
| | - Manuel J López-Pérez
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain ; Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza Zaragoza, Spain ; Centros de Investigación Biomédica en Red de Enfermedades Raras, Universidad de Zaragoza Zaragoza, Spain
| | - Julio Montoya
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain ; Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza Zaragoza, Spain ; Centros de Investigación Biomédica en Red de Enfermedades Raras, Universidad de Zaragoza Zaragoza, Spain
| | - Eduardo Ruiz-Pesini
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain ; Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza Zaragoza, Spain ; Centros de Investigación Biomédica en Red de Enfermedades Raras, Universidad de Zaragoza Zaragoza, Spain ; Fundación ARAID, Universidad de Zaragoza Zaragoza, Spain
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8
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Levin L, Zhidkov I, Gurman Y, Hawlena H, Mishmar D. Functional recurrent mutations in the human mitochondrial phylogeny: dual roles in evolution and disease. Genome Biol Evol 2013; 5:876-90. [PMID: 23563965 PMCID: PMC3673625 DOI: 10.1093/gbe/evt058] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mutations frequently reoccur in the human mitochondrial DNA (mtDNA). However, it is unclear whether recurrent mtDNA nodal mutations (RNMs), that is, recurrent mutations in stems of unrelated phylogenetic nodes, are functional and hence selectively constrained. To answer this question, we performed comprehensive parsimony and maximum likelihood analyses of 9,868 publicly available whole human mtDNAs revealing 1,606 single nodal mutations (SNMs) and 679 RNMs. We then evaluated the potential functionality of synonymous, nonsynonymous and RNA SNMs and RNMs. For synonymous mutations, we have implemented the Codon Adaptation Index. For nonsynonymous mutations, we assessed evolutionary conservation, and employed previously described pathogenicity score assessment tools. For RNA genes’ mutations, we designed a bioinformatic tool which compiled evolutionary conservation and potential effect on RNA structure. While comparing the functionality scores of nonsynonymous and RNA SNMs and RNMs with those of disease-causing mtDNA mutations, we found significant difference (P < 0.001). However, 24 RNMs and 67 SNMs had comparable values with disease-causing mutations reflecting their potential function thus being the best candidates to participate in adaptive events of unrelated lineages. Strikingly, some functional RNMs occurred in unrelated mtDNA lineages that independently altered susceptibility to the same diseases, thus suggesting common functionality. To our knowledge, this is the most comprehensive analysis of selective signatures in the mtDNA not only within proteins but also within RNA genes. For the first time, we discover virtually all positively selected RNMs in our phylogeny while emphasizing their dual role in past evolutionary events and in disease today.
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Affiliation(s)
- Liron Levin
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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9
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Pacheu-Grau D, Gomez-Duran A, Iglesias E, Lopez-Gallardo E, Montoya J, Ruiz-Pesini E. Mitochondrial antibiograms in personalized medicine. Hum Mol Genet 2012; 22:1132-9. [DOI: 10.1093/hmg/dds517] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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10
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Iglesias E, Llobet L, Pacheu-Grau D, Gómez-Durán A, Ruiz-Pesini E. Cybrids for Mitochondrial DNA Pharmacogenomics. Drug Dev Res 2012. [DOI: 10.1002/ddr.21037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Gutiérrez Cortés N, Pertuiset C, Dumon E, Börlin M, Hebert-Chatelain E, Pierron D, Feldmann D, Jonard L, Marlin S, Letellier T, Rocher C. Novel mitochondrial DNA mutations responsible for maternally inherited nonsyndromic hearing loss. Hum Mutat 2012; 33:681-9. [PMID: 22241583 DOI: 10.1002/humu.22023] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2011] [Accepted: 01/04/2012] [Indexed: 11/11/2022]
Abstract
Some cases of maternally inherited isolated deafness are caused by mtDNA mutations, frequently following an exposure to aminoglycosides. Two mitochondrial genes have been clearly described as being affected by mutations responsible for this pathology: the ribosomal RNA 12S gene and the transfer RNA serine (UCN) gene. A previous study identified several candidate novel mtDNA mutations, localized in a variety of mitochondrial genes, found in patients with no previous treatment with aminoglycosides. Five of these candidate mutations are characterized in the present study. These mutations are localized in subunit ND1 of complex I of the respiratory chain (m.3388C>A [p.MT-ND1:Leu28Met]), the tRNA for Isoleucine (m.4295A>G), subunit COII of complex IV (m.8078G>A [p.MT-CO2:Val165Ile]), the tRNA of Serine 2 (AGU/C) (m.12236G>A), and Cytochrome B, subunit of complex III (m.15077G>A [p.MT-CYB:Glu111Lys]). Cybrid cell lines have been constructed for each of the studied mtDNA mutations and functional studies have been performed to assess the possible consequences of these mutations on mitochondrial bioenergetics. This study shows that a variety of mitochondrial genes, including protein-coding genes, can be responsible for nonsyndromic deafness, and that exposure to aminoglycosides is not required to develop the disease, giving new insights on the molecular bases of this pathology.
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Affiliation(s)
- Nicolás Gutiérrez Cortés
- INSERM-U688 Physiopathologie Mitochondriale, Université Victor Segalen Bordeaux 2,146 rue Léo Saignat, Bordeaux, F-33076 France
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