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Prakash C, Soni M, Kumar V. Mitochondrial oxidative stress and dysfunction in arsenic neurotoxicity: A review. J Appl Toxicol 2015; 36:179-88. [DOI: 10.1002/jat.3256] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 09/01/2015] [Accepted: 09/28/2015] [Indexed: 01/19/2023]
Affiliation(s)
- Chandra Prakash
- Department of Biochemistry; Maharshi Dayanand University; Rohtak 124001 Haryana India
| | - Manisha Soni
- Department of Biochemistry; Maharshi Dayanand University; Rohtak 124001 Haryana India
| | - Vijay Kumar
- Department of Biochemistry; Maharshi Dayanand University; Rohtak 124001 Haryana India
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202
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Mishra M, Kowluru RA. Epigenetic Modification of Mitochondrial DNA in the Development of Diabetic Retinopathy. Invest Ophthalmol Vis Sci 2015; 56:5133-42. [PMID: 26241401 DOI: 10.1167/iovs.15-16937] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
PURPOSE Retinal mitochondria are dysfunctional in diabetes, and mitochondrial DNA (mtDNA) is damaged and its transcription is compromised. Our aim was to investigate the role of mtDNA methylation in the development of diabetic retinopathy. METHODS Effect of high glucose (20 mM) on mtDNA methylation was analyzed in retinal endothelial cells by methylation-specific PCR and by quantifying 5-methylcytosine (5mC). Dnmt1 binding at the D-loop and Cytb regions of mtDNA was analyzed by chromatin immunoprecipitation. The role of mtDNA methylation in transcription and cell death was confirmed by quantifying transcripts of mtDNA-encoded genes (Cytb, ND6, and CoxII) and apoptosis, using cells transfected with Dnmt1-small interfering RNA (siRNA), or incubated with a Dnmt inhibitor. The key parameters were validated in the retinal microvasculature from human donors with diabetic retinopathy. RESULTS High glucose increased mtDNA methylation, and methylation was significantly higher at the D-loop than at the Cytb and CoxII regions. Mitochondrial accumulation of Dnmt1 and its binding at the D-loop were also significantly increased. Inhibition of Dnmt by its siRNA or pharmacologic inhibitor ameliorated glucose-induced increase in 5mC levels and cell apoptosis. Retinal microvasculature from human donors with diabetic retinopathy presented similar increase in D-loop methylation and decrease in mtDNA transcription. CONCLUSIONS Hypermethylation of mtDNA in diabetes impairs its transcription, resulting in dysfunctional mitochondria and accelerated capillary cell apoptosis. Regulation of mtDNA methylation has potential to restore mitochondrial homeostasis and inhibit/retard the development of diabetic retinopathy.
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203
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Consequences of zygote injection and germline transfer of mutant human mitochondrial DNA in mice. Proc Natl Acad Sci U S A 2015; 112:E5689-98. [PMID: 26438859 DOI: 10.1073/pnas.1506129112] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Considerable evidence supports mutations in mitochondrial genes as the cause of maternally inherited diseases affecting tissues that rely primarily on oxidative energy metabolism, usually the nervous system, the heart, and skeletal muscles. Mitochondrial diseases are diverse, and animal models currently are limited. Here we introduced a mutant human mitochondrial gene responsible for Leber hereditary optic neuropathy (LHON) into the mouse germ line using fluorescence imaging for tissue-specific enrichment in the target retinal ganglion cells. A mitochondria-targeted adeno-associated virus (MTS-AAV) containing the mutant human NADH ubiquinone oxidoreductase subunit 4 (ND4) gene followed by mitochondrial-encoded mCherry was microinjected into zygotes. Female founders with mCherry fluorescence on ophthalmoscopy were backcrossed with normal males for eight generations. Mutant human ND4 DNA was 20% of mouse ND4 and did not integrate into the host genome. Translated human ND4 protein assembled into host respiratory complexes, decreasing respiratory chain function and increasing oxidative stress. Swelling of the optic nerve head was followed by progressive demise of ganglion cells and their axons, the hallmarks of human LHON. Early visual loss that began at 3 mo and progressed to blindness 8 mo after birth was reversed by intraocular injection of MTS-AAV expressing wild-type human ND4. The technology of introducing human mitochondrial genes into the mouse germ line has never been described, to our knowledge, and has implications not only for creating animal models recapitulating the counterpart human disorder but more importantly for reversing the adverse effects of the mutant gene using gene therapy to deliver the wild-type allele.
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204
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Ghaffari Novin M, Noruzinia M, Allahveisi A, Saremi A, Fadaei Fathabadi F, Mastery Farahani R, Dehghani Fard A, Pooladi A, Mazaherinezhad Fard R, Yousefian E. Comparison of mitochondrial-related transcriptional levels of TFAM, NRF1 and MT-CO1 genes in single human oocytes at various stages of the oocyte maturation. IRANIAN BIOMEDICAL JOURNAL 2015; 19:23-8. [PMID: 25605486 PMCID: PMC4322229 DOI: 10.6091/ibj.1400.2015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background: The aim of the current study was to assess the mRNA levels of two mitochondria-related genes, including nuclear-encoded NRF1 (nuclear respiratory factor 1), mitochondrial transcription factor A (TFAM), and mitochondrial-encoded cytochrome c oxidase subunit 1 (MT-CO1) genes in various stages of the human oocyte maturation. Methods: Oocytes were obtained from nine infertile women with male factor undergoing in vitro fertilization (IVF)/intra-cytoplasmic sperm injection protocol. Mitochondrial-related mRNA levels were performed by single-cell TaqMan real-time PCR. Results: the expression level of the target genes was low at the germinal vesicle stage (P>0.05). Although the mRNA level of NRF1gene remained stable in metaphase I, the mRNA level of TFAM and MT-CO1 increased significantly (P<0.05).In metaphase II, the expression level of all genes increased compared to metaphase I (P<0.05).Conclusion: The overexpression levels of NRF1, TFAM, and MT-CO1 genes are related to the oocyte maturation. Therefore, the current study could be used clinically to improve the success rate of IVF.
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Affiliation(s)
- Marefat Ghaffari Novin
- Dept. of Biology and Anatomical Sciences, Shahid Beheshti University of Medical Sciences, Velenjak, Tehran, Iran
| | - Mehrdad Noruzinia
- Dept. of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Azra Allahveisi
- Dept. of Biology and Anatomical Sciences, Shahid Beheshti University of Medical Sciences, Velenjak, Tehran, Iran
| | - Aboutaleb Saremi
- Sarem Cell Research Center (SCRC), Sarem Women’s Hospital, Tehran, Iran
| | - Fateme Fadaei Fathabadi
- Dept. of Biology and Anatomical Sciences, Shahid Beheshti University of Medical Sciences, Velenjak, Tehran, Iran
| | - Reza Mastery Farahani
- Dept. of Biology and Anatomical Sciences, Shahid Beheshti University of Medical Sciences, Velenjak, Tehran, Iran
| | - Ali Dehghani Fard
- Sarem Cell Research Center (SCRC), Sarem Women’s Hospital, Tehran, Iran
| | - Arash Pooladi
- Sarem Cell Research Center (SCRC), Sarem Women’s Hospital, Tehran, Iran
| | | | - Elham Yousefian
- Dept. of Biology and Anatomical Sciences, Shahid Beheshti University of Medical Sciences, Velenjak, Tehran, Iran
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205
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Kawahara M, Koyama S, Iimura S, Yamazaki W, Tanaka A, Kohri N, Sasaki K, Takahashi M. Preimplantation death of xenomitochondrial mouse embryo harbouring bovine mitochondria. Sci Rep 2015; 5:14512. [PMID: 26416548 PMCID: PMC4586891 DOI: 10.1038/srep14512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 09/02/2015] [Indexed: 11/09/2022] Open
Abstract
Mitochondria, cellular organelles playing essential roles in eukaryotic cell metabolism, are thought to have evolved from bacteria. The organization of mtDNA is remarkably uniform across species, reflecting its vital and conserved role in oxidative phosphorylation (OXPHOS). Our objectives were to evaluate the compatibility of xenogeneic mitochondria in the development of preimplantation embryos in mammals. Mouse embryos harbouring bovine mitochondria (mtB-M embryos) were prepared by the cell-fusion technique employing the haemagglutinating virus of Japan (HVJ). The mtB-M embryos showed developmental delay at embryonic days (E) 3.5 after insemination. Furthermore, none of the mtB-M embryos could implant into the maternal uterus after embryo transfer, whereas control mouse embryos into which mitochondria from another mouse had been transferred developed as well as did non-manipulated embryos. When we performed quantitative PCR (qPCR) of mouse and bovine ND5, we found that the mtB-M embryos contained 8.3% of bovine mitochondria at the blastocyst stage. Thus, contamination with mitochondria from another species induces embryonic lethality prior to implantation into the maternal uterus. The heteroplasmic state of these xenogeneic mitochondria could have detrimental effects on preimplantation development, leading to preservation of species-specific mitochondrial integrity in mammals.
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Affiliation(s)
- Manabu Kawahara
- Laboratory of Animal Breeding and Reproduction, Research Faculty of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo 060-8589, Japan
| | - Shiori Koyama
- Laboratory of Animal Breeding and Reproduction, Research Faculty of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo 060-8589, Japan
| | - Satomi Iimura
- Laboratory of Animal Breeding and Reproduction, Research Faculty of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo 060-8589, Japan
| | - Wataru Yamazaki
- Laboratory of Animal Breeding and Reproduction, Research Faculty of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo 060-8589, Japan
| | - Aiko Tanaka
- Laboratory of Animal Breeding and Reproduction, Research Faculty of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo 060-8589, Japan
| | - Nanami Kohri
- Laboratory of Animal Breeding and Reproduction, Research Faculty of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo 060-8589, Japan
| | - Keisuke Sasaki
- Laboratory of Animal Breeding and Reproduction, Research Faculty of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo 060-8589, Japan
| | - Masashi Takahashi
- Laboratory of Animal Breeding and Reproduction, Research Faculty of Agriculture, Hokkaido University, Kita-ku Kita 9 Nishi 9, Sapporo 060-8589, Japan
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206
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Rodríguez-Mora S, Mateos E, Moran M, Martín MÁ, López JA, Calvo E, Terrón MC, Luque D, Muriaux D, Alcamí J, Coiras M, López-Huertas MR. Intracellular expression of Tat alters mitochondrial functions in T cells: a potential mechanism to understand mitochondrial damage during HIV-1 replication. Retrovirology 2015; 12:78. [PMID: 26376973 PMCID: PMC4571071 DOI: 10.1186/s12977-015-0203-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 08/26/2015] [Indexed: 01/22/2023] Open
Abstract
Background HIV-1 replication results in mitochondrial damage that is enhanced during antiretroviral therapy (ART). The onset of HIV-1 replication is regulated by viral protein Tat, a 101-residue protein codified by two exons that elongates viral transcripts. Although the first exon of Tat (aa 1–72) forms itself an active protein, the presence of the second exon (aa 73–101) results in a more competent transcriptional protein with additional functions. Results Mitochondrial overall functions were analyzed in Jurkat cells stably expressing full-length Tat (Tat101) or one-exon Tat (Tat72). Representative results were confirmed in PBLs transiently expressing Tat101 and in HIV-infected Jurkat cells. The intracellular expression of Tat101 induced the deregulation of metabolism and cytoskeletal proteins which remodeled the function and distribution of mitochondria. Tat101 reduced the transcription of the mtDNA, resulting in low
ATP production. The total amount of mitochondria increased likely to counteract their functional impairment. These effects were enhanced when Tat second exon was expressed. Conclusions Intracellular Tat altered mtDNA transcription, mitochondrial content and distribution in CD4+ T cells. The importance of Tat second exon in non-transcriptional functions was confirmed. Tat101 may be responsible for mitochondrial dysfunctions found in HIV-1 infected patients. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0203-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sara Rodríguez-Mora
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
| | - Elena Mateos
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
| | - María Moran
- Laboratorio de Enfermedades Raras: mitocondriales y neuromusculares, Instituto de Investigación Hospital 12 de Octubre, "i + 12", Madrid, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) U723, Madrid, Spain.
| | - Miguel Ángel Martín
- Laboratorio de Enfermedades Raras: mitocondriales y neuromusculares, Instituto de Investigación Hospital 12 de Octubre, "i + 12", Madrid, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) U723, Madrid, Spain.
| | - Juan Antonio López
- Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain.
| | - Enrique Calvo
- Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain.
| | - María Carmen Terrón
- Unidad de Microscopía Electrónica y Confocal, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
| | - Daniel Luque
- Unidad de Microscopía Electrónica y Confocal, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
| | - Delphine Muriaux
- Unité de Virologie Humaine - INSERM U758/École Normale Supérieure, Lyon, France. .,Laboratoire de Domaines Membranaires et Assemblage Viral, Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé, Montpellier, France.
| | - José Alcamí
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
| | - Mayte Coiras
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
| | - María Rosa López-Huertas
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain. .,Unité de Virologie Humaine - INSERM U758/École Normale Supérieure, Lyon, France.
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207
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Gubellini P, Kachidian P. Animal models of Parkinson's disease: An updated overview. Rev Neurol (Paris) 2015; 171:750-61. [PMID: 26343921 DOI: 10.1016/j.neurol.2015.07.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 07/20/2015] [Accepted: 07/22/2015] [Indexed: 12/21/2022]
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder whose etiology, besides a minority of genetic cases, is still largely unknown. Animal models have contributed to elucidate PD etiology and pathogenesis, as well as its cellular and molecular mechanisms, leading to the general hypothesis that this neurological disorder is due to complex interactions between environmental and genetic factors. However, the full understanding of PD is still very far from being achieved, and new potential treatments need to be tested to further improve patients' quality of life and, possibly, slow down the neurodegenerative process. In this context, animal models of PD are required to address all these issues. "Classic" models are based on neurotoxins that selectively target catecholaminergic neurons (such as 6-hydroxydopamine, 1-methyl-1,2,3,6-tetrahydropiridine, agricultural pesticides, etc.), while more recent models employ genetic manipulations that either introduce mutations similar to those find in familial cases of PD (α-synuclein, DJ-1, PINK1, Parkin, etc.) or selectively disrupt nigrostriatal neurons (MitoPark, Pitx3, Nurr1, etc.). Each one of these models has its own advantages and limitations, thus some are better suited for studying PD pathogenesis, while others are more pertinent to test therapeutic treatments. Here, we provide a critical and updated review of the most used PD models.
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Affiliation(s)
- P Gubellini
- Aix-Marseille Université, CNRS, Institut de Biologie du Développement de Marseille (IBDM) UMR7288, case 907, parc scientifique de Luminy, 163, avenue de Luminy, 13009 Marseille, France
| | - P Kachidian
- Aix-Marseille Université, CNRS, Institut de Biologie du Développement de Marseille (IBDM) UMR7288, case 907, parc scientifique de Luminy, 163, avenue de Luminy, 13009 Marseille, France.
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208
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Lee WTY, St John J. The control of mitochondrial DNA replication during development and tumorigenesis. Ann N Y Acad Sci 2015; 1350:95-106. [PMID: 26335356 DOI: 10.1111/nyas.12873] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondrial DNA (mtDNA) copy number is strictly regulated during development and tumorigenesis. Pluripotent stem cells and cancer stem-like cells use glycolysis for energy metabolism, as they possess low mtDNA copy number, which promotes cell proliferation. As pluripotent stem cells can differentiate into all cell types of the body, they establish the mtDNA set point during early development, maintaining mtDNA copy number at low levels but enabling differentiating cells to acquire the appropriate numbers of mtDNA copy to meet their specific demands for OXPHOS-derived ATP, as they become specialized cells. This process is mediated by changes to DNA methylation at exon 2 of the catalytic subunit of the mitochondrial-specific polymerase, POLGA. Cancer stem-like cells, however, are hypermethylated and maintain low mtDNA copy number, resulting in their dependence on aerobic glycolysis. Their hypermethylation at exon 2 of POLGA also promotes their multipotent state. As a result, cancer cells are unable to increase their mtDNA content and differentiate into specific lineages unless they are treated with DNA demethylation agents or partially depleted of their mtDNA. This review describes these processes in depth and argues that DNA methylation of POLGA is instrumental in the fate of pluripotent stem cells and cancer cells.
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Affiliation(s)
- William T Y Lee
- Centre for Genetic Diseases, Hudson Institute of Medical Research, Victoria, Australia.,Department of Molecular and Translational Science, Monash University, Victoria, Australia
| | - Justin St John
- Centre for Genetic Diseases, Hudson Institute of Medical Research, Victoria, Australia.,Department of Molecular and Translational Science, Monash University, Victoria, Australia
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209
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Heinonen S, Buzkova J, Muniandy M, Kaksonen R, Ollikainen M, Ismail K, Hakkarainen A, Lundbom J, Lundbom N, Vuolteenaho K, Moilanen E, Kaprio J, Rissanen A, Suomalainen A, Pietiläinen KH. Impaired Mitochondrial Biogenesis in Adipose Tissue in Acquired Obesity. Diabetes 2015; 64:3135-45. [PMID: 25972572 DOI: 10.2337/db14-1937] [Citation(s) in RCA: 231] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 05/08/2015] [Indexed: 01/08/2023]
Abstract
Low mitochondrial number and activity have been suggested as underlying factors in obesity, type 2 diabetes, and metabolic syndrome. However, the stage at which mitochondrial dysfunction manifests in adipose tissue after the onset of obesity remains unknown. Here we examined subcutaneous adipose tissue (SAT) samples from healthy monozygotic twin pairs, 22.8-36.2 years of age, who were discordant (ΔBMI >3 kg/m(2), mean length of discordance 6.3 ± 0.3 years, n = 26) and concordant (ΔBMI <3 kg/m(2), n = 14) for body weight, and assessed their detailed mitochondrial metabolic characteristics: mitochondrial-related transcriptomes with dysregulated pathways, mitochondrial DNA (mtDNA) amount, mtDNA-encoded transcripts, and mitochondrial oxidative phosphorylation (OXPHOS) protein levels. We report global expressional downregulation of mitochondrial oxidative pathways with concomitant downregulation of mtDNA amount, mtDNA-dependent translation system, and protein levels of the OXPHOS machinery in the obese compared with the lean co-twins. Pathway analysis indicated downshifting of fatty acid oxidation, ketone body production and breakdown, and the tricarboxylic acid cycle, which inversely correlated with adiposity, insulin resistance, and inflammatory cytokines. Our results suggest that mitochondrial biogenesis, oxidative metabolic pathways, and OXPHOS proteins in SAT are downregulated in acquired obesity, and are associated with metabolic disturbances already at the preclinical stage.
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Affiliation(s)
- Sini Heinonen
- Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Jana Buzkova
- Research Programs Unit, Molecular Neurology, Biomedicum-Helsinki, University of Helsinki, Helsinki, Finland
| | - Maheswary Muniandy
- Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Risto Kaksonen
- Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland Siluetti Hospital, Helsinki, Finland
| | - Miina Ollikainen
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Khadeeja Ismail
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Antti Hakkarainen
- Helsinki Medical Imaging Center, University of Helsinki, Helsinki, Finland
| | - Jesse Lundbom
- Helsinki Medical Imaging Center, University of Helsinki, Helsinki, Finland Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research, Heinrich Heine University, Düsseldorf, Germany
| | - Nina Lundbom
- Helsinki Medical Imaging Center, University of Helsinki, Helsinki, Finland
| | - Katriina Vuolteenaho
- The Immunopharmacology Research Group, University of Tampere School of Medicine and Tampere University Hospital, Tampere, Finland
| | - Eeva Moilanen
- The Immunopharmacology Research Group, University of Tampere School of Medicine and Tampere University Hospital, Tampere, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland Finnish Twin Cohort Study, Department of Public Health, Hjelt Institute, University of Helsinki, Helsinki, Finland National Institute for Health and Welfare, Department of Mental Health and Substance Abuse Services, Helsinki, Finland
| | - Aila Rissanen
- Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland Department of Psychiatry, Helsinki University Central Hospital, Helsinki, Finland
| | - Anu Suomalainen
- Research Programs Unit, Molecular Neurology, Biomedicum-Helsinki, University of Helsinki, Helsinki, Finland Department of Neurology, Helsinki University Central Hospital, Helsinki, Finland
| | - Kirsi H Pietiläinen
- Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland Abdominal Center, Endocrinology, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
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210
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Computational DNA hole spectroscopy: A new tool to predict mutation hotspots, critical base pairs, and disease 'driver' mutations. Sci Rep 2015; 5:13571. [PMID: 26310834 PMCID: PMC4550865 DOI: 10.1038/srep13571] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/30/2015] [Indexed: 01/05/2023] Open
Abstract
We report on a new technique, computational DNA hole spectroscopy, which creates spectra of electron hole probabilities vs. nucleotide position. A hole is a site of positive charge created when an electron is removed. Peaks in the hole spectrum depict sites where holes tend to localize and potentially trigger a base pair mismatch during replication. Our studies of mitochondrial DNA reveal a correlation between L-strand hole spectrum peaks and spikes in the human mutation spectrum. Importantly, we also find that hole peak positions that do not coincide with large variant frequencies often coincide with disease-implicated mutations and/or (for coding DNA) encoded conserved amino acids. This enables combining hole spectra with variant data to identify critical base pairs and potential disease 'driver' mutations. Such integration of DNA hole and variance spectra could ultimately prove invaluable for pinpointing critical regions of the vast non-protein-coding genome. An observed asymmetry in correlations, between the spectrum of human mtDNA variations and the L- and H-strand hole spectra, is attributed to asymmetric DNA replication processes that occur for the leading and lagging strands.
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211
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Rutkai I, Dutta S, Katakam PV, Busija DW. Dynamics of enhanced mitochondrial respiration in female compared with male rat cerebral arteries. Am J Physiol Heart Circ Physiol 2015; 309:H1490-500. [PMID: 26276815 DOI: 10.1152/ajpheart.00231.2015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 08/13/2015] [Indexed: 02/07/2023]
Abstract
Mitochondrial respiration has never been directly examined in intact cerebral arteries. We tested the hypothesis that mitochondrial energetics of large cerebral arteries ex vivo are sex dependent. The Seahorse XFe24 analyzer was used to examine mitochondrial respiration in isolated cerebral arteries from adult male and female Sprague-Dawley rats. We examined the role of nitric oxide (NO) on mitochondrial respiration under basal conditions, using N(ω)-nitro-l-arginine methyl ester, and following pharmacological challenge using diazoxide (DZ), and also determined levels of mitochondrial and nonmitochondrial proteins using Western blot, and vascular diameter responses to DZ. The components of mitochondrial respiration including basal respiration, ATP production, proton leak, maximal respiration, and spare respiratory capacity were elevated in females compared with males, but increased in both male and female arteries in the presence of the NOS inhibitor. Although acute DZ treatment had little effect on mitochondrial respiration of male arteries, it decreased the respiration in female arteries. Levels of mitochondrial proteins in Complexes I-V and the voltage-dependent anion channel protein were elevated in female compared with male cerebral arteries. The DZ-induced vasodilation was greater in females than in males. Our findings show that substantial sex differences in mitochondrial respiratory dynamics exist in large cerebral arteries and may provide the mechanistic basis for observations that the female cerebral vasculature is more adaptable after injury.
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Affiliation(s)
- Ibolya Rutkai
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Somhrita Dutta
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, Louisiana
| | - Prasad V Katakam
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, Louisiana
| | - David W Busija
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, Louisiana
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212
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Primer removal during mammalian mitochondrial DNA replication. DNA Repair (Amst) 2015; 34:28-38. [PMID: 26303841 DOI: 10.1016/j.dnarep.2015.07.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 07/02/2015] [Indexed: 12/17/2022]
Abstract
The small circular mitochondrial genome in mammalian cells is replicated by a dedicated replisome, defects in which can cause mitochondrial disease in humans. A fundamental step in mitochondrial DNA (mtDNA) replication and maintenance is the removal of the RNA primers needed for replication initiation. The nucleases RNase H1, FEN1, DNA2, and MGME1 have been implicated in this process. Here we review the role of these nucleases in the light of primer removal pathways in mitochondria, highlight associations with disease, as well as consider the implications for mtDNA replication initiation.
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213
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Jemt E, Persson Ö, Shi Y, Mehmedovic M, Uhler JP, Dávila López M, Freyer C, Gustafsson CM, Samuelsson T, Falkenberg M. Regulation of DNA replication at the end of the mitochondrial D-loop involves the helicase TWINKLE and a conserved sequence element. Nucleic Acids Res 2015; 43:9262-75. [PMID: 26253742 PMCID: PMC4627069 DOI: 10.1093/nar/gkv804] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 07/28/2015] [Indexed: 11/12/2022] Open
Abstract
The majority of mitochondrial DNA replication events are terminated prematurely. The nascent DNA remains stably associated with the template, forming a triple-stranded displacement loop (D-loop) structure. However, the function of the D-loop region of the mitochondrial genome remains poorly understood. Using a comparative genomics approach we here identify two closely related 15 nt sequence motifs of the D-loop, strongly conserved among vertebrates. One motif is at the D-loop 5'-end and is part of the conserved sequence block 1 (CSB1). The other motif, here denoted coreTAS, is at the D-loop 3'-end. Both these sequences may prevent transcription across the D-loop region, since light and heavy strand transcription is terminated at CSB1 and coreTAS, respectively. Interestingly, the replication of the nascent D-loop strand, occurring in a direction opposite to that of heavy strand transcription, is also terminated at coreTAS, suggesting that coreTAS is involved in termination of both transcription and replication. Finally, we demonstrate that the loading of the helicase TWINKLE at coreTAS is reversible, implying that this site is a crucial component of a switch between D-loop formation and full-length mitochondrial DNA replication.
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Affiliation(s)
- Elisabeth Jemt
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Örjan Persson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Yonghong Shi
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Majda Mehmedovic
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Jay P Uhler
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Marcela Dávila López
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Christoph Freyer
- Department of Laboratory Medicine, Karolinska Institutet, Retzius väg 8, 171 77 Stockholm, Sweden
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Tore Samuelsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
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Abstract
In the past century, considerable efforts were made to understand the role of mitochondrial DNA (mtDNA) mutations and of oxidative stress in aging. The classic mitochondrial free radical theory of aging, in which mtDNA mutations cause genotoxic oxidative stress, which in turn creates more mutations, has been a central hypothesis in the field for decades. In the past few years, however, new elements have discredited this original theory. The major sources of mitochondrial DNA mutations seem to be replication errors and failure of the repair mechanisms, and the accumulation of these mutations as observed in aged organisms seems to occur by clonal expansion and not to be caused by a reactive oxygen species-dependent vicious cycle. New hypotheses of how age-associated mitochondrial dysfunction may lead to aging are based on the role of reactive oxygen species as signaling molecules and on their role in mediating stress responses to age-dependent damage. Here, we review the changes that mtDNA undergoes during aging and the past and most recent hypotheses linking these changes to the tissue failure observed in aging.
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Affiliation(s)
- Milena Pinto
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Carlos T Moraes
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; Department of Cell Biology and Anatomy, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.
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215
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Masotti A, Celluzzi A, Petrini S, Bertini E, Zanni G, Compagnucci C. Aged iPSCs display an uncommon mitochondrial appearance and fail to undergo in vitro neurogenesis. Aging (Albany NY) 2015; 6:1094-108. [PMID: 25567319 PMCID: PMC4298368 DOI: 10.18632/aging.100708] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Reprogramming of human fibroblasts into induced pluripotent stem cells (iPSCs) leads to mitochondrial rejuvenation, making iPSCs a candidate model to study the mitochondrial biology during stemness and differentiation. At present, it is generally accepted that iPSCs can be maintained and propagated indefinitely in culture, but no specific studies have addressed this issue. In our study, we investigated features related to the 'biological age' of iPSCs, culturing and analyzing iPSCs kept for prolonged periods in vitro. We have demonstrated that aged iPSCs present an increased number of mitochondria per cell with an altered mitochondrial membrane potential and fail to properly undergo in vitro neurogenesis. In aged iPSCs we have also found an altered expression of genes relevant to mitochondria biogenesis. Overall, our results shed light on the mitochondrial biology of young and aged iPSCs and explore how an altered mitochondrial status may influence neuronal differentiation. Our work suggests to deepen the understanding of the iPSCs biology before considering their use in clinical applications.
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216
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Müller-Höcker J, Schäfer S, Krebs S, Blum H, Zsurka G, Kunz WS, Prokisch H, Seibel P, Jung A. Oxyphil cell metaplasia in the parathyroids is characterized by somatic mitochondrial DNA mutations in NADH dehydrogenase genes and cytochrome c oxidase activity-impairing genes. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 184:2922-35. [PMID: 25418474 DOI: 10.1016/j.ajpath.2014.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/14/2014] [Accepted: 07/17/2014] [Indexed: 02/01/2023]
Abstract
Oxyphil cell transformation of epithelial cells due to the accumulation of mitochondria occurs often during cellular aging. To understand the pathogenic mechanisms, we studied mitochondrial DNA (mtDNA) alterations in the three cell types of the parathyroids using multiplex real-time PCR and next-generation sequencing. mtDNA was analyzed from cytochrome c oxidase (COX)-positive and COX-negative areas of 19 parathyroids. Mitochondria-rich pre-oxyphil/oxyphil cells were more prone to develop COX defects than the mitochondria-poor clear chief cells (P < 0.001). mtDNA increased approximately 2.5-fold from clear chief to oxyphil cells. In COX deficiency, the increase was even more pronounced, and COX-negative oxyphil cells had approximately two times more mtDNA than COX-positive oxyphil cells (P < 0.001), illustrating the influence of COX deficiency on mtDNA biosynthesis, probably as a consequence of insufficient ATP synthesis. Next-generation sequencing revealed a broad spectrum of putative pathogenic mtDNA point mutations affecting NADH dehydrogenase and COX genes as well as regulatory elements of mtDNA. NADH dehydrogenase gene mutations preferentially accumulated in COX-positive pre-oxyphil/oxyphil cells and, therefore, could be essential for inducing oxyphil cell transformation by increasing mtDNA/mitochondrial biogenesis. In contrast, COX-negative cells predominantly harbored mutations in the MT-CO1 and MT-CO3 genes and in regulatory mtDNA elements, but only rarely NADH dehydrogenase mutations. Thus, multiple hits in NADH dehydrogenase and COX activity-impairing genes represent the molecular basis of oxyphil cell transformation in the parathyroids.
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Affiliation(s)
- Josef Müller-Höcker
- Institute for Pathology of the Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sabine Schäfer
- Institute for Pathology of the Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stefan Krebs
- Gene Center of the Ludwig-Maximilians-Universität München, Campus Großhadern, Munich, Germany
| | - Helmut Blum
- Gene Center of the Ludwig-Maximilians-Universität München, Campus Großhadern, Munich, Germany
| | - Gábor Zsurka
- Division of Neurochemistry, Department of Epileptology and Life and Brain Center, University of Bonn, Bonn, Germany
| | - Wolfram S Kunz
- Division of Neurochemistry, Department of Epileptology and Life and Brain Center, University of Bonn, Bonn, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz-Zentrum München, Neuherberg, Germany
| | - Peter Seibel
- Molekulare Zellbiologie, Biotechnological Biomedical Center, Universität Leipzig, Leipzig, Germany
| | - Andreas Jung
- Institute for Pathology of the Ludwig-Maximilians-Universität München, Munich, Germany; German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany.
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217
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Olejár T, Pajuelo-Reguera D, Alán L, Dlasková A, Ježek P. Coupled aggregation of mitochondrial single-strand DNA-binding protein tagged with Eos fluorescent protein visualizes synchronized activity of mitochondrial nucleoids. Mol Med Rep 2015; 12:5185-90. [PMID: 26239383 DOI: 10.3892/mmr.2015.4085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 06/05/2015] [Indexed: 11/05/2022] Open
Abstract
Oligomer aggregation of green-to-red photoconvertible fluorescent protein Eos (EosFP) is a natural feature of the wild‑type variant. The aim of the present study was to follow up mitochondrial nucleoid behavior under natural conditions of living cells transfected with mitochondrial single‑strand DNA‑binding protein (mtSSB) conjugated with EosFP. HEPG2 and SH‑SY5Y cells were subjected to lentiviral transfection and subsequently immunostained with anti‑DNA, anti‑transcription factor A, mitochondrial (TFAM) or anti‑translocase of the inner membrane 23 antibodies. Fluorescent microscopy, conventional confocal microscopy, superresolution biplane fluorescence photo-activation localization microscopy and direct stochastic optical reconstruction microscopy were used for imaging. In the two cell types, apparent couples of equally‑sized mtSSB‑EosFP‑visualized dots were observed. During the time course of the ongoing transfection procedure, however, a small limited number of large aggregates of mtSSB‑EosFP‑tagged protein started to form in the cells, which exhibited a great co‑localization with the noted coupled positions. Antibody staining and 3D immunocytochemistry confirmed that nucleoid components such as TFAM and DNA were co‑localized with these aggregates. Furthermore, the observed reduction of the mtDNA copy number in mtSSB‑EosFP‑transfected cells suggested a possible impairment of nucleoid function. In conclusion, the present study demonstrated that coupled nucleoids are synchronized by mtSSB‑EosFP overexpression and visualized through their equal binding capacity to mtSSB‑EosFP‑tagged protein. This observation suggested parallel replication and transcription activity of nucleoid couples native from a parental one. Preserved coupling in late stages of artificial EosFP‑mediated aggregation of tagged proteins suggested a rational manner of mitochondrial branching that may be cell-type specifically dependent on hierarchical nucleoid replication.
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Affiliation(s)
- Tomáš Olejár
- Department of Membrane Transport Biophysics, Institute of Physiology, The Czech Academy of Sciences, Prague 14220, Czech Republic
| | - David Pajuelo-Reguera
- Department of Membrane Transport Biophysics, Institute of Physiology, The Czech Academy of Sciences, Prague 14220, Czech Republic
| | - Lukáš Alán
- Department of Membrane Transport Biophysics, Institute of Physiology, The Czech Academy of Sciences, Prague 14220, Czech Republic
| | - Andrea Dlasková
- Department of Membrane Transport Biophysics, Institute of Physiology, The Czech Academy of Sciences, Prague 14220, Czech Republic
| | - Petr Ježek
- Department of Membrane Transport Biophysics, Institute of Physiology, The Czech Academy of Sciences, Prague 14220, Czech Republic
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218
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Han LH, Dong LY, Yu H, Sun GY, Wu Y, Gao J, Thasler W, An W. Deceleration of liver regeneration by knockdown of augmenter of liver regeneration gene is associated with impairment of mitochondrial DNA synthesis in mice. Am J Physiol Gastrointest Liver Physiol 2015; 309:G112-22. [PMID: 25977511 DOI: 10.1152/ajpgi.00435.2014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 05/11/2015] [Indexed: 01/31/2023]
Abstract
Hepatic stimulator substance, also known as augmenter of liver regeneration (ALR), is a novel hepatic mitogen that stimulates liver regeneration after partial hepatectomy (PH). Recent work has indicated that a lack of ALR expression inhibited liver regeneration in rats, and the mechanism seems to be related to increased cell apoptosis. The mitochondria play an important role during liver regeneration. Adequate ATP supply, which is largely dependent on effective mitochondrial biogenesis, is essential for progress of liver regeneration. However, ALR gene expression during liver regeneration, particularly its function with mitochondrial DNA synthesis, remains poorly understood. In this study, ALR expression in hepatocytes of mice was suppressed with ALR short-hairpin RNA interference or ALR deletion (knockout, KO). The ALR-defective mice underwent PH, and the liver was allowed to regenerate for 1 wk. Analysis of liver growth and its correlation with mitochondrial biogenesis showed that both ALR mRNA and protein levels increased robustly in control mice with a maximum at days 3 and 4 post-PH. However, ALR knockdown inhibited hepatic DNA synthesis and decelerated liver regeneration after PH. Furthermore, both in the ALR-knockdown and ALR-KO mice, expression of mitochondrial transcription factor A and peroxisome proliferator-activated receptor-γ coactivator-1α were reduced, resulting in impaired mitochondrial biogenesis. In conclusion, ALR is apparently required to ensure appropriate liver regeneration following PH in mice, and deletion of the ALR gene may delay liver regeneration in part due to impaired mitochondrial biogenesis.
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Affiliation(s)
- Li-hong Han
- Department of Cell Biology and Municipal Laboratory of Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing, China; and
| | - Ling-yue Dong
- Department of Cell Biology and Municipal Laboratory of Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing, China; and
| | - Hao Yu
- Department of Cell Biology and Municipal Laboratory of Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing, China; and
| | - Guang-yong Sun
- Department of Cell Biology and Municipal Laboratory of Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing, China; and
| | - Yuan Wu
- Department of Cell Biology and Municipal Laboratory of Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing, China; and
| | - Jian Gao
- Department of Cell Biology and Municipal Laboratory of Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing, China; and
| | | | - Wei An
- Department of Cell Biology and Municipal Laboratory of Liver Protection and Regulation of Regeneration, Capital Medical University, Beijing, China; and
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219
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Clemente P, Pajak A, Laine I, Wibom R, Wedell A, Freyer C, Wredenberg A. SUV3 helicase is required for correct processing of mitochondrial transcripts. Nucleic Acids Res 2015; 43:7398-413. [PMID: 26152302 PMCID: PMC4551930 DOI: 10.1093/nar/gkv692] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/25/2015] [Indexed: 12/05/2022] Open
Abstract
Mitochondrial gene expression is largely regulated by post-transcriptional mechanisms that control the amount and translation of each mitochondrial mRNA. Despite its importance for mitochondrial function, the mechanisms and proteins involved in mRNA turnover are still not fully characterized. Studies in yeast and human cell lines have indicated that the mitochondrial helicase SUV3, together with the polynucleotide phosphorylase, PNPase, composes the mitochondrial degradosome. To further investigate the in vivo function of SUV3 we disrupted the homolog of SUV3 in Drosophila melanogaster (Dm). Loss of dmsuv3 led to the accumulation of mitochondrial mRNAs, without increasing rRNA levels, de novo transcription or decay intermediates. Furthermore, we observed a severe decrease in mitochondrial tRNAs accompanied by an accumulation of unprocessed precursor transcripts. These processing defects lead to reduced mitochondrial translation and a severe respiratory chain complex deficiency, resulting in a pupal lethal phenotype. In summary, our results propose that SUV3 is predominantly required for the processing of mitochondrial polycistronic transcripts in metazoan and that this function is independent of PNPase.
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Affiliation(s)
- Paula Clemente
- Division of Metabolic Diseases, Department of Laboratory Medicine; Karolinska Institutet, Stockholm 17177, Sweden
| | - Aleksandra Pajak
- Division of Metabolic Diseases, Department of Laboratory Medicine; Karolinska Institutet, Stockholm 17177, Sweden
| | - Isabelle Laine
- Division of Metabolic Diseases, Department of Laboratory Medicine; Karolinska Institutet, Stockholm 17177, Sweden
| | - Rolf Wibom
- Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Anna Wedell
- Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm 17176, Sweden Department of Molecular Medicine and Surgery, Science for Life Laboratory, Karolinska Institutet, Stockholm 17176, Sweden
| | - Christoph Freyer
- Division of Metabolic Diseases, Department of Laboratory Medicine; Karolinska Institutet, Stockholm 17177, Sweden Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Anna Wredenberg
- Division of Metabolic Diseases, Department of Laboratory Medicine; Karolinska Institutet, Stockholm 17177, Sweden Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm 17176, Sweden
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220
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Liu Z, Guo J, Sun H, Huang Y, Zhao R, Yang X. α-Lipoic acid attenuates LPS-induced liver injury by improving mitochondrial function in association with GR mitochondrial DNA occupancy. Biochimie 2015; 116:52-60. [PMID: 26133658 DOI: 10.1016/j.biochi.2015.06.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 06/22/2015] [Indexed: 12/21/2022]
Abstract
α-Lipoic acid (LA) has been demonstrated to be a key regulator of energy metabolism. However, whether LA can protect the liver from inflammation, as well as the underlying mechanism involved, are still largely unclear. In the present study, mice treated with lipopolysaccharide (LPS) and injected with LA were used as a model. Liver injury, energy metabolism and mitochondrial regulation were investigated to assess the protective effect of LA on the liver and explore the possible mechanisms involved. Our results showed that LA attenuated liver injury, as evidenced by the decreased plasma alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels after LA treatment compared with the LPS-treated group. The hepatic ATP and NADH levels, expression levels of most mitochondrial DNA (mtDNA)-encoded genes as well as mitochondrial complex I, IV and V activities were all significantly increased in the LA-treated group compared with the LPS-treated group. Levels of Sirt3 protein, which is essential for the regulation of mitochondrial metabolism, were also increased in the LA-treated group. Regarding the regulation of mtDNA-encoded genes expression, we observed no obvious change in the methylation status of the mtDNA D-loop region. However, compared to the LPS-treated group, LA treatment increased glucocorticoid receptor (GR) protein expression in the liver, as well as the level of GR occupancy on the mtDNA D-loop region. Our study demonstrates that LA exerts a liver-protective effect in an inflammation state by improving mitochondrial function. Furthermore, to the best of our knowledge, we demonstrate for the first time that GR may be involved in this effect via an enhanced binding to the mtDNA transcriptional control region, thereby regulating the expression of mtDNA-encoded genes.
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Affiliation(s)
- Zhiqing Liu
- Key Laboratory of Animal Physiology & Biochemistry, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Jun Guo
- Key Laboratory of Animal Physiology & Biochemistry, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Hailin Sun
- Key Laboratory of Animal Physiology & Biochemistry, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yanping Huang
- Key Laboratory of Animal Physiology & Biochemistry, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Ruqian Zhao
- Key Laboratory of Animal Physiology & Biochemistry, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xiaojing Yang
- Key Laboratory of Animal Physiology & Biochemistry, Nanjing Agricultural University, Nanjing 210095, PR China.
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221
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The exonuclease activity of DNA polymerase γ is required for ligation during mitochondrial DNA replication. Nat Commun 2015; 6:7303. [PMID: 26095671 PMCID: PMC4557304 DOI: 10.1038/ncomms8303] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 04/27/2015] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial DNA (mtDNA) polymerase γ (POLγ) harbours a 3′–5′ exonuclease proofreading activity. Here we demonstrate that this activity is required for the creation of ligatable ends during mtDNA replication. Exonuclease-deficient POLγ fails to pause on reaching a downstream 5′-end. Instead, the enzyme continues to polymerize into double-stranded DNA, creating an unligatable 5′-flap. Disease-associated mutations can both increase and decrease exonuclease activity and consequently impair DNA ligation. In mice, inactivation of the exonuclease activity causes an increase in mtDNA mutations and premature ageing phenotypes. These mutator mice also contain high levels of truncated, linear fragments of mtDNA. We demonstrate that the formation of these fragments is due to impaired ligation, causing nicks near the origin of heavy-strand DNA replication. In the subsequent round of replication, the nicks lead to double-strand breaks and linear fragment formation. Mitochondrial DNA (mtDNA) polymerase γ has a 3′–5′ exonuclease proofreading activity. Here, the authors show it is required for creating ligatable ends during mtDNA replication, and inactivation of the activity in mice causes strand-specific nicks in DNA and the formation of linear mtDNA fragments.
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222
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Gorkhali NA, Jiang L, Shrestha BS, He XH, Junzhao Q, Han JL, Ma YH. High occurrence of mitochondrial heteroplasmy in nepalese indigenous sheep (Ovis aries) compared to chinese sheep. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:2645-7. [DOI: 10.3109/19401736.2015.1041134] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Neena Amatya Gorkhali
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,
- Animal Breeding Division, National Animal Science Institute, Nepal Agriculture Research Council (NARC), Kathmandu, Nepal, and
| | - Lin Jiang
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,
| | - Bhola Shankar Shrestha
- Animal Breeding Division, National Animal Science Institute, Nepal Agriculture Research Council (NARC), Kathmandu, Nepal, and
| | - Xiao-Hong He
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,
| | - Qian Junzhao
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Yue-Hui Ma
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China,
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223
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Tryon LD, Crilly MJ, Hood DA. Effect of denervation on the regulation of mitochondrial transcription factor A expression in skeletal muscle. Am J Physiol Cell Physiol 2015; 309:C228-38. [PMID: 26063705 DOI: 10.1152/ajpcell.00266.2014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 06/03/2015] [Indexed: 11/22/2022]
Abstract
The purpose of this study was to determine how the expression of mitochondrial transcription factor A (Tfam), a protein that governs mitochondrial DNA (mtDNA) transcription and replication, is regulated during a state of reduced organelle content imposed by muscle disuse. We measured Tfam expression at 8 h, 16 h, 24 h, 3 days, or 7 days following denervation and hypothesized that decreases in Tfam expression would precede mitochondrial loss. Muscle mass was lowered by 13% and 38% at 3 and 7 days postdenervation, while cytochrome c oxidase activity fell by 33% and 39% at the same time points. Tfam promoter activation in vivo was reduced by 30-65% between 8 h and 3 days of denervation, while Tfam transcript half-life was increased following 8-24 h of denervation. Protein expression of RNA-binding proteins that promote mRNA degradation (CUG repeat-binding protein and K homology splicing regulator protein) was elevated at 3 and 7 days of denervation. Tfam localization within subsarcolemmal mitochondria was reduced after 3 and 7 days of denervation and was associated with suppression of the cytochrome c oxidase type I transcript at 3 days, indicating that denervation impairs both mitochondrial Tfam import and mtDNA transcription during an early period following denervation. These data suggest that putative signals downregulate Tfam transcription during the earliest stages following denervation but are counteracted by increases in Tfam mRNA stability. Import of Tfam into the mitochondrion seems to be the most critical point of regulation of this protein during the early onset of denervation, an impairment of which is coincident with the loss of mitochondria during muscle disuse.
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Affiliation(s)
- Liam D Tryon
- Muscle Health Research Centre, York University, Toronto, Ontario, Canada; and School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada
| | - Matthew J Crilly
- Muscle Health Research Centre, York University, Toronto, Ontario, Canada; and School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada
| | - David A Hood
- Muscle Health Research Centre, York University, Toronto, Ontario, Canada; and School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada
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224
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Moustafa IM, Uchida A, Wang Y, Yennawar N, Cameron CE. Structural models of mammalian mitochondrial transcription factor B2. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:987-1002. [PMID: 26066983 DOI: 10.1016/j.bbagrm.2015.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 05/22/2015] [Accepted: 05/25/2015] [Indexed: 11/26/2022]
Abstract
Mammalian mitochondrial DNA (mtDNA) encodes 13 core proteins of oxidative phosphorylation, 12S and 16S ribosomal RNAs, and 22 transfer RNAs. Mutations and deletions of mtDNA and/or nuclear genes encoding mitochondrial proteins have been implicated in a wide range of diseases. Thus, cell survival and health of the organism require some steady-state level of the mitochondrial genome and its expression. In mammalian systems, the mitochondrial transcription factor B2 (mtTFB2 or TFB2M) is indispensable for transcription initiation. TFB2M along with two other proteins, mitochondrial RNA polymerase (mtRNAP or POLRMT) and mitochondrial transcription factor A (mtTFA or TFAM), are key components of the core mitochondrial transcription apparatus. Structural information for POLRMT and TFAM from humans is available; however, there is no available structure for TFB2M. In the present study, three-dimensional structure of TFB2M from humans was modeled using a combination of homology modeling and small-angle X-ray scattering (SAXS). The TFB2M structural model adds substantively to our understanding of TFB2M function. An explanation for the low or absent RNA methyltransferase activity is provided. A putative nucleic acid-binding site is revealed. The amino and carboxy termini, while likely lacking defined secondary structure, appear to adopt compact, globular conformations, thus "capping" the ends of the protein. Finally, sites of interaction of TFB2M with other factors, protein and/or nucleic acid, are suggested by the identification of species-specific clusters on the surface of the protein.
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Affiliation(s)
- Ibrahim M Moustafa
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Akira Uchida
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Yao Wang
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Neela Yennawar
- Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
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225
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Szczepanowska K, Trifunovic A. Different faces of mitochondrial DNA mutators. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1362-72. [PMID: 26014346 DOI: 10.1016/j.bbabio.2015.05.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 05/15/2015] [Accepted: 05/17/2015] [Indexed: 10/23/2022]
Abstract
A number of studies have shown that ageing is associated with increased amounts of mtDNA deletions and/or point mutations in a variety of species as diverse as Caenorhabditis elegans, Drosophila melanogaster, mice, rats, dogs, primates and humans. This detected vulnerability of mtDNA has led to the suggestion that the accumulation of somatic mtDNA mutations might arise from increased oxidative damage and could play an important role in the ageing process by producing cells with a decreased oxidative capacity. However, the vast majority of DNA polymorphisms and disease-causing base-substitution mutations and age-associated mutations that have been detected in human mtDNA are transition mutations. They are likely arising from the slight infidelity of the mitochondrial DNA polymerase. Indeed, transition mutations are also the predominant type of mutation found in mtDNA mutator mice, a model for premature ageing caused by increased mutation load due to the error prone mitochondrial DNA synthesis. These particular misincorporation events could also be exacerbated by dNTP pool imbalances. The role of different repair, replication and maintenance mechanisms that contribute to mtDNA integrity and mutagenesis will be discussed in details in this article. This article is part of a Special Issue entitled: Mitochondrial Dysfunction in Aging.
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Affiliation(s)
- Karolina Szczepanowska
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD) and Institute for Mitochondrial Diseases and Ageing, Medical Faculty, University of Cologne, D-50931 Cologne, Germany
| | - Aleksandra Trifunovic
- Cologne Excellence Cluster on Cellular Stress Responses in Ageing-Associated Diseases (CECAD) and Institute for Mitochondrial Diseases and Ageing, Medical Faculty, University of Cologne, D-50931 Cologne, Germany.
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226
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Reversal of mitochondrial defects with CSB-dependent serine protease inhibitors in patient cells of the progeroid Cockayne syndrome. Proc Natl Acad Sci U S A 2015; 112:E2910-9. [PMID: 26038566 DOI: 10.1073/pnas.1422264112] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
UV-sensitive syndrome (UV(S)S) and Cockayne syndrome (CS) are human disorders caused by CSA or CSB gene mutations; both conditions cause defective transcription-coupled repair and photosensitivity. Patients with CS also display neurological and developmental abnormalities and dramatic premature aging, and their cells are hypersensitive to oxidative stress. We report CSA/CSB-dependent depletion of the mitochondrial DNA polymerase-γ catalytic subunit (POLG1), due to HTRA3 serine protease accumulation in CS, but not in UV(s)S or control fibroblasts. Inhibition of serine proteases restored physiological POLG1 levels in either CS fibroblasts and in CSB-silenced cells. Moreover, patient-derived CS cells displayed greater nitroso-redox imbalance than UV(S)S cells. Scavengers of reactive oxygen species and peroxynitrite normalized HTRA3 and POLG1 levels in CS cells, and notably, increased mitochondrial oxidative phosphorylation, which was altered in CS cells. These data reveal critical deregulation of proteases potentially linked to progeroid phenotypes in CS, and our results suggest rescue strategies as a therapeutic option.
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227
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Roberti M, Polosa PL, Bruni F, Deceglie S, Gadaleta MN, Cantatore P. MTERF factors: a multifunction protein family. Biomol Concepts 2015; 1:215-24. [PMID: 25961998 DOI: 10.1515/bmc.2010.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The MTERF family is a large protein family, identified in metazoans and plants, which consists of four subfamilies, MTERF1, 2, 3 and 4. Mitochondrial localisation was predicted for the vast majority of MTERF family members and demonstrated for the characterised MTERF proteins. The main structural feature of MTERF proteins is the presence of a modular architecture, based on repetitions of a 30-residue module, the mTERF motif, containing leucine zipper-like heptads. The MTERF family includes transcription termination factors: human mTERF, sea urchin mtDBP and Drosophila DmTTF. In addition to terminating transcription, they are involved in transcription initiation and in the control of mtDNA replication. This multiplicity of functions seems to flank differences in the gene organisation of mitochondrial genomes. MTERF2 and MTERF3 play antithetical roles in controlling mitochondrial transcription: that is, mammalian and Drosophila MTERF3 act as negative regulators, whereas mammalian MTERF2 functions as a positive regulator. Both proteins contact mtDNA in the promoter region, perhaps establishing interactions, either mutual or with other factors. Regulation of MTERF gene expression in human and Drosophila depends on nuclear transcription factors NRF-2 and DREF, respectively, and proceeds through pathways which appear to discriminate between factors positively or negatively acting in mitochondrial transcription. In this emerging scenario, it appears that MTERF proteins act to coordinate mitochondrial transcription.
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228
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Quiñones-Lombraña A, Blanco JG. Chromosome 21-derived hsa-miR-155-5p regulates mitochondrial biogenesis by targeting Mitochondrial Transcription Factor A (TFAM). Biochim Biophys Acta Mol Basis Dis 2015; 1852:1420-7. [PMID: 25869329 DOI: 10.1016/j.bbadis.2015.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 04/02/2015] [Accepted: 04/03/2015] [Indexed: 02/06/2023]
Abstract
The regulation of mitochondrial biogenesis is under the control of nuclear genes including the master Mitochondrial Transcription Factor A (TFAM). Recent evidence suggests that the expression of TFAM is regulated by microRNAs (miRNAs) in various cellular contexts. Here, we show that hsa-miR-155-5p, a prominent miRNA encoded in chromosome 21, controls the expression of TFAM at the post-transcriptional level. In human fibroblasts derived from a diploid donor, downregulation of TFAM by hsa-miR-155-5p decreased mitochondrial DNA (mtDNA) content. In contrast, downregulation of TFAM by hsa-miR-155-5p did not decrease mtDNA content in fibroblasts derived from a donor with Down syndrome (DS, trisomy 21). In line, downregulation of mitochondrial TFAM levels through hsa-miR-155-5p decreased mitochondrial mass in diploid fibroblasts but not in trisomic cells. Due to the prevalence of mitochondrial dysfunction and cardiac abnormalities in subjects with DS, we examined the presence of potential associations between hsa-miR-155-5p and TFAM expression in heart samples from donors with and without DS. There were significant negative associations between hsa-miR-155-5p and TFAM expression in heart samples from donors with and without DS. These results suggest that regulation of TFAM by hsa-miR-155-5p impacts mitochondrial biogenesis in the diploid setting but not in the DS setting.
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Affiliation(s)
- Adolfo Quiñones-Lombraña
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York, USA
| | - Javier G Blanco
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York, USA.
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229
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Truksa J, Dong LF, Rohlena J, Stursa J, Vondrusova M, Goodwin J, Nguyen M, Kluckova K, Rychtarcikova Z, Lettlova S, Spacilova J, Stapelberg M, Zoratti M, Neuzil J. Mitochondrially targeted vitamin E succinate modulates expression of mitochondrial DNA transcripts and mitochondrial biogenesis. Antioxid Redox Signal 2015; 22:883-900. [PMID: 25578105 DOI: 10.1089/ars.2013.5594] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
AIMS To assess the effect of mitochondrially targeted vitamin E (VE) analogs on mitochondrial function and biogenesis. RESULTS Mitochondrially targeted vitamin E succinate (MitoVES) is an efficient inducer of apoptosis in cancer cells. Here, we show that unlike its untargeted counterpart α-tocopheryl succinate, MitoVES suppresses proliferation of cancer cells at sub-apoptotic doses by way of affecting the mitochondrial DNA (mtDNA) transcripts. We found that MitoVES strongly suppresses the level of the displacement loop transcript followed by those of mtDNA genes coding for subunits of mitochondrial complexes. This process is coupled to the inhibition of mitochondrial respiration, dissipation of the mitochondrial membrane potential, and generation of reactive oxygen species. In addition, exposure of cancer cells to MitoVES led to decreased expression of TFAM and diminished mitochondrial biogenesis. The inhibition of mitochondrial transcription was replicated in vivo in a mouse model of HER2(high) breast cancer, where MitoVES lowered the level of mtDNA transcripts in cancer cells but not in normal tissue. INNOVATION Our data show that mitochondrially targeted VE analogs represent a novel class of mitocans that not only induce apoptosis at higher concentrations but also block proliferation and suppress normal mitochondrial function and transcription at low, non-apoptogenic doses. CONCLUSIONS Our data indicate a novel, selective anti-cancer activity of compounds that act by targeting mitochondria of cancer cells, inducing significant alterations in mitochondrial function associated with transcription of mtDNA-coded genes. These changes subsequently result in the arrest of cell proliferation.
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Affiliation(s)
- Jaroslav Truksa
- 1 Molecular Therapy Group, Institute of Biotechnology , Academy of Sciences of the Czech Republic, Prague, Czech Republic
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230
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How do changes in the mtDNA and mitochondrial dysfunction influence cancer and cancer therapy? Challenges, opportunities and models. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2015; 764:16-30. [DOI: 10.1016/j.mrrev.2015.01.001] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 01/11/2015] [Accepted: 01/12/2015] [Indexed: 12/28/2022]
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231
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Xu J, Chi F, Guo T, Punj V, Lee WNP, French SW, Tsukamoto H. NOTCH reprograms mitochondrial metabolism for proinflammatory macrophage activation. J Clin Invest 2015; 125:1579-90. [PMID: 25798621 DOI: 10.1172/jci76468] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 02/09/2015] [Indexed: 12/20/2022] Open
Abstract
Metabolic reprogramming is implicated in macrophage activation, but the underlying mechanisms are poorly understood. Here, we demonstrate that the NOTCH1 pathway dictates activation of M1 phenotypes in isolated mouse hepatic macrophages (HMacs) and in a murine macrophage cell line by coupling transcriptional upregulation of M1 genes with metabolic upregulation of mitochondrial oxidative phosphorylation and ROS (mtROS) to augment induction of M1 genes. Enhanced mitochondrial glucose oxidation was achieved by increased recruitment of the NOTCH1 intracellular domain (NICD1) to nuclear and mitochondrial genes that encode respiratory chain components and by NOTCH-dependent induction of pyruvate dehydrogenase phosphatase 1 (Pdp1) expression, pyruvate dehydrogenase activity, and glucose flux to the TCA cycle. As such, inhibition of the NOTCH pathway or Pdp1 knockdown abrogated glucose oxidation, mtROS, and M1 gene expression. Conditional NOTCH1 deficiency in the myeloid lineage attenuated HMac M1 activation and inflammation in a murine model of alcoholic steatohepatitis and markedly reduced lethality following endotoxin-mediated fulminant hepatitis in mice. In vivo monocyte tracking further demonstrated the requirement of NOTCH1 for the migration of blood monocytes into the liver and subsequent M1 differentiation. Together, these results reveal that NOTCH1 promotes reprogramming of mitochondrial metabolism for M1 macrophage activation.
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MESH Headings
- Animals
- Cell Line
- Electron Transport/genetics
- Endotoxemia/complications
- Fatty Liver, Alcoholic/immunology
- Fatty Liver, Alcoholic/metabolism
- Fatty Liver, Alcoholic/pathology
- Feedback, Physiological
- Gene Expression Regulation
- Glucose/metabolism
- Inflammation/immunology
- Inflammation/metabolism
- Liver Failure, Acute/etiology
- Liver Failure, Acute/immunology
- Liver Failure, Acute/metabolism
- Liver Failure, Acute/pathology
- Macrophage Activation/genetics
- Macrophage Activation/physiology
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mitochondria/metabolism
- Myeloid Cells/metabolism
- Myeloid Cells/pathology
- Nitric Oxide/metabolism
- Oxidative Phosphorylation
- Protein Structure, Tertiary
- Pyruvate Dehydrogenase (Lipoamide)-Phosphatase/antagonists & inhibitors
- Pyruvate Dehydrogenase (Lipoamide)-Phosphatase/genetics
- Pyruvate Dehydrogenase (Lipoamide)-Phosphatase/metabolism
- Pyruvate Dehydrogenase Complex/metabolism
- Reactive Oxygen Species/metabolism
- Receptor, Notch1/deficiency
- Receptor, Notch1/physiology
- Signal Transduction/physiology
- Transcription, Genetic
- Up-Regulation
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232
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Nargund AM, Fiorese CJ, Pellegrino MW, Deng P, Haynes CM. Mitochondrial and nuclear accumulation of the transcription factor ATFS-1 promotes OXPHOS recovery during the UPR(mt). Mol Cell 2015; 58:123-33. [PMID: 25773600 DOI: 10.1016/j.molcel.2015.02.008] [Citation(s) in RCA: 304] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 11/11/2014] [Accepted: 02/03/2015] [Indexed: 12/29/2022]
Abstract
Mitochondrial diseases and aging are associated with defects in the oxidative phosphorylation machinery (OXPHOS), which are the only complexes composed of proteins encoded by separate genomes. To better understand genome coordination and OXPHOS recovery during mitochondrial dysfunction, we examined ATFS-1, a transcription factor that regulates mitochondria-to-nuclear communication during the mitochondrial UPR, via ChIP-sequencing. Surprisingly, in addition to regulating mitochondrial chaperone, OXPHOS complex assembly factor, and glycolysis genes, ATFS-1 bound directly to OXPHOS gene promoters in both the nuclear and mitochondrial genomes. Interestingly, atfs-1 was required to limit the accumulation of OXPHOS transcripts during mitochondrial stress, which required accumulation of ATFS-1 in the nucleus and mitochondria. Because balanced ATFS-1 accumulation promoted OXPHOS complex assembly and function, our data suggest that ATFS-1 stimulates respiratory recovery by fine-tuning OXPHOS expression to match the capacity of the suboptimal protein-folding environment in stressed mitochondria, while simultaneously increasing proteostasis capacity.
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Affiliation(s)
- Amrita M Nargund
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christopher J Fiorese
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; BCMB Allied Program, Weill Cornell Medical College, New York, NY 10065, USA
| | - Mark W Pellegrino
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Pan Deng
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; BCMB Allied Program, Weill Cornell Medical College, New York, NY 10065, USA
| | - Cole M Haynes
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; BCMB Allied Program, Weill Cornell Medical College, New York, NY 10065, USA.
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233
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Lee D, Kim KY, Shim MS, Kim SY, Ellisman MH, Weinreb RN, Ju WK. Coenzyme Q10 ameliorates oxidative stress and prevents mitochondrial alteration in ischemic retinal injury. Apoptosis 2015; 19:603-14. [PMID: 24337820 PMCID: PMC3938850 DOI: 10.1007/s10495-013-0956-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Coenzyme Q10 (CoQ10) acts by scavenging reactive oxygen species for protecting neuronal cells against oxidative stress in neurodegenerative diseases. We tested whether a diet supplemented with CoQ10 ameliorates oxidative stress and mitochondrial alteration, as well as promotes retinal ganglion cell (RGC) survival in ischemic retina induced by intraocular pressure elevation. A CoQ10 significantly promoted RGC survival at 2 weeks after ischemia. Superoxide dismutase 2 (SOD2) and heme oxygenase-1 (HO-1) expression were significantly increased at 12 h after ischemic injury. In contrast, the CoQ10 significantly prevented the upregulation of SOD2 and HO-1 protein expression in ischemic retina. In addition, the CoQ10 significantly blocked activation of astroglial and microglial cells in ischemic retina. Interestingly, the CoQ10 blocked apoptosis by decreasing caspase-3 protein expression in ischemic retina. Bax and phosphorylated Bad (pBad) protein expression were significantly increased in ischemic retina at 12 h. Interestingly, while CoQ10 significantly decreased Bax protein expression in ischemic retina, CoQ10 showed greater increase of pBad protein expression. Of interest, ischemic injury significantly increased mitochondrial transcription factor A (Tfam) protein expression in the retina at 12 h, however, CoQ10 significantly preserved Tfam protein expression in ischemic retina. Interestingly, there were no differences in mitochondrial DNA content among control- or CoQ10-treated groups. Our findings demonstrate that CoQ10 protects RGCs against oxidative stress by modulating the Bax/Bad-mediated mitochondrial apoptotic pathway as well as prevents mitochondrial alteration by preserving Tfam protein expression in ischemic retina. Our results suggest that CoQ10 may provide neuroprotection against oxidative stress-mediated mitochondrial alterations in ischemic retinal injury.
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Affiliation(s)
- Dongwook Lee
- Laboratory for Optic Nerve Biology, Department of Ophthalmology, Hamilton Glaucoma Center, University of California San Diego, 9415 Campus Point Drive, La Jolla, CA 92037 USA
- Research Institute of Clinical Medicine of Chonbuk National University-Biomedical Research Institute, Chonbuk National University Hospital, Chonju, Chonbuk Republic of Korea
| | - Keun-Young Kim
- Department of Neuroscience, Center for Research on Biological Systems, National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA USA
| | - Myoung Sup Shim
- Laboratory for Optic Nerve Biology, Department of Ophthalmology, Hamilton Glaucoma Center, University of California San Diego, 9415 Campus Point Drive, La Jolla, CA 92037 USA
| | - Sang Yeop Kim
- Laboratory for Optic Nerve Biology, Department of Ophthalmology, Hamilton Glaucoma Center, University of California San Diego, 9415 Campus Point Drive, La Jolla, CA 92037 USA
| | - Mark H. Ellisman
- Department of Neuroscience, Center for Research on Biological Systems, National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA USA
| | - Robert N. Weinreb
- Laboratory for Optic Nerve Biology, Department of Ophthalmology, Hamilton Glaucoma Center, University of California San Diego, 9415 Campus Point Drive, La Jolla, CA 92037 USA
| | - Won-Kyu Ju
- Laboratory for Optic Nerve Biology, Department of Ophthalmology, Hamilton Glaucoma Center, University of California San Diego, 9415 Campus Point Drive, La Jolla, CA 92037 USA
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234
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Agaronyan K, Morozov YI, Anikin M, Temiakov D. Mitochondrial biology. Replication-transcription switch in human mitochondria. Science 2015; 347:548-51. [PMID: 25635099 DOI: 10.1126/science.aaa0986] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Coordinated replication and expression of the mitochondrial genome is critical for metabolically active cells during various stages of development. However, it is not known whether replication and transcription can occur simultaneously without interfering with each other and whether mitochondrial DNA copy number can be regulated by the transcription machinery. We found that interaction of human transcription elongation factor TEFM with mitochondrial RNA polymerase and nascent transcript prevents the generation of replication primers and increases transcription processivity and thereby serves as a molecular switch between replication and transcription, which appear to be mutually exclusive processes in mitochondria. TEFM may allow mitochondria to increase transcription rates and, as a consequence, respiration and adenosine triphosphate production without the need to replicate mitochondrial DNA, as has been observed during spermatogenesis and the early stages of embryogenesis.
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Affiliation(s)
- Karen Agaronyan
- Department of Cell Biology, School of Osteopathic Medicine, Rowan University, 2 Medical Center Drive, Stratford, NJ 08084, USA
| | - Yaroslav I Morozov
- Department of Cell Biology, School of Osteopathic Medicine, Rowan University, 2 Medical Center Drive, Stratford, NJ 08084, USA
| | - Michael Anikin
- Department of Cell Biology, School of Osteopathic Medicine, Rowan University, 2 Medical Center Drive, Stratford, NJ 08084, USA
| | - Dmitry Temiakov
- Department of Cell Biology, School of Osteopathic Medicine, Rowan University, 2 Medical Center Drive, Stratford, NJ 08084, USA.
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235
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Posse V, Shahzad S, Falkenberg M, Hällberg BM, Gustafsson CM. TEFM is a potent stimulator of mitochondrial transcription elongation in vitro. Nucleic Acids Res 2015; 43:2615-24. [PMID: 25690892 PMCID: PMC4357710 DOI: 10.1093/nar/gkv105] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
A single-subunit RNA polymerase, POLRMT, transcribes the mitochondrial genome in human cells. Recently, a factor termed as the mitochondrial transcription elongation factor, TEFM, was shown to stimulate transcription elongation in vivo, but its effect in vitro was relatively modest. In the current work, we have isolated active TEFM in recombinant form and used a reconstituted in vitro transcription system to characterize its activities. We show that TEFM strongly promotes POLRMT processivity as it dramatically stimulates the formation of longer transcripts. TEFM also abolishes premature transcription termination at conserved sequence block II, an event that has been linked to primer formation during initiation of mtDNA synthesis. We show that POLRMT pauses at a wide range of sites in a given DNA sequence. In the absence of TEFM, this leads to termination; however, the presence of TEFM abolishes this effect and aids POLRMT in continuation of transcription. Further, we show that TEFM substantially increases the POLRMT affinity to an elongation-like DNA:RNA template. In combination with previously published in vivo observations, our data establish TEFM as an essential component of the mitochondrial transcription machinery.
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Affiliation(s)
- Viktor Posse
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Saba Shahzad
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-17177 Stockholm, Sweden Röntgen-Ångström-Cluster, Karolinska Institutet Outstation, Centre for Structural Systems Biology, DESY-Campus, D-22603 Hamburg, Germany
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-17177 Stockholm, Sweden Röntgen-Ångström-Cluster, Karolinska Institutet Outstation, Centre for Structural Systems Biology, DESY-Campus, D-22603 Hamburg, Germany European Molecular Biology Laboratory, Hamburg Unit, D-22603 Hamburg, Germany
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-40530 Gothenburg, Sweden
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236
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Lewis SC, Joers P, Willcox S, Griffith JD, Jacobs HT, Hyman BC. A rolling circle replication mechanism produces multimeric lariats of mitochondrial DNA in Caenorhabditis elegans. PLoS Genet 2015; 11:e1004985. [PMID: 25693201 PMCID: PMC4334201 DOI: 10.1371/journal.pgen.1004985] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 01/05/2015] [Indexed: 11/24/2022] Open
Abstract
Mitochondrial DNA (mtDNA) encodes respiratory complex subunits essential to almost all eukaryotes; hence respiratory competence requires faithful duplication of this molecule. However, the mechanism(s) of its synthesis remain hotly debated. Here we have developed Caenorhabditis elegans as a convenient animal model for the study of metazoan mtDNA synthesis. We demonstrate that C. elegans mtDNA replicates exclusively by a phage-like mechanism, in which multimeric molecules are synthesized from a circular template. In contrast to previous mammalian studies, we found that mtDNA synthesis in the C. elegans gonad produces branched-circular lariat structures with multimeric DNA tails; we were able to detect multimers up to four mtDNA genome unit lengths. Further, we did not detect elongation from a displacement-loop or analogue of 7S DNA, suggesting a clear difference from human mtDNA in regard to the site(s) of replication initiation. We also identified cruciform mtDNA species that are sensitive to cleavage by the resolvase RusA; we suggest these four-way junctions may have a role in concatemer-to-monomer resolution. Overall these results indicate that mtDNA synthesis in C. elegans does not conform to any previously documented metazoan mtDNA replication mechanism, but instead are strongly suggestive of rolling circle replication, as employed by bacteriophages. As several components of the metazoan mitochondrial DNA replisome are likely phage-derived, these findings raise the possibility that the rolling circle mtDNA replication mechanism may be ancestral among metazoans.
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Affiliation(s)
- Samantha C. Lewis
- Department of Biology and Interdepartmental Graduate Program in Genetics, Genomics and Bioinformatics, University of California Riverside, Riverside, California, United States of America
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
| | - Priit Joers
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
- Estonian Biocentre, Tartu, Estonia
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jack D. Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Howard T. Jacobs
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
- Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
| | - Bradley C. Hyman
- Department of Biology and Interdepartmental Graduate Program in Genetics, Genomics and Bioinformatics, University of California Riverside, Riverside, California, United States of America
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237
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Mitochondrial dependency in progression of acute myeloid leukemia. Mitochondrion 2015; 21:41-8. [PMID: 25640960 DOI: 10.1016/j.mito.2015.01.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/23/2014] [Accepted: 01/21/2015] [Indexed: 11/20/2022]
Abstract
Acute myeloid leukemia (AML) is a clonal hematopoietic malignant disorder which arises due to dysregulated differentiation, uncontrolled growth and inhibition of apoptosis leading to the accumulation of immature myeloid progenitor in the bone marrow. The heterogeneity of the disease at the molecular and cytogenetic level has led to the identification of several alteration of biological and clinical significance. One of the alterations which have gained attention in recent times is the altered energy and metabolic dependency of cancer originally proposed by Warburg. Mitochondria are important cell organelles regulating cellular energetic level, metabolism and apoptosis which in turn can affect cell proliferation and differentiation, the major manifestations of diseases like AML. In recent times the importance of mitochondrial generated ATP and mitochondrial localized metabolic pathways has been shown to play important role in the progression of AML. These studies have also demonstrated the clinical significance of mitochondrial targets for its effectiveness in combating relapsed or refractory AML. Here we review the importance of the mitochondrial dependency for the progression of AML and the emergence of the mitochondrial molecular targets which holds therapeutic importance.
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238
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Iommarini L, Peralta S, Torraco A, Diaz F. Mitochondrial Diseases Part II: Mouse models of OXPHOS deficiencies caused by defects in regulatory factors and other components required for mitochondrial function. Mitochondrion 2015; 22:96-118. [PMID: 25640959 DOI: 10.1016/j.mito.2015.01.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 01/22/2015] [Indexed: 01/21/2023]
Abstract
Mitochondrial disorders are defined as defects that affect the oxidative phosphorylation system (OXPHOS). They are characterized by a heterogeneous array of clinical presentations due in part to a wide variety of factors required for proper function of the components of the OXPHOS system. There is no cure for these disorders owing to our poor knowledge of the pathogenic mechanisms of disease. To understand the mechanisms of human disease numerous mouse models have been developed in recent years. Here we summarize the features of several mouse models of mitochondrial diseases directly related to those factors affecting mtDNA maintenance, replication, transcription, translation as well as other proteins that are involved in mitochondrial dynamics and quality control which affect mitochondrial OXPHOS function without being intrinsic components of the system. We discuss how these models have contributed to our understanding of mitochondrial diseases and their pathogenic mechanisms.
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Affiliation(s)
- Luisa Iommarini
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Via Irnerio 42, 40128 Bologna, Italy.
| | - Susana Peralta
- Department of Neurology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA.
| | - Alessandra Torraco
- Unit for Neuromuscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Viale di San Paolo, 15 - 00146, Rome, Italy.
| | - Francisca Diaz
- Department of Neurology, University of Miami, Miller School of Medicine, Miami, FL 33136, USA.
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Tan AS, Baty JW, Dong LF, Bezawork-Geleta A, Endaya B, Goodwin J, Bajzikova M, Kovarova J, Peterka M, Yan B, Pesdar EA, Sobol M, Filimonenko A, Stuart S, Vondrusova M, Kluckova K, Sachaphibulkij K, Rohlena J, Hozak P, Truksa J, Eccles D, Haupt LM, Griffiths LR, Neuzil J, Berridge MV. Mitochondrial genome acquisition restores respiratory function and tumorigenic potential of cancer cells without mitochondrial DNA. Cell Metab 2015; 21:81-94. [PMID: 25565207 DOI: 10.1016/j.cmet.2014.12.003] [Citation(s) in RCA: 521] [Impact Index Per Article: 57.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 07/10/2014] [Accepted: 12/09/2014] [Indexed: 10/24/2022]
Abstract
We report that tumor cells without mitochondrial DNA (mtDNA) show delayed tumor growth, and that tumor formation is associated with acquisition of mtDNA from host cells. This leads to partial recovery of mitochondrial function in cells derived from primary tumors grown from cells without mtDNA and a shorter lag in tumor growth. Cell lines from circulating tumor cells showed further recovery of mitochondrial respiration and an intermediate lag to tumor growth, while cells from lung metastases exhibited full restoration of respiratory function and no lag in tumor growth. Stepwise assembly of mitochondrial respiratory (super)complexes was correlated with acquisition of respiratory function. Our findings indicate horizontal transfer of mtDNA from host cells in the tumor microenvironment to tumor cells with compromised respiratory function to re-establish respiration and tumor-initiating efficacy. These results suggest pathophysiological processes for overcoming mtDNA damage and support the notion of high plasticity of malignant cells.
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Affiliation(s)
- An S Tan
- Malaghan Institute of Medical Research, P.O. Box 7060, Wellington 6242, New Zealand
| | - James W Baty
- Malaghan Institute of Medical Research, P.O. Box 7060, Wellington 6242, New Zealand
| | - Lan-Feng Dong
- School of Medical Science, Griffith University, Southport, QLD 4222, Australia
| | | | - Berwini Endaya
- School of Medical Science, Griffith University, Southport, QLD 4222, Australia
| | - Jacob Goodwin
- School of Medical Science, Griffith University, Southport, QLD 4222, Australia
| | - Martina Bajzikova
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Jaromira Kovarova
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Martin Peterka
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Bing Yan
- School of Medical Science, Griffith University, Southport, QLD 4222, Australia
| | | | - Margarita Sobol
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Anatolyj Filimonenko
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Shani Stuart
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD 4059, Australia
| | - Magdalena Vondrusova
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Katarina Kluckova
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | | | - Jakub Rohlena
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Pavel Hozak
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - Jaroslav Truksa
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic
| | - David Eccles
- Malaghan Institute of Medical Research, P.O. Box 7060, Wellington 6242, New Zealand
| | - Larisa M Haupt
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD 4059, Australia
| | - Lyn R Griffiths
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD 4059, Australia
| | - Jiri Neuzil
- School of Medical Science, Griffith University, Southport, QLD 4222, Australia; Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague 142 20, Czech Republic.
| | - Michael V Berridge
- Malaghan Institute of Medical Research, P.O. Box 7060, Wellington 6242, New Zealand.
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240
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Ajaz S, Czajka A, Malik A. Accurate measurement of circulating mitochondrial DNA content from human blood samples using real-time quantitative PCR. Methods Mol Biol 2015; 1264:117-31. [PMID: 25631009 DOI: 10.1007/978-1-4939-2257-4_12] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We describe a protocol to accurately measure the amount of human mitochondrial DNA (MtDNA) in peripheral blood samples which can be modified to quantify MtDNA from other body fluids, human cells, and tissues. This protocol is based on the use of real-time quantitative PCR (qPCR) to quantify the amount of MtDNA relative to nuclear DNA (designated the Mt/N ratio). In the last decade, there have been increasing numbers of studies describing altered MtDNA or Mt/N in circulation in common nongenetic diseases where mitochondrial dysfunction may play a role (for review see Malik and Czajka, Mitochondrion 13:481-492, 2013). These studies are distinct from those looking at genetic mitochondrial disease and are attempting to identify acquired changes in circulating MtDNA content as an indicator of mitochondrial function. However, the methodology being used is not always specific and reproducible. As more than 95 % of the human mitochondrial genome is duplicated in the human nuclear genome, it is important to avoid co-amplification of nuclear pseudogenes. Furthermore, template preparation protocols can also affect the results because of the size and structural differences between the mitochondrial and nuclear genomes. Here we describe how to (1) prepare DNA from blood samples; (2) pretreat the DNA to prevent dilution bias; (3) prepare dilution standards for absolute quantification using the unique primers human mitochondrial genome forward primer (hMitoF3) and human mitochondrial genome reverse primer(hMitoR3) for the mitochondrial genome, and human nuclear genome forward primer (hB2MF1) and human nuclear genome reverse primer (hB2MR1) primers for the human nuclear genome; (4) carry out qPCR for either relative or absolute quantification from test samples; (5) analyze qPCR data; and (6) calculate the sample size to adequately power studies. The protocol presented here is suitable for high-throughput use.
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Affiliation(s)
- Saima Ajaz
- Diabetes Research Group, Faculty of Life Sciences & Medicine, King's College London, Hodgkin Building, Guy's Campus, London Bridge, London, SE1 1UL, UK
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241
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Li L, Yu Q, Liang W. Molecular pathways of mitochondrial dysfunctions: Possible cause of cell death in anesthesia-induced developmental neurotoxicity. Brain Res Bull 2015; 110:14-9. [DOI: 10.1016/j.brainresbull.2014.10.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 10/20/2014] [Accepted: 10/21/2014] [Indexed: 02/05/2023]
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242
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Ferreira A, Serafim TL, Sardão VA, Cunha-Oliveira T. Role of mtDNA-related mitoepigenetic phenomena in cancer. Eur J Clin Invest 2015; 45 Suppl 1:44-9. [PMID: 25524586 DOI: 10.1111/eci.12359] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 10/20/2014] [Indexed: 12/25/2022]
Abstract
BACKGROUND Abnormal mitochondrial function has long been associated with the development and the progression of cancer. Multiple defects in the mitochondrial genome have been reported for various cancers, however the often disregarded mitochondrial epigenetic landscape provides an additional source of deregulation that may contribute to carcinogenesis. DESIGN This article reviews the current understanding of mitochondrial epigenetics and how it may relate to cancer progression and development. Relevant studies were found through electronic databases (Web of Science and PubMed). RESULTS AND CONCLUSIONS The remarkably unexplored field of mitochondrial epigenetics has the potential to shed light on several cancer-related mitochondrial abnormalities. More studies using innovative, genome-wide sequencing technologies are highly warranted to assess whether and how altered mtDNA methylation patterns affect cancer initiation and progression.
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Affiliation(s)
- André Ferreira
- CNC, Center for Neuroscience and Cell Biology, University of Coimbra, Cantanhede, Portugal
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243
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Chatre L, Ricchetti M. mTRIP: an imaging tool to investigate mitochondrial DNA dynamics in physiology and disease at the single-cell resolution. Methods Mol Biol 2015; 1264:133-47. [PMID: 25631010 DOI: 10.1007/978-1-4939-2257-4_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Mitochondrial physiology and metabolism are closely linked to replication and transcription of the genome of the organelle, the mitochondrial DNA (mtDNA). However, the characterization of mtDNA processing is poorly defined at the single-cell level. Here, we describe mTRIP (mitochondrial transcription and replication imaging protocol), an imaging approach based on modified fluorescence in situ hybridization (FISH), which simultaneously reveals mitochondrial structures engaged in mtDNA initiation of replication and global mitochondrial RNA (mtRNA) content at the single-cell level in human cells. In addition, mTRIP can be coupled to immunofluorescence for in situ protein tracking, or to MitoTracker, thereby allowing simultaneous labelling of mtDNA, mtRNA, and proteins or mitochondria, respectively. Altogether, qualitative and quantitative alterations of the dynamics of mtDNA processing are detected by mTRIP in human cells undergoing physiological changes, as well as stress and dysfunction, with a potential for diagnostic of mitochondrial diseases.
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MESH Headings
- Cell Line, Transformed
- DNA Replication
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/isolation & purification
- DNA, Mitochondrial/metabolism
- Genome, Mitochondrial
- Humans
- Image Processing, Computer-Assisted
- Microscopy, Fluorescence/instrumentation
- Microscopy, Fluorescence/methods
- Mitochondrial Diseases/genetics
- Mitochondrial Diseases/metabolism
- Molecular Imaging/instrumentation
- Molecular Imaging/methods
- Nucleic Acid Hybridization/methods
- Single-Cell Analysis/instrumentation
- Single-Cell Analysis/methods
- Transcription, Genetic
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Affiliation(s)
- Laurent Chatre
- Team "Stability of Nuclear and Mitochondrial," Unité de Génétique Moléculaire des Levures, Institut Pasteur, CNRS UMR3525, 25-28 Rue du Dr. Roux, Paris, France,
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244
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Biolistic Transformation of Candida glabrata for Homoplasmic Mitochondrial Genome Transformants. Fungal Biol 2015. [DOI: 10.1007/978-3-319-10142-2_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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245
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Baggio F, Bratic A, Mourier A, Kauppila TES, Tain LS, Kukat C, Habermann B, Partridge L, Larsson NG. Drosophila melanogaster LRPPRC2 is involved in coordination of mitochondrial translation. Nucleic Acids Res 2014; 42:13920-38. [PMID: 25428350 PMCID: PMC4267620 DOI: 10.1093/nar/gku1132] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Members of the pentatricopeptide repeat domain (PPR) protein family bind RNA and are important for post-transcriptional control of organelle gene expression in unicellular eukaryotes, metazoans and plants. They also have a role in human pathology, as mutations in the leucine-rich PPR-containing (LRPPRC) gene cause severe neurodegeneration. We have previously shown that the mammalian LRPPRC protein and its Drosophila melanogaster homolog DmLRPPRC1 (also known as bicoid stability factor) are necessary for mitochondrial translation by controlling stability and polyadenylation of mRNAs. We here report characterization of DmLRPPRC2, a second fruit fly homolog of LRPPRC, and show that it has a predominant mitochondrial localization and interacts with a stem-loop interacting RNA binding protein (DmSLIRP2). Ubiquitous downregulation of DmLrpprc2 expression causes respiratory chain dysfunction, developmental delay and shortened lifespan. Unexpectedly, decreased DmLRPPRC2 expression does not globally affect steady-state levels or polyadenylation of mitochondrial transcripts. However, some mitochondrial transcripts abnormally associate with the mitochondrial ribosomes and some products are dramatically overproduced and other ones decreased, which, in turn, results in severe deficiency of respiratory chain complexes. The function of DmLRPPRC2 thus seems to be to ensure that mitochondrial transcripts are presented to the mitochondrial ribosomes in an orderly fashion to avoid poorly coordinated translation.
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Affiliation(s)
- Francesca Baggio
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Ana Bratic
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Arnaud Mourier
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Timo E S Kauppila
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Luke S Tain
- Department of the Biological Mechanisms of Ageing, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Christian Kukat
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Bianca Habermann
- Department of Computational Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Linda Partridge
- Department of the Biological Mechanisms of Ageing, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne 50931, Germany Department of Laboratory Medicine, Karolinska Institutet, Stockholm 17177, Sweden
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246
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Venø ST, Witt MB, Kulikowicz T, Bohr VA, Stevnsner T. Regulation of the human Suv3 helicase on DNA by inorganic cofactors. Biochimie 2014; 108:160-8. [PMID: 25446650 DOI: 10.1016/j.biochi.2014.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 11/05/2014] [Indexed: 11/19/2022]
Abstract
Mitochondria are essential organelles and consequently proper expression and maintenance of the mitochondrial genome are indispensable for proper cell function. The mitochondrial Suv3 (SUPV3L1) helicase is known to have a central role in mitochondrial RNA metabolism and to be essential for maintenance of mitochondrial DNA stability. Here we have performed biochemical investigations to determine the potential regulation of the human Suv3 (hSuv3) helicase function by inorganic cofactors. We find that hSuv3 helicase and ATPase activity in vitro is strictly dependent on the presence of specific divalent cations. Interestingly, we show that divalent cations and nucleotide concentration have a direct effect on helicase substrate stability. Also, hSuv3 helicase is able to utilize several different nucleotide cofactors including both NTPs and dNTPs. Intriguingly, the potency of the individual nucleotide as energy source for hSuv3 unwinding differed depending on the included divalent cation and nucleotide concentration. At low concentrations, all four NTPs could support helicase activity with varying effectiveness depending on the included divalent cation. However, at higher nucleotide concentrations, only ATP was able to elicit the helicase activity of hSuv3. Consequently, we speculate that the capacity of hSuv3 DNA unwinding activity might be sensitive to the local availability of specific inorganic cofactors.
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Affiliation(s)
- Susanne T Venø
- Danish Center of Molecular Gerontology and Danish Aging Research Center, University of Aarhus, Department of Molecular Biology and Genetics, Aarhus C DK-8000, Denmark
| | - Marie B Witt
- Danish Center of Molecular Gerontology and Danish Aging Research Center, University of Aarhus, Department of Molecular Biology and Genetics, Aarhus C DK-8000, Denmark
| | - Tomasz Kulikowicz
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Tinna Stevnsner
- Danish Center of Molecular Gerontology and Danish Aging Research Center, University of Aarhus, Department of Molecular Biology and Genetics, Aarhus C DK-8000, Denmark.
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247
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Bliksøen M, Baysa A, Eide L, Bjørås M, Suganthan R, Vaage J, Stensløkken KO, Valen G. Mitochondrial DNA damage and repair during ischemia-reperfusion injury of the heart. J Mol Cell Cardiol 2014; 78:9-22. [PMID: 25446179 DOI: 10.1016/j.yjmcc.2014.11.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/10/2014] [Accepted: 11/11/2014] [Indexed: 11/28/2022]
Abstract
Ischemia-reperfusion (IR) injury of the heart generates reactive oxygen species that oxidize macromolecules including mitochondrial DNA (mtDNA). The 8-oxoguanine DNA glycosylase (OGG1) works synergistically with MutY DNA glycosylase (MYH) to maintain mtDNA integrity. Our objective was to study the functional outcome of lacking the repair enzymes OGG1 and MYH after myocardial IR and we hypothesized that OGG1 and MYH are important enzymes to preserve mtDNA and heart function after IR. Ex vivo global ischemia for 30min followed by 10min of reperfusion induced mtDNA damage that was removed within 60min of reperfusion in wild-type mice. After 60min of reperfusion the ogg1(-/-) mice demonstrated increased mtDNA copy number and decreased mtDNA damage removal suggesting that OGG1 is responsible for removal of IR-induced mtDNA damage and copy number regulation. mtDNA damage was not detected in the ogg1(-/-)/myh(-/-), inferring that adenine opposite 8-oxoguanine is an abundant mtDNA lesion upon IR. The level and integrity of mtDNA were restored in all genotypes after 35min of regional ischemia and six week reperfusion with no change in cardiac function. No consistent upregulation of other mitochondrial base excision repair enzymes in any of our knockout models was found. Thus repair of mtDNA oxidative base lesions may not be important for maintenance of cardiac function during IR injury in vivo. This article is part of a Special Issue entitled "Mitochondria: From Basic Mitochondrial Biology to Cardiovascular Disease."
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Affiliation(s)
- M Bliksøen
- Department of Physiology, Institute of Basic Medical Sciences, Norway; Center for Heart Failure Research, University of Oslo, Norway
| | - A Baysa
- Department of Physiology, Institute of Basic Medical Sciences, Norway; Center for Heart Failure Research, University of Oslo, Norway
| | - L Eide
- Department of Medical Biochemistry, University of Oslo, Norway
| | - M Bjørås
- Department of Microbiology, University of Oslo and Oslo University Hospital Rikshospitalet, Norway
| | - R Suganthan
- Department of Microbiology, University of Oslo and Oslo University Hospital Rikshospitalet, Norway
| | - J Vaage
- Department of Emergency Medicine and Intensive Care, University of Oslo and Oslo University Hospital, Ullevål, Oslo, Norway
| | - K O Stensløkken
- Department of Physiology, Institute of Basic Medical Sciences, Norway; Center for Heart Failure Research, University of Oslo, Norway.
| | - G Valen
- Department of Physiology, Institute of Basic Medical Sciences, Norway; Center for Heart Failure Research, University of Oslo, Norway
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248
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249
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Bi R, Zhang W, Yu D, Li X, Wang HZ, Hu QX, Zhang C, Lu W, Ni J, Fang Y, Li T, Yao YG. Mitochondrial DNA haplogroup B5 confers genetic susceptibility to Alzheimer's disease in Han Chinese. Neurobiol Aging 2014; 36:1604.e7-16. [PMID: 25457022 DOI: 10.1016/j.neurobiolaging.2014.10.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Revised: 09/07/2014] [Accepted: 10/10/2014] [Indexed: 02/05/2023]
Abstract
Mitochondrial dysfunction has been widely reported in psychiatric and neurodegenerative diseases. We aimed to investigate the association between matrilineal structures of Han Chinese populations and Alzheimer's disease (AD) by a 2-stage case-control study: A total of 341 AD patients and 435 normal individuals from Southwest China were analyzed for mitochondrial DNA sequence variations and were classified into respective haplogroups. A total of 371 AD patients and 470 normal individuals from East China, as validation samples, were genotyped for the variants defining the risk haplogroup. Haplogroup B5 had a significantly higher frequency in AD patients (7.33%) than in control subjects (3.68%) from Southwest China, and we found a similar pattern of higher frequency of B5 in patients in the case-control sample from East China. In the combined population, association of haplogroup B5 with AD risk was strengthened (p = 0.02; odds ratio = 1.74; 95% confidence interval = 1.10-2.76). In lymphoblastoid cell lines belonging to haplogroup B5a, we observed significantly increased reactive oxygen species and decreased mitochondrial mass. Hela cells with stable expression of the MT-ATP6 gene with B5-defining variant m.8584G>A also showed a significantly decreased mitochondrial function. Taken together, our results indicated that haplogroup B5 conferred genetic susceptibility to AD in Han Chinese, and this effect was most likely mediated by ancient variant m.8584G>A. The predisposing effect of B5 to AD is consistent with the ancestral-susceptibility model of complex diseases.
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Affiliation(s)
- Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Wen Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Dandan Yu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Xiao Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hui-Zhen Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China; School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Qiu-Xiang Hu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chen Zhang
- Division of Mood Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong, University School of Medicine, Shanghai, China
| | - Weihong Lu
- Division of Mood Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong, University School of Medicine, Shanghai, China
| | - Jianliang Ni
- First Geriatric Department, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yiru Fang
- Division of Mood Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong, University School of Medicine, Shanghai, China
| | - Tao Li
- The Mental Health Center & Psychiatric Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China.
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250
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Xu Y, Lu S. Transforming growth factor-β1-induced epithelial to mesenchymal transition increases mitochondrial content in the A549 non-small cell lung cancer cell line. Mol Med Rep 2014; 11:417-21. [PMID: 25323156 DOI: 10.3892/mmr.2014.2678] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 07/30/2014] [Indexed: 11/06/2022] Open
Abstract
The mitochondrial genome DNA copy number is critical for the functional maintenance of the mitochondria and energy acquisition for cell metabolism. Epithelial to mesenchymal transition (EMT) is an important process during embryonic development and has also been hypothesized to exhibit a significant role in cancer cell invasion and metastasis. In the present study, EMT was induced in the A549 non-small cell lung cancer (NSCLC) cell line, using transforming growth factor-β1 (TGF-β1) and changes in mitochondrial content, mitochondrial DNA (mtDNA) copy number and protein cytochrome c (Cyt c) were determined by reverse transcription-quantitative polymerase chain reaction and western blot analysis, respectively. mtDNA copy number and Cyt c protein levels were observed to increase following the induction of EMT in NSCLC cells. Results of the current study indicate that energy metabolism is adapted to facilitate EMT in NSCLC cells.
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Affiliation(s)
- Yunhua Xu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, P.R. China
| | - Shun Lu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, P.R. China
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