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Giulivi C, Wang JY, Hagerman RJ. Artificial neural network applied to fragile X-associated tremor/ataxia syndrome stage diagnosis based on peripheral mitochondrial bioenergetics and brain imaging outcomes. Sci Rep 2022; 12:21382. [PMID: 36496525 PMCID: PMC9741636 DOI: 10.1038/s41598-022-25615-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022] Open
Abstract
No proven prognosis is available for the neurodegenerative disorder fragile X-associated tremor/ataxia syndrome (FXTAS). Artificial neural network analyses (ANN) were used to predict FXTAS progression using data from 127 adults (noncarriers and FMR1 premutation carriers with and without FXTAS) with five outcomes from brain MRI imaging and 22 peripheral bioenergetic outcomes from two cell types. Diagnosis accuracy by ANN predictions ranged from 41.7 to 86.3% (depending on the algorithm used), and those misclassified usually presented a higher FXTAS stage. ANN prediction of FXTAS stages was based on a combination of two imaging findings (white matter hyperintensity and whole-brain volumes adjusted for intracranial volume) and four bioenergetic outcomes. Those at Stage 3 vs. 0-2 showed lower mitochondrial mass, higher oxidative stress, and an altered electron transfer consistent with mitochondrial unfolded protein response activation. Those at Stages 4-5 vs. 3 had higher oxidative stress and glycerol-3-phosphate-linked ATP production, suggesting that targeting mGPDH activity may prevent a worse prognosis. This was confirmed by the bioenergetic improvement of inhibiting mGPDH with metformin in affected fibroblasts. ANN supports the prospect of an unbiased molecular definition in diagnosing FXTAS stages while identifying potential targets for personalized medicine.
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Affiliation(s)
- Cecilia Giulivi
- grid.27860.3b0000 0004 1936 9684Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA USA ,grid.413079.80000 0000 9752 8549MIND Institute, University of California at Davis Medical Center, Sacramento, CA USA
| | - Jun Yi Wang
- grid.413079.80000 0000 9752 8549MIND Institute, University of California at Davis Medical Center, Sacramento, CA USA ,grid.27860.3b0000 0004 1936 9684Center for Mind and Brain, University of California Davis, Davis, CA USA
| | - Randi J. Hagerman
- grid.413079.80000 0000 9752 8549MIND Institute, University of California at Davis Medical Center, Sacramento, CA USA ,grid.413079.80000 0000 9752 8549Department of Pediatrics, University of California at Davis Medical Center, Sacramento, CA USA
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De Benedittis G, Latini A, Colafrancesco S, Priori R, Perricone C, Novelli L, Borgiani P, Ciccacci C. Alteration of Mitochondrial DNA Copy Number and Increased Expression Levels of Mitochondrial Dynamics-Related Genes in Sjögren's Syndrome. Biomedicines 2022; 10:2699. [PMID: 36359219 PMCID: PMC9687724 DOI: 10.3390/biomedicines10112699] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 07/26/2023] Open
Abstract
Sjögren's syndrome (SS) is a chronic autoimmune multifactorial disease characterized by inflammation and lymphocytic infiltration of the exocrine glands. Several studies have highlighted the involvement of oxidative stress in this pathology, suggesting that it could induce mitochondrial dysfunctions. Mitochondria could have a role in inflammatory and immune processes. Since the mitochondrial DNA (mtDNA) copy number could change in response to physiological or environmental stimuli, this study aimed to evaluate possible alterations in the mtDNA copy number in SS. We have analyzed the amount of mtDNA in the peripheral blood of 74 SS patients and 61 healthy controls by qPCR. Then, since mitochondrial fusion and fission play a crucial role in maintaining the number of mitochondria, we investigated the expression variability of the genes most commonly involved in mitochondrial dynamics in a subgroup of SS patients and healthy controls. Interestingly, we observed a highly significant decrease in mtDNA copies in the SS patients compared to healthy controls (p = 1.44 × 10-12). Expression levels of mitochondrial fission factor (MFF), mitofusin-1 (MFN1), and mitochondrial transcription factor A (TFAM) genes were analyzed, showing a statistically significant increase in the expression of MFF (p = 0.003) and TFAM (p = 0.022) in the SS patients compared to healthy controls. These results give further insight into the possible involvement of mitochondrial dysfunctions in SS disease.
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Affiliation(s)
- Giada De Benedittis
- Genetics Section, Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Andrea Latini
- Genetics Section, Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Serena Colafrancesco
- Division of Rheumatology, Department of Clinical Internal, Anaesthesiologic and Cardiovascular Sciences, Sapienza University, 00133 Rome, Italy
| | - Roberta Priori
- Division of Rheumatology, Department of Clinical Internal, Anaesthesiologic and Cardiovascular Sciences, Sapienza University, 00133 Rome, Italy
- UniCamillus—Saint Camillus International University of Health Sciences, 00131 Rome, Italy
| | - Carlo Perricone
- Rheumatology Department of Medicine, University of Perugia, Piazzale Giorgio Menghini 1, 06129 Perugia, Italy
| | - Lucia Novelli
- UniCamillus—Saint Camillus International University of Health Sciences, 00131 Rome, Italy
| | - Paola Borgiani
- Genetics Section, Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Cinzia Ciccacci
- UniCamillus—Saint Camillus International University of Health Sciences, 00131 Rome, Italy
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Orlando A, Chimienti G, Pesce V, Fracasso F, Lezza AMS, Russo F. An In Vitro Study on Mitochondrial Compensatory Response Induced by Gliadin Peptides in Caco-2 Cells. Int J Mol Sci 2019; 20:ijms20081862. [PMID: 30991726 PMCID: PMC6514596 DOI: 10.3390/ijms20081862] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/10/2019] [Accepted: 04/11/2019] [Indexed: 02/07/2023] Open
Abstract
Dietary gliadin may show a broad spectrum of toxicity. The interplay between mitochondria and gliadin-induced oxidative stress has not been thoroughly examined in the intestinal epithelium. In this kinetic study, Caco-2 cells were exposed for 24 h to pepsin-trypsin-digested gliadin, alone or in combination with the antioxidant 2,6-di-tbutyl-p-cresol (BHT), and the effects on mitochondrial biogenesis and mtDNA were studied. Cells ability to recover from stress was determined after 24 h and 48 h of incubation in the culture medium. Gliadin-induced oxidative stress evoked a compensatory response. The stressor triggered a rapid and significant increase of Peroxisome proliferator-activated receptor γ coactivator-1alpha (PGC-1α) and Peroxiredoxin III (PrxIII) proteins, and mtDNA amount. As for the effects of gliadin on mtDNA integrity, strand breaks, abasic sites, and modified bases were analyzed in three mtDNA regions. D-loop appeared a more fragile target than Ori-L and ND1/ND2. The temporal trend of the damage at D-loop paralleled that of the amount of mtDNA. Overall, a trend toward control values was shown 48 h after gliadin exposure. Finally, BHT was able to counteract the effects of gliadin. Results from this study highlighted the effects of gliadin-induced oxidative stress on mitochondria, providing valuable evidence that might improve the knowledge of the pathophysiology of gluten-related disorders.
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Affiliation(s)
- Antonella Orlando
- Laboratory of Nutritional Pathophysiology, National Institute of Gastroenterology "S. de Bellis", Research Hospital, 70013 Castellana Grotte (Bari), Italy.
| | - Guglielmina Chimienti
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70100 Bari, Italy.
| | - Vito Pesce
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70100 Bari, Italy.
| | - Flavio Fracasso
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70100 Bari, Italy.
| | - Angela Maria Serena Lezza
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Via Orabona 4, 70100 Bari, Italy.
| | - Francesco Russo
- Laboratory of Nutritional Pathophysiology, National Institute of Gastroenterology "S. de Bellis", Research Hospital, 70013 Castellana Grotte (Bari), Italy.
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Cobley JN, Fiorello ML, Bailey DM. 13 reasons why the brain is susceptible to oxidative stress. Redox Biol 2018; 15:490-503. [PMID: 29413961 PMCID: PMC5881419 DOI: 10.1016/j.redox.2018.01.008] [Citation(s) in RCA: 659] [Impact Index Per Article: 109.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 12/12/2022] Open
Abstract
The human brain consumes 20% of the total basal oxygen (O2) budget to support ATP intensive neuronal activity. Without sufficient O2 to support ATP demands, neuronal activity fails, such that, even transient ischemia is neurodegenerative. While the essentiality of O2 to brain function is clear, how oxidative stress causes neurodegeneration is ambiguous. Ambiguity exists because many of the reasons why the brain is susceptible to oxidative stress remain obscure. Many are erroneously understood as the deleterious result of adventitious O2 derived free radical and non-radical species generation. To understand how many reasons underpin oxidative stress, one must first re-cast free radical and non-radical species in a positive light because their deliberate generation enables the brain to achieve critical functions (e.g. synaptic plasticity) through redox signalling (i.e. positive functionality). Using free radicals and non-radical derivatives to signal sensitises the brain to oxidative stress when redox signalling goes awry (i.e. negative functionality). To advance mechanistic understanding, we rationalise 13 reasons why the brain is susceptible to oxidative stress. Key reasons include inter alia unsaturated lipid enrichment, mitochondria, calcium, glutamate, modest antioxidant defence, redox active transition metals and neurotransmitter auto-oxidation. We review RNA oxidation as an underappreciated cause of oxidative stress. The complex interplay between each reason dictates neuronal susceptibility to oxidative stress in a dynamic context and neural identity dependent manner. Our discourse sets the stage for investigators to interrogate the biochemical basis of oxidative stress in the brain in health and disease.
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Affiliation(s)
- James Nathan Cobley
- Free Radical Laboratory, Departments of Diabetes and Cardiovascular Sciences, Centre for Health Sciences, University of the Highlands and Islands, Inverness IV2 3HJ, UK.
| | - Maria Luisa Fiorello
- Free Radical Laboratory, Departments of Diabetes and Cardiovascular Sciences, Centre for Health Sciences, University of the Highlands and Islands, Inverness IV2 3HJ, UK
| | - Damian Miles Bailey
- Neurovascular Research Laboratory, Faculty of Life Sciences and Education, University of South Wales, Wales, CF37 4AT, UK
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Pastukh VM, Gorodnya OM, Gillespie MN, Ruchko MV. Regulation of mitochondrial genome replication by hypoxia: The role of DNA oxidation in D-loop region. Free Radic Biol Med 2016; 96:78-88. [PMID: 27091693 PMCID: PMC4912408 DOI: 10.1016/j.freeradbiomed.2016.04.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 03/18/2016] [Accepted: 04/14/2016] [Indexed: 02/04/2023]
Abstract
Mitochondria of mammalian cells contain multiple copies of mitochondrial (mt) DNA. Although mtDNA copy number can fluctuate dramatically depending on physiological and pathophysiologic conditions, the mechanisms regulating mitochondrial genome replication remain obscure. Hypoxia, like many other physiologic stimuli that promote growth, cell proliferation and mitochondrial biogenesis, uses reactive oxygen species as signaling molecules. Emerging evidence suggests that hypoxia-induced transcription of nuclear genes requires controlled DNA damage and repair in specific sequences in the promoter regions. Whether similar mechanisms are operative in mitochondria is unknown. Here we test the hypothesis that controlled oxidative DNA damage and repair in the D-loop region of the mitochondrial genome are required for mitochondrial DNA replication and transcription in hypoxia. We found that hypoxia had little impact on expression of mitochondrial proteins in pulmonary artery endothelial cells, but elevated mtDNA content. The increase in mtDNA copy number was accompanied by oxidative modifications in the D-loop region of the mitochondrial genome. To investigate the role of this sequence-specific oxidation of mitochondrial genome in mtDNA replication, we overexpressed mitochondria-targeted 8-oxoguanine glycosylase Ogg1 in rat pulmonary artery endothelial cells, enhancing the mtDNA repair capacity of transfected cells. Overexpression of Ogg1 resulted in suppression of hypoxia-induced mtDNA oxidation in the D-loop region and attenuation of hypoxia-induced mtDNA replication. Ogg1 overexpression also reduced binding of mitochondrial transcription factor A (TFAM) to both regulatory and coding regions of the mitochondrial genome without altering total abundance of TFAM in either control or hypoxic cells. These observations suggest that oxidative DNA modifications in the D-loop region during hypoxia are important for increased TFAM binding and ensuing replication of the mitochondrial genome.
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Affiliation(s)
- Viktor M Pastukh
- Department of Pharmacology and Center for Lung Biology, University of South Alabama College of Medicine, Mobile, AL 36688, USA.
| | - Olena M Gorodnya
- Department of Pharmacology and Center for Lung Biology, University of South Alabama College of Medicine, Mobile, AL 36688, USA.
| | - Mark N Gillespie
- Department of Pharmacology and Center for Lung Biology, University of South Alabama College of Medicine, Mobile, AL 36688, USA.
| | - Mykhaylo V Ruchko
- Department of Pharmacology and Center for Lung Biology, University of South Alabama College of Medicine, Mobile, AL 36688, USA.
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Wong S, Napoli E, Krakowiak P, Tassone F, Hertz-Picciotto I, Giulivi C. Role of p53, Mitochondrial DNA Deletions, and Paternal Age in Autism: A Case-Control Study. Pediatrics 2016; 137:peds.2015-1888. [PMID: 27033107 PMCID: PMC4811307 DOI: 10.1542/peds.2015-1888] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/06/2016] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The tumor suppressor p53 responds to a variety of environmental stressors by regulating cell cycle arrest, apoptosis, senescence, DNA repair, bioenergetics and mitochondrial DNA (mtDNA) copy number maintenance. Developmental abnormalities have been reported in p53-deficient mice, and altered p53 and p53-associated pathways in autism (AU). Furthermore, via the Pten-p53 crosstalk, Pten haploinsufficient-mice have autisticlike behavior accompanied by brain mitochondrial dysfunction with accumulation of mtDNA deletions. METHODS mtDNA copy number and deletions, and p53 gene copy ratios were evaluated in peripheral blood monocytic cells from children aged 2-5 years with AU (n = 66), race-, gender-, and age-matched typically neurodeveloping children (n = 46), and both parents from each diagnostic group, recruited by the Childhood Autism Risk from Genes and Environment study at the University of California, Davis. RESULTS mtDNA deletions and higher p53 gene copy ratios were more common in children with AU and their fathers. The incidence of mtDNA deletions in fathers of children with AU was increased 1.9-fold over fathers of typically neurodeveloping children, suggesting a role for deficient DNA repair capacity not driven by paternal age. Deletions in mtDNA and altered p53 gene copy ratios seem to result from genetics (children with severity scores ≥8) and/or act in concert with environmental factors (children with 6-7 severity scores). CONCLUSIONS Given pro- and antioxidant activities of p53, and associations of genomic instability with disorders other than AU, our study suggests a link between DNA repair capacity, genomic instability in the 17p13.1 region influenced by environmental triggers, and AU diagnosis.
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Affiliation(s)
- Sarah Wong
- Department of Molecular Biosciences, School of Veterinary Medicine
| | - Eleonora Napoli
- Department of Molecular Biosciences, School of Veterinary Medicine
| | | | - Flora Tassone
- Biochemistry and Molecular Medicine, School of Medicine, and,Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, Davis, California
| | - Irva Hertz-Picciotto
- Departments of Public Health Sciences and,Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, Davis, California
| | - Cecilia Giulivi
- Department of Molecular Biosciences, School of Veterinary Medicine, Medical Investigations of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, Davis, California
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Picca A, Lezza AMS. Regulation of mitochondrial biogenesis through TFAM-mitochondrial DNA interactions: Useful insights from aging and calorie restriction studies. Mitochondrion 2015; 25:67-75. [PMID: 26437364 DOI: 10.1016/j.mito.2015.10.001] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/24/2015] [Accepted: 10/01/2015] [Indexed: 11/24/2022]
Abstract
Mitochondrial biogenesis is regulated to adapt mitochondrial population to cell energy demands. Mitochondrial transcription factor A (TFAM) performs several functions for mtDNA and interactions between TFAM and mtDNA participate to regulation of mitochondrial biogenesis. Such interactions are modulated through different mechanisms: regulation of TFAM expression and turnover, modulation of TFAM binding activity to mtDNA through post-translational modifications and differential affinity of TFAM, occurrence of TFAM sliding on mtDNA filaments and of cooperative binding among TFAM molecules, modulation of protein-protein interactions. The tissue-specific regulation of mitochondrial biogenesis in aging and calorie restriction (CR) highlights the relevance of modulation of TFAM-mtDNA interactions.
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Affiliation(s)
- Anna Picca
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona, 4, 70125, Bari, Italy
| | - Angela Maria Serena Lezza
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona, 4, 70125, Bari, Italy.
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8
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Gleave JA, Perri PD, Nash JE. Mitochondrial dysfunction in Parkinson’s disease: a possible target for neuroprotection. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11515-014-1337-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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10
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Gebhard D, Matt K, Burger K, Bergemann J. Shortwave UV-Induced Damage as Part of the Solar Damage Spectrum Is Not a Major Contributor to Mitochondrial Dysfunction. J Biochem Mol Toxicol 2014; 28:256-62. [DOI: 10.1002/jbt.21561] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 02/07/2014] [Accepted: 02/11/2014] [Indexed: 01/22/2023]
Affiliation(s)
- Daniel Gebhard
- Department of Life Sciences; Albstadt-Sigmaringen University of Applied Sciences; 72488 Sigmaringen Germany
| | - Katja Matt
- Department of Life Sciences; Albstadt-Sigmaringen University of Applied Sciences; 72488 Sigmaringen Germany
| | - Katharina Burger
- Department of Life Sciences; Albstadt-Sigmaringen University of Applied Sciences; 72488 Sigmaringen Germany
| | - Jörg Bergemann
- Department of Life Sciences; Albstadt-Sigmaringen University of Applied Sciences; 72488 Sigmaringen Germany
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11
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Shi CM, Xu GF, Yang L, Fu ZY, Chen L, Fu HL, Shen YH, Zhu L, Ji CB, Guo XR. Overexpression of TFAM protects 3T3-L1 adipocytes from NYGGF4 (PID1) overexpression-induced insulin resistance and mitochondrial dysfunction. Cell Biochem Biophys 2014; 66:489-97. [PMID: 23274913 DOI: 10.1007/s12013-012-9496-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
NYGGF4, also known as phosphotyrosine interaction domain containing 1(PID1), is a recently discovered gene which is involved in obesity-related insulin resistance (IR) and mitochondrial dysfunction. We aimed to further elucidate the effects and mechanisms underlying NYGGF4-induced IR by investigating the effect of overexpressing mitochondrial transcription factor A (TFAM), which is essential for mitochondrial DNA transcription and replication, on NYGGF4-induced IR and mitochondrial abnormalities in 3T3-L1 adipocytes. Overexpression of TFAM increased the mitochondrial copy number and ATP content in both control 3T3-L1 adipocytes and NYGGF4-overexpressing adipocytes. Reactive oxygen species (ROS) production was enhanced in NYGGF4-overexpressing adipocytes and reduced in TFAM-overexpressing adipocytes; co-overexpression of TFAM significantly attenuated ROS production in NYGGF4-overexpressing adipocytes. However, overexpression of TFAM did not affect the mitochondrial transmembrane potential (ΔΨm) in control 3T3-L1 adipocytes or NYGGF4-overexpressing adipocytes. In addition, co-overexpression of TFAM-enhanced insulin-stimulated glucose uptake by increasing Glucose transporter type 4 (GLUT4) translocation to the PM in NYGGF4-overexpressing adipocytes. Overexpression of NYGGF4 significantly inhibited tyrosine phosphorylation of Insulin receptor substrate 1 (IRS-1) and serine phosphorylation of Akt, whereas overexpression of TFAM strongly induced phosphorylation of IRS-1 and Akt in NYGGF4-overexpressing adipocytes. This study demonstrates that NYGGF4 plays a role in IR by impairing mitochondrial function, and that overexpression of TFAM can restore mitochondrial function to normal levels in NYGGF4-overexpressing adipocytes via activation of the IRS-1/PI3K/Akt signaling pathway.
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Affiliation(s)
- Chun-Mei Shi
- State Key Laboratory of Reproductive Medicine, Department of Pediatrics, Nanjing Maternity and Child Health Hospital Affiliated to Nanjing Medical University, Nanjing, China
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Gaweda-Walerych K, Zekanowski C. The impact of mitochondrial DNA and nuclear genes related to mitochondrial functioning on the risk of Parkinson's disease. Curr Genomics 2014; 14:543-59. [PMID: 24532986 PMCID: PMC3924249 DOI: 10.2174/1389202914666131210211033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 07/30/2013] [Accepted: 08/29/2013] [Indexed: 12/21/2022] Open
Abstract
Mitochondrial dysfunction and oxidative stress are the major factors implicated in Parkinson’s disease (PD)
pathogenesis. The maintenance of healthy mitochondria is a very complex process coordinated bi-genomically. Here, we
review association studies on mitochondrial haplogroups and subhaplogroups, discussing the underlying molecular
mechanisms. We also focus on variation in the nuclear genes (NDUFV2, PGC-1alpha, HSPA9, LRPPRC, MTIF3,
POLG1, and TFAM encoding NADH dehydrogenase (ubiquinone) flavoprotein 2, peroxisome proliferator-activated receptor
gamma coactivator 1-alpha, mortalin, leucine-rich pentatricopeptide repeat containing protein, translation initiation
factor 3, mitochondrial DNA polymerase gamma, and mitochondrial transcription factor A, respectively) primarily linked
to regulation of mitochondrial functioning that recently have been associated with PD risk. Possible interactions between
mitochondrial and nuclear genetic variants and related proteins are discussed.
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Affiliation(s)
- Katarzyna Gaweda-Walerych
- Laboratory of Neurogenetics, Mossakowski Medical Research Centre, Polish Academy of Sciences, Pawinskiego 5 str., 02-106 Warszawa, Poland
| | - Cezary Zekanowski
- Laboratory of Neurogenetics, Mossakowski Medical Research Centre, Polish Academy of Sciences, Pawinskiego 5 str., 02-106 Warszawa, Poland
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Genome-wide expression profiling and functional characterization of SCA28 lymphoblastoid cell lines reveal impairment in cell growth and activation of apoptotic pathways. BMC Med Genomics 2013; 6:22. [PMID: 23777634 PMCID: PMC3689607 DOI: 10.1186/1755-8794-6-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 06/05/2013] [Indexed: 11/10/2022] Open
Abstract
Background SCA28 is an autosomal dominant ataxia associated with AFG3L2 gene mutations. We performed a whole genome expression profiling using lymphoblastoid cell lines (LCLs) from four SCA28 patients and six unrelated healthy controls matched for sex and age. Methods Gene expression was evaluated with the Affymetrix GeneChip Human Genome U133A 2.0 Arrays and data were validated by real-time PCR. Results We found 66 genes whose expression was statistically different in SCA28 LCLs, 35 of which were up-regulated and 31 down-regulated. The differentially expressed genes were clustered in five functional categories: (1) regulation of cell proliferation; (2) regulation of programmed cell death; (3) response to oxidative stress; (4) cell adhesion, and (5) chemical homeostasis. To validate these data, we performed functional experiments that proved an impaired SCA28 LCLs growth compared to controls (p < 0.005), an increased number of cells in the G0/G1 phase (p < 0.001), and an increased mortality because of apoptosis (p < 0.05). We also showed that respiratory chain activity and reactive oxygen species levels was not altered, although lipid peroxidation in SCA28 LCLs was increased in basal conditions (p < 0.05). We did not detect mitochondrial DNA large deletions. An increase of TFAM, a crucial protein for mtDNA maintenance, and of DRP1, a key regulator of mitochondrial dynamic mechanism, suggested an alteration of fission/fusion pathways. Conclusions Whole genome expression profiling, performed on SCA28 LCLs, allowed us to identify five altered functional categories that characterize the SCA28 LCLs phenotype, the first reported in human cells to our knowledge.
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U-turn DNA bending by human mitochondrial transcription factor A. Curr Opin Struct Biol 2013; 23:116-24. [PMID: 23333034 DOI: 10.1016/j.sbi.2012.12.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 12/19/2012] [Accepted: 12/20/2012] [Indexed: 02/03/2023]
Abstract
Transcription factor A (TFAM) is involved in the transcription regulation, maintenance and compaction of the mitochondrial genome. Recent structural data on TFAM showed its mode of operation and clarified previous biochemical and genetic results. In solution, TFAM is highly dynamic. According to crystal structures of its complex with the cognate light-strand promoter (LSP) binding sequence, it intertwines and dramatically bends DNA, thereby allowing interactions with the transcription initiation machinery. Recent studies have shown TFAM sliding on non-specific DNA, which induces compaction by increasing DNA flexibility. Finally, the structural localization of disease-related TFAM mutations suggests functional impairment at the molecular level.
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Napoli E, Ross-Inta C, Wong S, Hung C, Fujisawa Y, Sakaguchi D, Angelastro J, Omanska-Klusek A, Schoenfeld R, Giulivi C. Mitochondrial dysfunction in Pten haplo-insufficient mice with social deficits and repetitive behavior: interplay between Pten and p53. PLoS One 2012; 7:e42504. [PMID: 22900024 PMCID: PMC3416855 DOI: 10.1371/journal.pone.0042504] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 07/09/2012] [Indexed: 11/30/2022] Open
Abstract
Etiology of aberrant social behavior consistently points to a strong polygenetic component involved in fundamental developmental pathways, with the potential of being enhanced by defects in bioenergetics. To this end, the occurrence of social deficits and mitochondrial outcomes were evaluated in conditional Pten (Phosphatase and tensin homolog) haplo-insufficient mice, in which only one allele was selectively knocked-out in neural tissues. Pten mutations have been linked to Alzheimer's disease and syndromic autism spectrum disorders, among others. By 4–6 weeks of age, Pten insufficiency resulted in the increase of several mitochondrial Complex activities (II–III, IV and V) not accompanied by increases in mitochondrial mass, consistent with an activation of the PI3K/Akt pathway, of which Pten is a negative modulator. At 8–13 weeks of age, Pten haplo-insufficient mice did not show significant behavioral abnormalities or changes in mitochondrial outcomes, but by 20–29 weeks, they displayed aberrant social behavior (social avoidance, failure to recognize familiar mouse, and repetitive self-grooming), macrocephaly, increased oxidative stress, decreased cytochrome c oxidase (CCO) activity (50%) and increased mtDNA deletions in cerebellum and hippocampus. Mitochondrial dysfunction was the result of a downregulation of p53-signaling pathway evaluated by lower protein expression of p21 (65% of controls) and the CCO chaperone SCO2 (47% of controls), two p53-downstream targets. This mechanism was confirmed in Pten-deficient striatal neurons and, HCT 116 cells with different p53 gene dosage. These results suggest a unique pathogenic mechanism of the Pten-p53 axis in mice with aberrant social behavior: loss of Pten (via p53) impairs mitochondrial function elicited by an early defective assembly of CCO and later enhanced by the accumulation of mtDNA deletions. Consistent with our results, (i) SCO2 deficiency and/or CCO activity defects have been reported in patients with learning disabilities including autism and (ii) mutated proteins in ASD have been found associated with p53-signaling pathways.
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Affiliation(s)
- Eleonora Napoli
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Catherine Ross-Inta
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Sarah Wong
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Connie Hung
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Yasuko Fujisawa
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Danielle Sakaguchi
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - James Angelastro
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Alicja Omanska-Klusek
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Robert Schoenfeld
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Cecilia Giulivi
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
- Medical Investigations of Neurodevelopmental Disorders Institute, School of Medicine, University of California Davis, Davis, California, United States of America
- * E-mail:
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16
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Pohjoismäki JLO, Boettger T, Liu Z, Goffart S, Szibor M, Braun T. Oxidative stress during mitochondrial biogenesis compromises mtDNA integrity in growing hearts and induces a global DNA repair response. Nucleic Acids Res 2012; 40:6595-607. [PMID: 22508755 PMCID: PMC3413112 DOI: 10.1093/nar/gks301] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cardiomyocyte development in mammals is characterized by a transition from hyperplastic to hypertrophic growth soon after birth. The rise of cardiomyocyte cell mass in postnatal life goes along with a proportionally bigger increase in the mitochondrial mass in response to growing energy requirements. Relatively little is known about the molecular processes regulating mitochondrial biogenesis and mitochondrial DNA (mtDNA) maintenance during developmental cardiac hypertrophy. Genome-wide transcriptional profiling revealed the activation of transcriptional regulatory circuits controlling mitochondrial biogenesis in growing rat hearts. In particular, we detected a specific upregulation of factors involved in mtDNA expression and translation. More surprisingly, we found a specific upregulation of DNA repair proteins directly linked to increased oxidative damage during heart mitochondrial biogenesis, but only relatively minor changes in the mtDNA replication machinery. Our study paves the way for improved understanding of mitochondrial biogenesis, mtDNA maintenance and physiological adaptation processes in the heart and provides the first evidence for the recruitment of nucleotide excision repair proteins to mtDNA in cardiomyocytes upon DNA damage.
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Affiliation(s)
- Jaakko L O Pohjoismäki
- Department of Cardiac Development and Remodelling, Max-Planck-Institute for Heart and Lung Research, Ludwigstrasse 43, 61231 Bad Nauheim, Germany.
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17
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Lane N. Mitonuclear match: optimizing fitness and fertility over generations drives ageing within generations. Bioessays 2011; 33:860-9. [PMID: 21922504 DOI: 10.1002/bies.201100051] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Many conserved eukaryotic traits, including apoptosis, two sexes, speciation and ageing, can be causally linked to a bioenergetic requirement for mitochondrial genes. Mitochondrial genes encode proteins involved in cell respiration, which interact closely with proteins encoded by nuclear genes. Functional respiration requires the coadaptation of mitochondrial and nuclear genes, despite divergent tempi and modes of evolution. Free-radical signals emerge directly from the biophysics of mosaic respiratory chains encoded by two genomes prone to mismatch, with apoptosis being the default penalty for compromised respiration. Selection for genomic matching is facilitated by two sexes, and optimizes fitness, adaptability and fertility in youth. Mismatches cause infertility, low fitness, hybrid breakdown, and potentially speciation. The dynamics of selection for mitonuclear function optimize fitness over generations, but the same selective processes also operate within generations, driving ageing and age-related diseases. This coherent view of eukaryotic energetics offers striking insights into infertility and age-related diseases.
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Affiliation(s)
- Nick Lane
- Department of Genetics, Evolution and Environment, University College London, London, UK.
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18
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Napoli E, Ross-Inta C, Wong S, Omanska-Klusek A, Barrow C, Iwahashi C, Garcia-Arocena D, Sakaguchi D, Berry-Kravis E, Hagerman R, Hagerman PJ, Giulivi C. Altered zinc transport disrupts mitochondrial protein processing/import in fragile X-associated tremor/ataxia syndrome. Hum Mol Genet 2011; 20:3079-92. [PMID: 21558427 DOI: 10.1093/hmg/ddr211] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Fragile X-associated tremor/ataxia syndrome (FXTAS) is a late-onset neurodegenerative disorder that affects individuals who are carriers of small CGG premutation expansions in the fragile X mental retardation 1 (FMR1) gene. Mitochondrial dysfunction was observed as an incipient pathological process occurring in individuals who do not display overt features of FXTAS (1). Fibroblasts from premutation carriers had lower oxidative phosphorylation capacity (35% of controls) and Complex IV activity (45%), and higher precursor-to-mature ratios (P:M) of nDNA-encoded mitochondrial proteins (3.1-fold). However, fibroblasts from carriers with FXTAS symptoms presented higher FMR1 mRNA expression (3-fold) and lower Complex V (38%) and aconitase activities (43%). Higher P:M of ATPase β-subunit (ATPB) and frataxin were also observed in cortex from patients that died with FXTAS symptoms. Biochemical findings observed in FXTAS cells (lower mature frataxin, lower Complex IV and aconitase activities) along with common phenotypic traits shared by Friedreich's ataxia and FXTAS carriers (e.g. gait ataxia, loss of coordination) are consistent with a defective iron homeostasis in both diseases. Higher P:M, and lower ZnT6 and mature frataxin protein expression suggested defective zinc and iron metabolism arising from altered ZnT protein expression, which in turn impairs the activity of mitochondrial Zn-dependent proteases, critical for the import and processing of cytosolic precursors, such as frataxin. In support of this hypothesis, Zn-treated fibroblasts showed a significant recovery of ATPB P:M, ATPase activity and doubling time, whereas Zn and desferrioxamine extended these recoveries and rescued Complex IV activity.
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Affiliation(s)
- Eleonora Napoli
- Department of Molecular Biosciences, School of Veterinary Medicine, School of Medicine, University of California Davis, Davis, CA 95616, USA
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19
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Liu P, Demple B. DNA repair in mammalian mitochondria: Much more than we thought? ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2010; 51:417-426. [PMID: 20544882 DOI: 10.1002/em.20576] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
For many years, the repair of most damage in mitochondrial DNA (mtDNA) was thought limited to short-patch base excision repair (SP-BER), which replaces a single nucleotide by the sequential action of DNA glycosylases, an apurinic/apyrimidinic (AP) endonuclease, the mitochondrial DNA polymerase gamma, an abasic lyase activity, and mitochondrial DNA ligase. However, the likely array of lesions inflicted on mtDNA by oxygen radicals and the possibility of replication errors and disruptions indicated that such a restricted repair repertoire would be inadequate. Recent studies have considerably expanded our knowledge of mtDNA repair to include long-patch base excision repair (LP-BER), mismatch repair, and homologous recombination and nonhomologous end-joining. In addition, elimination of mutagenic 8-oxodeoxyguanosine triphosphate (8-oxodGTP) helps prevent cell death due to the accumulation of this oxidation product in mtDNA. Although it was suspected for many years that irreparably damaged mtDNA might be targeted for degradation, only recently was clear evidence provided for this hypothesis. Therefore, multiple DNA repair pathways and controlled degradation of mtDNA function together to maintain the integrity of mitochondrial genome.
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Affiliation(s)
- Pingfang Liu
- Department of Radiation Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
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20
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Gaweda-Walerych K, Safranow K, Maruszak A, Bialecka M, Klodowska-Duda G, Czyzewski K, Slawek J, Rudzinska M, Styczynska M, Opala G, Drozdzik M, Kurzawski M, Szczudlik A, Canter JA, Barcikowska M, Zekanowski C. Mitochondrial transcription factor A variants and the risk of Parkinson's disease. Neurosci Lett 2010; 469:24-9. [DOI: 10.1016/j.neulet.2009.11.037] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Accepted: 11/12/2009] [Indexed: 10/20/2022]
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21
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Rebelo AP, Williams SL, Moraes CT. In vivo methylation of mtDNA reveals the dynamics of protein-mtDNA interactions. Nucleic Acids Res 2009; 37:6701-15. [PMID: 19740762 PMCID: PMC2777446 DOI: 10.1093/nar/gkp727] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To characterize the organization of mtDNA–protein complexes (known as nucleoids) in vivo, we have probed the mtDNA surface exposure using site-specific DNA methyltransferases targeted to the mitochondria. We have observed that DNA methyltransferases have different accessibility to different sites on the mtDNA based on the levels of protein occupancy. We focused our studies on selected regions of mtDNA that are believed to be major regulatory regions involved in transcription and replication. The transcription termination region (TERM) within the tRNALeu(UUR) gene was consistently and strongly protected from methylation, suggesting frequent and high affinity binding of mitochondrial transcription termination factor 1 (mTERF1) to the site. Protection from methylation was also observed in other regions of the mtDNA, including the light and heavy strand promoters (LSP, HSP) and the origin of replication of the light strand (OL). Manipulations aiming at increasing or decreasing the levels of the mitochondrial transcription factor A (TFAM) led to decreased in vivo methylation, whereas manipulations that stimulated mtDNA replication led to increased methylation. We also analyzed the effect of ATAD3 and oxidative stress in mtDNA exposure. Our data provide a map of human mtDNA accessibility and demonstrate that nucleoids are dynamically associated with proteins.
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Affiliation(s)
- Adriana P Rebelo
- Department of Cell Biology and Anatomy, University of Miami School of Medicine, Miami, FL 33136, USA
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22
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Jeng JY, Yeh TS, Lee JW, Lin SH, Fong TH, Hsieh RH. Maintenance of mitochondrial DNA copy number and expression are essential for preservation of mitochondrial function and cell growth. J Cell Biochem 2008; 103:347-57. [PMID: 18072287 DOI: 10.1002/jcb.21625] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To examine whether a reduction in the mtDNA level will compromise mitochondrial biogenesis and mitochondrial function, we created a cell model with depleted mtDNA. Stable transfection of small interfering (si)RNA of mitochondrial transcription factor A (Tfam) was used to interfere with Tfam gene expression. Selected stable clones showed 60-95% reduction in Tfam gene expression and 50-90% reduction in cytochrome b (Cyt b) gene expression. Tfam gene knockdown clones also showed decreased mtDNA-encoded cytochrome c oxidase subunit I (COX I) protein expression. However, no significant differences in protein expression were observed in nuclear DNA (nDNA)-encoded mitochondrial respiratory enzyme subunits. The cell morphology changed from a rhombus-like to a spindle-like form as determined in clones with decreased expressions of Tfam, mtRNA, and mitochondrial proteins. The mitochondrial respiratory enzyme activities and ATP production in such clones were significantly lower. The proportions of mtDNA mutations including 8-hydroxy-2'-deoxyguanosine (8-OHdG), a 4,977-bp deletion, and a 3,243-point mutation were also examined in these clones. No obvious increase in mtDNA mutations was observed in mitochondrial dysfunctional cell clones. The mitochondrial respiratory activity and ATP production ability recovered in cells with increased mtDNA levels after removal of the specific siRNA treatment. These experimental results provide direct evidence to substantiate that downregulation of mtDNA copy number and expression may compromise mitochondrial function and subsequent cell growth and morphology.
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Affiliation(s)
- Jaan-Yeh Jeng
- Department of General Surgery, Cathay General Hospital, Taipei, Taiwan, Republic of China
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23
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Gasiev AI, Shaikhaev GO. Lesions of the mitochondrial genome and ways of its preservation. RUSS J GENET+ 2008. [DOI: 10.1134/s1022795408040017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Ohgaki K, Kanki T, Fukuoh A, Kurisaki H, Aoki Y, Ikeuchi M, Kim SH, Hamasaki N, Kang D. The C-terminal Tail of Mitochondrial Transcription Factor A Markedly Strengthens its General Binding to DNA. ACTA ACUST UNITED AC 2006; 141:201-11. [PMID: 17167045 DOI: 10.1093/jb/mvm020] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Mitochondrial transcription factor A (TFAM) contains a basic C-terminal tail which is essential for the promoter-specific transcription. TFAM is also a major component of a protein-mitochondrial DNA (mtDNA) complex, called nucleoid, as a non-specific DNA-binding protein. However, little is known about a role of the C-tail in the nucleoid. Overexpression of full-length TFAM decreased the amount of a D-loop form of mtDNA in cells, while overexpression of TFAM lacking its C-tail (TFAM-DeltaC) did not, suggesting that the C-tail is involved in destabilization or formation of the D-loop. An mRNA for mtDNA-derived ND1 was hardly decreased in the former but rather decreased in the latter. Given that the D-loop formation is coupled with the transcription, the decrease in the D-loop is likely due to its destabilization. The recombinant full-length TFAM much strongly unwound DNA than TFAM-DeltaC, which is consistent with the above idea because D-loop is resolved by unwinding of the supercoiling state. Notably, truncation of the C-tail decreased DNA-binding activity of TFAM by three orders of magnitude. Thus, the C-terminal tail of TFAM is important for the strong general binding to mtDNA. This strong DNA-binding conferred by the C-tail may play an important role in the nucleoid structure.
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Affiliation(s)
- Kippei Ohgaki
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
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25
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Pohjoismäki JLO, Wanrooij S, Hyvärinen AK, Goffart S, Holt IJ, Spelbrink JN, Jacobs HT. Alterations to the expression level of mitochondrial transcription factor A, TFAM, modify the mode of mitochondrial DNA replication in cultured human cells. Nucleic Acids Res 2006; 34:5815-28. [PMID: 17062618 PMCID: PMC1635303 DOI: 10.1093/nar/gkl703] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Mitochondrial transcription factor A (TFAM) is an abundant mitochondrial protein of the HMG superfamily, with various putative roles in mitochondrial DNA (mtDNA) metabolism. In this study we have investigated the effects on mtDNA replication of manipulating TFAM expression in cultured human cells. Mammalian mtDNA replication intermediates (RIs) fall into two classes, whose mechanistic relationship is not properly understood. One class is characterized by extensive RNA incorporation on the lagging strand, whereas the other has the structure of products of conventional, strand-coupled replication. TFAM overexpression increased the overall abundance of RIs and shifted them substantially towards those of the conventional, strand-coupled type. The shift was most pronounced in the rDNA region and at various replication pause sites and was accompanied by a drop in the relative amount of replication-termination intermediates, a substantial reduction in mitochondrial transcripts, mtDNA decatenation and progressive copy number depletion. TFAM overexpression could be partially phenocopied by treatment of cells with dideoxycytidine, suggesting that its effects are partially attributable to a decreased rate of fork progression. TFAM knockdown also resulted in mtDNA depletion, but RIs remained mainly of the ribosubstituted type, although termination intermediates were enhanced. We propose that TFAM influences the mode of mtDNA replication via its combined effects on different aspects of mtDNA metabolism.
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Affiliation(s)
- Jaakko L. O. Pohjoismäki
- Institute of Medical Technology and Tampere University HospitalFI-33014 University of Tampere, Finland
| | - Sjoerd Wanrooij
- Institute of Medical Technology and Tampere University HospitalFI-33014 University of Tampere, Finland
| | - Anne K. Hyvärinen
- Institute of Medical Technology and Tampere University HospitalFI-33014 University of Tampere, Finland
| | - Steffi Goffart
- Institute of Medical Technology and Tampere University HospitalFI-33014 University of Tampere, Finland
| | - Ian J. Holt
- MRC-Dunn Human Nutrition Unit, Hill RoadCambridge CB2 2XY, England, UK
| | - Johannes N. Spelbrink
- Institute of Medical Technology and Tampere University HospitalFI-33014 University of Tampere, Finland
| | - Howard T. Jacobs
- Institute of Medical Technology and Tampere University HospitalFI-33014 University of Tampere, Finland
- IBLS Division of Molecular Genetics, University of GlasgowGlasgow G12 8QQ, Scotland, UK
- To whom correspondence should be addressed. Tel: +358 33 55 17 731; Fax: +358 32 15 77 10;
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