151
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Roubicek DA, Souza-Pinto NCD. Mitochondria and mitochondrial DNA as relevant targets for environmental contaminants. Toxicology 2017; 391:100-108. [PMID: 28655544 DOI: 10.1016/j.tox.2017.06.012] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/20/2017] [Accepted: 06/21/2017] [Indexed: 10/19/2022]
Abstract
The mitochondrial DNA (mtDNA) is a closed circular molecule that encodes, in humans, 13 polypeptides components of the oxidative phosphorylation complexes. Integrity of the mitochondrial genome is essential for mitochondrial function and cellular homeostasis, and mutations and deletions in the mtDNA lead to oxidative stress, mitochondrial dysfunction and cell death. In vitro and in situ studies suggest that when exposed to certain genotoxins, mtDNA accumulates more damage than nuclear DNA, likely owing to its organization and localization in the mitochondrial matrix, which tends to accumulate lipophilic, positively charged molecules. In that regard, several relevant environmental and occupational contaminants have physical-chemical characteristics that indicate that they might accumulate in mitochondria and target mtDNA. Nonetheless, very little is known so far about mtDNA damage and mitochondrial dysfunction due to environmental exposure, either in model organisms or in humans. In this article, we discuss some of the characteristics of mtDNA which render it a potentially relevant target for damage by environmental contaminants, as well as possible functional consequences of damage/mutation accumulation. In addition, we review the data available in the literature focusing on mitochondrial effects of the most common classes of environmental pollutants. From that, we conclude that several lines of experimental evidence support the idea that mitochondria and mtDNA are susceptible and biologically relevant targets for pollutants, and more studies, including mechanistic ones, are needed to shed more light into the contribution of mitochondrial dysfunction to the environmental and human health effects of chemical exposure.
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Affiliation(s)
- Deborah A Roubicek
- Dept. of Environmental Analyses, São Paulo State Environmental Agency, CETESB, Av. Prof. Frederico Hermann Jr, 345, 05459-900, São Paulo, SP, Brazil
| | - Nadja C de Souza-Pinto
- Depto. de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo SP 05508-000, Brazil.
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152
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Mitochondrial Nucleoid: Shield and Switch of the Mitochondrial Genome. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:8060949. [PMID: 28680532 PMCID: PMC5478868 DOI: 10.1155/2017/8060949] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/06/2017] [Accepted: 04/03/2017] [Indexed: 11/18/2022]
Abstract
Mitochondria preserve very complex and distinctively unique machinery to maintain and express the content of mitochondrial DNA (mtDNA). Similar to chromosomes, mtDNA is packaged into discrete mtDNA-protein complexes referred to as a nucleoid. In addition to its role as a mtDNA shield, over 50 nucleoid-associated proteins play roles in mtDNA maintenance and gene expression through either temporary or permanent association with mtDNA or other nucleoid-associated proteins. The number of mtDNA(s) contained within a single nucleoid is a fundamental question but remains a somewhat controversial issue. Disturbance in nucleoid components and mutations in mtDNA were identified as significant in various diseases, including carcinogenesis. Significant interest in the nucleoid structure and its regulation has been stimulated in relation to mitochondrial diseases, which encompass diseases in multicellular organisms and are associated with accumulation of numerous mutations in mtDNA. In this review, mitochondrial nucleoid structure, nucleoid-associated proteins, and their regulatory roles in mitochondrial metabolism are briefly addressed to provide an overview of the emerging research field involving mitochondrial biology.
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153
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Fiorese CJ, Haynes CM. Integrating the UPR mt into the mitochondrial maintenance network. Crit Rev Biochem Mol Biol 2017; 52:304-313. [PMID: 28276702 DOI: 10.1080/10409238.2017.1291577] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Mitochondrial function is central to many different processes in the cell, from oxidative phosphorylation to the synthesis of iron-sulfur clusters. Therefore, mitochondrial dysfunction underlies a diverse array of diseases, from neurodegenerative diseases to cancer. Stress can be communicated to the cytosol and nucleus from the mitochondria through many different signals, and in response the cell can effect everything from transcriptional to post-transcriptional responses to protect the mitochondrial network. How these responses are coordinated have only recently begun to be understood. In this review, we explore how the cell maintains mitochondrial function, focusing on the mitochondrial unfolded protein response (UPRmt), a transcriptional response that can activate a wide array of programs to repair and restore mitochondrial function.
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Affiliation(s)
- Christopher J Fiorese
- a Department of Molecular Cell and Cancer Biology , University of Massachusetts Medical School , Worcester , MA , USA.,b BCMB Allied Program , Weill Cornell Medical College , New York , NY , USA
| | - Cole M Haynes
- a Department of Molecular Cell and Cancer Biology , University of Massachusetts Medical School , Worcester , MA , USA.,b BCMB Allied Program , Weill Cornell Medical College , New York , NY , USA
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154
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Adrian-Kalchhauser I, Svensson O, Kutschera VE, Alm Rosenblad M, Pippel M, Winkler S, Schloissnig S, Blomberg A, Burkhardt-Holm P. The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish. BMC Genomics 2017; 18:177. [PMID: 28209125 PMCID: PMC5314710 DOI: 10.1186/s12864-017-3550-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/02/2017] [Indexed: 11/15/2022] Open
Abstract
Background Vertebrate mitochondrial genomes are optimized for fast replication and low cost of RNA expression. Accordingly, they are devoid of introns, are transcribed as polycistrons and contain very little intergenic sequences. Usually, vertebrate mitochondrial genomes measure between 16.5 and 17 kilobases (kb). Results During genome sequencing projects for two novel vertebrate models, the invasive round goby and the sand goby, we found that the sand goby genome is exceptionally small (16.4 kb), while the mitochondrial genome of the round goby is much larger than expected for a vertebrate. It is 19 kb in size and is thus one of the largest fish and even vertebrate mitochondrial genomes known to date. The expansion is attributable to a sequence insertion downstream of the putative transcriptional start site. This insertion carries traces of repeats from the control region, but is mostly novel. To get more information about this phenomenon, we gathered all available mitochondrial genomes of Gobiidae and of nine gobioid species, performed phylogenetic analyses, analysed gene arrangements, and compared gobiid mitochondrial genome sizes, ecological information and other species characteristics with respect to the mitochondrial phylogeny. This allowed us amongst others to identify a unique arrangement of tRNAs among Ponto-Caspian gobies. Conclusions Our results indicate that the round goby mitochondrial genome may contain novel features. Since mitochondrial genome organisation is tightly linked to energy metabolism, these features may be linked to its invasion success. Also, the unique tRNA arrangement among Ponto-Caspian gobies may be helpful in studying the evolution of this highly adaptive and invasive species group. Finally, we find that the phylogeny of gobiids can be further refined by the use of longer stretches of linked DNA sequence. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3550-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irene Adrian-Kalchhauser
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, Basel, 4051, Switzerland.
| | - Ola Svensson
- Department of Biological and Environmental Sciences, University of Gothenburg, Medicinaregatan 18A, 41390, Göteborg, Sweden.,The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, P.O. Box 460, 40530, Gothenburg, Sweden
| | - Verena E Kutschera
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Magnus Alm Rosenblad
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, P.O. Box 460, 40530, Gothenburg, Sweden.,Department of Marine Sciences, NBIS Bioinformatics Infrastructure for Life Sciences, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Martin Pippel
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Siegfried Schloissnig
- Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany
| | - Anders Blomberg
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, P.O. Box 460, 40530, Gothenburg, Sweden.,Department of Marine Sciences, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Patricia Burkhardt-Holm
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, Basel, 4051, Switzerland.,Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB, Canada
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155
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Phillips AF, Millet AR, Tigano M, Dubois SM, Crimmins H, Babin L, Charpentier M, Piganeau M, Brunet E, Sfeir A. Single-Molecule Analysis of mtDNA Replication Uncovers the Basis of the Common Deletion. Mol Cell 2017; 65:527-538.e6. [PMID: 28111015 DOI: 10.1016/j.molcel.2016.12.014] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 10/04/2016] [Accepted: 12/16/2016] [Indexed: 11/30/2022]
Abstract
Mutations in mtDNA lead to muscular and neurological diseases and are linked to aging. The most frequent aberrancy is the "common deletion" that involves a 4,977-bp region flanked by 13-bp repeats. To investigate the basis of this deletion, we developed a single-molecule mtDNA combing method. The analysis of replicating mtDNA molecules provided in vivo evidence in support of the asymmetric mode of replication. Furthermore, we observed frequent fork stalling at the junction of the common deletion, suggesting that impaired replication triggers the formation of this toxic lesion. In parallel experiments, we employed mito-TALENs to induce breaks in distinct loci of the mitochondrial genome and found that breaks adjacent to the 5' repeat trigger the common deletion. Interestingly, this process was mediated by the mitochondrial replisome independent of canonical DSB repair. Altogether, our data underscore a unique replication-dependent repair pathway that leads to the mitochondrial common deletion.
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Affiliation(s)
- Aaron F Phillips
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Armêl R Millet
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 75005 Paris, France; Genome Dynamics in the Immune System Laboratory, INSERM, UMR 1163, Institut Imagine, 75015 Paris, France
| | - Marco Tigano
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Sonia M Dubois
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 75005 Paris, France
| | - Hannah Crimmins
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Loelia Babin
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 75005 Paris, France; Genome Dynamics in the Immune System Laboratory, INSERM, UMR 1163, Institut Imagine, 75015 Paris, France
| | - Marine Charpentier
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 75005 Paris, France
| | - Marion Piganeau
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 75005 Paris, France
| | - Erika Brunet
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, INSERM U 1154, CNRS UMR 7196, 75005 Paris, France; Genome Dynamics in the Immune System Laboratory, INSERM, UMR 1163, Institut Imagine, 75015 Paris, France.
| | - Agnel Sfeir
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA.
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156
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Guilliam TA, Doherty AJ. PrimPol-Prime Time to Reprime. Genes (Basel) 2017; 8:genes8010020. [PMID: 28067825 PMCID: PMC5295015 DOI: 10.3390/genes8010020] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/09/2016] [Accepted: 12/16/2016] [Indexed: 01/16/2023] Open
Abstract
The complex molecular machines responsible for genome replication encounter many obstacles during their progression along DNA. Tolerance of these obstructions is critical for efficient and timely genome duplication. In recent years, primase-polymerase (PrimPol) has emerged as a new player involved in maintaining eukaryotic replication fork progression. This versatile replicative enzyme, a member of the archaeo-eukaryotic primase (AEP) superfamily, has the capacity to perform a range of template-dependent and independent synthesis activities. Here, we discuss the emerging roles of PrimPol as a leading strand repriming enzyme and describe the mechanisms responsible for recruiting and regulating the enzyme during this process. This review provides an overview and update of the current PrimPol literature, as well as highlighting unanswered questions and potential future avenues of investigation.
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Affiliation(s)
- Thomas A Guilliam
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK.
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK.
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157
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Shokolenko IN, Alexeyev MF. Mitochondrial transcription in mammalian cells. Front Biosci (Landmark Ed) 2017; 22:835-853. [PMID: 27814650 DOI: 10.2741/4520] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
As a consequence of recent discoveries of intimate involvement of mitochondria with key cellular processes, there has been a resurgence of interest in all aspects of mitochondrial biology, including the intricate mechanisms of mitochondrial DNA maintenance and expression. Despite four decades of research, there remains a lot to be learned about the processes that enable transcription of genetic information from mitochondrial DNA to RNA, as well as their regulation. These processes are vitally important, as evidenced by the lethality of inactivating the central components of mitochondrial transcription machinery. Here, we review the current understanding of mitochondrial transcription and its regulation in mammalian cells. We also discuss key theories in the field and highlight controversial subjects and future directions as we see them.
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Affiliation(s)
- Inna N Shokolenko
- University of South Alabama, Patt Capps Covey College of Allied Health Professions, Biomedical Sciences Department, 5721 USA Drive N, HAHN 4021, Mobile, AL 36688-0002, USA
| | - Mikhail F Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, 5851 USA Dr. North, MSB3074, Mobile, AL 36688, USA,
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158
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Heinonen S, Muniandy M, Buzkova J, Mardinoglu A, Rodríguez A, Frühbeck G, Hakkarainen A, Lundbom J, Lundbom N, Kaprio J, Rissanen A, Pietiläinen KH. Mitochondria-related transcriptional signature is downregulated in adipocytes in obesity: a study of young healthy MZ twins. Diabetologia 2017; 60:169-181. [PMID: 27734103 DOI: 10.1007/s00125-016-4121-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/09/2016] [Indexed: 01/04/2023]
Abstract
AIMS/HYPOTHESIS Low mitochondrial activity in adipose tissue is suggested to be an underlying factor in obesity and its metabolic complications. We aimed to find out whether mitochondrial measures are downregulated in obesity also in isolated adipocytes. METHODS We studied young adult monozygotic (MZ) twin pairs discordant (n = 14, intrapair difference ΔBMI ≥ 3 kg/m2) and concordant (n = 5, ΔBMI < 3 kg/m2) for BMI, identified from ten birth cohorts of 22- to 36-year-old Finnish twins. Abdominal body fat distribution (MRI), liver fat content (magnetic resonance spectroscopy), insulin sensitivity (OGTT), high-sensitivity C-reactive protein, serum lipids and adipokines were measured. Subcutaneous abdominal adipose tissue biopsies were obtained to analyse the transcriptomics patterns of the isolated adipocytes as well as of the whole adipose tissue. Mitochondrial DNA transcript levels in adipocytes were measured by quantitative real-time PCR. Western blots of oxidative phosphorylation (OXPHOS) protein levels in adipocytes were performed in obese and lean unrelated individuals. RESULTS The heavier (BMI 29.9 ± 1.0 kg/m2) co-twins of the discordant twin pairs had more subcutaneous, intra-abdominal and liver fat and were more insulin resistant (p < 0.01 for all measures) than the lighter (24.1 ± 0.9 kg/m2) co-twins. Altogether, 2538 genes in adipocytes and 2135 in adipose tissue were significantly differentially expressed (nominal p < 0.05) between the co-twins. Pathway analysis of these transcripts in both isolated adipocytes and adipose tissue revealed that the heavier co-twins displayed reduced expression of genes relating to mitochondrial pathways, a result that was replicated when analysing the pathways behind the most consistently downregulated genes in the heavier co-twins (in at least 12 out of 14 pairs). Consistently upregulated genes in adipocytes were related to inflammation. We confirmed that mitochondrial DNA transcript levels (12S RNA, 16S RNA, COX1, ND5, CYTB), expression of mitochondrial ribosomal protein transcripts and a major mitochondrial regulator PGC-1α (also known as PPARGC1A) were reduced in the heavier co-twins' adipocytes (p < 0.05). OXPHOS protein levels of complexes I and III in adipocytes were lower in obese than in lean individuals. CONCLUSIONS/INTERPRETATION Subcutaneous abdominal adipocytes in obesity show global expressional downregulation of oxidative pathways, mitochondrial transcripts and OXPHOS protein levels and upregulation of inflammatory pathways. DATA AVAILABILITY The datasets analysed and generated during the current study are available in the figshare repository, https://dx.doi.org/10.6084/m9.figshare.3806286.v1.
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Affiliation(s)
- Sini Heinonen
- Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, Biomedicum Helsinki, C424b, P.O. Box 63, Haartmaninkatu 8, 00014, Helsinki, Finland
| | - Maheswary Muniandy
- Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, Biomedicum Helsinki, C424b, P.O. Box 63, Haartmaninkatu 8, 00014, Helsinki, Finland
| | - Jana Buzkova
- Research Programs Unit, Molecular Neurology, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Adil Mardinoglu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Amaia Rodríguez
- Metabolic Research Laboratory, Clínica Universidad de Navarra, Pamplona, Spain
- CIBEROBN, Instituto de Salud Carlos III, Pamplona, Spain
| | - Gema Frühbeck
- Metabolic Research Laboratory, Clínica Universidad de Navarra, Pamplona, Spain
- CIBEROBN, Instituto de Salud Carlos III, Pamplona, Spain
| | - Antti Hakkarainen
- HUS Medical Imaging Center, Radiology, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Jesper Lundbom
- HUS Medical Imaging Center, Radiology, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research, Heinrich Heine University, Düsseldorf, Germany
| | - Nina Lundbom
- HUS Medical Imaging Center, Radiology, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Jaakko Kaprio
- FIMM, Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
- Finnish Twin Cohort Study, Department of Public Health, University of Helsinki, Helsinki, Finland
- National Institute for Health and Welfare, Department of Health, Helsinki, Finland
| | - Aila Rissanen
- Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, Biomedicum Helsinki, C424b, P.O. Box 63, Haartmaninkatu 8, 00014, Helsinki, Finland
- Department of Psychiatry, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
| | - Kirsi H Pietiläinen
- Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, Biomedicum Helsinki, C424b, P.O. Box 63, Haartmaninkatu 8, 00014, Helsinki, Finland.
- FIMM, Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland.
- Endocrinology, Abdominal Center, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland.
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159
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E GX, Zhao YJ, Huang YF. Sheep mitochondrial heteroplasmy arises from tandem motifs and unspecific PCR amplification. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 29:91-95. [PMID: 27841052 DOI: 10.1080/24701394.2016.1242582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The mitochondrial DNA control region (D-loop) is a widely used molecular marker in evolutionary and phylogeographic research. However, the occurrence of heteroplasmy of the D-loop region within individuals has rarely been investigated. In this study, a total of 85 Chinese sheep were used to amplify a partial D-loop region, and 15 heteroplasmic animals (17.64%) were identified. A comparative analysis of the PCR amplification and cloning of the D-loop sequences from the heteroplasmic samples revealed most of the sequencing profile from the heteroplasmic regions started at the beginning of a 75-bp random repeat motif. In addition, a total of 22 nonsyngeneic sequences with a D-loop were found in 61 of the clones obtained from the 4 random heteroplasmic and 3 homozygote animals, and their genomic locations were compared for homology. In summary, the D-Loop sequencing profiles appear to be heteroplasmic and could arise from tandem repeat motifs and unspecific replication during PCR amplification; however, they are not likely due to the presence of multiple mitochondrial genomes within an individual.
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Affiliation(s)
- Guang-Xin E
- a College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Yong-Ju Zhao
- a College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
| | - Yong-Fu Huang
- a College of Animal Science and Technology, Chongqing Key Laboratory of Forage & Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization , Southwest University , Chongqing , China
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160
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Cividini F, Scott BT, Dai A, Han W, Suarez J, Diaz-Juarez J, Diemer T, Casteel DE, Dillmann WH. O-GlcNAcylation of 8-Oxoguanine DNA Glycosylase (Ogg1) Impairs Oxidative Mitochondrial DNA Lesion Repair in Diabetic Hearts. J Biol Chem 2016; 291:26515-26528. [PMID: 27816939 DOI: 10.1074/jbc.m116.754481] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/03/2016] [Indexed: 11/06/2022] Open
Abstract
mtDNA damage in cardiac myocytes resulting from increased oxidative stress is emerging as an important factor in the pathogenesis of diabetic cardiomyopathy. A prevalent lesion that occurs in mtDNA damage is the formation of 8-hydroxy-2'-deoxyguanosine (8-OHdG), which can cause mutations when not repaired properly by 8-oxoguanine DNA glycosylase (Ogg1). Although the mtDNA repair machinery has been described in cardiac myocytes, the regulation of this repair has been incompletely investigated. Here we report that the hearts of type 1 diabetic mice, despite having increased Ogg1 protein levels, had significantly lower Ogg1 activity than the hearts of control, non-type 1 diabetic mice. In diabetic hearts, we further observed increased levels of 8-OHdG and an increased amount of mtDNA damage. Interestingly, Ogg1 was found to be highly O-GlcNAcylated in diabetic mice compared with controls. In vitro experiments demonstrated that O-GlcNAcylation inhibits Ogg1 activity, which could explain the mtDNA lesion accumulation observed in vivo Reducing Ogg1 O-GlcNAcylation in vivo by introducing a dominant negative O-GlcNAc transferase mutant (F460A) restored Ogg1 enzymatic activity and, consequently, reduced 8-OHdG and mtDNA damage despite the adverse hyperglycemic milieu. Taken together, our results implicate hyperglycemia-induced O-GlcNAcylation of Ogg1 in increased mtDNA damage and, therefore, provide a new plausible biochemical mechanism for diabetic cardiomyopathy.
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Affiliation(s)
- Federico Cividini
- From the Department of Medicine, University of California, San Diego, La Jolla, California 92093-0671 and
| | - Brian T Scott
- From the Department of Medicine, University of California, San Diego, La Jolla, California 92093-0671 and
| | - Anzhi Dai
- From the Department of Medicine, University of California, San Diego, La Jolla, California 92093-0671 and
| | - Wenlong Han
- From the Department of Medicine, University of California, San Diego, La Jolla, California 92093-0671 and
| | - Jorge Suarez
- From the Department of Medicine, University of California, San Diego, La Jolla, California 92093-0671 and
| | - Julieta Diaz-Juarez
- the Department of Pharmacology, Instituto Nacional de Cardiología, Juan Badiano 41, Barrio Belisario Domínguez Secc XVI, 14080 Tlalpan, DF, Mexico
| | - Tanja Diemer
- From the Department of Medicine, University of California, San Diego, La Jolla, California 92093-0671 and
| | - Darren E Casteel
- From the Department of Medicine, University of California, San Diego, La Jolla, California 92093-0671 and
| | - Wolfgang H Dillmann
- From the Department of Medicine, University of California, San Diego, La Jolla, California 92093-0671 and
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161
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Cao X, Qin Y. Mitochondrial translation factors reflect coordination between organelles and cytoplasmic translation via mTOR signaling: Implication in disease. Free Radic Biol Med 2016; 100:231-237. [PMID: 27101739 DOI: 10.1016/j.freeradbiomed.2016.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/11/2016] [Accepted: 04/13/2016] [Indexed: 12/24/2022]
Abstract
Mitochondria are semi-autonomous organelle possessing their own translation machinery to biosynthesize mitochondrial DNA (mtDNA)-encoded polypeptides, which are the core subunits of oxidative phosphorylation (OXPHOS) complexes. Mitochondrial translation elongation factor 4 (mtEF4) is a key quality control factor in mitochondrial translation (mt-translation) that regulates mitochondrial tRNA translocation and modulates cellular responses by influencing cytoplasmic translation (ct-translation). In addition to mtEF4, mt-translational activators, mitochondrial microRNAs (mitomiRs), and MITRAC have been reported recently as crucial mt-translation regulators. Here, we focus on the novel ways how these factors regulate mt-translation, discuss the main cellular response of mammalian target of rapamycin (mTOR) signalling upon mt-translation defects, and summarize the related human diseases.
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Affiliation(s)
- Xintao Cao
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Qin
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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162
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Nuclear but not mitochondrial-encoded oxidative phosphorylation genes are altered in aging, mild cognitive impairment, and Alzheimer's disease. Alzheimers Dement 2016; 13:510-519. [PMID: 27793643 DOI: 10.1016/j.jalz.2016.09.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/30/2016] [Accepted: 09/12/2016] [Indexed: 01/01/2023]
Abstract
INTRODUCTION We have comprehensively described the expression profiles of mitochondrial DNA and nuclear DNA genes that encode subunits of the respiratory oxidative phosphorylation (OXPHOS) complexes (I-V) in the hippocampus from young controls, age matched, mild cognitively impaired (MCI), and Alzheimer's disease (AD) subjects. METHODS Hippocampal tissues from 44 non-AD controls (NC), 10 amnestic MCI, and 18 AD cases were analyzed on Affymetrix Hg-U133 plus 2.0 arrays. RESULTS The microarray data revealed significant down regulation in OXPHOS genes in AD, particularly those encoded in the nucleus. In contrast, there was up regulation of the same gene(s) in MCI subjects compared to AD and ND cases. No significant differences were observed in mtDNA genes identified in the array between AD, ND, and MCI subjects except one mt-ND6. DISCUSSION Our findings suggest that restoration of the expression of nuclear-encoded OXPHOS genes in aging could be a viable strategy for blunting AD progression.
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163
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Human mitochondrial ribosomes can switch their structural RNA composition. Proc Natl Acad Sci U S A 2016; 113:12198-12201. [PMID: 27729525 DOI: 10.1073/pnas.1609338113] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The recent developments in cryo-EM have revolutionized our access to previously refractory structures. In particular, such studies of mammalian mitoribosomes have confirmed the absence of any 5S rRNA species and revealed the unexpected presence of a mitochondrially encoded tRNA (mt-tRNA) that usurps this position. Although the cryo-EM structures resolved the conundrum of whether mammalian mitoribosomes contain a 5S rRNA, they introduced a new dilemma: Why do human and porcine mitoribosomes integrate contrasting mt-tRNAs? Human mitoribosomes have been shown to integrate mt-tRNAVal compared with the porcine use of mt-tRNAPhe We have explored this observation further. Our studies examine whether a range of mt-tRNAs are used by different mammals, or whether the mt-tRNA selection is strictly limited to only these two species of the 22 tRNAs encoded by the mitochondrial genome (mtDNA); whether there is tissue-specific variation within a single organism; and what happens to the human mitoribosome when levels of the mt-tRNAVal are depleted. Our data demonstrate that only mt-tRNAVal or mt-tRNAPhe are found in the mitoribosomes of five different mammals, each mammal favors the same mt-tRNA in all tissue types, and strikingly, when steady-state levels of mt-tRNAVal are reduced, human mitoribosome biogenesis displays an adaptive response by switching to the incorporation of mt-tRNAPhe to generate translationally competent machinery.
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164
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Mazunin IO, Levitskii SA, Patrushev MV, Kamenski PA. Mitochondrial Matrix Processes. BIOCHEMISTRY (MOSCOW) 2016; 80:1418-28. [PMID: 26615433 DOI: 10.1134/s0006297915110036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Mitochondria possess their own genome that, despite its small size, is critically important for their functioning, as it encodes several dozens of RNAs and proteins. All biochemical processes typical for bacterial and nuclear DNA are described in mitochondrial matrix: replication, repair, recombination, and transcription. Commonly, their mechanisms are similar to those found in bacteria, but they are characterized by several unique features. In this review, we provide an overall description of mitochondrial matrix processes paying special attention to the typical features of such mechanisms.
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Affiliation(s)
- I O Mazunin
- Immanuil Kant Baltic Federal University, Institute of Chemistry and Biology, Kaliningrad, 236038, Russia.
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165
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Zhang XC, Li W, Zhao J, Chen HG, Zhu XP. Novel duplication pattern of the mitochondrial control region in Cantor's Giant softshell turtle Pelochelys cantorii. Gene 2016; 593:242-248. [PMID: 27565702 DOI: 10.1016/j.gene.2016.08.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/06/2016] [Accepted: 08/22/2016] [Indexed: 10/21/2022]
Abstract
Cantor's Giant Softshell Turtle, Pelochelys cantorii has become one of the most critically endangered species in the world. When comparative analyses of the P. cantorii complete mitochondrial genome sequences were conducted, we discovered a duplication of a segment of the control region in the mitochondrial genome of P. cantorii. The duplication is characterized by two copies of conserved sequence box 2 (CSB2) and CSB3 in a single control region. In contrast to previous reports of duplications involving the control regions of other animals, this particular pattern of duplications appears to be unique to P. cantorii. Copies of the CSB2 and CSB3 show many of the conserved sequence features typically found in mitochondrial control regions, and rare differences were found between the paralogous copies. Using the primer design principle of simple sequence repeats (SSR) and the reference sequence of the duplicated CSBs, specific primers were designed to amplify the duplicated CSBs. These primers were validated among different individuals and populations of P. cantorii. This unique duplication structure suggests the two copies of the CSB2 and CSB3 may have arisen through occasional tandem duplication and subsequent concerted evolution.
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Affiliation(s)
- Xin-Cheng Zhang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu 214081, PR China; Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, PR China
| | - Wei Li
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, PR China
| | - Jian Zhao
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, PR China
| | - Hai-Gang Chen
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu 214081, PR China; Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, PR China
| | - Xin-Ping Zhu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu 214081, PR China; Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, PR China.
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166
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Guo J, Gao S, Liu Z, Zhao R, Yang X. Alpha-Lipoic Acid Alleviates Acute Inflammation and Promotes Lipid Mobilization During the Inflammatory Response in White Adipose Tissue of Mice. Lipids 2016; 51:1145-1152. [DOI: 10.1007/s11745-016-4185-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 08/05/2016] [Indexed: 12/22/2022]
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167
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Bioenergetic roles of mitochondrial fusion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1277-1283. [DOI: 10.1016/j.bbabio.2016.04.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/18/2016] [Accepted: 04/05/2016] [Indexed: 11/17/2022]
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168
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Kühl I, Miranda M, Posse V, Milenkovic D, Mourier A, Siira SJ, Bonekamp NA, Neumann U, Filipovska A, Polosa PL, Gustafsson CM, Larsson NG. POLRMT regulates the switch between replication primer formation and gene expression of mammalian mtDNA. SCIENCE ADVANCES 2016; 2:e1600963. [PMID: 27532055 PMCID: PMC4975551 DOI: 10.1126/sciadv.1600963] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/01/2016] [Indexed: 05/27/2023]
Abstract
Mitochondria are vital in providing cellular energy via their oxidative phosphorylation system, which requires the coordinated expression of genes encoded by both the nuclear and mitochondrial genomes (mtDNA). Transcription of the circular mammalian mtDNA depends on a single mitochondrial RNA polymerase (POLRMT). Although the transcription initiation process is well understood, it is debated whether POLRMT also serves as the primase for the initiation of mtDNA replication. In the nucleus, the RNA polymerases needed for gene expression have no such role. Conditional knockout of Polrmt in the heart results in severe mitochondrial dysfunction causing dilated cardiomyopathy in young mice. We further studied the molecular consequences of different expression levels of POLRMT and found that POLRMT is essential for primer synthesis to initiate mtDNA replication in vivo. Furthermore, transcription initiation for primer formation has priority over gene expression. Surprisingly, mitochondrial transcription factor A (TFAM) exists in an mtDNA-free pool in the Polrmt knockout mice. TFAM levels remain unchanged despite strong mtDNA depletion, and TFAM is thus protected from degradation of the AAA(+) Lon protease in the absence of POLRMT. Last, we report that mitochondrial transcription elongation factor may compensate for a partial depletion of POLRMT in heterozygous Polrmt knockout mice, indicating a direct regulatory role of this factor in transcription. In conclusion, we present in vivo evidence that POLRMT has a key regulatory role in the replication of mammalian mtDNA and is part of a transcriptional mechanism that provides a switch between primer formation for mtDNA replication and mitochondrial gene expression.
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Affiliation(s)
- Inge Kühl
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Maria Miranda
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Viktor Posse
- Department of Medical Biochemistry and Cell Biology, Göteborgs Universitet, 40530 Göteborg, Sweden
| | - Dusanka Milenkovic
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Arnaud Mourier
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
- Université de Bordeaux and the Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires UMR 5095, Saint-Saëns, F-33077 Bordeaux, France
| | - Stefan J. Siira
- Harry Perkins Institute of Medical Research, Centre for Medical Research and School of Chemistry and Biochemistry, The University of Western Australia, Perth 6009, Australia
| | - Nina A. Bonekamp
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Ulla Neumann
- Central Microscopy, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, Centre for Medical Research and School of Chemistry and Biochemistry, The University of Western Australia, Perth 6009, Australia
| | - Paola Loguercio Polosa
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari Aldo Moro, 70125 Bari, Italy
| | - Claes M. Gustafsson
- Department of Medical Biochemistry and Cell Biology, Göteborgs Universitet, 40530 Göteborg, Sweden
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
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169
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Abstract
Oxidative phosphorylation (OXPHOS) is the mechanism whereby ATP, the major energy source for the cell, is produced by harnessing cellular respiration in the mitochondrion. This is facilitated by five multi-subunit complexes housed within the inner mitochondrial membrane. These complexes, with the exception of complex II, are of a dual genetic origin, requiring expression from nuclear and mitochondrial genes. Mitochondrially encoded mRNA is translated on the mitochondrial ribosome (mitoribosome) and the recent release of the near atomic resolution structure of the mammalian mitoribosome has highlighted its peculiar features. However, whereas some aspects of mitochondrial translation are understood, much is to be learnt about the presentation of mitochondrial mRNA to the mitoribosome, the biogenesis of the machinery, the exact role of the membrane, the constitution of the translocon/insertion machinery and the regulation of translation in the mitochondrion. This review addresses our current knowledge of mammalian mitochondrial gene expression, highlights key questions and indicates how defects in this process can result in profound mitochondrial disease.
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170
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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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171
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Li H, Bi R, Fan Y, Wu Y, Tang Y, Li Z, He Y, Zhou J, Tang J, Chen X, Yao YG. mtDNA Heteroplasmy in Monozygotic Twins Discordant for Schizophrenia. Mol Neurobiol 2016; 54:4343-4352. [DOI: 10.1007/s12035-016-9996-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 06/14/2016] [Indexed: 12/30/2022]
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172
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Skarpengland T, Holm S, Scheffler K, Gregersen I, Dahl TB, Suganthan R, Segers FM, Østlie I, Otten JJT, Luna L, Ketelhuth DFJ, Lundberg AM, Neurauter CG, Hildrestrand G, Skjelland M, Bjørndal B, Svardal AM, Iversen PO, Hedin U, Nygård S, Olstad OK, Krohg-Sørensen K, Slupphaug G, Eide L, Kuśnierczyk A, Folkersen L, Ueland T, Berge RK, Hansson GK, Biessen EAL, Halvorsen B, Bjørås M, Aukrust P. Neil3-dependent base excision repair regulates lipid metabolism and prevents atherosclerosis in Apoe-deficient mice. Sci Rep 2016; 6:28337. [PMID: 27328939 PMCID: PMC4916448 DOI: 10.1038/srep28337] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 06/01/2016] [Indexed: 12/23/2022] Open
Abstract
Increasing evidence suggests that oxidative DNA damage accumulates in atherosclerosis. Recently, we showed that a genetic variant in the human DNA repair enzyme NEIL3 was associated with increased risk of myocardial infarction. Here, we explored the role of Neil3/NEIL3 in atherogenesis by both clinical and experimental approaches. Human carotid plaques revealed increased NEIL3 mRNA expression which significantly correlated with mRNA levels of the macrophage marker CD68. Apoe−/−Neil3−/− mice on high-fat diet showed accelerated plaque formation as compared to Apoe−/− mice, reflecting an atherogenic lipid profile, increased hepatic triglyceride levels and attenuated macrophage cholesterol efflux capacity. Apoe−/−Neil3−/− mice showed marked alterations in several pathways affecting hepatic lipid metabolism, but no genotypic alterations in genome integrity or genome-wide accumulation of oxidative DNA damage. These results suggest a novel role for the DNA glycosylase Neil3 in atherogenesis in balancing lipid metabolism and macrophage function, potentially independently of genome-wide canonical base excision repair of oxidative DNA damage.
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Affiliation(s)
- Tonje Skarpengland
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Sverre Holm
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Katja Scheffler
- Department of Medical Biochemistry, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Institute of Basic Medical Research, University of Oslo, Oslo, Norway.,Department of Informatics, University of Oslo, Oslo, Norway
| | - Ida Gregersen
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tuva B Dahl
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,K.G. Jebsen Inflammatory Research Center, University of Oslo, Oslo, Norway
| | - Rajikala Suganthan
- Department of Microbiology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Filip M Segers
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Ingunn Østlie
- Department of Pathology,Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Jeroen J T Otten
- Department of Experimental Vascular Pathology, University of Maastricht, Maastricht, The Netherlands
| | - Luisa Luna
- Department of Microbiology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Daniel F J Ketelhuth
- Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Anna M Lundberg
- Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | | | - Gunn Hildrestrand
- Department of Microbiology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Mona Skjelland
- Department of Neurology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Bodil Bjørndal
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Asbjørn M Svardal
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Per O Iversen
- Institute of Basic Medical Research, University of Oslo, Oslo, Norway.,Department of Hematology, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Department of Nutrition, University of Oslo, Oslo, Norway
| | - Ulf Hedin
- Department of Surgery, Karolinska University Hospital, Stockholm, Sweden
| | - Ståle Nygård
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Ole K Olstad
- Department of Medical Biochemistry, Oslo University Hospital Ullevål, Oslo, Norway
| | - Kirsten Krohg-Sørensen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Thoracic and Cardiovascular Surgery, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Geir Slupphaug
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Metabolomics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Lars Eide
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Medical Biochemistry, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Anna Kuśnierczyk
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Metabolomics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Lasse Folkersen
- Center for Biological Sequence Analysis, Technical University of Denmark, Copenhagen, Denmark
| | - Thor Ueland
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,K.G. Jebsen Inflammatory Research Center, University of Oslo, Oslo, Norway
| | - Rolf K Berge
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Heart Disease, Haukeland University Hospital, Bergen, Norway
| | - Göran K Hansson
- Center for Molecular Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Erik A L Biessen
- Department of Experimental Vascular Pathology, University of Maastricht, Maastricht, The Netherlands
| | - Bente Halvorsen
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,K.G. Jebsen Inflammatory Research Center, University of Oslo, Oslo, Norway
| | - Magnar Bjørås
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Microbiology, Oslo University Hospital Rikshospitalet, Oslo, Norway.,PROMEC Core Facility for Proteomics and Metabolomics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Pål Aukrust
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,K.G. Jebsen Inflammatory Research Center, University of Oslo, Oslo, Norway.,Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital Rikshospitalet, Oslo, Norway
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173
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Chaperone-Mediated Autophagy and Mitochondrial Homeostasis in Parkinson's Disease. PARKINSONS DISEASE 2016; 2016:2613401. [PMID: 27413575 PMCID: PMC4927950 DOI: 10.1155/2016/2613401] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 04/04/2016] [Accepted: 05/29/2016] [Indexed: 12/20/2022]
Abstract
Parkinson's disease (PD), a complex neurodegenerative disorder, is pathologically characterized by the formation of Lewy bodies and loss of dopaminergic neurons in the substantia nigra pars compacta (SNc). Mitochondrial dysfunction is considered to be one of the most important causative mechanisms. In addition, dysfunction of chaperone-mediated autophagy (CMA), one of the lysosomal proteolytic pathways, has been shown to play an important role in the pathogenesis of PD. An exciting and important development is recent finding that CMA and mitochondrial quality control may be linked. This review summarizes the studies revealing the link between autophagy and mitochondrial function. Discussions are focused on the connections between CMA and mitochondrial failure and on the role of MEF2D, a neuronal survival factor, in mediating the regulation of mitochondria in the context of CMA. These new findings highlight the need to further explore the possibility of targeting the MEF2D-mitochondria-CMA network in both understanding the PD pathogenesis and developing novel therapeutic strategies.
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174
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Wisnovsky S, Jean SR, Liyanage S, Schimmer A, Kelley SO. Mitochondrial DNA repair and replication proteins revealed by targeted chemical probes. Nat Chem Biol 2016; 12:567-73. [DOI: 10.1038/nchembio.2102] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 03/24/2016] [Indexed: 01/16/2023]
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175
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Hämäläinen RH. Mitochondria and mtDNA integrity in stem cell function and differentiation. Curr Opin Genet Dev 2016; 38:83-89. [PMID: 27219871 DOI: 10.1016/j.gde.2016.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 04/21/2016] [Accepted: 04/24/2016] [Indexed: 01/19/2023]
Abstract
Stem cells require tight control of energy metabolism to maintain homeostasis. They possess few immature mitochondria, repress mitochondrial respiration and instead use glycolysis to produce energy, yet mitochondrial defects can lead to severe stem cell dysfunction. Recent studies have shown that mitochondrial mass, function and integrity are tightly controlled in stem cells and the integrity of the mitochondrial genome is equally important to nuclear genome integrity for proper stem cell homeostasis. Mitochondria are now considered central in regulating stem cell function and governing cellular fate choices. This review will summarize recent advances highlighting the importance of mitochondrial integrity in stem cells.
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Affiliation(s)
- Riikka H Hämäläinen
- Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.
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176
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Gaidutšik I, Sedman T, Sillamaa S, Sedman J. Irc3 is a mitochondrial DNA branch migration enzyme. Sci Rep 2016; 6:26414. [PMID: 27194389 PMCID: PMC4872236 DOI: 10.1038/srep26414] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 05/03/2016] [Indexed: 01/03/2023] Open
Abstract
Integrity of mitochondrial DNA (mtDNA) is essential for cellular energy metabolism. In the budding yeast Saccharomyces cerevisiae, a large number of nuclear genes influence the stability of mitochondrial genome; however, most corresponding gene products act indirectly and the actual molecular mechanisms of mtDNA inheritance remain poorly characterized. Recently, we found that a Superfamily II helicase Irc3 is required for the maintenance of mitochondrial genome integrity. Here we show that Irc3 is a mitochondrial DNA branch migration enzyme. Irc3 modulates mtDNA metabolic intermediates by preferential binding and unwinding Holliday junctions and replication fork structures. Furthermore, we demonstrate that the loss of Irc3 can be complemented with mitochondrially targeted RecG of Escherichia coli. We suggest that Irc3 could support the stability of mtDNA by stimulating fork regression and branch migration or by inhibiting the formation of irregular branched molecules.
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Affiliation(s)
- Ilja Gaidutšik
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b, Tartu 51010, Estonia
| | - Tiina Sedman
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b, Tartu 51010, Estonia
| | - Sirelin Sillamaa
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b, Tartu 51010, Estonia
| | - Juhan Sedman
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b, Tartu 51010, Estonia
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177
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Erlich AT, Tryon LD, Crilly MJ, Memme JM, Moosavi ZSM, Oliveira AN, Beyfuss K, Hood DA. Function of specialized regulatory proteins and signaling pathways in exercise-induced muscle mitochondrial biogenesis. Integr Med Res 2016; 5:187-197. [PMID: 28462117 PMCID: PMC5390460 DOI: 10.1016/j.imr.2016.05.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 05/04/2016] [Indexed: 12/19/2022] Open
Abstract
Skeletal muscle mitochondrial content and function are regulated by a number of specialized molecular pathways that remain to be fully defined. Although a number of proteins have been identified to be important for the maintenance of mitochondria in quiescent muscle, the requirement for these appears to decrease with the activation of multiple overlapping signaling events that are triggered by exercise. This makes exercise a valuable therapeutic tool for the treatment of mitochondrially based metabolic disorders. In this review, we summarize some of the traditional and more recently appreciated pathways that are involved in mitochondrial biogenesis in muscle, particularly during exercise.
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Affiliation(s)
| | | | | | | | | | | | | | - David A. Hood
- Corresponding author. Muscle Health Research Centre, School of Kinesiology and Health Science York University, Toronto, Ontario M3J1P3, Canada.
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178
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Morozov YI, Temiakov D. Human Mitochondrial Transcription Initiation Complexes Have Similar Topology on the Light and Heavy Strand Promoters. J Biol Chem 2016; 291:13432-5. [PMID: 27226527 DOI: 10.1074/jbc.c116.727966] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Indexed: 11/06/2022] Open
Abstract
Transcription is a highly regulated process in all domains of life. In human mitochondria, transcription of the circular genome involves only two promoters, called light strand promoter (LSP) and heavy strand promoter (HSP), located in the opposite DNA strands. Initiation of transcription occurs upon sequential assembly of an initiation complex that includes mitochondrial RNA polymerase (mtRNAP) and the initiation factors mitochondrial transcription factor A (TFAM) and TFB2M. It has been recently suggested that the transcription initiation factor TFAM binds to HSP and LSP in opposite directions, implying that the mechanisms of transcription initiation are drastically dissimilar at these promoters. In contrast, we found that binding of TFAM to HSP and the subsequent recruitment of mtRNAP results in a pre-initiation complex that is remarkably similar in topology and properties to that formed at the LSP promoter. Our data suggest that assembly of the pre-initiation complexes on LSP and HSP brings these transcription units in close proximity, providing an opportunity for regulatory proteins to simultaneously control transcription initiation in both mtDNA strands.
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Affiliation(s)
- Yaroslav I Morozov
- From the Department of Cell Biology, Rowan University, School of Osteopathic Medicine, Stratford, New Jersey 08084
| | - Dmitry Temiakov
- From the Department of Cell Biology, Rowan University, School of Osteopathic Medicine, Stratford, New Jersey 08084
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179
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Accurate quantification of mouse mitochondrial DNA without co-amplification of nuclear mitochondrial insertion sequences. Mitochondrion 2016; 29:59-64. [PMID: 27181048 DOI: 10.1016/j.mito.2016.05.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 05/03/2016] [Accepted: 05/11/2016] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mitochondria contain an extra-nuclear genome in the form of mitochondrial DNA (MtDNA), damage to which can lead to inflammation and bioenergetic deficit. Changes in MtDNA levels are increasingly used as a biomarker of mitochondrial dysfunction. We previously reported that in humans, fragments in the nuclear genome known as nuclear mitochondrial insertion sequences (NumtS) affect accurate quantification of MtDNA. In the current paper our aim was to determine whether mouse NumtS affect the quantification of MtDNA and to establish a method designed to avoid this. METHODS The existence of NumtS in the mouse genome was confirmed using blast N, unique MtDNA regions were identified using FASTA, and MtDNA primers which do not co-amplify NumtS were designed and tested. MtDNA copy numbers were determined in a range of mouse tissues as the ratio of the mitochondrial and nuclear genome using real time qPCR and absolute quantification. RESULTS Approximately 95% of mouse MtDNA was duplicated in the nuclear genome as NumtS which were located in 15 out of 21 chromosomes. A unique region was identified and primers flanking this region were used. MtDNA levels differed significantly in mouse tissues being the highest in the heart, with levels in descending order (highest to lowest) in kidney, liver, blood, brain, islets and lung. CONCLUSION The presence of NumtS in the nuclear genome of mouse could lead to erroneous data when studying MtDNA content or mutation. The unique primers described here will allow accurate quantification of MtDNA content in mouse models without co-amplification of NumtS.
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180
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Shi Y, Posse V, Zhu X, Hyvärinen AK, Jacobs HT, Falkenberg M, Gustafsson CM. Mitochondrial transcription termination factor 1 directs polar replication fork pausing. Nucleic Acids Res 2016; 44:5732-42. [PMID: 27112570 PMCID: PMC4937320 DOI: 10.1093/nar/gkw302] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/12/2016] [Indexed: 12/01/2022] Open
Abstract
During replication of nuclear ribosomal DNA (rDNA), clashes with the transcription apparatus can cause replication fork collapse and genomic instability. To avoid this problem, a replication fork barrier protein is situated downstream of rDNA, there preventing replication in the direction opposite rDNA transcription. A potential candidate for a similar function in mitochondria is the mitochondrial transcription termination factor 1 (MTERF1, also denoted mTERF), which binds to a sequence just downstream of the ribosomal transcription unit. Previous studies have shown that MTERF1 prevents antisense transcription over the ribosomal RNA genes, a process which we here show to be independent of the transcription elongation factor TEFM. Importantly, we now demonstrate that MTERF1 arrests mitochondrial DNA (mtDNA) replication with distinct polarity. The effect is explained by the ability of MTERF1 to act as a directional contrahelicase, blocking mtDNA unwinding by the mitochondrial helicase TWINKLE. This conclusion is also supported by in vivo evidence that MTERF1 stimulates TWINKLE pausing. We conclude that MTERF1 can direct polar replication fork arrest in mammalian mitochondria.
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Affiliation(s)
- Yonghong Shi
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden Center for Molecular Medicine, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Viktor Posse
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Xuefeng Zhu
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden Center for Molecular Medicine, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Anne K Hyvärinen
- BioMediTech and Tampere University Hospital, FI-33014, University of Tampere, Finland
| | - Howard T Jacobs
- BioMediTech and Tampere University Hospital, FI-33014, University of Tampere, Finland Institute of Biotechnology, FI-00014, University of Helsinki, Finland
| | - Maria Falkenberg
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Claes M Gustafsson
- Institute of Biomedicine, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
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181
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Young MJ, Copeland WC. Human mitochondrial DNA replication machinery and disease. Curr Opin Genet Dev 2016; 38:52-62. [PMID: 27065468 DOI: 10.1016/j.gde.2016.03.005] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/03/2016] [Accepted: 03/08/2016] [Indexed: 12/21/2022]
Abstract
The human mitochondrial genome is replicated by DNA polymerase γ in concert with key components of the mitochondrial DNA (mtDNA) replication machinery. Defects in mtDNA replication or nucleotide metabolism cause deletions, point mutations, or depletion of mtDNA. The resulting loss of cellular respiration ultimately induces mitochondrial genetic diseases, including mtDNA depletion syndromes (MDS) such as Alpers or early infantile hepatocerebral syndromes, and mtDNA deletion disorders such as progressive external ophthalmoplegia, ataxia-neuropathy, or mitochondrial neurogastrointestinal encephalomyopathy. Here we review the current literature regarding human mtDNA replication and heritable disorders caused by genetic changes of the POLG, POLG2, Twinkle, RNASEH1, DNA2, and MGME1 genes.
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Affiliation(s)
- Matthew J Young
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, P.O. Box 12233, Research Triangle Park, NC 27709, United States
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, P.O. Box 12233, Research Triangle Park, NC 27709, United States.
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182
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Haig D. Intracellular evolution of mitochondrial DNA (mtDNA) and the tragedy of the cytoplasmic commons. Bioessays 2016; 38:549-55. [DOI: 10.1002/bies.201600003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- David Haig
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge MA USA
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183
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Carter HN, Chen CCW, Hood DA. Mitochondria, muscle health, and exercise with advancing age. Physiology (Bethesda) 2016; 30:208-23. [PMID: 25933821 DOI: 10.1152/physiol.00039.2014] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Skeletal muscle health is dependent on the optimal function of its mitochondria. With advancing age, decrements in numerous mitochondrial variables are evident in muscle. Part of this decline is due to reduced physical activity, whereas the remainder appears to be attributed to age-related alterations in mitochondrial synthesis and degradation. Exercise is an important strategy to stimulate mitochondrial adaptations in older individuals to foster improvements in muscle function and quality of life.
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Affiliation(s)
- Heather N Carter
- Muscle Health Research Centre, School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada
| | - Chris C W Chen
- Muscle Health Research Centre, School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada
| | - David A Hood
- Muscle Health Research Centre, School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada
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184
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Abstract
Mammalian mitochondrial DNA (mtDNA) encodes 13 proteins that are essential for the function of the oxidative phosphorylation system, which is composed of four respiratory-chain complexes and adenosine triphosphate (ATP) synthase. Remarkably, the maintenance and expression of mtDNA depend on the mitochondrial import of hundreds of nuclear-encoded proteins that control genome maintenance, replication, transcription, RNA maturation, and mitochondrial translation. The importance of this complex regulatory system is underscored by the identification of numerous mutations of nuclear genes that impair mtDNA maintenance and expression at different levels, causing human mitochondrial diseases with pleiotropic clinical manifestations. The basic scientific understanding of the mechanisms controlling mtDNA function has progressed considerably during the past few years, thanks to advances in biochemistry, genetics, and structural biology. The challenges for the future will be to understand how mtDNA maintenance and expression are regulated and to what extent direct intramitochondrial cross talk between different processes, such as transcription and translation, is important.
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Affiliation(s)
- Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 405 30 Gothenburg, Sweden; ,
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 405 30 Gothenburg, Sweden; ,
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany; .,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
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185
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Restoration of normal embryogenesis by mitochondrial supplementation in pig oocytes exhibiting mitochondrial DNA deficiency. Sci Rep 2016; 6:23229. [PMID: 26987907 PMCID: PMC4796791 DOI: 10.1038/srep23229] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/03/2016] [Indexed: 11/08/2022] Open
Abstract
An increasing number of women fail to achieve pregnancy due to either failed fertilization or embryo arrest during preimplantation development. This often results from decreased oocyte quality. Indeed, reduced mitochondrial DNA copy number (mitochondrial DNA deficiency) may disrupt oocyte quality in some women. To overcome mitochondrial DNA deficiency, whilst maintaining genetic identity, we supplemented pig oocytes selected for mitochondrial DNA deficiency, reduced cytoplasmic maturation and lower developmental competence, with autologous populations of mitochondrial isolate at fertilization. Supplementation increased development to blastocyst, the final stage of preimplantation development, and promoted mitochondrial DNA replication prior to embryonic genome activation in mitochondrial DNA deficient oocytes but not in oocytes with normal levels of mitochondrial DNA. Blastocysts exhibited transcriptome profiles more closely resembling those of blastocysts from developmentally competent oocytes. Furthermore, mitochondrial supplementation reduced gene expression patterns associated with metabolic disorders that were identified in blastocysts from mitochondrial DNA deficient oocytes. These results demonstrate the importance of the oocyte’s mitochondrial DNA investment in fertilization outcome and subsequent embryo development to mitochondrial DNA deficient oocytes.
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186
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Wu X, Xu H, Zhang Z, Chang Q, Liao S, Zhang L, Li Y, Wu D, Liang B. Transcriptome Profiles Using Next-Generation Sequencing Reveal Liver Changes in the Early Stage of Diabetes in Tree Shrew (Tupaia belangeri chinensis). J Diabetes Res 2016; 2016:6238526. [PMID: 27069931 PMCID: PMC4812456 DOI: 10.1155/2016/6238526] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 02/06/2016] [Accepted: 02/18/2016] [Indexed: 01/05/2023] Open
Abstract
Determining the liver changes during the early stages of diabetes is critical to understand the nature of the disease and development of novel treatments for it. Advances in the use of animal models and next-generation sequencing technologies offer a powerful tool in connection between liver changes and the diabetes. Here, we created a tree shrew diabetes model akin to type 1 diabetes by using streptozotocin to induce hyperglycemia and hyperlipidemia. Using RNA-seq, we compiled liver transcriptome profiles to determine the differentially expressed genes and to explore the role of hyperglycemia in liver changes. Our results, respectively, identified 14,060 and 14,335 genes in healthy tree shrews and those with diabetes, with 70 genes differentially expressed between the two groups. Gene orthology and KEGG annotation revealed that several of the main biological processes of these genes were related to translational processes, steroid metabolic processes, oxidative stress, inflammation, and hypertension, all of which are highly associated with diabetes and its complications. These results collectively suggest that STZ induces hyperglycemia in tree shrew and that hyperglycemia induced oxidative stress led to high expression of aldose reductase, inflammation, and even cell death in liver tissues during the early stage of diabetes.
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Affiliation(s)
- Xiaoyun Wu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Key Laboratory of Puer Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Haibo Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Zhiguo Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Qing Chang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Shasha Liao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Linqiang Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Yunhai Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Bin Liang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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187
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Ferreira RM, Chiaratti MR, Macabelli CH, Rodrigues CA, Ferraz ML, Watanabe YF, Smith LC, Meirelles FV, Baruselli PS. The Infertility of Repeat-Breeder Cows During Summer Is Associated with Decreased Mitochondrial DNA and Increased Expression of Mitochondrial and Apoptotic Genes in Oocytes1. Biol Reprod 2016; 94:66. [DOI: 10.1095/biolreprod.115.133017] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 01/29/2016] [Indexed: 11/01/2022] Open
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188
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Wachsmuth M, Hübner A, Li M, Madea B, Stoneking M. Age-Related and Heteroplasmy-Related Variation in Human mtDNA Copy Number. PLoS Genet 2016; 12:e1005939. [PMID: 26978189 PMCID: PMC4792396 DOI: 10.1371/journal.pgen.1005939] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 02/24/2016] [Indexed: 12/17/2022] Open
Abstract
The mitochondrial (mt) genome is present in many copies in human cells, and intra-individual variation in mtDNA sequences is known as heteroplasmy. Recent studies found that heteroplasmies are highly tissue-specific, site-specific, and allele-specific, however the functional implications have not been explored. This study investigates variation in mtDNA copy numbers (mtCN) in 12 different tissues obtained at autopsy from 152 individuals (ranging in age from 3 days to 96 years). Three different methods to estimate mtCN were compared: shotgun sequencing (in 4 tissues), capture-enriched sequencing (in 12 tissues) and droplet digital PCR (ddPCR, in 2 tissues). The highest precision in mtCN estimation was achieved using shotgun sequencing data. However, capture-enrichment data provide reliable estimates of relative (albeit not absolute) mtCNs. Comparisons of mtCN from different tissues of the same individual revealed that mtCNs in different tissues are, with few exceptions, uncorrelated. Hence, each tissue of an individual seems to regulate mtCN in a tissue-related rather than an individual-dependent manner. Skeletal muscle (SM) samples showed an age-related decrease in mtCN that was especially pronounced in males, while there was an age-related increase in mtCN for liver (LIV) samples. MtCN in SM samples was significantly negatively correlated with both the total number of heteroplasmic sites and with minor allele frequency (MAF) at two heteroplasmic sites, 408 and 16327. Heteroplasmies at both sites are highly specific for SM, accumulate with aging and are part of functional elements that regulate mtDNA replication. These data support the hypothesis that selection acting on these heteroplasmic sites is reducing mtCN in SM of older individuals.
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Affiliation(s)
- Manja Wachsmuth
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Burkhard Madea
- Institut für Rechtsmedizin, Universitätsklinikum Bonn, Bonn, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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189
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Amberger A, Deutschmann AJ, Traunfellner P, Moser P, Feichtinger RG, Kofler B, Zschocke J. 17β-Hydroxysteroid dehydrogenase type 10 predicts survival of patients with colorectal cancer and affects mitochondrial DNA content. Cancer Lett 2016; 374:149-155. [PMID: 26884257 DOI: 10.1016/j.canlet.2016.02.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 02/04/2023]
Abstract
Mitochondrial energy production is reduced in tumor cells, and altered mitochondrial respiration contributes to tumor progression. Synthesis of proteins coded by mitochondrial DNA (mtDNA) requires the correct processing of long polycistronic precursor RNA molecules. Mitochondrial RNase P, composed of three different proteins (MRPP1, HSD10, and MRPP3), is necessary for correct RNA processing. Here we analyzed the role of RNase P proteins in colorectal cancer. High HSD10 expression was found in 28%; high MRPP1 expression in 40% of colorectal cancers, respectively. Expression of both proteins was not significantly associated with clinicopathological parameters. Survival analysis revealed that loss of HSD10 expression is associated with poor prognosis. Cox regression demonstrated that patients with high HSD10 tumors are at lower risk. High HSD10 expression was significantly associated with high mtDNA content in tumor tissue. A causal effect of HSD10 overexpression or knock down with increased or reduced mtDNA levels, respectively, was confirmed in tumor cell lines. Our data suggest that HSD10 plays a role in alterations of energy metabolism by regulating mtDNA content in colorectal carcinomas, and HSD10 protein analysis may be of prognostic value.
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Affiliation(s)
- Albert Amberger
- Division of Human Genetics, Medical University Innsbruck, Peter Mayr Straße 1, 6020 Innsbruck, Austria.
| | - Andrea J Deutschmann
- Division of Human Genetics, Medical University Innsbruck, Peter Mayr Straße 1, 6020 Innsbruck, Austria
| | - Pia Traunfellner
- Division of Human Genetics, Medical University Innsbruck, Peter Mayr Straße 1, 6020 Innsbruck, Austria
| | - Patrizia Moser
- Institute of General Pathology, Medical University Innsbruck, Müllerstraße 44, 6020 Innsbruck, Austria
| | - René G Feichtinger
- Laura-Bassi Centre of Expertise-THERAPEP, Research Program for Receptor Biochemistry and Tumor Metabolism, Department of Pediatrics, Paracelsus Medical University Salzburg, Müllner Hauptstraße 48, 5020 Salzburg, Austria
| | - Barbara Kofler
- Laura-Bassi Centre of Expertise-THERAPEP, Research Program for Receptor Biochemistry and Tumor Metabolism, Department of Pediatrics, Paracelsus Medical University Salzburg, Müllner Hauptstraße 48, 5020 Salzburg, Austria
| | - Johannes Zschocke
- Division of Human Genetics, Medical University Innsbruck, Peter Mayr Straße 1, 6020 Innsbruck, Austria.
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190
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Botsios S, Manuelidis L. CJD and Scrapie Require Agent-Associated Nucleic Acids for Infection. J Cell Biochem 2016; 117:1947-58. [PMID: 26773845 DOI: 10.1002/jcb.25495] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 01/15/2016] [Indexed: 01/18/2023]
Abstract
Unlike Alzheimer's and most other neurodegenerative diseases, Transmissible Spongiform Encephalopathies (TSEs) are all caused by actively replicating infectious particles of viral size and density. Different strain-specific TSE agents cause CJD, kuru, scrapie and BSE, and all behave as latent viruses that evade adaptive immune responses and can persist for years in lymphoreticular tissues. A foreign viral structure with a nucleic acid genome best explains these TSE strains and their endemic and epidemic spread in susceptible species. Nevertheless, it is widely believed that host prion protein (PrP), without any genetic material, encodes all these strains. We developed rapid infectivity assays that allowed us to reproducibly isolate infectious particles where >85% of the starting titer separated from the majority of host components, including PrP. Remarkably, digestion of all forms of PrP did not reduce brain particle titers. To ask if TSE agents, as other viruses, require nucleic acids, we exposed high titer FU-CJD and 22L scrapie particles to potent nucleases. Both agent-strains were propagated in GT1 neuronal cells to avoid interference by complex degenerative brain changes that can impede nuclease digestions. After exposure to nucleases that are active in sarkosyl, infectivity of both agents was reproducibly reduced by ≥99%. No gold-stained host proteins or any form of PrP were visibly altered by these nucleases. In contrast, co-purifying protected mitochondrial DNA and circular SPHINX DNAs were destroyed. These findings demonstrate that TSE agents require protected genetic material to infect their hosts, and should reopen investigation of essential agent nucleic acids. J. Cell. Biochem. 117: 1947-1958, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Sotirios Botsios
- Department of Surgery, Section of Neuropathology, Yale Medical School, New Haven, 06510, Connecticut
| | - Laura Manuelidis
- Department of Surgery, Section of Neuropathology, Yale Medical School, New Haven, 06510, Connecticut
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191
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Yamazaki M, Munetsuna E, Yamada H, Ando Y, Mizuno G, Murase Y, Kondo K, Ishikawa H, Teradaira R, Suzuki K, Ohashi K. Fructose consumption induces hypomethylation of hepatic mitochondrial DNA in rats. Life Sci 2016; 149:146-52. [PMID: 26869391 DOI: 10.1016/j.lfs.2016.02.020] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 12/11/2015] [Accepted: 02/06/2016] [Indexed: 10/22/2022]
Abstract
AIMS Fructose may play a crucial role in the pathogenesis of metabolic syndrome (MetS). However, the pathogenic mechanism of the fructose-induced MetS has not yet been investigated fully. Recently, several reports have investigated the association between mitochondrial DNA (mtDNA) and MetS. We examined the effect of fructose-rich diets on mtDNA content, transcription, and epigenetic changes. MAIN METHODS Four-week-old male Sprague-Dawley rats were offered a 20% fructose solution for 14weeks. We quantified mRNAs for hepatic mitochondrial genes and analyzed the mtDNA methylation (5-mC and 5-hmC) levels using ELISA kits. KEY FINDINGS Histological analysis revealed non-alcoholic fatty liver disease (NAFLD) in fructose-fed rats. Hepatic mtDNA content and transcription were higher in fructose-fed rats than in the control group. Global hypomethylation of mtDNA was also observed in fructose-fed rats. SIGNIFICANCE We showed that fructose consumption stimulates hepatic mtDNA-encoded gene expression. This phenomenon might be due to epigenetic changes in mtDNA. Fructose-induced mitochondrial epigenetic changes appear to be a novel mechanism underlying the pathology of MetS and NAFLD.
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Affiliation(s)
- Mirai Yamazaki
- Department of Clinical Biochemistry, Fujita Health University School of Health Sciences, Toyoake, Japan
| | - Eiji Munetsuna
- Department of Biochemistry, Fujita Health University School of Medicine, Toyoake, Japan
| | - Hiroya Yamada
- Department of Hygiene, Fujita Health University School of Medicine, Toyoake, Japan.
| | - Yoshitaka Ando
- Department of Joint Research Laboratory of Clinical Medicine, Fujita Health University School of Medicine, Toyoake, Japan
| | - Genki Mizuno
- Department of Clinical Biochemistry, Fujita Health University School of Health Sciences, Toyoake, Japan
| | - Yuri Murase
- Department of Clinical Biochemistry, Fujita Health University School of Health Sciences, Toyoake, Japan
| | - Kanako Kondo
- Department of Clinical Biochemistry, Fujita Health University School of Health Sciences, Toyoake, Japan
| | - Hiroaki Ishikawa
- Department of Clinical Biochemistry, Fujita Health University School of Health Sciences, Toyoake, Japan
| | - Ryoji Teradaira
- Department of Clinical Biochemistry, Fujita Health University School of Health Sciences, Toyoake, Japan
| | - Koji Suzuki
- Department of Public Health, Fujita Health University School of Health Sciences, Toyoake, Japan
| | - Koji Ohashi
- Department of Clinical Biochemistry, Fujita Health University School of Health Sciences, Toyoake, Japan.
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192
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Qu J, Yasukawa T, Kang D. Suppression of mitochondrial transcription initiation complexes changes the balance of replication intermediates of mitochondrial DNA and reduces 7S DNA in cultured human cells. J Biochem 2016; 160:49-57. [PMID: 26861994 DOI: 10.1093/jb/mvw010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 01/20/2016] [Indexed: 11/13/2022] Open
Abstract
Analysis of replicating mammalian mitochondrial DNA (mtDNA) suggested that initiation of the replication occurs not only at the specific position, Ori-H but also across a broad zone in mtDNA. We investigated relationship of mitochondrial transcription initiation which takes place upstream of Ori-H and mtDNA replication initiation through analysing the effect of knockdown of mitochondrial transcription factor B2, TFB2M and mitochondrial RNA polymerase, POLRMT, components of the transcription initiation complexes in cultured human cells. Under the conditions where suppression of the transcription initiation complexes was achieved by simultaneous depletion of TFB2M and POLRMT, decrease of replication intermediates of mtDNA RITOLS replication mode accompanied reduction in mtDNA copy number. On the other hand, replication intermediates of coupled leading and lagging strand DNA replication, another proposed replication mode, appeared to be less affected. The findings support the view that the former mode involves transcription from the light strand promoter (LSP), and suggest that initiation of the latter mode is independent from the transcription and has distinct regulation. Further, knockdown of TFB2M alone caused significant decrease of 7S DNA, which implies that transcription initiation complexes formed at the LSP engage 7S DNA synthesis more frequently than the initiation of productive replication and transcription.
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Affiliation(s)
- Jianhua Qu
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takehiro Yasukawa
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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193
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Alán L, Špaček T, Ježek P. Delaunay algorithm and principal component analysis for 3D visualization of mitochondrial DNA nucleoids by Biplane FPALM/dSTORM. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 45:443-61. [PMID: 26846371 DOI: 10.1007/s00249-016-1114-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 12/21/2015] [Accepted: 01/12/2016] [Indexed: 12/16/2022]
Abstract
Data segmentation and object rendering is required for localization super-resolution microscopy, fluorescent photoactivation localization microscopy (FPALM), and direct stochastic optical reconstruction microscopy (dSTORM). We developed and validated methods for segmenting objects based on Delaunay triangulation in 3D space, followed by facet culling. We applied them to visualize mitochondrial nucleoids, which confine DNA in complexes with mitochondrial (mt) transcription factor A (TFAM) and gene expression machinery proteins, such as mt single-stranded-DNA-binding protein (mtSSB). Eos2-conjugated TFAM visualized nucleoids in HepG2 cells, which was compared with dSTORM 3D-immunocytochemistry of TFAM, mtSSB, or DNA. The localized fluorophores of FPALM/dSTORM data were segmented using Delaunay triangulation into polyhedron models and by principal component analysis (PCA) into general PCA ellipsoids. The PCA ellipsoids were normalized to the smoothed volume of polyhedrons or by the net unsmoothed Delaunay volume and remodeled into rotational ellipsoids to obtain models, termed DVRE. The most frequent size of ellipsoid nucleoid model imaged via TFAM was 35 × 45 × 95 nm; or 35 × 45 × 75 nm for mtDNA cores; and 25 × 45 × 100 nm for nucleoids imaged via mtSSB. Nucleoids encompassed different point density and wide size ranges, speculatively due to different activity stemming from different TFAM/mtDNA stoichiometry/density. Considering twofold lower axial vs. lateral resolution, only bulky DVRE models with an aspect ratio >3 and tilted toward the xy-plane were considered as two proximal nucleoids, suspicious occurring after division following mtDNA replication. The existence of proximal nucleoids in mtDNA-dSTORM 3D images of mtDNA "doubling"-supported possible direct observations of mt nucleoid division after mtDNA replication.
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Affiliation(s)
- Lukáš Alán
- Department of Membrane Transport Biophysics, No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Tomáš Špaček
- Department of Membrane Transport Biophysics, No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Petr Ježek
- Department of Membrane Transport Biophysics, No. 75, Institute of Physiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague 4, Czech Republic.
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194
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Chatre L, Montagne B, Ricchetti M. A Single-Cell Resolution Imaging Protocol of Mitochondrial DNA Dynamics in Physiopathology, mTRIP, Which Also Evaluates Sublethal Cytotoxicity. Methods Mol Biol 2016; 1351:49-65. [PMID: 26530674 DOI: 10.1007/978-1-4939-3040-1_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Mitochondria autonomously replicate and transcribe their own genome, which is present in multiple copies in the organelle. Transcription and replication of the mitochondrial DNA (mtDNA), which are defined here as mtDNA processing, are essential for mitochondrial function. The extent, efficiency, and coordination of mtDNA processing are key parameters of the mitochondrial state in living cells. Recently, single-cell analysis of mtDNA processing revealed a large and dynamic heterogeneity of mitochondrial populations in single cells, which is linked to mitochondrial function and is altered during disease. This was achieved using mitochondrial Transcription and Replication Imaging Protocol (mTRIP), a modified fluorescence in situ hybridization (FISH) approach that simultaneously reveals the mitochondrial RNA content and mtDNA engaged in initiation of replication at the single-cell level. mTRIP can also be coupled to immunofluorescence or MitoTracker, resulting in the additional labeling of proteins or active mitochondria, respectively. Therefore, mTRIP detects quantitative and qualitative alterations of the dynamics of mtDNA processing in human cells that respond to physiological changes or result from diseases. In addition, we show here that mTRIP is a rather sensitive tool for detecting mitochondrial alterations that may lead to loss of cell viability, and is thereby a useful tool for monitoring sublethal cytotoxicity for instance during chronic drug treatment.
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Affiliation(s)
- Laurent Chatre
- Team "Stability of Nuclear and Mitochondrial DNA" CNRS UMR 3525, Paris, France
- Stem Cells and Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, 25-28 Rue du Dr. Roux, Paris, France
| | - Benjamin Montagne
- Team "Stability of Nuclear and Mitochondrial DNA" CNRS UMR 3525, Paris, France
- Stem Cells and Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, 25-28 Rue du Dr. Roux, Paris, France
| | - Miria Ricchetti
- Team "Stability of Nuclear and Mitochondrial DNA" CNRS UMR 3525, Paris, France.
- Stem Cells and Development, Department of Developmental & Stem Cell Biology, Institut Pasteur, 25-28 Rue du Dr. Roux, Paris, France.
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195
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Perera OP, Walsh TK, Luttrell RG. Complete Mitochondrial Genome of Helicoverpa zea (Lepidoptera: Noctuidae) and Expression Profiles of Mitochondrial-Encoded Genes in Early and Late Embryos. JOURNAL OF INSECT SCIENCE (ONLINE) 2016; 16:iew023. [PMID: 27126963 PMCID: PMC4864584 DOI: 10.1093/jisesa/iew023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 03/06/2016] [Indexed: 05/06/2023]
Abstract
The mitochondrial genome (mitogenome) of the bollworm, Helicoverpa zea (Boddie), was assembled using paired-end nucleotide sequence reads generated with a next-generation sequencing platform. Assembly resulted in a mitogenome of 15,348 bp with greater than 17,000-fold average coverage. Organization of the H. zea mitogenome (gene order and orientation) was identical to other known lepidopteran mitogenome sequences. Compared with Helicoverpa armigera (Hübner) mitogenome, there were a few differences in the lengths of gaps between genes, but the lengths of nucleotide overlaps were essentially conserved between the two species. Nucleotide composition of the H. zea mitochondrial genome was very similar to those of the related species H. armigera and Helicoverpa punctigera Wallengren. Mapping of RNA-Seq reads obtained from 2-h eggs and 48-h embryos to protein coding genes (PCG) revealed that all H. zea PCGs were processed as single mature gene transcripts except for the bicistronic atp8 + atp6 transcript. A tRNA-like sequence predicted to form a hammer-head-like secondary structure that may play a role in transcription start and mitogenome replication was identified within the control region of the H. zea mitogenome. Similar structures were also found within the control regions of several other lepidopteran species. Expression analysis revealed significant differences in levels of expression of PCGs within each developmental stage, but the pattern of variation was similar in both developmental stages analyzed in this study. Mapping of RNA-Seq reads to PCG transcripts also identified transcription termination and polyadenylation sites that differed from the sites described in other lepidopteran species.
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Affiliation(s)
- Omaththage P Perera
- Southern Insect Management Research Unit, USDA-ARS, Stoneville, MS 38776 (; ; ),
| | - Thomas K Walsh
- Land and Water Flagship, Commonwealth Scientific and Industrial Research Organization, Clunies Ross Street, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Randall G Luttrell
- Southern Insect Management Research Unit, USDA-ARS, Stoneville, MS 38776 (; ; )
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196
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Abstract
Methods of in vivo visualization and manipulation of mitochondrial genetic machinery are limited due to the need to surpass not only the cytoplasmic membrane but also two mitochondrial membranes. Here, we employ the matrix-addressing sequence of mitochondrial ribosomal 5S-rRNA (termed MAM), which is naturally imported into mammalian mitochondria, to construct an import system for in vivo targeting of mitochondrial (mt) DNA or mtRNA, in order to provide fluorescence hybridization of the desired sequences.
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Affiliation(s)
- Jaroslav Zelenka
- Department No. 75, Membrane Transprot Biophysics, Institute of Physiology, Academy of Sciences of the Czech Republic, Videnska 1084, Prague 4, 14220, Czech Republic
| | - Petr Ježek
- Department No. 75, Membrane Transprot Biophysics, Institute of Physiology, Academy of Sciences of the Czech Republic, Videnska 1084, Prague 4, 14220, Czech Republic.
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197
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198
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Novin MG, Allahveisi A, Noruzinia M, Farhadifar F, Yousefian E, Fard AD, Salimi M. The relationship between transcript expression levels of nuclear encoded (TFAM, NRF1) and mitochondrial encoded (MT-CO1) genes in single human oocytes during oocyte maturation. Balkan J Med Genet 2015; 18:39-46. [PMID: 26929904 PMCID: PMC4768824 DOI: 10.1515/bjmg-2015-0004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In some cases of infertility in women, human oocytes fail to mature when they reach the metaphase II (MII) stage. Mitochondria plays an important role in oocyte maturation. A large number of mitochondrial DNA (mtDNA), copied in oocytes, is essential for providing adenosine triphosphate (ATP) during oocyte maturation. The purpose of this study was to identify the relationship between transcript expression levels of the mitochondrial encoded gene (MT-CO1) and two nuclear encoded genes, nuclear respiratory factor 1 (NRF1) and mitochondrial transcription factor A (TFAM) in various stages of human oocyte maturation. Nine consenting patients, age 21–35 years old, with male factors were selected for ovarian stimulation and intracytoplasmic sperm injection (ICSI) procedures. mRNA levels of mitochondrial-related genes were performed by singlecell TaqMan® quantitative real-time polymerase chain reaction (qRT-PCR). There was no significant relationship between the relative expression levels in germinal vesicle (GV) stage oocytes (p = 0.62). On the contrary, a significant relationship was seen between the relative expression levels of TFAM and NRF1 and the MT-CO1 genes at the stages of metaphase I (MI) and MII (p = 0.03 and p = 0.002). A relationship exists between the transcript expression levels of TFAM and NRF1, and MT-CO1 genes in various stages of human oocyte maturation.
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Affiliation(s)
- M Ghaffari Novin
- Department of Biology and Anatomical Sciences, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - A Allahveisi
- Department of Anatomical Sciences, Faculty of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - M Noruzinia
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - F Farhadifar
- Deptartment of Obstetrics and Gynecology, School of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - E Yousefian
- Department of Anatomical Sciences, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - A Dehghani Fard
- Sarem Cell Research Center (SCRC), Sarem Women's Hospital, Tehran, Iran
| | - M Salimi
- Department of Biology and Anatomical Sciences, Shahid Beheshti University of Medical Science, Tehran, Iran
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199
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Nakahira K, Hisata S, Choi AMK. The Roles of Mitochondrial Damage-Associated Molecular Patterns in Diseases. Antioxid Redox Signal 2015; 23:1329-50. [PMID: 26067258 PMCID: PMC4685486 DOI: 10.1089/ars.2015.6407] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
SIGNIFICANCE Mitochondria, vital cellular power plants to generate energy, are involved in immune responses. Mitochondrial damage-associated molecular patterns (DAMPs) are molecules that are released from mitochondria to extracellular space during cell death and include not only proteins but also DNA or lipids. Mitochondrial DAMPs induce inflammatory responses and are critically involved in the pathogenesis of various diseases. RECENT ADVANCES Recent studies elucidate the molecular mechanisms by which mitochondrial DAMPs are released and initiate immune responses by use of genetically modulated cells or animals. Importantly, the levels of mitochondrial DAMPs in patients are often associated with severity and prognosis of human diseases, such as infection, asthma, ischemic heart disease, and cancer. CRITICAL ISSUES Although mitochondrial DAMPs can represent proinflammatory molecules in various experimental models, their roles in human diseases may be multifunctional and complex. It remains unclear where and how mitochondrial DAMPs are liberated into extracellular spaces and exert their biological functions particularly in vivo. In addition, while mitochondria can secrete several types of DAMPs during cell death, the interaction of each mitochondrial DAMP (e.g., synergistic effects) remains unclear. FUTURE DIRECTIONS Regulation of mitochondrial DAMP-mediated immune responses may be important to alter the progression of human diseases. In addition, measuring mitochondrial DAMPs in patients may be clinically useful as biomarkers to predict prognosis or response to therapies. Further studies of the mechanisms by which mitochondrial DAMPs impact the initiation and progression of diseases may lead to the development of therapeutics specifically targeting this pathway. Antioxid.
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Affiliation(s)
- Kiichi Nakahira
- 1 Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College and New York-Presbyterian Hospital , New York, New York.,2 Division of Pulmonary and Critical Care Medicine, Weill Cornell Medical College , New York, New York
| | - Shu Hisata
- 1 Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College and New York-Presbyterian Hospital , New York, New York.,2 Division of Pulmonary and Critical Care Medicine, Weill Cornell Medical College , New York, New York
| | - Augustine M K Choi
- 1 Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College and New York-Presbyterian Hospital , New York, New York.,2 Division of Pulmonary and Critical Care Medicine, Weill Cornell Medical College , New York, New York
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200
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Malik AN, Parsade CK, Ajaz S, Crosby-Nwaobi R, Gnudi L, Czajka A, Sivaprasad S. Altered circulating mitochondrial DNA and increased inflammation in patients with diabetic retinopathy. Diabetes Res Clin Pract 2015; 110:257-65. [PMID: 26625720 DOI: 10.1016/j.diabres.2015.10.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 08/21/2015] [Accepted: 10/02/2015] [Indexed: 12/20/2022]
Abstract
AIMS We previously showed that circulating mitochondrial DNA (MtDNA) levels are altered in diabetic nephropathy. The aim of the current study was to determine if circulating MtDNA levels are altered in patients with diabetic retinopathy. METHODS Patients with diabetes (n=220) were studied in a clinical setting using a cross-sectional study design as the following groups: DR-0 (no retinopathy, n=53), DR-m (mild non-proliferative diabetic retinopathy NPDR, n=98) and DR-s (severe proliferative diabetic retinopathy, n=69). MtDNA content in peripheral blood DNA was measured as the mitochondrial to nuclear genome ratio using real time qPCR. Circulating cytokines were measured using the luminex assay and MtDNA damage was assessed using PCR. Differences were considered significant at P<0.05. RESULTS Circulating MtDNA values were higher in DR-m compared to DR-0 (P=0.02) and decreased in DR-s compared to DR-m (P=0.001). These changes remained significant after adjusting for associated parameters. In parallel there were increased levels of circulating cytokines IL-4 (P=0.005) and TNF-α (P=0.02) in the DR-s group and increased MtDNA damage in DR-m patients compared to DR-0 (P=0.03). CONCLUSIONS Our data show that circulating MtDNA levels are independently associated with diabetic retinopathy, showing an increase in DR-m and decrease in DR-s with a parallel increase in MtDNA damage and inflammation. Hyperglycemia-induced changes in MtDNA in early diabetes may contribute to inflammation and progression of diabetic retinopathy. Longitudinal studies should be carried out to determine a potential causality of MtDNA in diabetic retinopathy.
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Affiliation(s)
- Afshan N Malik
- King's College London, Diabetes Research Group, Division of Diabetes and Nutritional Sciences, Faculty of Life Sciences and Medicine, UK.
| | - Chandani K Parsade
- King's College London, Diabetes Research Group, Division of Diabetes and Nutritional Sciences, Faculty of Life Sciences and Medicine, UK
| | - Saima Ajaz
- King's College London, Diabetes Research Group, Division of Diabetes and Nutritional Sciences, Faculty of Life Sciences and Medicine, UK
| | - Roxanne Crosby-Nwaobi
- King's College London, Laser and Retinal Research Unit, Department of Ophthalmology, UK; King's College London, NIHR Moorfields Biomedical Research Centre, UK
| | - Luigi Gnudi
- King's College London, Cardiovascular Division, Faculty of Life Science & Medicine, UK
| | - Anna Czajka
- King's College London, Diabetes Research Group, Division of Diabetes and Nutritional Sciences, Faculty of Life Sciences and Medicine, UK
| | - Sobha Sivaprasad
- King's College London, Laser and Retinal Research Unit, Department of Ophthalmology, UK; King's College London, NIHR Moorfields Biomedical Research Centre, UK
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