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Ferreira T, Rodriguez S. Mitochondrial DNA: Inherent Complexities Relevant to Genetic Analyses. Genes (Basel) 2024; 15:617. [PMID: 38790246 PMCID: PMC11121663 DOI: 10.3390/genes15050617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Mitochondrial DNA (mtDNA) exhibits distinct characteristics distinguishing it from the nuclear genome, necessitating specific analytical methods in genetic studies. This comprehensive review explores the complex role of mtDNA in a variety of genetic studies, including genome-wide, epigenome-wide, and phenome-wide association studies, with a focus on its implications for human traits and diseases. Here, we discuss the structure and gene-encoding properties of mtDNA, along with the influence of environmental factors and epigenetic modifications on its function and variability. Particularly significant are the challenges posed by mtDNA's high mutation rate, heteroplasmy, and copy number variations, and their impact on disease susceptibility and population genetic analyses. The review also highlights recent advances in methodological approaches that enhance our understanding of mtDNA associations, advocating for refined genetic research techniques that accommodate its complexities. By providing a comprehensive overview of the intricacies of mtDNA, this paper underscores the need for an integrated approach to genetic studies that considers the unique properties of mitochondrial genetics. Our findings aim to inform future research and encourage the development of innovative methodologies to better interpret the broad implications of mtDNA in human health and disease.
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Affiliation(s)
- Tomas Ferreira
- Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0SL, UK
| | - Santiago Rodriguez
- Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1QU, UK
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2
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Lee W, Zamudio-Ochoa A, Buchel G, Podlesniy P, Marti Gutierrez N, Puigròs M, Calderon A, Tang HY, Li L, Mikhalchenko A, Koski A, Trullas R, Mitalipov S, Temiakov D. Molecular basis for maternal inheritance of human mitochondrial DNA. Nat Genet 2023; 55:1632-1639. [PMID: 37723262 PMCID: PMC10763495 DOI: 10.1038/s41588-023-01505-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 08/17/2023] [Indexed: 09/20/2023]
Abstract
Uniparental inheritance of mitochondrial DNA (mtDNA) is an evolutionary trait found in nearly all eukaryotes. In many species, including humans, the sperm mitochondria are introduced to the oocyte during fertilization1,2. The mechanisms hypothesized to prevent paternal mtDNA transmission include ubiquitination of the sperm mitochondria and mitophagy3,4. However, the causative mechanisms of paternal mtDNA elimination have not been defined5,6. We found that mitochondria in human spermatozoa are devoid of intact mtDNA and lack mitochondrial transcription factor A (TFAM)-the major nucleoid protein required to protect, maintain and transcribe mtDNA. During spermatogenesis, sperm cells express an isoform of TFAM, which retains the mitochondrial presequence, ordinarily removed upon mitochondrial import. Phosphorylation of this presequence prevents mitochondrial import and directs TFAM to the spermatozoon nucleus. TFAM relocalization from the mitochondria of spermatogonia to the spermatozoa nucleus directly correlates with the elimination of mtDNA, thereby explaining maternal inheritance in this species.
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Affiliation(s)
- William Lee
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Angelica Zamudio-Ochoa
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Gina Buchel
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Petar Podlesniy
- Neurobiology Unit, Institut d'Investigacions Biomèdiques de Barcelona (IIBB-CSIC-IDIBAPS) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Nuria Marti Gutierrez
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, OR, USA
| | - Margalida Puigròs
- Neurobiology Unit, Institut d'Investigacions Biomèdiques de Barcelona (IIBB-CSIC-IDIBAPS) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Anna Calderon
- Neurobiology Unit, Institut d'Investigacions Biomèdiques de Barcelona (IIBB-CSIC-IDIBAPS) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Hsin-Yao Tang
- Molecular & Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Li Li
- Department of Pathology and Genomic Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Aleksei Mikhalchenko
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, OR, USA
| | - Amy Koski
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, OR, USA
| | - Ramon Trullas
- Neurobiology Unit, Institut d'Investigacions Biomèdiques de Barcelona (IIBB-CSIC-IDIBAPS) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Shoukhrat Mitalipov
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, Portland, OR, USA
| | - Dmitry Temiakov
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
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3
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Seel A, Padovani F, Mayer M, Finster A, Bureik D, Thoma F, Osman C, Klecker T, Schmoller KM. Regulation with cell size ensures mitochondrial DNA homeostasis during cell growth. Nat Struct Mol Biol 2023; 30:1549-1560. [PMID: 37679564 PMCID: PMC10584693 DOI: 10.1038/s41594-023-01091-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/07/2023] [Indexed: 09/09/2023]
Abstract
To maintain stable DNA concentrations, proliferating cells need to coordinate DNA replication with cell growth. For nuclear DNA, eukaryotic cells achieve this by coupling DNA replication to cell-cycle progression, ensuring that DNA is doubled exactly once per cell cycle. By contrast, mitochondrial DNA replication is typically not strictly coupled to the cell cycle, leaving the open question of how cells maintain the correct amount of mitochondrial DNA during cell growth. Here, we show that in budding yeast, mitochondrial DNA copy number increases with cell volume, both in asynchronously cycling populations and during G1 arrest. Our findings suggest that cell-volume-dependent mitochondrial DNA maintenance is achieved through nuclear-encoded limiting factors, including the mitochondrial DNA polymerase Mip1 and the packaging factor Abf2, whose amount increases in proportion to cell volume. By directly linking mitochondrial DNA maintenance to nuclear protein synthesis and thus cell growth, constant mitochondrial DNA concentrations can be robustly maintained without a need for cell-cycle-dependent regulation.
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Affiliation(s)
- Anika Seel
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Francesco Padovani
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Moritz Mayer
- Institute of Cell Biology, University of Bayreuth, Bayreuth, Germany
| | - Alissa Finster
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Daniela Bureik
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Felix Thoma
- Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Christof Osman
- Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Till Klecker
- Institute of Cell Biology, University of Bayreuth, Bayreuth, Germany
| | - Kurt M Schmoller
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany.
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4
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Kozhukhar N, Alexeyev MF. 35 Years of TFAM Research: Old Protein, New Puzzles. BIOLOGY 2023; 12:823. [PMID: 37372108 DOI: 10.3390/biology12060823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/29/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023]
Abstract
Transcription Factor A Mitochondrial (TFAM), through its contributions to mtDNA maintenance and expression, is essential for cellular bioenergetics and, therefore, for the very survival of cells. Thirty-five years of research on TFAM structure and function generated a considerable body of experimental evidence, some of which remains to be fully reconciled. Recent advancements allowed an unprecedented glimpse into the structure of TFAM complexed with promoter DNA and TFAM within the open promoter complexes. These novel insights, however, raise new questions about the function of this remarkable protein. In our review, we compile the available literature on TFAM structure and function and provide some critical analysis of the available data.
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Affiliation(s)
- Natalya Kozhukhar
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Mikhail F Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
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5
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Kozhukhar N, Alexeyev MF. The C-Terminal Tail of Mitochondrial Transcription Factor A Is Dispensable for Mitochondrial DNA Replication and Transcription In Situ. Int J Mol Sci 2023; 24:9430. [PMID: 37298383 PMCID: PMC10253692 DOI: 10.3390/ijms24119430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/04/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Mitochondrial transcription factor A (TFAM) is one of the widely studied but still incompletely understood mitochondrial protein, which plays a crucial role in the maintenance and transcription of mitochondrial DNA (mtDNA). The available experimental evidence is often contradictory in assigning the same function to various TFAM domains, partly owing to the limitations of those experimental systems. Recently, we developed the GeneSwap approach, which enables in situ reverse genetic analysis of mtDNA replication and transcription and is devoid of many of the limitations of the previously used techniques. Here, we utilized this approach to analyze the contributions of the TFAM C-terminal (tail) domain to mtDNA transcription and replication. We determined, at a single amino acid (aa) resolution, the TFAM tail requirements for in situ mtDNA replication in murine cells and established that tail-less TFAM supports both mtDNA replication and transcription. Unexpectedly, in cells expressing either C-terminally truncated murine TFAM or DNA-bending human TFAM mutant L6, HSP1 transcription was impaired to a greater extent than LSP transcription. Our findings are incompatible with the prevailing model of mtDNA transcription and thus suggest the need for further refinement.
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Affiliation(s)
| | - Mikhail F. Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
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6
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Abu Shelbayeh O, Arroum T, Morris S, Busch KB. PGC-1α Is a Master Regulator of Mitochondrial Lifecycle and ROS Stress Response. Antioxidants (Basel) 2023; 12:antiox12051075. [PMID: 37237941 DOI: 10.3390/antiox12051075] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/20/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Mitochondria play a major role in ROS production and defense during their life cycle. The transcriptional activator PGC-1α is a key player in the homeostasis of energy metabolism and is therefore closely linked to mitochondrial function. PGC-1α responds to environmental and intracellular conditions and is regulated by SIRT1/3, TFAM, and AMPK, which are also important regulators of mitochondrial biogenesis and function. In this review, we highlight the functions and regulatory mechanisms of PGC-1α within this framework, with a focus on its involvement in the mitochondrial lifecycle and ROS metabolism. As an example, we show the role of PGC-1α in ROS scavenging under inflammatory conditions. Interestingly, PGC-1α and the stress response factor NF-κB, which regulates the immune response, are reciprocally regulated. During inflammation, NF-κB reduces PGC-1α expression and activity. Low PGC-1α activity leads to the downregulation of antioxidant target genes resulting in oxidative stress. Additionally, low PGC-1α levels and concomitant oxidative stress promote NF-κB activity, which exacerbates the inflammatory response.
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Affiliation(s)
- Othman Abu Shelbayeh
- Institute of Integrative Cell Biology and Physiology, University of Münster, Schlossplatz 5, 48149 Münster, Germany
| | - Tasnim Arroum
- Institute of Integrative Cell Biology and Physiology, University of Münster, Schlossplatz 5, 48149 Münster, Germany
- Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48202, USA
| | - Silke Morris
- Institute of Integrative Cell Biology and Physiology, University of Münster, Schlossplatz 5, 48149 Münster, Germany
| | - Karin B Busch
- Institute of Integrative Cell Biology and Physiology, University of Münster, Schlossplatz 5, 48149 Münster, Germany
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7
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Effect of prebiotics administered during embryo development on mitochondria in intestinal and immune tissues of adult broiler chickens. Poult Sci 2023; 102:102663. [PMID: 37030257 PMCID: PMC10105484 DOI: 10.1016/j.psj.2023.102663] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Mitochondria are cellular organelles that are the place of many metabolic processes and thus have a significant impact on the proper functioning of the organism. These organelles respond easily to environmental stimuli and cellular energy demands. To ensure the proper functioning of mitochondria, a high supply of specific nutrients is needed. Literature reports suggest that a favorable profile of the intestinal microbiota may improve the functioning of the mitochondria. The gut microbiota transmits a signal to the mitochondria of the mucosa cells. This signaling alters mitochondrial metabolism, activates cells of the immune system, and alters intestinal epithelial barrier functions. The aim of the study is to determine the relative number of mtDNA copies and to analyze the mitochondrial expression of genes related to respiratory chain proteins and energy metabolism in the intestinal mucosa and cecal tonsils of broiler chickens injected on the d 12 of egg incubation with various prebiotics. 300 incubated eggs of Ross 308 broiler chicken on d 12 of incubation were injected with: control group with physiological saline, prebiotics: XOS3, XOS4, MOS3, and MOS4. On d 42 after hatching, 8 individuals from each group were sacrificed. Cecal mucosa and cecal tonsils were collected postmortem for DNA and RNA isolation. Relative mitochondrial DNA copy number analysis was performed by qPCR method using 2 calculation methods. Gene expression analysis of the cecal tonsils and cecal mucosa was performed by RT-qPCR for the gene panel selected based on literature data and gene functions related to mitochondria: CS, EPX (MPO), CYCS, TFAM, NRF1, ND2, MnSOD (SOD2). As the results showed the overall mt DNA copy number is stable in both tissues. The significant change in gene expression in cecal mucosa was induced by XOS4 and MOS3. Both prebiotics caused upregulation of gene expression. In cecal tonsils all prebiotics caused downregulation of entire set of genes under the analysis. Statistically significant results of gene expression were detected for CYCS, ND2, NRF, TFAM for all experimental groups.
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8
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Seike H, Ishimori K, Watanabe A, Kiryu M, Hatakeyama S, Tanaka S, Yoshihara R. Two high-mobility group domains of MHG1 are necessary to maintain mtDNA in Neurospora crassa. Fungal Biol 2022; 126:826-833. [PMID: 36517150 DOI: 10.1016/j.funbio.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 10/13/2022] [Accepted: 11/08/2022] [Indexed: 11/15/2022]
Abstract
The mhg1 (NCU02695/ada-23) gene encodes the mitochondrial high-mobility group box (HMG-box or HMGB) protein in Neurospora crassa. The mhg1 KO strain (mhg1KO) has mitochondrial DNA (mtDNA) instability and a short lifespan; however, the function of MHG1 remains unclear. To investigate the role of this protein in the maintenance of mtDNA, domain deleted MHG1 proteins were expressed in the mhg1KO strain, and their effects were analyzed. We identified two putative HMG-domains, HMGBI and HMGBII. Although deletion of the HMG-box did not abolish MHG1's mitochondrial localization, the mhg1KO phenotype of a severe growth defect and a high sensitivity to mutagens could not be restored by introduction of HMG-box deleted mhg1 gene into the KO strain. It was indicated that recombinant full-length MHG1, i.e., mitochondrial targeting sequence (MTS) containing protein, did not exhibit explicit DNA binding, whereas the MHG1 protein truncated for the MTS sequence did in vitro by an electrophoretic mobility shift assay. Furthermore, recombinant MHG1 protein lacking MTS and HMG-domains, either HMGBI or HMGBII, had DNA affinity and an altered band shift pattern compared with MTS-truncated MHG1 protein. These results suggest that cleavage of MTS and appropriate DNA binding via HMG-domains are indispensable for maintaining mtDNA in N. crassa.
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Affiliation(s)
- Hayami Seike
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Keisuke Ishimori
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Asagi Watanabe
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Mao Kiryu
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Shin Hatakeyama
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Shuuitsu Tanaka
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan
| | - Ryouhei Yoshihara
- Department of Regulatory Biology, Faculty of Science, Saitama University, Shimo-Ohkubo 255, Sakura-ku, Saitama, Saitama, 338-8570, Japan.
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9
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Kozhukhar N, Spadafora D, Rodriguez YAR, Alexeyev MF. A Method for In Situ Reverse Genetic Analysis of Proteins Involved mtDNA Replication. Cells 2022; 11:2168. [PMID: 35883613 PMCID: PMC9316749 DOI: 10.3390/cells11142168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/29/2022] [Accepted: 07/10/2022] [Indexed: 02/01/2023] Open
Abstract
The unavailability of tractable reverse genetic analysis approaches represents an obstacle to a better understanding of mitochondrial DNA replication. Here, we used CRISPR-Cas9 mediated gene editing to establish the conditional viability of knockouts in the key proteins involved in mtDNA replication. This observation prompted us to develop a set of tools for reverse genetic analysis in situ, which we called the GeneSwap approach. The technique was validated by identifying 730 amino acid (aa) substitutions in the mature human TFAM that are conditionally permissive for mtDNA replication. We established that HMG domains of TFAM are functionally independent, which opens opportunities for engineering chimeric TFAMs with customized properties for studies on mtDNA replication, mitochondrial transcription, and respiratory chain function. Finally, we present evidence that the HMG2 domain plays the leading role in TFAM species-specificity, thus indicating a potential pathway for TFAM-mtDNA evolutionary co-adaptations.
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Affiliation(s)
| | | | | | - Mikhail F. Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA; (N.K.); (D.S.); (Y.A.R.R.)
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10
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Abstract
In the course of its short history, mitochondrial DNA (mtDNA) has made a long journey from obscurity to the forefront of research on major biological processes. mtDNA alterations have been found in all major disease groups, and their significance remains the subject of intense research. Despite remarkable progress, our understanding of the major aspects of mtDNA biology, such as its replication, damage, repair, transcription, maintenance, etc., is frustratingly limited. The path to better understanding mtDNA and its role in cells, however, remains torturous and not without errors, which sometimes leave a long trail of controversy behind them. This review aims to provide a brief summary of our current knowledge of mtDNA and highlight some of the controversies that require attention from the mitochondrial research community.
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Affiliation(s)
- Inna Shokolenko
- Department of Biomedical Sciences, Pat Capps Covey College of Allied Health Professions, University of South Alabama, Mobile, AL 36688, USA
| | - Mikhail Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
- Correspondence:
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11
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Miranda M, Bonekamp NA, Kühl I. Starting the engine of the powerhouse: mitochondrial transcription and beyond. Biol Chem 2022; 403:779-805. [PMID: 35355496 DOI: 10.1515/hsz-2021-0416] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/09/2022] [Indexed: 12/25/2022]
Abstract
Mitochondria are central hubs for cellular metabolism, coordinating a variety of metabolic reactions crucial for human health. Mitochondria provide most of the cellular energy via their oxidative phosphorylation (OXPHOS) system, which requires the coordinated expression of genes encoded by both the nuclear (nDNA) and mitochondrial genomes (mtDNA). Transcription of mtDNA is not only essential for the biogenesis of the OXPHOS system, but also generates RNA primers necessary to initiate mtDNA replication. Like the prokaryotic system, mitochondria have no membrane-based compartmentalization to separate the different steps of mtDNA maintenance and expression and depend entirely on nDNA-encoded factors imported into the organelle. Our understanding of mitochondrial transcription in mammalian cells has largely progressed, but the mechanisms regulating mtDNA gene expression are still poorly understood despite their profound importance for human disease. Here, we review mechanisms of mitochondrial gene expression with a focus on the recent findings in the field of mammalian mtDNA transcription and disease phenotypes caused by defects in proteins involved in this process.
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Affiliation(s)
- Maria Miranda
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, D-50931, Germany
| | - Nina A Bonekamp
- Department of Neuroanatomy, Mannheim Center for Translational Neurosciences (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, D-68167, Germany
| | - Inge Kühl
- Department of Cell Biology, Institute of Integrative Biology of the Cell (I2BC), UMR9198, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, F-91190, France
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12
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Nomiyama T, Setoyama D, Yasukawa T, Kang D. Mitochondria Metabolomics Reveals a Role of β-Nicotinamide Mononucleotide Metabolism in Mitochondrial DNA Replication. J Biochem 2021; 171:325-338. [PMID: 34865026 DOI: 10.1093/jb/mvab136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/30/2021] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial DNA (mtDNA) replication is tightly regulated and necessary for cellular homeostasis; however, its relationship with mitochondrial metabolism remains unclear. Advances in metabolomics integrated with the rapid isolation of mitochondria will allow for remarkable progress in analyzing mitochondrial metabolism. Here, we propose a novel methodology for mitochondria-targeted metabolomics, which employs a quick isolation procedure using a hemolytic toxin from Streptococcus pyogenes streptolysin O (SLO). SLO-isolation of mitochondria from cultured HEK293 cells is time- and labor-saving for simultaneous multi-sample processing and has been applied to various other cell lines in this study. Furthermore, our method can detect the time-dependent reduction in mitochondrial ATP in response to a glycolytic inhibitor 2-deoxyglucose, indicating the suitability to prepare metabolite analysis-competent mitochondria. Using this methodology, we searched for specific mitochondrial metabolites associated with mtDNA replication activation, and nucleotides and NAD+ were identified to be prominently altered. Most notably, treatment of β-Nicotinamide Mononucleotide (β-NMN), a precursor of NAD+, to HEK293 cells activated and improved the rate of mtDNA replication by increasing nucleotides in mitochondria and decreasing their degradation products: nucleosides. Our results suggest that β-NMN metabolism play a role in supporting mtDNA replication by maintaining the nucleotide pool balance in the mitochondria.
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Affiliation(s)
- Tomoko Nomiyama
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Fukuoka, Japan.,Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, 3-1-1 Maidashi, Fukuoka, Japan
| | - Daiki Setoyama
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Fukuoka, Japan.,Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, 3-1-1 Maidashi, Fukuoka, Japan
| | - Takehiro Yasukawa
- Department of Pathology and Oncology, Juntendo University School of Medicine, 2-1-1 Hongo, Tokyo, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Fukuoka, Japan.,Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, 3-1-1 Maidashi, Fukuoka, Japan
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13
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Bonekamp NA, Jiang M, Motori E, Garcia Villegas R, Koolmeister C, Atanassov I, Mesaros A, Park CB, Larsson NG. High levels of TFAM repress mammalian mitochondrial DNA transcription in vivo. Life Sci Alliance 2021; 4:4/11/e202101034. [PMID: 34462320 PMCID: PMC8408345 DOI: 10.26508/lsa.202101034] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 01/04/2023] Open
Abstract
Mitochondrial transcription factor A (TFAM) is compacting mitochondrial DNA (dmtDNA) into nucleoids and directly controls mtDNA copy number. Here, we show that the TFAM-to-mtDNA ratio is critical for maintaining normal mtDNA expression in different mouse tissues. Moderately increased TFAM protein levels increase mtDNA copy number but a normal TFAM-to-mtDNA ratio is maintained resulting in unaltered mtDNA expression and normal whole animal metabolism. Mice ubiquitously expressing very high TFAM levels develop pathology leading to deficient oxidative phosphorylation (OXPHOS) and early postnatal lethality. The TFAM-to-mtDNA ratio varies widely between tissues in these mice and is very high in skeletal muscle leading to strong repression of mtDNA expression and OXPHOS deficiency. In the heart, increased mtDNA copy number results in a near normal TFAM-to-mtDNA ratio and maintained OXPHOS capacity. In liver, induction of LONP1 protease and mitochondrial RNA polymerase expression counteracts the silencing effect of high TFAM levels. TFAM thus acts as a general repressor of mtDNA expression and this effect can be counterbalanced by tissue-specific expression of regulatory factors.
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Affiliation(s)
- Nina A Bonekamp
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Min Jiang
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany.,Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Key Laboratory of Growth Regulation and Transformation Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Elisa Motori
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | | | - Camilla Koolmeister
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ilian Atanassov
- Proteomics Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Andrea Mesaros
- Phenotyping Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany .,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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14
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Filograna R, Mennuni M, Alsina D, Larsson NG. Mitochondrial DNA copy number in human disease: the more the better? FEBS Lett 2020; 595:976-1002. [PMID: 33314045 PMCID: PMC8247411 DOI: 10.1002/1873-3468.14021] [Citation(s) in RCA: 207] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/02/2020] [Accepted: 11/26/2020] [Indexed: 12/19/2022]
Abstract
Most of the genetic information has been lost or transferred to the nucleus during the evolution of mitochondria. Nevertheless, mitochondria have retained their own genome that is essential for oxidative phosphorylation (OXPHOS). In mammals, a gene‐dense circular mitochondrial DNA (mtDNA) of about 16.5 kb encodes 13 proteins, which constitute only 1% of the mitochondrial proteome. Mammalian mtDNA is present in thousands of copies per cell and mutations often affect only a fraction of them. Most pathogenic human mtDNA mutations are recessive and only cause OXPHOS defects if present above a certain critical threshold. However, emerging evidence strongly suggests that the proportion of mutated mtDNA copies is not the only determinant of disease but that also the absolute copy number matters. In this review, we critically discuss current knowledge of the role of mtDNA copy number regulation in various types of human diseases, including mitochondrial disorders, neurodegenerative disorders and cancer, and during ageing. We also provide an overview of new exciting therapeutic strategies to directly manipulate mtDNA to restore OXPHOS in mitochondrial diseases.
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Affiliation(s)
- Roberta Filograna
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Mara Mennuni
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - David Alsina
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Nils-Göran Larsson
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
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15
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Kozhukhar N, Alexeyev MF. Limited predictive value of TFAM in mitochondrial biogenesis. Mitochondrion 2019; 49:156-165. [PMID: 31419493 PMCID: PMC6885536 DOI: 10.1016/j.mito.2019.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/23/2019] [Accepted: 08/12/2019] [Indexed: 12/16/2022]
Abstract
Mitochondrial transcription factor A (TFAM) plays an important role in mitochondrial DNA (mtDNA) transcription and replication. In some experimental settings, TFAM expression parallels parameters of mitochondrial biogenesis, which led to a widespread acceptance of TFAM as marker of mitochondrial biogenesis. We modulated TFAM expression in several experimental systems and observed that it fails to consistently parallel mtDNA copy number and expression of mtDNA-encoded polypeptides. We suggest that the use of TFAM as a marker of mitochondrial biogenesis should be avoided outside of systems in which its performance has been carefully validated.
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Affiliation(s)
- Natalya Kozhukhar
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA.
| | - Mikhail F Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA.
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16
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Duan Y, Sun L, Liu J, Fu W, Wang S, Ni Y, Zhao R. Effects of tonic immobility and corticosterone on mitochondria metabolism in pectoralis major muscle of broiler chickens. ANIMAL PRODUCTION SCIENCE 2018. [DOI: 10.1071/an16401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Tonic immobility (TI), which can be divided into short (STI) or long (LTI) duration, is a trait related to fear and stress response. In a previous study, we found that in broilers that LTI phenotype and chronic corticosterone (CORT) administration caused retarded growth and lower muscle weight compared with their control counterparts. The aim of this study is to determine whether the mitochondrial DNA (mtDNA) copy number and mitochondrial oxidative phosphorylation (OXPHOS), the vital factors involved in regulating energy homeostasis, have been changed by LTI or CORT treatment. The results showed that STI broilers had higher mtDNA copy number and cytochrome c oxidase (COX) enzyme activity compared with LTI broilers. Analysis of mtDNA-encoded OXPHOS genes revealed that the mRNA expression of the COX subunit 1, 2, NADH dehydrogenase (ND) subunits 1, 3 and 6, were also increased in STI broilers compared with LTI broilers. Regarding the transcriptional regulation of mtDNA-encoded OXPHOS genes, no difference was found in the methylation of the mitochondria control region between the TI phenotypes or the CORT treatments. The PGC-1α protein level was higher in STI broilers, but the av uncoupling proteins, did not show significant difference at the protein level between TI phenotypes. These results suggest that the mitochondrial function in pectoralis major muscle of STI broilers is better than that of LTI counterparts. However, chronic CORT administration did not affect the mitochondrial metabolism, indicating the mitochondrial insensitivity to CORT treatment in pectoralis major muscle.
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17
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Karácsony Z, Gácser A, Vágvölgyi C, Scazzocchio C, Hamari Z. A dually located multi-HMG-box protein of Aspergillus nidulans has a crucial role in conidial and ascospore germination. Mol Microbiol 2014; 94:383-402. [PMID: 25156107 DOI: 10.1111/mmi.12772] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2014] [Indexed: 11/28/2022]
Abstract
Seven HMG-box proteins of Aspergillus nidulans have been identified in the genomic databases. Three of these have the characteristics of non-specific DNA-binding proteins. One of these, AN1267 (HmbB), comprises one canonical HMG-box in its C-terminus and upstream of the canonical box two structurally related boxes, to be called Shadow-HMG-boxes. This protein defines, together with the Podospora anserina mtHMG1, a clade of proteins present in the Pezizomycotina, with orthologues in some of the Taphrinomycotina. HmbB localizes primarily to the mitochondria but occasionally in nuclei. The deletion of the cognate gene results in a number of pleiotropic effects, including those on hyphal morphology, sensitivity to oxidative stress, absence of sterigmatocystin production and changes in the profile of conidial metabolites. The most striking phenotype of deletion strains is a dramatic decrease in conidial and ascospore viability. We show that this is most likely due to the protein being essential to maintain mitochondrial DNA in spores.
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Affiliation(s)
- Zoltán Karácsony
- University of Szeged Faculty of Sciences and Informatics, Department of Microbiology, H-6726, Szeged, Közép fasor 52, Hungary
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18
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Liu Z, Liu J, Wang J, Xu J, Liu Y, Sun X, Su L, Wang JH, Jiang Y. Role of testis-specific high-mobility-group protein in transcriptional regulation of inducible nitric oxide synthase expression in the liver of endotoxic shock mice. FEBS J 2014; 281:2202-13. [PMID: 24605775 DOI: 10.1111/febs.12774] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 02/24/2014] [Accepted: 02/26/2014] [Indexed: 01/13/2023]
Abstract
Inducible nitric oxide synthase (iNOS) plays a central role in tissue damage during endotoxic shock. However, the underlying mechanisms that control transcription of iNOS are not completely defined. A screening strategy with DNA pull-down technology and two-dimensional difference in gel electrophorcsis (2D-DIGE) analysis was used to identify regulators that interact with the iNOS promoter. We found 14 proteins that bind to the iNOS promoter in the liver of endotoxic shock mice. After matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) analysis, one of these proteins was identified as testis-specific high-mobility-group protein (tsHMG), an alternative splicing isoform encoded by the mitochondrial transcription factor A gene. We identified the binding sites of tsHMG on the iNOS promoter using a LiquiChip system, and further confirmed interactions between tsHMG and iNOS by RT-PCR, western blotting and immunofluorescence. Functional analysis by over-expression and RNA interference of tsHMG revealed that tsHMG regulates lipopolysaccharide-stimulated iNOS expression. These results indicate that tsHMG participates in modulation of iNOS expression in the early stage of endotoxic shock.
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Affiliation(s)
- Zhifeng Liu
- Key Laboratory of Functional Proteomics of Guangdong Province, Department of Pathophysiology, Southern Medical University, Guangzhou, China; Department of Intensive Care Unit, General Hospital of Guangzhou Military Command, Guangzhou, China
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19
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Kasashima K, Nagao Y, Endo H. Dynamic regulation of mitochondrial genome maintenance in germ cells. Reprod Med Biol 2013; 13:11-20. [PMID: 24482608 PMCID: PMC3890057 DOI: 10.1007/s12522-013-0162-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 07/04/2013] [Indexed: 12/11/2022] Open
Abstract
Mitochondria play a crucial role in the development and function of germ cells. Mitochondria contain a maternally inherited genome that should be transmitted to offspring without reactive oxygen species‐induced damage during germ line development. Germ cells are also involved in the mitochondrial DNA (mtDNA) bottleneck; thus, the appropriate regulation of mtDNA in these cells is very important for this characteristic transmission. In this review, we focused on unique regulation of the mitochondrial genome in animal germ cells; paternal elimination and the mtDNA bottleneck in females. We also summarized the mitochondrial nucleoid factors involved in various mtDNA regulation pathways. Among them, mitochondrial transcription factor A (TFAM), which has pleiotropic and essential roles in mtDNA maintenance, appears to have putative roles in germ cell regulation.
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Affiliation(s)
- Katsumi Kasashima
- Department of Biochemistry, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498 Japan
| | - Yasumitsu Nagao
- Center for Experimental Medicine, Jichi Medical University, Shimotsuke, Tochigi 329-0498 Japan
| | - Hitoshi Endo
- Department of Biochemistry, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498 Japan
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20
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Kukat C, Larsson NG. mtDNA makes a U-turn for the mitochondrial nucleoid. Trends Cell Biol 2013; 23:457-63. [PMID: 23721879 DOI: 10.1016/j.tcb.2013.04.009] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/17/2013] [Accepted: 04/22/2013] [Indexed: 11/29/2022]
Abstract
Mitochondria contain mtDNA derived from the ancestral endosymbiont genome. Important subunits of the oxidative phosphorylation system, which supplies cells with the energy currency ATP, are encoded by mtDNA. A naked mtDNA molecule is longer than a typical mitochondrion and is therefore compacted in vivo to form a nucleoprotein complex, denoted the mitochondrial nucleoid. Mitochondrial transcription factor A (TFAM) is the main factor packaging mtDNA into nucleoids and is also essential for mtDNA transcription initiation. The crystal structure of TFAM shows that it bends mtDNA in a sharp U-turn, which likely provides the structural basis for its dual functions. Super-resolution imaging studies have revealed that the nucleoid has an average diameter of ∼100nm and frequently contains a single copy of mtDNA. In this review the structure of the mitochondrial nucleoid and its possible regulatory roles in mtDNA expression will be discussed.
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Affiliation(s)
- Christian Kukat
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9b, 50931 Cologne, Germany
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21
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Effects of overexpression of mitochondrial transcription factor A on lifespan and oxidative stress response in Drosophila melanogaster. Biochem Biophys Res Commun 2012. [PMID: 23206694 DOI: 10.1016/j.bbrc.2012.11.084] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mitochondrial transcription factor A (TFAM) plays a role in the maintenance of mitochondrial DNA (mtDNA) by packaging mtDNA, forming the mitochondrial nucleoid. There have been many reports about a function of TFAM at the cellular level, but only a few studies have been done in individual organisms. Here we examined the effects of TFAM on the Drosophila lifespan and oxidative stress response, by overexpressing TFAM using the GAL4/UAS system. Under standard conditions, the lifespan of TFAM-overexpressing flies was shorter than that of the control flies. However, the lifespan of TFAM-overexpressing flies was longer when they were treated with 1% H(2)O(2). These results suggest that even though excess TFAM has a negative influence on lifespan, it has a defensive function under strong oxidative stress. In the TFAM-overexpressing flies, no significant changes in mtDNA copy number or mtDNA transcription were observed. However, the results of a total antioxidant activity assay suggest the possibility that TFAM is involved in the elimination of oxidative stress. The present results clearly show the effects of TFAM overexpression on the lifespan of Drosophila under both standard conditions and oxidative stress conditions, and our findings contribute to the understanding of the physiological mechanisms involving TFAM in mitochondria.
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22
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Campbell CT, Kolesar JE, Kaufman BA. Mitochondrial transcription factor A regulates mitochondrial transcription initiation, DNA packaging, and genome copy number. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:921-9. [DOI: 10.1016/j.bbagrm.2012.03.002] [Citation(s) in RCA: 236] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 03/08/2012] [Accepted: 03/15/2012] [Indexed: 10/28/2022]
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23
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Artuso L, Romano A, Verri T, Domenichini A, Argenton F, Santorelli FM, Petruzzella V. Mitochondrial DNA metabolism in early development of zebrafish (Danio rerio). BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1002-11. [DOI: 10.1016/j.bbabio.2012.03.019] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 03/12/2012] [Accepted: 03/14/2012] [Indexed: 10/28/2022]
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24
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Matsushima Y, Kaguni LS. Matrix proteases in mitochondrial DNA function. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:1080-7. [PMID: 22172992 DOI: 10.1016/j.bbagrm.2011.11.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 11/22/2011] [Accepted: 11/23/2011] [Indexed: 10/14/2022]
Abstract
Lon, ClpXP and m-AAA are the three major ATP-dependent proteases in the mitochondrial matrix. All three are involved in general quality control by degrading damaged or abnormal proteins. In addition to this role, they are proposed to serve roles in mitochondrial DNA functions including packaging and stability, replication, transcription and translation. In particular, Lon has been implicated in mtDNA metabolism in yeast, fly and humans. Here, we review the role of Lon protease in mitochondrial DNA functions, and discuss a putative physiological role for mitochondrial transcription factor A (TFAM) degradation by Lon protease. We also discuss the possible roles of m-AAA and ClpXP in mitochondrial DNA functions, and the putative candidate substrates for the three matrix proteases. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
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Affiliation(s)
- Yuichi Matsushima
- Department of Mental Retardation & Birth Defect Research, National Institute of Neuroscience, National Center of Neurology & Psychiatry, Tokyo 187-8502, Japan
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25
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Super-resolution microscopy reveals that mammalian mitochondrial nucleoids have a uniform size and frequently contain a single copy of mtDNA. Proc Natl Acad Sci U S A 2011; 108:13534-9. [PMID: 21808029 DOI: 10.1073/pnas.1109263108] [Citation(s) in RCA: 379] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Mammalian mtDNA is packaged in DNA-protein complexes denoted mitochondrial nucleoids. The organization of the nucleoid is a very fundamental question in mitochondrial biology and will determine tissue segregation and transmission of mtDNA. We have used a combination of stimulated emission depletion microscopy, enabling a resolution well below the diffraction barrier, and molecular biology to study nucleoids in a panel of mammalian tissue culture cells. We report that the nucleoids labeled with antibodies against DNA, mitochondrial transcription factor A (TFAM), or incorporated BrdU, have a defined, uniform mean size of ∼100 nm in mammals. Interestingly, the nucleoid frequently contains only a single copy of mtDNA (average ∼1.4 mtDNA molecules per nucleoid). Furthermore, we show by molecular modeling and volume calculations that TFAM is a main constituent of the nucleoid, besides mtDNA. These fundamental insights into the organization of mtDNA have broad implications for understanding mitochondrial dysfunction in disease and aging.
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26
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Itoh K, Izumi A, Mori T, Dohmae N, Yui R, Maeda-Sano K, Shirai Y, Kanaoka MM, Kuroiwa T, Higashiyama T, Sugita M, Murakami-Murofushi K, Kawano S, Sasaki N. DNA packaging proteins Glom and Glom2 coordinately organize the mitochondrial nucleoid of Physarum polycephalum. Mitochondrion 2011; 11:575-86. [PMID: 21406253 DOI: 10.1016/j.mito.2011.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 02/03/2011] [Accepted: 03/04/2011] [Indexed: 10/18/2022]
Abstract
Mitochondrial DNA (mtDNA) is generally packaged into the mitochondrial nucleoid (mt-nucleoid) by a high-mobility group (HMG) protein. Glom is an mtDNA-packaging HMG protein in Physarum polycephalum. Here we identified a new mtDNA-packaging protein, Glom2, which had a region homologous with yeast Mgm101. Glom2 could bind to an entire mtDNA and worked synergistically with Glom for condensation of mtDNA in vitro. Down-regulation of Glom2 enhanced the alteration of mt-nucleoid morphology and the loss of mtDNA induced by down-regulation of Glom, and impaired mRNA accumulation of some mtDNA-encoded genes. These data suggest that Glom2 may organize the mt-nucleoid coordinately with Glom.
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Affiliation(s)
- Kie Itoh
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.
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27
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Mitochondrial Lon protease regulates mitochondrial DNA copy number and transcription by selective degradation of mitochondrial transcription factor A (TFAM). Proc Natl Acad Sci U S A 2010; 107:18410-5. [PMID: 20930118 DOI: 10.1073/pnas.1008924107] [Citation(s) in RCA: 207] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Lon is the major protease in the mitochondrial matrix in eukaryotes, and is well conserved among species. Although a role for Lon in mitochondrial biogenesis has been proposed, the mechanistic basis is unclear. Here, we demonstrate a role for Lon in mtDNA metabolism. An RNA interference (RNAi) construct was designed that reduces Lon to less than 10% of its normal level in Drosophila Schneider cells. RNAi knockdown of Lon results in increased abundance of mitochondrial transcription factor A (TFAM) and mtDNA copy number. In a corollary manner, overexpression of Lon reduces TFAM levels and mtDNA copy number. Notably, induction of mtDNA depletion in Lon knockdown cells does not result in degradation of TFAM, thereby causing a dramatic increase in the TFAMmtDNA ratio. The increased TFAMmtDNA ratio in turn causes inhibition of mitochondrial transcription. We conclude that Lon regulates mitochondrial transcription by stabilizing the mitochondrial TFAMmtDNA ratio via selective degradation of TFAM.
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28
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Freyer C, Park CB, Ekstrand MI, Shi Y, Khvorostova J, Wibom R, Falkenberg M, Gustafsson CM, Larsson NG. Maintenance of respiratory chain function in mouse hearts with severely impaired mtDNA transcription. Nucleic Acids Res 2010; 38:6577-88. [PMID: 20566479 PMCID: PMC2965244 DOI: 10.1093/nar/gkq527] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The basal mitochondrial transcription machinery is essential for biogenesis of the respiratory chain and consists of mitochondrial RNA polymerase, mitochondrial transcription factor A (TFAM) and mitochondrial transcription factor B2. This triad of proteins is sufficient and necessary for mtDNA transcription initiation. Abolished mtDNA transcription caused by tissue-specific knockout of TFAM in the mouse heart leads to early onset of a severe mitochondrial cardiomyopathy with lethality within the first post-natal weeks. Here, we describe a mouse model expressing human TFAM instead of the endogenous mouse TFAM in heart. These rescue mice have severe reduction in mtDNA transcription initiation, but, surprisingly, are healthy at the age of 52 weeks with near-normal steady-state levels of transcripts. In addition, we demonstrate that heavy-strand mtDNA transcription normally terminates at the termination-associated sequence in the control region. This termination is abolished in rescue animals resulting in heavy (H)-strand transcription of the entire control region. In conclusion, we demonstrate here the existence of an unexpected mtDNA transcript stabilization mechanism that almost completely compensates for the severely reduced transcription initiation in rescue hearts. Future elucidation of the underlying molecular mechanism may provide a novel pathway to treat mitochondrial dysfunction in human pathology.
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Affiliation(s)
- Christoph Freyer
- Department of Laboratory Medicine, Karolinska Institutet, Retzius väg 8, 171 65 Solna, Sweden
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29
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Norrbom J, Wallman SE, Gustafsson T, Rundqvist H, Jansson E, Sundberg CJ. Training response of mitochondrial transcription factors in human skeletal muscle. Acta Physiol (Oxf) 2010; 198:71-9. [PMID: 19681768 DOI: 10.1111/j.1748-1716.2009.02030.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIM Mitochondrial function is essential for physical performance and health. Aerobic fitness is positively associated with mitochondrial (mt) biogenesis in muscle cells through partly unknown regulatory mechanisms. The present study aimed to investigate the influence of exercise and training status on key mt transcription factors in relation to oxidative capacity in human skeletal muscle. METHODS The basal mRNA and protein levels of mitochondrial transcription factor A (TFAM), mitochondrial transcription factors B1 (TFB1M) or B2 (TFB2M), and mRNA levels of mitochondrial transcription termination factor (mTERF), were measured in a cross-sectional study with elite athletes (EA) and moderately active (MA) and the basal mRNA levels of these factors were measured during a 10-day endurance training programme with (R-leg) and without (NR-leg) restricted blood flow to the working leg. RESULTS TFAM protein expression was significantly higher in the EA than in the MA, while protein levels of TFB1M and TFB2M were not different between the groups. There was no difference between EA and MA, or any effect with training on TFAM mRNA levels. However, the mRNA levels of TFB1M, TFB2M and mTERF were higher in EA compared with MA. For TFB1M and TFB2M, the mRNA expression was increased in the R-leg after 10 days of training, but not in the NR-leg. mTERF mRNA levels were higher in EA compared with MA. CONCLUSION This study further establishes that TFAM protein levels are higher in conditions with enhanced oxidative capacity. The mRNA levels of TFB1M and TFB2M are influenced by endurance training, possibly suggesting a role for these factors in the regulation of exercise-induced mitochondrial biogenesis.
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Affiliation(s)
- J Norrbom
- Division of Clinical Physiology, Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden.
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30
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Xu S, Zhong M, Zhang L, Wang Y, Zhou Z, Hao Y, Zhang W, Yang X, Wei A, Pei L, Yu Z. Overexpression of Tfam protects mitochondria against beta-amyloid-induced oxidative damage in SH-SY5Y cells. FEBS J 2009; 276:3800-9. [PMID: 19496804 DOI: 10.1111/j.1742-4658.2009.07094.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
There is strong evidence that beta-amyloid (Abeta) causes oxidative stress and induces mitochondrial dysfunction in the pathogenesis of Alzheimer's disease. Mitochondrial transcription factor A (Tfam) has multiple roles in the maintenance of mtDNA. To study the protective roles of Tfam against amyloid neurotoxicity, we established SH-SY5Y cell lines stably overexpressing Tfam and exposed them to 10 microm Abeta1-42 for 24 h. We found that Tfam overexpression attenuated Abeta1-42-induced cell viability damage and apoptosis. In addition, Tfam overexpression significantly suppressed the increase in excess reactive oxygen species and reversed the reduction in cytochrome c oxidase activity and ATP production induced by Abeta1-42. Furthermore, overexpression of DeltaC-Tfam, which has no functional domain for stimulating mtDNA transcription but can still maintain the mtDNA nucleoid formation and mtDNA copy number, also exhibited protective effects against Abeta1-42 cytotoxicity in SH-SY5Y cells. Together, our data suggest that Tfam overexpression protects mitochondria against Abeta-induced oxidative damage in SH-SY5Y cells. These beneficial effects may be attributable to the roles of Tfam in maintaining mtDNA nucleoid formation and mtDNA copy number.
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Affiliation(s)
- Shangcheng Xu
- Department of Occupational Health, Third Military Medical University, Chongqing, China
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31
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Torraco A, Diaz F, Vempati UD, Moraes CT. Mouse models of oxidative phosphorylation defects: powerful tools to study the pathobiology of mitochondrial diseases. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1793:171-80. [PMID: 18601959 PMCID: PMC2652735 DOI: 10.1016/j.bbamcr.2008.06.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Revised: 05/28/2008] [Accepted: 06/04/2008] [Indexed: 01/14/2023]
Abstract
Defects in the oxidative phosphorylation system (OXPHOS) are responsible for a group of extremely heterogeneous and pleiotropic pathologies commonly known as mitochondrial diseases. Although many mutations have been found to be responsible for OXPHOS defects, their pathogenetic mechanisms are still poorly understood. An important contribution to investigate the in vivo function of several mitochondrial proteins and their role in mitochondrial dysfunction, has been provided by mouse models. Thanks to their genetic and physiologic similarity to humans, mouse models represent a powerful tool to investigate the impact of pathological mutations on metabolic pathways. In this review we discuss the main mouse models of mitochondrial disease developed, focusing on the ones that directly affect the OXPHOS system.
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Affiliation(s)
- Alessandra Torraco
- Department of Neurology, University of Miami Miller School of Medicine, 1095 NW 14th Terrace, Miami, FL 33136, USA
| | - Francisca Diaz
- Department of Neurology, University of Miami Miller School of Medicine, 1095 NW 14th Terrace, Miami, FL 33136, USA
| | - Uma D. Vempati
- Department of Neurology, University of Miami Miller School of Medicine, 1095 NW 14th Terrace, Miami, FL 33136, USA
| | - Carlos T. Moraes
- Department of Neurology, University of Miami Miller School of Medicine, 1095 NW 14th Terrace, Miami, FL 33136, USA
- Department of Cell Biology and Anatomy, University of Miami Miller School of Medicine, 1095 NW 14th Terrace, Miami, FL 33136, USA
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32
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Pastukh V, Shokolenko I, Wang B, Wilson G, Alexeyev M. Human mitochondrial transcription factor A possesses multiple subcellular targeting signals. FEBS J 2007; 274:6488-99. [PMID: 18028422 DOI: 10.1111/j.1742-4658.2007.06167.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The mitochondrial transcription factor A (TFAM) is a member of a high-mobility group (HMG) family represented mostly by nuclear proteins. Although nuclear localization of TFAM has been demonstrated in some tumors and after treatment of tumor cells with anticancer drugs, the significance of these observations has not been fully elucidated. Here we report that both TFAM overexpression and impairment of its mitochondrial targeting can result in nuclear accumulation of the protein. Both M1 and M7 methionines of human TFAM (hTFAM) can be used for translation initiation with almost equal efficiency resulting in two polypeptides. The shorter polypeptide, however, is not located in the nucleus, despite truncation in the mitochondrial targeting sequence, and both isoforms are targeted to mitochondria with similar efficiency. We further demonstrate that nuclear TFAM confers significant cytoprotection against the chemotherapeutic drugs etoposide, camptothecin, and cisplatin. Three regions of hTFAM [HMG-like domain 1 (HMG1) and HMG-like domain 2 (HMG2), as well as the tail region] can effect nuclear accumulation of enhanced green fluorescent protein (EGFP) fusions. The HMG1 domain contains a bipartite nuclear localization sequence whose identity is supported by site-directed mutagenesis. However, this bipartite nuclear localization sequence is weak, and both N-terminal and C-terminal flanking sequences enhance the nuclear targeting of EGFP. Finally, several mutations in the HMG1 domain increased the mitochondrial targeting of the EGFP fusions, suggesting that the mitochondrial targeting sequence of hTFAM may extend beyond the cleavable presequence.
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Affiliation(s)
- Viktoriya Pastukh
- Department of Cell Biology and Neuroscience, University of South Alabama, Mobile, AL 36688, USA
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Kaufman BA, Durisic N, Mativetsky JM, Costantino S, Hancock MA, Grutter P, Shoubridge EA. The mitochondrial transcription factor TFAM coordinates the assembly of multiple DNA molecules into nucleoid-like structures. Mol Biol Cell 2007; 18:3225-36. [PMID: 17581862 PMCID: PMC1951767 DOI: 10.1091/mbc.e07-05-0404] [Citation(s) in RCA: 300] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Packaging DNA into condensed structures is integral to the transmission of genomes. The mammalian mitochondrial genome (mtDNA) is a high copy, maternally inherited genome in which mutations cause a variety of multisystem disorders. In all eukaryotic cells, multiple mtDNAs are packaged with protein into spheroid bodies called nucleoids, which are the fundamental units of mtDNA segregation. The mechanism of nucleoid formation, however, remains unknown. Here, we show that the mitochondrial transcription factor TFAM, an abundant and highly conserved High Mobility Group box protein, binds DNA cooperatively with nanomolar affinity as a homodimer and that it is capable of coordinating and fully compacting several DNA molecules together to form spheroid structures. We use noncontact atomic force microscopy, which achieves near cryo-electron microscope resolution, to reveal the structural details of protein-DNA compaction intermediates. The formation of these complexes involves the bending of the DNA backbone, and DNA loop formation, followed by the filling in of proximal available DNA sites until the DNA is compacted. These results indicate that TFAM alone is sufficient to organize mitochondrial chromatin and provide a mechanism for nucleoid formation.
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Affiliation(s)
- Brett A. Kaufman
- *Department of Neurology and Neurosurgery and Program in NeuroEngineering, Montreal Neurological Institute
| | | | | | - Santiago Costantino
- *Department of Neurology and Neurosurgery and Program in NeuroEngineering, Montreal Neurological Institute
- Department of Physics
| | | | | | - Eric A. Shoubridge
- *Department of Neurology and Neurosurgery and Program in NeuroEngineering, Montreal Neurological Institute
- Department of Human Genetics, McGill University, Montreal, QC, H3A 2B4, Canada
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Hisada-Ishii S, Ebihara M, Kobayashi N, Kitagawa Y. Bipartite nuclear localization signal of matrin 3 is essential for vertebrate cells. Biochem Biophys Res Commun 2007; 354:72-6. [PMID: 17223080 DOI: 10.1016/j.bbrc.2006.12.191] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Accepted: 12/15/2006] [Indexed: 11/16/2022]
Abstract
Matrin 3, a nuclear matrix protein has potential (1) to withhold promiscuously edited RNAs within the nucleus in cooperation with p54(nrb) and PSF, (2) to mediate NMDA-induced neuronal death, and (3) to modulate promoter activity of genes proximal to matrix/scaffold attachment region (MAR/SAR). We identified a bipartite nuclear localization signal (NLS) of chicken matrin 3 (cmatr3) at residues 583-602. By expressing green fluorescent protein (GFP) fused to the NLS mutant in chicken DT40 cells, we showed an essential role of the NLS for cell proliferation. Furthermore, we showed that both clusters of basic amino acids and a linker of the bipartite NLS were essential and sufficient for the nuclear import of GFP. Exogenous cmatr3 rescued the HeLa cells where human matrin 3 was suppressed by RNA interference, but cmatr3 containing deletions at either of the basic amino acid clusters or the linker could not.
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Affiliation(s)
- Shoji Hisada-Ishii
- Department of Bioengineering Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
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Kang D, Kim SH, Hamasaki N. Mitochondrial transcription factor A (TFAM): Roles in maintenance of mtDNA and cellular functions. Mitochondrion 2007; 7:39-44. [PMID: 17280879 DOI: 10.1016/j.mito.2006.11.017] [Citation(s) in RCA: 308] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2006] [Accepted: 09/21/2006] [Indexed: 10/23/2022]
Abstract
A growing body of evidence suggests that mammalian mitochondrial DNA takes on higher structure called nucleoid or mitochromosome corresponding to that of nuclear DNA. Mitochondrial transcription factor A (TFAM), which was cloned as a transcription factor for mitochondrial DNA, has known to be essential for the maintenance of mitochondrial DNA. Human TFAM has an ability to bind to DNA in a sequence-independent manner and is abundant enough to cover whole region of mitochondrial DNA, owing to which TFAM stabilizes mitochondrial DNA through formation of nucleoid and regulates (or titrates) the amount of mitochondrial DNA. Overexpression of human TFAM in mice increases the amount of mitochondrial DNA and dramatically ameliorates the cardiac dysfunctions caused by myocardial infarction. The maintenance of integrity of mitochondrial DNA is important for keeping proper cellular functions both under physiological and pathological conditions. TFAM may play a crucial role in maintaining mitochondrial DNA as a main component of the nucleoid.
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Affiliation(s)
- Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan.
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36
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Matsushima Y, Kaguni LS. Differential phenotypes of active site and human autosomal dominant progressive external ophthalmoplegia mutations in Drosophila mitochondrial DNA helicase expressed in Schneider cells. J Biol Chem 2007; 282:9436-9444. [PMID: 17272269 PMCID: PMC4853901 DOI: 10.1074/jbc.m610550200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report the cloning and molecular analysis of Drosophila mitochondrial DNA helicase (d-mtDNA helicase) homologous to human TWINKLE, which encodes one of the genes responsible for autosomal dominant progressive external ophthalmoplegia. An RNA interference construct was designed that reduces expression of d-mtDNA helicase to an undetectable level in Schneider cells. RNA interference knockdown of d-mtDNA helicase decreases the copy number of mitochondrial DNA (mtDNA) approximately 5-fold. In a corollary manner, overexpression of d-mtDNA helicase increases mtDNA levels 1.4-fold. Overexpression of helicase active site mutants K388A and D483A results in a severe depletion of mtDNA and a dominant negative lethal phenotype. Overexpression of mutants analogous to human autosomal dominant progressive external ophthalmoplegia mutations shows differential effects. Overexpression of I334T and A442P mutants yields a dominant negative effect as for the active site mutants. In contrast, overexpression of A326T, R341Q, and W441C mutants results in increased mtDNA copy number, as observed with wild-type overexpression. Our dominant negative analysis of d-mtDNA helicase in cultured cells provides a tractable model for understanding human autosomal dominant progressive external ophthalmoplegia mutations.
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Affiliation(s)
- Yuichi Matsushima
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Laurie S Kaguni
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824.
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Bonawitz ND, Clayton DA, Shadel GS. Initiation and beyond: multiple functions of the human mitochondrial transcription machinery. Mol Cell 2007; 24:813-25. [PMID: 17189185 DOI: 10.1016/j.molcel.2006.11.024] [Citation(s) in RCA: 266] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mitochondria contain their own DNA (mtDNA) that is expressed and replicated by nucleus-encoded factors imported into the organelle. Recently, the core human mitochondrial transcription machinery has been defined, comprising a bacteriophage-related mtRNA polymerase (POLRMT), an HMG-box transcription factor (h-mtTFA), and two transcription factors (h-mtTFB1 and h-mtTFB2) that also serve as rRNA methyltransferases. Here, we describe these transcription components as well as recent insights into the mechanism of human mitochondrial transcription initiation and its regulation. We also discuss novel roles for the mitochondrial transcription machinery beyond transcription initiation, including priming of mtDNA replication, packaging of mtDNA, coordination of ribosome biogenesis, and coupling of transcription to translation.
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Affiliation(s)
- Nicholas D Bonawitz
- Department of Pathology, Yale University School of Medicine, 310 Cedar Street, P.O. Box 208023, New Haven, Connecticut 06520, USA
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Pohjoismäki JLO, Wanrooij S, Hyvärinen AK, Goffart S, Holt IJ, Spelbrink JN, Jacobs HT. Alterations to the expression level of mitochondrial transcription factor A, TFAM, modify the mode of mitochondrial DNA replication in cultured human cells. Nucleic Acids Res 2006; 34:5815-28. [PMID: 17062618 PMCID: PMC1635303 DOI: 10.1093/nar/gkl703] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Mitochondrial transcription factor A (TFAM) is an abundant mitochondrial protein of the HMG superfamily, with various putative roles in mitochondrial DNA (mtDNA) metabolism. In this study we have investigated the effects on mtDNA replication of manipulating TFAM expression in cultured human cells. Mammalian mtDNA replication intermediates (RIs) fall into two classes, whose mechanistic relationship is not properly understood. One class is characterized by extensive RNA incorporation on the lagging strand, whereas the other has the structure of products of conventional, strand-coupled replication. TFAM overexpression increased the overall abundance of RIs and shifted them substantially towards those of the conventional, strand-coupled type. The shift was most pronounced in the rDNA region and at various replication pause sites and was accompanied by a drop in the relative amount of replication-termination intermediates, a substantial reduction in mitochondrial transcripts, mtDNA decatenation and progressive copy number depletion. TFAM overexpression could be partially phenocopied by treatment of cells with dideoxycytidine, suggesting that its effects are partially attributable to a decreased rate of fork progression. TFAM knockdown also resulted in mtDNA depletion, but RIs remained mainly of the ribosubstituted type, although termination intermediates were enhanced. We propose that TFAM influences the mode of mtDNA replication via its combined effects on different aspects of mtDNA metabolism.
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Affiliation(s)
- Jaakko L. O. Pohjoismäki
- Institute of Medical Technology and Tampere University HospitalFI-33014 University of Tampere, Finland
| | - Sjoerd Wanrooij
- Institute of Medical Technology and Tampere University HospitalFI-33014 University of Tampere, Finland
| | - Anne K. Hyvärinen
- Institute of Medical Technology and Tampere University HospitalFI-33014 University of Tampere, Finland
| | - Steffi Goffart
- Institute of Medical Technology and Tampere University HospitalFI-33014 University of Tampere, Finland
| | - Ian J. Holt
- MRC-Dunn Human Nutrition Unit, Hill RoadCambridge CB2 2XY, England, UK
| | - Johannes N. Spelbrink
- Institute of Medical Technology and Tampere University HospitalFI-33014 University of Tampere, Finland
| | - Howard T. Jacobs
- Institute of Medical Technology and Tampere University HospitalFI-33014 University of Tampere, Finland
- IBLS Division of Molecular Genetics, University of GlasgowGlasgow G12 8QQ, Scotland, UK
- To whom correspondence should be addressed. Tel: +358 33 55 17 731; Fax: +358 32 15 77 10;
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McCarthy FM, Cooksey AM, Wang N, Bridges SM, Pharr GT, Burgess SC. Modeling a whole organ using proteomics: the avian bursa of Fabricius. Proteomics 2006; 6:2759-71. [PMID: 16596704 DOI: 10.1002/pmic.200500648] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
While advances in proteomics have improved proteome coverage and enhanced biological modeling, modeling function in multicellular organisms requires understanding how cells interact. Here we used the chicken bursa of Fabricius, a common experimental system for B cell function, to model organ function from proteomics data. The bursa has two major functional cell types: B cells and the supporting stromal cells. We used differential detergent fractionation-multidimensional protein identification technology (DDF-MudPIT) to identify 5198 proteins from all cellular compartments. Of these, 1753 were B cell specific, 1972 were stroma specific and 1473 were shared between the two. By modeling programmed cell death (PCD), cell differentiation and proliferation, and transcriptional activation, we have improved functional annotation of chicken proteins and placed chicken-specific death receptors into the PCD process using phylogenetics. We have identified 114 transcription factors (TFs); 42 of the bursal B cell TFs have not been reported before in any B cells. We have also improved the structural annotation of a newly sequenced genome by confirming the in vivo expression of 4006 "predicted", and 6623 ab initio, ORFs. Finally, we have developed a novel method for facilitating structural annotation, "expressed peptide sequence tags" (ePSTs) and demonstrate its utility by identifying 521 potential novel proteins from the chicken "unassigned chromosome".
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Affiliation(s)
- Fiona M McCarthy
- Department of Basic Science, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762-6100, USA.
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Kang D, Hamasaki N. Mitochondrial Transcription Factor A in the Maintenance of Mitochondrial DNA. Ann N Y Acad Sci 2006; 1042:101-8. [PMID: 15965051 DOI: 10.1196/annals.1338.010] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Mitochondria have their own genome, which is essential for proper oxidative phosphorylation needed for a large part of ATP production in a cell. Although mitochondrial DNA-less (rho0) cells can survive under special conditions, the integrity of the mitochondrial genome is critical for survival of multicellular organisms. Mitochondrial transcription factor A (TFAM), originally cloned as transcription factor, is essential for the maintenance of mtDNA. Recently, it has become known that TFAM plays critical roles in multiple aspects to maintain the integrity of mitochondrial DNA: transcription, replication, nucleoid formation, damage sensing, and DNA repair. The effects of TFAM in these aspects are intimately related to each other and to function as a whole for the purpose of maintenance of mtDNA.
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Affiliation(s)
- Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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Abstract
Mitochondrial DNA (mtDNA) encodes essential components of the cellular energy-producing apparatus, and lesions in mtDNA and mitochondrial dysfunction contribute to numerous human diseases. Understanding mtDNA organization and inheritance is therefore an important goal. Recent studies have revealed that mitochondria use diverse metabolic enzymes to organize and protect mtDNA, drive the segregation of the organellar genome, and couple the inheritance of mtDNA with cellular metabolism. In addition, components of a membrane-associated mtDNA segregation apparatus that might link mtDNA transmission to mitochondrial movements are beginning to be identified. These findings provide new insights into the mechanisms of mtDNA maintenance and inheritance.
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Affiliation(s)
- Xin Jie Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, Texas 75390-9148, USA
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42
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Piantadosi CA, Suliman HB. Mitochondrial transcription factor A induction by redox activation of nuclear respiratory factor 1. J Biol Chem 2005; 281:324-33. [PMID: 16230352 DOI: 10.1074/jbc.m508805200] [Citation(s) in RCA: 182] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nuclear expression of mitochondrial transcription factor A (Tfam), which is required for mitochondrial DNA (mtDNA) transcription and replication, must be linked to cellular energy needs. Because respiration generates reactive oxygen species as a side-product, we tested the idea that reactive oxygen species regulate Tfam expression through phosphorylation of nuclear respiratory factor (NRF-1) and binding to the Tfam promoter. In mitochondria-rich rat hepatoma cells that overexpress NRF-1, basal and oxidant-induced increases were found in Tfam expression and mtDNA content. Specific binding of NRF-1 to Tfam promoter was demonstrated by electrophoretic mobility shift assay and chromatin immunoprecipitation. NRF-1-Tfam binding was augmented under pro-oxidant conditions. NRF-1 gene silencing produced 1:1 knockdown of Tfam expression and decreased mtDNA content. To evaluate oxidation-reduction (redox) regulation of NRF-1 in Tfam expression, blockade of upstream phosphatidylinositol 3-kinase was used to demonstrate loss of oxidant stimulation of NRF-1 phosphorylation and Tfam expression. The oxidant response was also abrogated by specific inhibition of Akt/protein kinase B. Examination of the NRF-1 amino acid sequence revealed an Akt phosphorylation consensus at which site-directed mutagenesis abolished NRF-1 phosphorylation by Akt. Finally, Akt phosphorylation and NRF-1 translocation predictably lacked oxidant regulation in a cancer line having no PTEN tumor suppressor (HCC1937 cells). This study discloses novel redox regulation of NRF-1 phosphorylation and nuclear translocation by phosphatidylinositol 3,4,5-triphosphate kinase/Akt signaling in controlling Tfam induction by an anti-oxidant pro-survival network.
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Affiliation(s)
- Claude A Piantadosi
- Department of Medicine, Duke University, Medical Center, Durham, North Carolina 27710, USA.
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Taanman JW, Llewelyn Williams S. The Human Mitochondrial Genome. OXIDATIVE STRESS AND DISEASE 2005. [DOI: 10.1201/9781420028843.ch3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Kanki T, Ohgaki K, Gaspari M, Gustafsson CM, Fukuoh A, Sasaki N, Hamasaki N, Kang D. Architectural role of mitochondrial transcription factor A in maintenance of human mitochondrial DNA. Mol Cell Biol 2004; 24:9823-34. [PMID: 15509786 PMCID: PMC525493 DOI: 10.1128/mcb.24.22.9823-9834.2004] [Citation(s) in RCA: 233] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mitochondrial transcription factor A (TFAM), a transcription factor for mitochondrial DNA (mtDNA) that also possesses the property of nonspecific DNA binding, is essential for maintenance of mtDNA. To clarify the role of TFAM, we repressed the expression of endogenous TFAM in HeLa cells by RNA interference. The amount of TFAM decreased maximally to about 15% of the normal level at day 3 after RNA interference and then recovered gradually. The amount of mtDNA changed closely in parallel with the daily change in TFAM while in organello transcription of mtDNA at day 3 was maintained at about 50% of the normal level. TFAM lacking its C-terminal 25 amino acids (TFAM-DeltaC) marginally activated transcription in vitro. When TFAM-DeltaC was expressed at levels comparable to those of endogenous TFAM in HeLa cells, mtDNA increased twofold, suggesting that TFAM-DeltaC is as competent in maintaining mtDNA as endogenous TFAM under these conditions. The in organello transcription of TFAM-DeltaC-expressing cells was no more than that in the control. Thus, the mtDNA amount is finely correlated with the amount of TFAM but not with the transcription level. We discuss an architectural role for TFAM in the maintenance of mtDNA in addition to its role in transcription activation.
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Affiliation(s)
- Tomotake Kanki
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Tyynismaa H, Sembongi H, Bokori-Brown M, Granycome C, Ashley N, Poulton J, Jalanko A, Spelbrink JN, Holt IJ, Suomalainen A. Twinkle helicase is essential for mtDNA maintenance and regulates mtDNA copy number. Hum Mol Genet 2004; 13:3219-27. [PMID: 15509589 DOI: 10.1093/hmg/ddh342] [Citation(s) in RCA: 180] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mechanisms of mitochondrial DNA (mtDNA) maintenance have recently gained wide interest owing to their role in inherited diseases as well as in aging. Twinkle is a new mitochondrial 5'-3' DNA helicase, defects of which we have previously shown to underlie a mitochondrial disease, progressive external ophthalmoplegia with multiple mtDNA deletions. Mouse Twinkle is highly similar to the human counterpart, suggesting conserved function. Here, we have characterized the mouse Twinkle gene and expression profile and report that the expression patterns are not conserved between human and mouse, but are synchronized with the adjacent gene MrpL43, suggesting a shared promoter. To elucidate the in vivo role of Twinkle in mtDNA maintenance, we generated two transgenic mouse lines overexpressing wild-type Twinkle. We could demonstrate for the first time that increased expression of Twinkle in muscle and heart increases mtDNA copy number up to 3-fold higher than controls, more than any other factor reported to date. Additionally, we utilized cultured human cells and observed that reduced expression of Twinkle by RNA interference mediated a rapid drop in mtDNA copy number, further supporting the in vivo results. These data demonstrate that Twinkle helicase is essential for mtDNA maintenance, and that it may be a key regulator of mtDNA copy number in mammals.
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Affiliation(s)
- Henna Tyynismaa
- Department of Neurology and Programme of Neurosciences, University of Helsinki, 00290 Helsinki, Finland
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Matsushima Y, Garesse R, Kaguni LS. Drosophila Mitochondrial Transcription Factor B2 Regulates Mitochondrial DNA Copy Number and Transcription in Schneider Cells. J Biol Chem 2004; 279:26900-5. [PMID: 15060065 DOI: 10.1074/jbc.m401643200] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report the cloning and molecular analysis of Drosophila mitochondrial transcription factor B2 (d-mt-TFB2), a protein that plays a role in mitochondrial transcription and mitochondrial DNA (mtDNA) replication in Drosophila. An RNA interference (RNAi) construct was designed that reduces expression of d-mtTFB2 to 5% of its normal level in Schneider cells. RNAi knock-down of d-mtTFB2 reduces the abundance of specific mitochondrial RNA transcripts 2- to 8-fold and decreases the copy number of mtDNA approximately 3-fold. In a corollary manner, we find that overexpression of d-mtTFB2 increases both the abundance of mitochondrial RNA transcripts and the copy number of mtDNA. In a comparative experiment, we find that overexpression of Drosophila mitochondrial transcription factor A (d-TFAM) increases mtDNA copy number with no significant effect on mitochondrial transcripts. This argues for a direct role for mtTFB2 in mitochondrial transcription and suggests that, if TFAM serves a role in transcription, its endogenous level limits mtDNA copy number but not transcription. Furthermore, we suggest that mtTFB2 increases mtDNA copy number by increasing the frequency of initiation of DNA replication, whereas TFAM serves to stabilize and package mtDNA in mitochondrial nucleoids. Our work represents the first study to document the function of mtTFB2 in vivo, establishing a dual role in regulation of both transcription and replication, and provides a benchmark for comparative biochemical studies in various animal systems.
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Affiliation(s)
- Yuichi Matsushima
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA
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