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Marinov GK, Ramalingam V, Greenleaf WJ, Kundaje A. An updated compendium and reevaluation of the evidence for nuclear transcription factor occupancy over the mitochondrial genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597442. [PMID: 38895386 PMCID: PMC11185660 DOI: 10.1101/2024.06.04.597442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
In most eukaryotes, mitochondrial organelles contain their own genome, usually circular, which is the remnant of the genome of the ancestral bacterial endosymbiont that gave rise to modern mitochondria. Mitochondrial genomes are dramatically reduced in their gene content due to the process of endosymbiotic gene transfer to the nucleus; as a result most mitochondrial proteins are encoded in the nucleus and imported into mitochondria. This includes the components of the dedicated mitochondrial transcription and replication systems and regulatory factors, which are entirely distinct from the information processing systems in the nucleus. However, since the 1990s several nuclear transcription factors have been reported to act in mitochondria, and previously we identified 8 human and 3 mouse transcription factors (TFs) with strong localized enrichment over the mitochondrial genome using ChIP-seq (Chromatin Immunoprecipitation) datasets from the second phase of the ENCODE (Encyclopedia of DNA Elements) Project Consortium. Here, we analyze the greatly expanded in the intervening decade ENCODE compendium of TF ChIP-seq datasets (a total of 6,153 ChIP experiments for 942 proteins, of which 763 are sequence-specific TFs) combined with interpretative deep learning models of TF occupancy to create a comprehensive compendium of nuclear TFs that show evidence of association with the mitochondrial genome. We find some evidence for chrM occupancy for 50 nuclear TFs and two other proteins, with bZIP TFs emerging as most likely to be playing a role in mitochondria. However, we also observe that in cases where the same TF has been assayed with multiple antibodies and ChIP protocols, evidence for its chrM occupancy is not always reproducible. In the light of these findings, we discuss the evidential criteria for establishing chrM occupancy and reevaluate the overall compendium of putative mitochondrial-acting nuclear TFs.
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Affiliation(s)
- Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
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2
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Bernardino Gomes TM, Vincent AE, Menger KE, Stewart JB, Nicholls TJ. Mechanisms and pathologies of human mitochondrial DNA replication and deletion formation. Biochem J 2024; 481:683-715. [PMID: 38804971 DOI: 10.1042/bcj20230262] [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: 03/22/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
Human mitochondria possess a multi-copy circular genome, mitochondrial DNA (mtDNA), that is essential for cellular energy metabolism. The number of copies of mtDNA per cell, and their integrity, are maintained by nuclear-encoded mtDNA replication and repair machineries. Aberrant mtDNA replication and mtDNA breakage are believed to cause deletions within mtDNA. The genomic location and breakpoint sequences of these deletions show similar patterns across various inherited and acquired diseases, and are also observed during normal ageing, suggesting a common mechanism of deletion formation. However, an ongoing debate over the mechanism by which mtDNA replicates has made it difficult to develop clear and testable models for how mtDNA rearrangements arise and propagate at a molecular and cellular level. These deletions may impair energy metabolism if present in a high proportion of the mtDNA copies within the cell, and can be seen in primary mitochondrial diseases, either in sporadic cases or caused by autosomal variants in nuclear-encoded mtDNA maintenance genes. These mitochondrial diseases have diverse genetic causes and multiple modes of inheritance, and show notoriously broad clinical heterogeneity with complex tissue specificities, which further makes establishing genotype-phenotype relationships challenging. In this review, we aim to cover our current understanding of how the human mitochondrial genome is replicated, the mechanisms by which mtDNA replication and repair can lead to mtDNA instability in the form of large-scale rearrangements, how rearranged mtDNAs subsequently accumulate within cells, and the pathological consequences when this occurs.
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Affiliation(s)
- Tiago M Bernardino Gomes
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- NHS England Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4HH, U.K
| | - Amy E Vincent
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Katja E Menger
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - James B Stewart
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Thomas J Nicholls
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
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3
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Tan BG, Gustafsson CM, Falkenberg M. Mechanisms and regulation of human mitochondrial transcription. Nat Rev Mol Cell Biol 2024; 25:119-132. [PMID: 37783784 DOI: 10.1038/s41580-023-00661-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2023] [Indexed: 10/04/2023]
Abstract
The expression of mitochondrial genes is regulated in response to the metabolic needs of different cell types, but the basic mechanisms underlying this process are still poorly understood. In this Review, we describe how different layers of regulation cooperate to fine tune initiation of both mitochondrial DNA (mtDNA) transcription and replication in human cells. We discuss our current understanding of the molecular mechanisms that drive and regulate transcription initiation from mtDNA promoters, and how the packaging of mtDNA into nucleoids can control the number of mtDNA molecules available for both transcription and replication. Indeed, a unique aspect of the mitochondrial transcription machinery is that it is coupled to mtDNA replication, such that mitochondrial RNA polymerase is additionally required for primer synthesis at mtDNA origins of replication. We discuss how the choice between replication-primer formation and genome-length RNA synthesis is controlled at the main origin of replication (OriH) and how the recent discovery of an additional mitochondrial promoter (LSP2) in humans may change this long-standing model.
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Affiliation(s)
- Benedict G Tan
- Institute for Mitochondrial Diseases and Ageing, Faculty of Medicine and University Hospital Cologne, Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
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4
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Kong Y, Li X, Zhang H, Fu B, Jiang HY, Yang HL, Dai J. Targeting POLRMT by a first-in-class inhibitor IMT1 inhibits osteosarcoma cell growth in vitro and in vivo. Cell Death Dis 2024; 15:57. [PMID: 38228583 PMCID: PMC10791695 DOI: 10.1038/s41419-024-06444-9] [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: 09/18/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/18/2024]
Abstract
Osteosarcoma (OS) is a highly aggressive form of bone cancer that predominantly affects adolescents and young adults. In this study, we have undertaken an investigation into the potential anti-OS cell activity of IMT1 (inhibitor of mitochondrial transcription 1), a first-in-class inhibitor of RNA polymerase mitochondrial (POLRMT). IMT1 exhibited a profound inhibitory effect on cell survival, proliferation, cell cycle progression, and migration in primary and immortalized OS cells. Furthermore, this POLRMT inhibitor elicited apoptosis in the OS cells, without, however, inducing cytotoxicity in human osteoblasts or osteoblastic cells. IMT1 disrupted mitochondrial functions in OS cells, resulting in mitochondrial depolarization, oxidative injury, lipid peroxidation, and ATP reduction in OS cells. Silencing POLRMT using targeted shRNA closely mimicked the actions of IMT1 and exerted potent anti-OS cell activity. Importantly, IMT1's effectiveness was diminished in POLRMT-silenced OS cells. Subsequent investigations revealed that IMT1 suppressed the activation of the Akt-mammalian target of rapamycin (mTOR) cascade in OS cells. IMT1 treatment or POLRMT silencing in primary OS cells led to a significant reduction in Akt1-S6K-S6 phosphorylation. Conversely, it was enhanced upon POLRMT overexpression. The restoration of Akt-mTOR activation through the introduction of a constitutively active S473D mutant Akt1 (caAkt1) mitigated IMT1-induced cytotoxicity in OS cells. In vivo, oral administration of IMT1 robustly curtailed the growth of OS xenografts in nude mice. Furthermore, IMT1 suppressed POLRMT activity, impaired mitochondrial function, repressed Akt-mTOR activation, and induced apoptosis within xenograft tissues. Collectively, these findings underscore the potent growth-inhibitory effects attributed to IMT1 via targeted POLRMT inhibition. The utilization of this POLRMT inhibitor carries substantial therapeutic promise in the context of OS treatment.
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Affiliation(s)
- Yang Kong
- Department of Orthopedics, the First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Orthopedics, The First People's Hospital of ChuZhou, ChuZhou, China
| | - Xiangrong Li
- Department of Pharmacy, Kongjiang Hospital of Yangpu District, Shanghai, China
| | - Huanle Zhang
- Department of Radiotherapy, Suzhou Ninth People's Hospital, Suzhou, China
| | - Bin Fu
- Department of Orthopedics, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hua-Ye Jiang
- Department of Orthopedics, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hui-Lin Yang
- Department of Orthopedics, the First Affiliated Hospital of Soochow University, Suzhou, China.
- Orthopedic Institute, Medical College, Soochow University, Suzhou, China.
| | - Jin Dai
- Department of Orthopedics, Suzhou Wujiang District Children's Hospital, Suzhou, China.
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5
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Schrott S, Osman C. Two mitochondrial HMG-box proteins, Cim1 and Abf2, antagonistically regulate mtDNA copy number in Saccharomyces cerevisiae. Nucleic Acids Res 2023; 51:11813-11835. [PMID: 37850632 PMCID: PMC10681731 DOI: 10.1093/nar/gkad849] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/21/2023] [Accepted: 09/24/2023] [Indexed: 10/19/2023] Open
Abstract
The mitochondrial genome, mtDNA, is present in multiple copies in cells and encodes essential subunits of oxidative phosphorylation complexes. mtDNA levels have to change in response to metabolic demands and copy number alterations are implicated in various diseases. The mitochondrial HMG-box proteins Abf2 in yeast and TFAM in mammals are critical for mtDNA maintenance and packaging and have been linked to mtDNA copy number control. Here, we discover the previously unrecognized mitochondrial HMG-box protein Cim1 (copy number influence on mtDNA) in Saccharomyces cerevisiae, which exhibits metabolic state dependent mtDNA association. Surprisingly, in contrast to Abf2's supportive role in mtDNA maintenance, Cim1 negatively regulates mtDNA copy number. Cells lacking Cim1 display increased mtDNA levels and enhanced mitochondrial function, while Cim1 overexpression results in mtDNA loss. Intriguingly, Cim1 deletion alleviates mtDNA maintenance defects associated with loss of Abf2, while defects caused by Cim1 overexpression are mitigated by simultaneous overexpression of Abf2. Moreover, we find that the conserved LON protease Pim1 is essential to maintain low Cim1 levels, thereby preventing its accumulation and concomitant repressive effects on mtDNA. We propose a model in which the protein ratio of antagonistically acting Cim1 and Abf2 determines mtDNA copy number.
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Affiliation(s)
- Simon Schrott
- Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, Planegg-Martinsried 82152, Germany
| | - Christof Osman
- Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, Planegg-Martinsried 82152, Germany
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6
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Li X, Yao L, Wang T, Gu X, Wu Y, Jiang T. Identification of the mitochondrial protein POLRMT as a potential therapeutic target of prostate cancer. Cell Death Dis 2023; 14:665. [PMID: 37816734 PMCID: PMC10564732 DOI: 10.1038/s41419-023-06203-2] [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: 05/21/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
RNA polymerase mitochondria (POLRMT) is essential for mitochondrial transcription machinery and other mitochondrial functions. Its expression and potential functions in prostate cancer were explored here. The Cancer Genome Atlas prostate cancer cohort (TCGA PRAD) shows that POLRMT mRNA expression is upregulated in prostate cancer tissues and POLRMT upregulation is correlated with poor patients' survival. POLRMT mRNA and protein levels were upregulated in local prostate cancer tissues and different primary/immortalized prostate cancer cells. Genetic depletion of POLRMT, using viral shRNA or CRISPR/Cas9 gene editing methods, impaired mitochondrial functions in prostate cancer cells, leading to mitochondrial depolarization, oxidative stress, mitochondria complex I inhibition, and ATP depletion. Moreover, POLRMT depletion resulted in robust inhibition of prostate cancer cell viability, proliferation, and migration, and provoked apoptosis. Conversely, prostate cancer cell proliferation, migration, and ATP contents were strengthened following ectopic POLRMT overexpression. In vivo, intratumoral injection of POLRMT shRNA adeno-associated virus impeded prostate cancer xenograft growth in nude mice. POLRMT silencing, oxidative stress, and ATP depletion were detected in POLRMT shRNA-treated prostate cancer xenograft tissues. IMT1 (inhibitor of mitochondrial transcription 1), the first-in-class POLRMT inhibitor, inhibited prostate cancer cell growth in vitro and in vivo. Together, overexpressed POLRMT is an important mitochondrial protein for prostate cancer cell growth, representing a novel and promising diagnostic and therapeutic oncotarget.
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Affiliation(s)
- Xiaojun Li
- Department of Urology, Taicang Affiliated Hospital of Soochow University, The First People's Hospital of Taicang, Taicang, China
| | - Linya Yao
- Department of Urology, Kunshan Hospital of Traditional Chinese Medicine Affiliated to Yangzhou University, Kunshan, China
| | - Tao Wang
- Department of Urology, Taicang Affiliated Hospital of Soochow University, The First People's Hospital of Taicang, Taicang, China
| | - Xiaolei Gu
- Department of Urology, Taicang Affiliated Hospital of Soochow University, The First People's Hospital of Taicang, Taicang, China
| | - Yufan Wu
- Department of Urology, Kunshan Hospital of Traditional Chinese Medicine Affiliated to Yangzhou University, Kunshan, China
| | - Ting Jiang
- Department of Urology, Taicang Affiliated Hospital of Soochow University, The First People's Hospital of Taicang, Taicang, China.
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7
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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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8
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Burr SP, Klimm F, Glynos A, Prater M, Sendon P, Nash P, Powell CA, Simard ML, Bonekamp NA, Charl J, Diaz H, Bozhilova LV, Nie Y, Zhang H, Frison M, Falkenberg M, Jones N, Minczuk M, Stewart JB, Chinnery PF. Cell lineage-specific mitochondrial resilience during mammalian organogenesis. Cell 2023; 186:1212-1229.e21. [PMID: 36827974 DOI: 10.1016/j.cell.2023.01.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 10/28/2022] [Accepted: 01/26/2023] [Indexed: 02/25/2023]
Abstract
Mitochondrial activity differs markedly between organs, but it is not known how and when this arises. Here we show that cell lineage-specific expression profiles involving essential mitochondrial genes emerge at an early stage in mouse development, including tissue-specific isoforms present before organ formation. However, the nuclear transcriptional signatures were not independent of organelle function. Genetically disrupting intra-mitochondrial protein synthesis with two different mtDNA mutations induced cell lineage-specific compensatory responses, including molecular pathways not previously implicated in organellar maintenance. We saw downregulation of genes whose expression is known to exacerbate the effects of exogenous mitochondrial toxins, indicating a transcriptional adaptation to mitochondrial dysfunction during embryonic development. The compensatory pathways were both tissue and mutation specific and under the control of transcription factors which promote organelle resilience. These are likely to contribute to the tissue specificity which characterizes human mitochondrial diseases and are potential targets for organ-directed treatments.
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Affiliation(s)
- Stephen P Burr
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Florian Klimm
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Department of Mathematics, Imperial College London, London, UK; EPSRC Centre for Mathematics of Precision Healthcare, Imperial College, London, UK; Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, D-14195 Berlin, Germany; Department of Computer Science, Freie Universität Berlin, Arnimallee 3, D-14195 Berlin, Germany
| | - Angelos Glynos
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Malwina Prater
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Pamella Sendon
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Pavel Nash
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Christopher A Powell
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Nina A Bonekamp
- Max Planck Institute for Biology of Ageing, Cologne, Germany; Department of Neuroanatomy, Mannheim Centre for Translational Neuroscience (MCTN), Medical Faculty Mannheim/Heidelberg University, Heidelberg, Germany
| | - Julia Charl
- Institute of Biochemistry, University of Cologne, Otto-Fischer-Strasse 12-14, Cologne, Germany
| | - Hector Diaz
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Lyuba V Bozhilova
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Yu Nie
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Haixin Zhang
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Michele Frison
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Nick Jones
- Department of Mathematics, Imperial College London, London, UK
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - James B Stewart
- Max Planck Institute for Biology of Ageing, Cologne, Germany; Biosciences Institute, Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
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9
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Tan BG, Mutti CD, Shi Y, Xie X, Zhu X, Silva-Pinheiro P, Menger KE, Díaz-Maldonado H, Wei W, Nicholls TJ, Chinnery PF, Minczuk M, Falkenberg M, Gustafsson CM. The human mitochondrial genome contains a second light strand promoter. Mol Cell 2022; 82:3646-3660.e9. [PMID: 36044900 DOI: 10.1016/j.molcel.2022.08.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/21/2022] [Accepted: 08/07/2022] [Indexed: 11/30/2022]
Abstract
The human mitochondrial genome must be replicated and expressed in a timely manner to maintain energy metabolism and supply cells with adequate levels of adenosine triphosphate. Central to this process is the idea that replication primers and gene products both arise via transcription from a single light strand promoter (LSP) such that primer formation can influence gene expression, with no consensus as to how this is regulated. Here, we report the discovery of a second light strand promoter (LSP2) in humans, with features characteristic of a bona fide mitochondrial promoter. We propose that the position of LSP2 on the mitochondrial genome allows replication and gene expression to be orchestrated from two distinct sites, which expands our long-held understanding of mitochondrial gene expression in humans.
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Affiliation(s)
- Benedict G Tan
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Christian D Mutti
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Yonghong Shi
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Xie Xie
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Xuefeng Zhu
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Pedro Silva-Pinheiro
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Katja E Menger
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Héctor Díaz-Maldonado
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden
| | - Wei Wei
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Thomas J Nicholls
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Patrick F Chinnery
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK; Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK.
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden.
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg 405 30, Sweden.
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10
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Erić P, Patenković A, Erić K, Tanasković M, Davidović S, Rakić M, Savić Veselinović M, Stamenković-Radak M, Jelić M. Temperature-Specific and Sex-Specific Fitness Effects of Sympatric Mitochondrial and Mito-Nuclear Variation in Drosophila obscura. INSECTS 2022; 13:insects13020139. [PMID: 35206713 PMCID: PMC8880146 DOI: 10.3390/insects13020139] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/20/2022] [Accepted: 01/22/2022] [Indexed: 12/28/2022]
Abstract
Simple Summary Does variation in the mitochondrial DNA sequence influence the survival and reproduction of an individual? What is the purpose of genetic variation of the mitochondrial DNA between individuals from the same population? As a simple laboratory model, Drosophila species can give us the answer to this question. Creating experimental lines with different combinations of mitochondrial and nuclear genomic DNA and testing how successful these lines were in surviving in different experimental set-ups enables us to deduce the effect that both genomes have on fitness. This study on D. obscura experimentally validates theoretical models that explain the persistence of mitochondrial DNA variation within populations. Our results shed light on the various mechanisms that maintain this type of variation. Finally, by conducting the experiments on two experimental temperatures, we have shown that environmental variations can support mitochondrial DNA variation within populations. Abstract The adaptive significance of sympatric mitochondrial (mtDNA) variation and the role of selective mechanisms that maintain it are debated to this day. Isofemale lines of Drosophila obscura collected from four populations were backcrossed within populations to construct experimental lines, with all combinations of mtDNA Cyt b haplotypes and nuclear genetic backgrounds (nuDNA). Individuals of both sexes from these lines were then subjected to four fitness assays (desiccation resistance, developmental time, egg-to-adult viability and sex ratio) on two experimental temperatures to examine the role of temperature fluctuations and sex-specific selection, as well as the part that interactions between the two genomes play in shaping mtDNA variation. The results varied across populations and fitness components. In the majority of comparisons, they show that sympatric mitochondrial variants affect fitness. However, their effect should be examined in light of interactions with nuDNA, as mito-nuclear genotype was even more influential on fitness across all components. We found both sex-specific and temperature-specific differences in mitochondrial and mito-nuclear genotype ranks in all fitness components. The effect of temperature-specific selection was found to be more prominent, especially in desiccation resistance. From the results of different components tested, we can also infer that temperature-specific mito-nuclear interactions rather than sex-specific selection on mito-nuclear genotypes have a more substantial role in preserving mtDNA variation in this model species.
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Affiliation(s)
- Pavle Erić
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”–National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.P.); (K.E.); (M.T.); (S.D.); (M.R.)
- Correspondence: ; Tel.: +381-112-078-334
| | - Aleksandra Patenković
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”–National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.P.); (K.E.); (M.T.); (S.D.); (M.R.)
| | - Katarina Erić
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”–National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.P.); (K.E.); (M.T.); (S.D.); (M.R.)
| | - Marija Tanasković
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”–National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.P.); (K.E.); (M.T.); (S.D.); (M.R.)
| | - Slobodan Davidović
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”–National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.P.); (K.E.); (M.T.); (S.D.); (M.R.)
| | - Mina Rakić
- Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research “Siniša Stanković”–National Institute of the Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11060 Belgrade, Serbia; (A.P.); (K.E.); (M.T.); (S.D.); (M.R.)
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (M.S.V.); (M.S.-R.); (M.J.)
| | - Marija Savić Veselinović
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (M.S.V.); (M.S.-R.); (M.J.)
| | - Marina Stamenković-Radak
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (M.S.V.); (M.S.-R.); (M.J.)
| | - Mihailo Jelić
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia; (M.S.V.); (M.S.-R.); (M.J.)
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11
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Singh M, Posse V, Peter B, Falkenberg M, Gustafsson C. Ribonucleotides embedded in template DNA impair mitochondrial RNA polymerase progression. Nucleic Acids Res 2022; 50:989-999. [PMID: 35018464 PMCID: PMC8789056 DOI: 10.1093/nar/gkab1251] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 11/30/2021] [Accepted: 12/07/2021] [Indexed: 11/12/2022] Open
Abstract
Human mitochondria lack ribonucleotide excision repair pathways, causing misincorporated ribonucleotides (rNMPs) to remain embedded in the mitochondrial genome. Previous studies have demonstrated that human mitochondrial DNA polymerase γ can bypass a single rNMP, but that longer stretches of rNMPs present an obstacle to mitochondrial DNA replication. Whether embedded rNMPs also affect mitochondrial transcription has not been addressed. Here we demonstrate that mitochondrial RNA polymerase elongation activity is affected by a single, embedded rNMP in the template strand. The effect is aggravated at stretches with two or more consecutive rNMPs in a row and cannot be overcome by addition of the mitochondrial transcription elongation factor TEFM. Our findings lead us to suggest that impaired transcription may be of functional relevance in genetic disorders associated with imbalanced nucleotide pools and higher levels of embedded rNMPs.
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Affiliation(s)
- Meenakshi Singh
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Viktor Posse
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Bradley Peter
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, SE-405 30, Sweden
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, SE-405 30, Sweden
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12
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Zamudio-Ochoa A, Morozov YI, Sarfallah A, Anikin M, Temiakov D. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2765-2781. [PMID: 35191499 PMCID: PMC8934621 DOI: 10.1093/nar/gkac103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/27/2022] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
Recognition of mammalian mitochondrial promoters requires the concerted action of mitochondrial RNA polymerase (mtRNAP) and transcription initiation factors TFAM and TFB2M. In this work, we found that transcript slippage results in heterogeneity of the human mitochondrial transcripts in vivo and in vitro. This allowed us to correctly interpret the RNAseq data, identify the bona fide transcription start sites (TSS), and assign mitochondrial promoters for > 50% of mammalian species and some other vertebrates. The divergent structure of the mammalian promoters reveals previously unappreciated aspects of mtDNA evolution. The correct assignment of TSS also enabled us to establish the precise register of the DNA in the initiation complex and permitted investigation of the sequence-specific protein-DNA interactions. We determined the molecular basis of promoter recognition by mtRNAP and TFB2M, which cooperatively recognize bases near TSS in a species-specific manner. Our findings reveal a role of mitochondrial transcription machinery in mitonuclear coevolution and speciation.
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Affiliation(s)
- Angelica Zamudio-Ochoa
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Yaroslav I Morozov
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Azadeh Sarfallah
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Michael Anikin
- Department of Cell Biology and Neuroscience, Rowan University, School of Osteopathic Medicine, 42 E Laurel Rd, Stratford, NJ 08084, USA
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13
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Menger KE, Rodríguez-Luis A, Chapman J, Nicholls TJ. Controlling the topology of mammalian mitochondrial DNA. Open Biol 2021; 11:210168. [PMID: 34547213 PMCID: PMC8455175 DOI: 10.1098/rsob.210168] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The genome of mitochondria, called mtDNA, is a small circular DNA molecule present at thousands of copies per human cell. MtDNA is packaged into nucleoprotein complexes called nucleoids, and the density of mtDNA packaging affects mitochondrial gene expression. Genetic processes such as transcription, DNA replication and DNA packaging alter DNA topology, and these topological problems are solved by a family of enzymes called topoisomerases. Within mitochondria, topoisomerases are involved firstly in the regulation of mtDNA supercoiling and secondly in disentangling interlinked mtDNA molecules following mtDNA replication. The loss of mitochondrial topoisomerase activity leads to defects in mitochondrial function, and variants in the dual-localized type IA topoisomerase TOP3A have also been reported to cause human mitochondrial disease. We review the current knowledge on processes that alter mtDNA topology, how mtDNA topology is modulated by the action of topoisomerases, and the consequences of altered mtDNA topology for mitochondrial function and human health.
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Affiliation(s)
- Katja E. Menger
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Alejandro Rodríguez-Luis
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - James Chapman
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Thomas J. Nicholls
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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14
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Zhou T, Sang YH, Cai S, Xu C, Shi MH. The requirement of mitochondrial RNA polymerase for non-small cell lung cancer cell growth. Cell Death Dis 2021; 12:751. [PMID: 34326320 PMCID: PMC8322058 DOI: 10.1038/s41419-021-04039-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 12/25/2022]
Abstract
POLRMT (RNA polymerase mitochondrial) is responsible for the transcription of mitochondrial genome encoding key components of oxidative phosphorylation. This process is important for cancer cell growth. The current study tested expression and potential functions of POLRMT in non-small cell lung cancer (NSCLC). TCGA cohorts and the results from the local lung cancer tissues showed that POLRMT is overexpressed in human lung cancer tissues. In both primary human NSCLC cells and A549 cells, POLRMT silencing (by targeted lentiviral shRNAs) or knockout (through CRSIPR/Cas9 gene editing method) potently inhibited cell viability, proliferation, migration, and invasion, and induced apoptosis activation. On the contrast, ectopic overexpression of POLRMT using a lentiviral construct accelerated cell proliferation and migration in NSCLC cells. The mtDNA contents, mRNA levels of mitochondrial transcripts, and subunits of respiratory chain complexes, as well as S6 phosphorylation, were decreased in POLRMT-silenced or -knockout NSCLC cells, but increased after ectopic POLRMT overexpression. In vivo, intratumoral injection of POLRMT shRNA adeno-associated virus (AAV) potently inhibited NSCLC xenograft growth in severe combined immune deficiency mice. The mtDNA contents, mRNA levels of mitochondria respiratory chain complex subunits, and S6 phosphorylation were decreased in POLRMT shRNA AAV-injected NSCLC xenograft tissues. These results show that POLRMT is a novel and important oncogene required for NSCLC cell growth in vitro and in vivo.
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Affiliation(s)
- Tong Zhou
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yong-Hua Sang
- Department of Thoracic Surgery, The Second affiliated Hospital of Soochow University, Suzhou, China
| | - Shang Cai
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Chun Xu
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.
| | - Min-Hua Shi
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China.
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15
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Kotrasová V, Keresztesová B, Ondrovičová G, Bauer JA, Havalová H, Pevala V, Kutejová E, Kunová N. Mitochondrial Kinases and the Role of Mitochondrial Protein Phosphorylation in Health and Disease. Life (Basel) 2021; 11:life11020082. [PMID: 33498615 PMCID: PMC7912454 DOI: 10.3390/life11020082] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 02/07/2023] Open
Abstract
The major role of mitochondria is to provide cells with energy, but no less important are their roles in responding to various stress factors and the metabolic changes and pathological processes that might occur inside and outside the cells. The post-translational modification of proteins is a fast and efficient way for cells to adapt to ever changing conditions. Phosphorylation is a post-translational modification that signals these changes and propagates these signals throughout the whole cell, but it also changes the structure, function and interaction of individual proteins. In this review, we summarize the influence of kinases, the proteins responsible for phosphorylation, on mitochondrial biogenesis under various cellular conditions. We focus on their role in keeping mitochondria fully functional in healthy cells and also on the changes in mitochondrial structure and function that occur in pathological processes arising from the phosphorylation of mitochondrial proteins.
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Affiliation(s)
- Veronika Kotrasová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
| | - Barbora Keresztesová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
- First Faculty of Medicine, Institute of Biology and Medical Genetics, Charles University, 128 00 Prague, Czech Republic
| | - Gabriela Ondrovičová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
| | - Jacob A. Bauer
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
| | - Henrieta Havalová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
| | - Vladimír Pevala
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
| | - Eva Kutejová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
- Correspondence: (E.K.); (N.K.)
| | - Nina Kunová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (V.K.); (B.K.); (G.O.); (J.A.B.); (H.H.); (V.P.)
- First Faculty of Medicine, Institute of Biology and Medical Genetics, Charles University, 128 00 Prague, Czech Republic
- Correspondence: (E.K.); (N.K.)
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16
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Basu U, Bostwick AM, Das K, Dittenhafer-Reed KE, Patel SS. Structure, mechanism, and regulation of mitochondrial DNA transcription initiation. J Biol Chem 2020; 295:18406-18425. [PMID: 33127643 PMCID: PMC7939475 DOI: 10.1074/jbc.rev120.011202] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/29/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are specialized compartments that produce requisite ATP to fuel cellular functions and serve as centers of metabolite processing, cellular signaling, and apoptosis. To accomplish these roles, mitochondria rely on the genetic information in their small genome (mitochondrial DNA) and the nucleus. A growing appreciation for mitochondria's role in a myriad of human diseases, including inherited genetic disorders, degenerative diseases, inflammation, and cancer, has fueled the study of biochemical mechanisms that control mitochondrial function. The mitochondrial transcriptional machinery is different from nuclear machinery. The in vitro re-constituted transcriptional complexes of Saccharomyces cerevisiae (yeast) and humans, aided with high-resolution structures and biochemical characterizations, have provided a deeper understanding of the mechanism and regulation of mitochondrial DNA transcription. In this review, we will discuss recent advances in the structure and mechanism of mitochondrial transcription initiation. We will follow up with recent discoveries and formative findings regarding the regulatory events that control mitochondrial DNA transcription, focusing on those involved in cross-talk between the mitochondria and nucleus.
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Affiliation(s)
- Urmimala Basu
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA; Graduate School of Biomedical Sciences, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | | | - Kalyan Das
- Department of Microbiology, Immunology, and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA.
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17
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Gupta A, Shrivastava D, Shakya AK, Gupta K, Pratap JV, Habib S. PfKsgA1 functions as a transcription initiation factor and interacts with the N-terminal region of the mitochondrial RNA polymerase of Plasmodium falciparum. Int J Parasitol 2020; 51:23-37. [PMID: 32896572 DOI: 10.1016/j.ijpara.2020.07.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 10/23/2022]
Abstract
The small mitochondrial genome (mtDNA) of the malaria parasite is known to transcribe its genes polycistonically, although promoter element(s) have not yet been identified. An unusually large Plasmodium falciparum candidate mitochondrial phage-like RNA polymerase (PfmtRNAP) with an extended N-terminal region is encoded by the parasite nuclear genome. Using specific antibodies against the enzyme, we established that PfmtRNAP was targeted exclusively to the mitochondrion and interacted with mtDNA. Phylogenetic analysis showed that it is part of a separate apicomplexan clade. A search for PfmtRNAP-associated transcription initiation factors using sequence homology and in silico protein-protein interaction network analysis identified PfKsgA1. PfKsgA1 is a dual cytosol- and mitochondrion-targeted protein that functions as a small subunit rRNA dimethyltransferase in ribosome biogenesis. Chromatin immunoprecipitation showed that PfKsgA1 interacts with mtDNA, and in vivo crosslinking and pull-down experiments confirmed PfmtRNAP-PfKsgA1 interaction. The ability of PfKsgA1 to serve as a transcription initiation factor was demonstrated by complementation of yeast mitochondrial transcription factor Mtf1 function in Rpo41-driven in vitro transcription. Pull-down experiments using PfKsgA1 and PfmtRNAP domains indicated that the N-terminal region of PfmtRNAP interacts primarily with the PfKsgA1 C-terminal domain with some contacts being made with the linker and N-terminal domain of PfKsgA1. In the absence of full-length recombinant PfmtRNAP, solution structures of yeast mitochondrial RNA polymerase Rpo41 complexes with Mtf1 or PfKsgA1 were determined by small-angle X-ray scattering. Protein interaction interfaces thus identified matched with those reported earlier for Rpo41-Mtf1 interaction and overlaid with the PfmtRNAP-interfacing region identified experimentally for PfKsgA1. Our results indicate that in addition to a role in mitochondrial ribosome biogenesis, PfKsgA1 has an independent function as a transcription initiation factor for PfmtRNAP.
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Affiliation(s)
- Ankit Gupta
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Deepti Shrivastava
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anil Kumar Shakya
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Kirti Gupta
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - J V Pratap
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Saman Habib
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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18
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Hill GE. Genetic hitchhiking, mitonuclear coadaptation, and the origins of mt DNA barcode gaps. Ecol Evol 2020; 10:9048-9059. [PMID: 32953045 PMCID: PMC7487244 DOI: 10.1002/ece3.6640] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 01/02/2023] Open
Abstract
DNA barcoding based on mitochondrial (mt) nucleotide sequences is an enigma. Neutral models of mt evolution predict DNA barcoding cannot work for recently diverged taxa, and yet, mt DNA barcoding accurately delimits species for many bilaterian animals. Meanwhile, mt DNA barcoding often fails for plants and fungi. I propose that because mt gene products must cofunction with nuclear gene products, the evolution of mt genomes is best understood with full consideration of the two environments that impose selective pressure on mt genes: the external environment and the internal genomic environment. Moreover, it is critical to fully consider the potential for adaptive evolution of not just protein products of mt genes but also of mt transfer RNAs and mt ribosomal RNAs. The tight linkage of genes on mt genomes that do not engage in recombination could facilitate selective sweeps whenever there is positive selection on any element in the mt genome, leading to the purging of mt genetic diversity within a population and to the rapid fixation of novel mt DNA sequences. Accordingly, the most important factor determining whether or not mt DNA sequences diagnose species boundaries may be the extent to which the mt chromosomes engage in recombination.
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19
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Karakaidos P, Rampias T. Mitonuclear Interactions in the Maintenance of Mitochondrial Integrity. Life (Basel) 2020; 10:life10090173. [PMID: 32878185 PMCID: PMC7555762 DOI: 10.3390/life10090173] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 08/28/2020] [Indexed: 12/27/2022] Open
Abstract
In eukaryotic cells, mitochondria originated in an α-proteobacterial endosymbiont. Although these organelles harbor their own genome, the large majority of genes, originally encoded in the endosymbiont, were either lost or transferred to the nucleus. As a consequence, mitochondria have become semi-autonomous and most of their processes require the import of nuclear-encoded components to be functional. Therefore, the mitochondrial-specific translation has evolved to be coordinated by mitonuclear interactions to respond to the energetic demands of the cell, acquiring unique and mosaic features. However, mitochondrial-DNA-encoded genes are essential for the assembly of the respiratory chain complexes. Impaired mitochondrial function due to oxidative damage and mutations has been associated with numerous human pathologies, the aging process, and cancer. In this review, we highlight the unique features of mitochondrial protein synthesis and provide a comprehensive insight into the mitonuclear crosstalk and its co-evolution, as well as the vulnerabilities of the animal mitochondrial genome.
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20
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Medini H, Cohen T, Mishmar D. Mitochondria Are Fundamental for the Emergence of Metazoans: On Metabolism, Genomic Regulation, and the Birth of Complex Organisms. Annu Rev Genet 2020; 54:151-166. [PMID: 32857636 DOI: 10.1146/annurev-genet-021920-105545] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Out of many intracellular bacteria, only the mitochondria and chloroplasts abandoned their independence billions of years ago and became endosymbionts within the host eukaryotic cell. Consequently, one cannot grow eukaryotic cells without their mitochondria, and the mitochondria cannot divide outside of the cell, thus reflecting interdependence. Here, we argue that such interdependence underlies the fundamental role of mitochondrial activities in the emergence of metazoans. Several lines of evidence support our hypothesis: (a) Differentiation and embryogenesis rely on mitochondrial function; (b) mitochondrial metabolites are primary precursors for epigenetic modifications (such as methyl and acetyl), which are critical for chromatin remodeling and gene expression, particularly during differentiation and embryogenesis; and (c) mitonuclear coregulation adapted to accommodate both housekeeping and tissue-dependent metabolic needs. We discuss the evolution of the unique mitochondrial genetic system, mitochondrial metabolites, mitonuclear coregulation, and their critical roles in the emergence of metazoans and in human disorders.
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Affiliation(s)
- Hadar Medini
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501 Israel;
| | - Tal Cohen
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501 Israel;
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501 Israel;
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21
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Vozáriková V, Kunová N, Bauer JA, Frankovský J, Kotrasová V, Procházková K, Džugasová V, Kutejová E, Pevala V, Nosek J, Tomáška Ľ. Mitochondrial HMG-Box Containing Proteins: From Biochemical Properties to the Roles in Human Diseases. Biomolecules 2020; 10:biom10081193. [PMID: 32824374 PMCID: PMC7463775 DOI: 10.3390/biom10081193] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial DNA (mtDNA) molecules are packaged into compact nucleo-protein structures called mitochondrial nucleoids (mt-nucleoids). Their compaction is mediated in part by high-mobility group (HMG)-box containing proteins (mtHMG proteins), whose additional roles include the protection of mtDNA against damage, the regulation of gene expression and the segregation of mtDNA into daughter organelles. The molecular mechanisms underlying these functions have been identified through extensive biochemical, genetic, and structural studies, particularly on yeast (Abf2) and mammalian mitochondrial transcription factor A (TFAM) mtHMG proteins. The aim of this paper is to provide a comprehensive overview of the biochemical properties of mtHMG proteins, the structural basis of their interaction with DNA, their roles in various mtDNA transactions, and the evolutionary trajectories leading to their rapid diversification. We also describe how defects in the maintenance of mtDNA in cells with dysfunctional mtHMG proteins lead to different pathologies at the cellular and organismal level.
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Affiliation(s)
- Veronika Vozáriková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Nina Kunová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Jacob A. Bauer
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Ján Frankovský
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Veronika Kotrasová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Katarína Procházková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Vladimíra Džugasová
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
| | - Eva Kutejová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Vladimír Pevala
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia; (N.K.); (J.A.B.); (V.K.); (E.K.); (V.P.)
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina CH-1, 842 15 Bratislava, Slovakia;
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina B-1, 842 15 Bratislava, Slovakia; (V.V.); (J.F.); (K.P.); (V.D.)
- Correspondence: ; Tel.: +421-2-90149-433
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22
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Luo Y, Ma J, Lu W. The Significance of Mitochondrial Dysfunction in Cancer. Int J Mol Sci 2020; 21:ijms21165598. [PMID: 32764295 PMCID: PMC7460667 DOI: 10.3390/ijms21165598] [Citation(s) in RCA: 133] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 02/06/2023] Open
Abstract
As an essential organelle in nucleated eukaryotic cells, mitochondria play a central role in energy metabolism, maintenance of redox balance, and regulation of apoptosis. Mitochondrial dysfunction, either due to the TCA cycle enzyme defects, mitochondrial DNA genetic mutations, defective mitochondrial electron transport chain, oxidative stress, or aberrant oncogene and tumor suppressor signaling, has been observed in a wide spectrum of human cancers. In this review, we summarize mitochondrial dysfunction induced by these alterations that promote human cancers.
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Affiliation(s)
- Yongde Luo
- School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou 325000, China
- Division of Gastroenterology and Hepatology, Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA;
- Correspondence: (Y.L.); (W.L.)
| | - Jianjia Ma
- Division of Gastroenterology and Hepatology, Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA;
| | - Weiqin Lu
- Division of Gastroenterology and Hepatology, Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA;
- Correspondence: (Y.L.); (W.L.)
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23
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Durairajanayagam D, Singh D, Agarwal A, Henkel R. Causes and consequences of sperm mitochondrial dysfunction. Andrologia 2020; 53:e13666. [PMID: 32510691 DOI: 10.1111/and.13666] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 05/07/2020] [Indexed: 12/15/2022] Open
Abstract
Mitochondria have multiple functions, including synthesis of adenine triphosphate, production of reactive oxygen species, calcium signalling, thermogenesis and apoptosis. Mitochondria have a significant contribution in regulating the various physiological aspects of reproductive function, from spermatogenesis up to fertilisation. Mitochondrial functionality and intact mitochondrial membrane potential are a pre-requisite for sperm motility, hyperactivation, capacitation, acrosin activity, acrosome reaction and DNA integrity. Optimal mitochondrial activity is therefore crucial for human sperm function and semen quality. However, the precise role of mitochondria in spermatozoa remains to be fully explored. Defects in sperm mitochondrial function severely impair the maintenance of energy production required for sperm motility and may be an underlying cause of asthenozoospermia. Sperm mtDNA is susceptible to oxidative damage and mutations that could compromise sperm function leading to infertility. Males with abnormal semen parameters have increased mtDNA copy number and reduced mtDNA integrity. This review discusses the role of mitochondria in sperm function, along with the causes and impact of its dysfunction on male fertility. Greater understanding of sperm mitochondrial function and its correlation with sperm quality could provide further insights into their contribution in the assessment of the infertile male.
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Affiliation(s)
- Damayanthi Durairajanayagam
- Department of Physiology, Faculty of Medicine, Universiti Teknologi MARA, Cawangan Selangor, Kampus Sungai Buloh, Sungai Buloh, Malaysia
| | - Dipty Singh
- Department of Neuroendocrinology, Indian Council of Medical Research (ICMR)-National Institute for Research in Reproductive Health (NIRRH), Mumbai, India
| | - Ashok Agarwal
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Ralf Henkel
- American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA.,Department of Medical Bioscience, Faculty of Natural Science, University of the Western Cape, Belville, South Africa
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24
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Nicholls TJ, Spåhr H, Jiang S, Siira SJ, Koolmeister C, Sharma S, Kauppila JHK, Jiang M, Kaever V, Rackham O, Chabes A, Falkenberg M, Filipovska A, Larsson NG, Gustafsson CM. Dinucleotide Degradation by REXO2 Maintains Promoter Specificity in Mammalian Mitochondria. Mol Cell 2019; 76:784-796.e6. [PMID: 31588022 PMCID: PMC6900737 DOI: 10.1016/j.molcel.2019.09.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/12/2019] [Accepted: 09/04/2019] [Indexed: 12/12/2022]
Abstract
Oligoribonucleases are conserved enzymes that degrade short RNA molecules of up to 5 nt in length and are assumed to constitute the final stage of RNA turnover. Here we demonstrate that REXO2 is a specialized dinucleotide-degrading enzyme that shows no preference between RNA and DNA dinucleotide substrates. A heart- and skeletal-muscle-specific knockout mouse displays elevated dinucleotide levels and alterations in gene expression patterns indicative of aberrant dinucleotide-primed transcription initiation. We find that dinucleotides act as potent stimulators of mitochondrial transcription initiation in vitro. Our data demonstrate that increased levels of dinucleotides can be used to initiate transcription, leading to an increase in transcription levels from both mitochondrial promoters and other, nonspecific sequence elements in mitochondrial DNA. Efficient RNA turnover by REXO2 is thus required to maintain promoter specificity and proper regulation of transcription in mammalian mitochondria.
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Affiliation(s)
- Thomas J Nicholls
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Henrik Spåhr
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden; Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm 17177, Sweden
| | - Shan Jiang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden; Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm 17177, Sweden
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia; Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Camilla Koolmeister
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden; Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm 17177, Sweden
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå 901 87, Sweden
| | - Johanna H K Kauppila
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Min Jiang
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Hannover Medical School, 30625 Hannover, Germany
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia; School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, WA 6102, Australia; Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå 901 87, Sweden
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia; School of Molecular Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Nils-Göran Larsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden; Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm 17177, Sweden.
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden.
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25
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Bouda E, Stapon A, Garcia-Diaz M. Mechanisms of mammalian mitochondrial transcription. Protein Sci 2019; 28:1594-1605. [PMID: 31309618 DOI: 10.1002/pro.3688] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 01/06/2023]
Abstract
Numerous age-related human diseases have been associated with deficiencies in cellular energy production. Moreover, genetic alterations resulting in mitochondrial dysfunction are the cause of inheritable disorders commonly known as mitochondrial diseases. Many of these deficiencies have been directly or indirectly linked to deficits in mitochondrial gene expression. Transcription is an essential step in gene expression and elucidating the molecular mechanisms involved in this process is critical for understanding defects in energy production. For the past five decades, substantial efforts have been invested in the field of mitochondrial transcription. These efforts have led to the discovery of the main protein factors responsible for transcription as well as to a basic mechanistic understanding of the transcription process. They have also revealed various mechanisms of transcriptional regulation as well as the links that exist between the transcription process and downstream processes of RNA maturation. Here, we review the knowledge gathered in early mitochondrial transcription studies and focus on recent findings that shape our current understanding of mitochondrial transcription, posttranscriptional processing, as well as transcriptional regulation in mammalian systems.
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Affiliation(s)
- Emilie Bouda
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York
| | - Anthony Stapon
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York
| | - Miguel Garcia-Diaz
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York
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26
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Al-Behadili A, Uhler JP, Berglund AK, Peter B, Doimo M, Reyes A, Wanrooij S, Zeviani M, Falkenberg M. A two-nuclease pathway involving RNase H1 is required for primer removal at human mitochondrial OriL. Nucleic Acids Res 2018; 46:9471-9483. [PMID: 30102370 PMCID: PMC6182146 DOI: 10.1093/nar/gky708] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/21/2018] [Accepted: 07/24/2018] [Indexed: 11/12/2022] Open
Abstract
The role of Ribonuclease H1 (RNase H1) during primer removal and ligation at the mitochondrial origin of light-strand DNA synthesis (OriL) is a key, yet poorly understood, step in mitochondrial DNA maintenance. Here, we reconstitute the replication cycle of L-strand synthesis in vitro using recombinant mitochondrial proteins and model OriL substrates. The process begins with initiation of DNA replication at OriL and ends with primer removal and ligation. We find that RNase H1 partially removes the primer, leaving behind the last one to three ribonucleotides. These 5'-end ribonucleotides disturb ligation, a conclusion which is supported by analysis of RNase H1-deficient patient cells. A second nuclease is therefore required to remove the last ribonucleotides and we demonstrate that Flap endonuclease 1 (FEN1) can execute this function in vitro. Removal of RNA primers at OriL thus depends on a two-nuclease model, which in addition to RNase H1 requires FEN1 or a FEN1-like activity. These findings define the role of RNase H1 at OriL and help to explain the pathogenic consequences of disease causing mutations in RNase H1.
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Affiliation(s)
- Ali Al-Behadili
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, Sweden
| | - Jay P Uhler
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, Sweden
| | - Anna-Karin Berglund
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, Sweden
| | - Bradley Peter
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, Sweden
| | - Mara Doimo
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Aurelio Reyes
- MRC-Mitochondrial Biology Unit, University of Cambridge, MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Massimo Zeviani
- MRC-Mitochondrial Biology Unit, University of Cambridge, MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, Sweden
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27
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Kumar RP, Ray S, Home P, Saha B, Bhattacharya B, Wilkins HM, Chavan H, Ganguly A, Milano-Foster J, Paul A, Krishnamurthy P, Swerdlow RH, Paul S. Regulation of energy metabolism during early mammalian development: TEAD4 controls mitochondrial transcription. Development 2018; 145:dev.162644. [PMID: 30201685 DOI: 10.1242/dev.162644] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 08/31/2018] [Indexed: 12/27/2022]
Abstract
Early mammalian development is crucially dependent on the establishment of oxidative energy metabolism within the trophectoderm (TE) lineage. Unlike the inner cell mass, TE cells enhance ATP production via mitochondrial oxidative phosphorylation (OXPHOS) and this metabolic preference is essential for blastocyst maturation. However, molecular mechanisms that regulate establishment of oxidative energy metabolism in TE cells are incompletely understood. Here, we show that conserved transcription factor TEAD4, which is essential for pre-implantation mammalian development, regulates this process by promoting mitochondrial transcription. In developing mouse TE and TE-derived trophoblast stem cells (TSCs), TEAD4 localizes to mitochondria, binds to mitochondrial DNA (mtDNA) and facilitates its transcription by recruiting mitochondrial RNA polymerase (POLRMT). Loss of TEAD4 impairs recruitment of POLRMT, resulting in reduced expression of mtDNA-encoded electron transport chain components, thereby inhibiting oxidative energy metabolism. Our studies identify a novel TEAD4-dependent molecular mechanism that regulates energy metabolism in the TE lineage to ensure mammalian development.
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Affiliation(s)
- Ram P Kumar
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Soma Ray
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Pratik Home
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Biswarup Saha
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Bhaswati Bhattacharya
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Heather M Wilkins
- University of Kansas Alzheimer's Disease Center and the Departments of Neurology, Molecular and Integrative Physiology, and Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Hemantkumar Chavan
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Avishek Ganguly
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jessica Milano-Foster
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Arindam Paul
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Partha Krishnamurthy
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Russell H Swerdlow
- University of Kansas Alzheimer's Disease Center and the Departments of Neurology, Molecular and Integrative Physiology, and Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Soumen Paul
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA .,Institute of Reproductive Health and Regenerative Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
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28
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Structural basis of mitochondrial transcription. Nat Struct Mol Biol 2018; 25:754-765. [PMID: 30190598 DOI: 10.1038/s41594-018-0122-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/29/2018] [Indexed: 01/17/2023]
Abstract
The mitochondrial genome is transcribed by a single-subunit DNA-dependent RNA polymerase (mtRNAP) and its auxiliary factors. Structural studies have elucidated how mtRNAP cooperates with its dedicated transcription factors to direct RNA synthesis: initiation factors TFAM and TFB2M assist in promoter-DNA binding and opening by mtRNAP while the elongation factor TEFM increases polymerase processivity to the levels required for synthesis of long polycistronic mtRNA transcripts. Here, we review the emerging body of structural and functional studies of human mitochondrial transcription, provide a molecular movie that can be used for teaching purposes and discuss the open questions to guide future directions of investigation.
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29
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Barshad G, Marom S, Cohen T, Mishmar D. Mitochondrial DNA Transcription and Its Regulation: An Evolutionary Perspective. Trends Genet 2018; 34:682-692. [DOI: 10.1016/j.tig.2018.05.009] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/19/2018] [Accepted: 05/31/2018] [Indexed: 12/15/2022]
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30
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Liu H, Li S, Liu X, Chen Y, Deng H. SIRT3 Overexpression Inhibits Growth of Kidney Tumor Cells and Enhances Mitochondrial Biogenesis. J Proteome Res 2018; 17:3143-3152. [DOI: 10.1021/acs.jproteome.8b00260] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Huan Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Siying Li
- University of California, Davis, Davis, California 95616, United States
| | - Xiaohui Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yuling Chen
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua University−Peking University Joint Center for Life Sciences, Beijing 100084, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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31
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Blumberg A, Danko CG, Kundaje A, Mishmar D. A common pattern of DNase I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization. Genome Res 2018; 28:1158-1168. [PMID: 30002158 PMCID: PMC6071632 DOI: 10.1101/gr.230409.117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 06/13/2018] [Indexed: 12/16/2022]
Abstract
Human mitochondrial DNA (mtDNA) is believed to lack chromatin and histones. Instead, it is coated solely by the transcription factor TFAM. We asked whether mtDNA packaging is more regulated than once thought. To address this, we analyzed DNase-seq experiments in 324 human cell types and found, for the first time, a pattern of 29 mtDNA Genomic footprinting (mt-DGF) sites shared by ∼90% of the samples. Their syntenic conservation in mouse DNase-seq experiments reflect selective constraints. Colocalization with known mtDNA regulatory elements, with G-quadruplex structures, in TFAM-poor sites (in HeLa cells) and with transcription pausing sites, suggest a functional regulatory role for such mt-DGFs. Altered mt-DGF pattern in interleukin 3-treated CD34+ cells, certain tissue differences, and significant prevalence change in fetal versus nonfetal samples, offer first clues to their physiological importance. Taken together, human mtDNA has a conserved protein-DNA organization, which is likely involved in mtDNA regulation.
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Affiliation(s)
- Amit Blumberg
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105 Israel
| | - Charles G Danko
- Baker Institute for Animal Health, Cornell University, Ithaca, New York 14853, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, California 94305-5120, USA
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105 Israel
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32
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Julius C, Riaz-Bradley A, Yuzenkova Y. RNA capping by mitochondrial and multi-subunit RNA polymerases. Transcription 2018; 9:292-297. [PMID: 29624107 PMCID: PMC6150613 DOI: 10.1080/21541264.2018.1456258] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2022] Open
Abstract
Recently, it was found that bacterial and eukaryotic transcripts are capped with cellular cofactors installed by their respective RNA polymerases (RNAPs) during transcription initiation. We now show that mitochondrial RNAP efficiently caps transcripts with ADP - containing cofactors. However, a functional role of universal RNAP - catalysed capping is not yet clear.
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Affiliation(s)
- Christina Julius
- a Centre for Bacterial Cell Biology , Institute for Cell and Molecular Biosciences , Newcastle University , Newcastle upon Tyne , NE2 4AX , UK
| | - Amber Riaz-Bradley
- a Centre for Bacterial Cell Biology , Institute for Cell and Molecular Biosciences , Newcastle University , Newcastle upon Tyne , NE2 4AX , UK
| | - Yulia Yuzenkova
- a Centre for Bacterial Cell Biology , Institute for Cell and Molecular Biosciences , Newcastle University , Newcastle upon Tyne , NE2 4AX , UK
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33
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Hillen HS, Morozov YI, Sarfallah A, Temiakov D, Cramer P. Structural Basis of Mitochondrial Transcription Initiation. Cell 2017; 171:1072-1081.e10. [PMID: 29149603 DOI: 10.1016/j.cell.2017.10.036] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/18/2017] [Accepted: 10/22/2017] [Indexed: 12/31/2022]
Abstract
Transcription in human mitochondria is driven by a single-subunit, factor-dependent RNA polymerase (mtRNAP). Despite its critical role in both expression and replication of the mitochondrial genome, transcription initiation by mtRNAP remains poorly understood. Here, we report crystal structures of human mitochondrial transcription initiation complexes assembled on both light and heavy strand promoters. The structures reveal how transcription factors TFAM and TFB2M assist mtRNAP to achieve promoter-dependent initiation. TFAM tethers the N-terminal region of mtRNAP to recruit the polymerase to the promoter whereas TFB2M induces structural changes in mtRNAP to enable promoter opening and trapping of the DNA non-template strand. Structural comparisons demonstrate that the initiation mechanism in mitochondria is distinct from that in the well-studied nuclear, bacterial, or bacteriophage transcription systems but that similarities are found on the topological and conceptual level. These results provide a framework for studying the regulation of gene expression and DNA replication in mitochondria.
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Affiliation(s)
- Hauke S Hillen
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Yaroslav I Morozov
- Department of Cell Biology, Rowan University, School of Osteopathic Medicine, 2 Medical Center Dr., Stratford, NJ 08084, USA
| | - Azadeh Sarfallah
- Department of Cell Biology, Rowan University, School of Osteopathic Medicine, 2 Medical Center Dr., Stratford, NJ 08084, USA
| | - Dmitry Temiakov
- Department of Cell Biology, Rowan University, School of Osteopathic Medicine, 2 Medical Center Dr., Stratford, NJ 08084, USA.
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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34
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Comparative biochemistry of cytochrome c oxidase in animals. Comp Biochem Physiol B Biochem Mol Biol 2017; 224:170-184. [PMID: 29180239 DOI: 10.1016/j.cbpb.2017.11.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 12/19/2022]
Abstract
Cytochrome c oxidase (COX), the terminal enzyme of the electron transport system, is central to aerobic metabolism of animals. Many aspects of its structure and function are highly conserved, yet, paradoxically, it is also an important model for studying the evolution of the metabolic phenotype. In this review, part of a special issue honouring Peter Hochachka, we consider the biology of COX from the perspective of comparative and evolutionary biochemistry. The approach is to consider what is known about the enzyme in the context of conventional biochemistry, but focus on how evolutionary researchers have used this background to explore the role of the enzyme in biochemical adaptation of animals. In synthesizing the conventional and evolutionary biochemistry, we hope to identify synergies and future research opportunities. COX represents a rare opportunity for researchers to design studies that span the breadth of biology: molecular genetics, protein biochemistry, enzymology, metabolic physiology, organismal performance, evolutionary biology, and phylogeography.
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35
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Uchida A, Murugesapillai D, Kastner M, Wang Y, Lodeiro MF, Prabhakar S, Oliver GV, Arnold JJ, Maher LJ, Williams MC, Cameron CE. Unexpected sequences and structures of mtDNA required for efficient transcription from the first heavy-strand promoter. eLife 2017; 6. [PMID: 28745586 PMCID: PMC5552277 DOI: 10.7554/elife.27283] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/25/2017] [Indexed: 12/16/2022] Open
Abstract
Human mtDNA contains three promoters, suggesting a need for differential expression of the mitochondrial genome. Studies of mitochondrial transcription have used a reductionist approach, perhaps masking differential regulation. Here we evaluate transcription from light-strand (LSP) and heavy-strand (HSP1) promoters using templates that mimic their natural context. These studies reveal sequences upstream, hypervariable in the human population (HVR3), and downstream of the HSP1 transcription start site required for maximal yield. The carboxy-terminal tail of TFAM is essential for activation of HSP1 but not LSP. Images of the template obtained by atomic force microscopy show that TFAM creates loops in a discrete region, the formation of which correlates with activation of HSP1; looping is lost in tail-deleted TFAM. Identification of HVR3 as a transcriptional regulatory element may contribute to between-individual variability in mitochondrial gene expression. The unique requirement of HSP1 for the TFAM tail may enable its regulation by post-translational modifications. DOI:http://dx.doi.org/10.7554/eLife.27283.001
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Affiliation(s)
- Akira Uchida
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, United States
| | | | - Markus Kastner
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, United States
| | - Yao Wang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, United States
| | - Maria F Lodeiro
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, United States
| | - Shaan Prabhakar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, United States
| | - Guinevere V Oliver
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, United States
| | - Jamie J Arnold
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, United States
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, United States
| | - Mark C Williams
- Department of Physics, Northeastern University, Boston, United States
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, State College, United States
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36
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Mulder H. Transcribing β-cell mitochondria in health and disease. Mol Metab 2017; 6:1040-1051. [PMID: 28951827 PMCID: PMC5605719 DOI: 10.1016/j.molmet.2017.05.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 05/13/2017] [Accepted: 05/22/2017] [Indexed: 12/17/2022] Open
Abstract
Background The recent genome-wide association studies (GWAS) of Type 2 Diabetes (T2D) have identified the pancreatic β-cell as the culprit in the pathogenesis of the disease. Mitochondrial metabolism plays a crucial role in the processes controlling release of insulin and β-cell mass. This notion implies that mechanisms controlling mitochondrial function have the potential to play a decisive pathogenetic role in T2D. Scope of the review This article reviews studies demonstrating that there is indeed mitochondrial dysfunction in islets in T2D, and that GWAS have identified a variant in the gene encoding transcription factor B1 mitochondrial (TFB1M), predisposing to T2D due to mitochondrial dysfunction and impaired insulin secretion. Mechanistic studies of the nature of this pathogenetic link, as well as of other mitochondrial transcription factors, are described. Major conclusions Based on this, it is argued that transcription and translation in mitochondria are critical processes determining mitochondrial function in β-cells in health and disease.
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Key Words
- AMPK, AMP-dependent protein kinase
- ATGL, adipocyte triglyceride lipase
- COX, Cytochrome c oxidase
- CYTB, Cytochrome b
- ERR-α, Estrogen-related receptor-α
- Expression quantitative trait locus (eQTL)
- GDH, Glutamate dehydrogenase
- GSIS, Glucose-stimulated insulin secretion
- GWAS, Genome-wide association study
- Genome-wide association study (GWAS)
- HSL, Hormone-sensitive lipase
- ICDc, Cytosolic isocitrate dehydrogenase
- Insulin secretion
- Islets
- KATP, ATP-dependent K+-channel
- MTERF, Mitochondrial transcription termination factor
- Mitochondria
- ND, NADH dehydrogenase
- NRF, Nuclear respiratory factor
- NSUN4, NOP2/Sun RNA methyltransferase family member 4
- OXPHOS, Oxidative phosphorylation
- PC, Pyruvate carboxylase
- PDH, pyruvate dehydrogenase
- PGC, Peroxisome proliferator-activated receptor-γ co-activator
- POLRMT, Mitochondrial RNA polymerase
- POLγ, DNA polymerase-γ
- PPARγ, Peroxisome proliferator-activated receptor-γ
- PRC, PGC1-related coactivator
- SENP1, Sentrin/SUMO-specific protease-1
- SNP, Single Nucleotide Polymorphism
- SUR1, Sulphonylurea receptor-1
- T2D, Type 2 Diabetes
- TCA, Tricarboxylic acid
- TEFM, Mitochondrial transcription elongation factor
- TFAM, Transcription factor A mitochondrial
- TFB1M, Transcription factor B1 mitochondrial
- TFB2M, Transcription factor B2 mitochondrial
- eQTL, Expression quantitative trait locus
- β-Cell
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Affiliation(s)
- Hindrik Mulder
- Unit of Molecular Metabolism, Lund University Diabetes Centre, Malmö, Sweden
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37
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Regulation of Mammalian Mitochondrial Gene Expression: Recent Advances. Trends Biochem Sci 2017; 42:625-639. [PMID: 28285835 PMCID: PMC5538620 DOI: 10.1016/j.tibs.2017.02.003] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/02/2017] [Accepted: 02/10/2017] [Indexed: 01/03/2023]
Abstract
Perturbation of mitochondrial DNA (mtDNA) gene expression can lead to human pathologies. Therefore, a greater appreciation of the basic mechanisms of mitochondrial gene expression is desirable to understand the pathophysiology of associated disorders. Although the purpose of the mitochondrial gene expression machinery is to provide only 13 proteins of the oxidative phosphorylation (OxPhos) system, recent studies have revealed its remarkable and unexpected complexity. We review here the latest breakthroughs in our understanding of the post-transcriptional processes of mitochondrial gene expression, focusing on advances in analyzing the mitochondrial epitranscriptome, the role of mitochondrial RNA granules (MRGs), the benefits of recently obtained structures of the mitochondrial ribosome, and the coordination of mitochondrial and cytosolic translation to orchestrate the biogenesis of OxPhos complexes. The genetic system required for mitochondrial gene expression is housed within the mitochondrial matrix, with all the necessary RNAs being provided by transcription of the mtDNA itself. Our understanding of the extent and nature of post-transcriptional modifications of mtRNA, the epitranscriptome, is rapidly expanding. Several required nucleus-encoded enzymes have recently been identified. mtRNA maturation factors localize in distinct foci, termed mtRNA granules, with newly transcribed RNA. These foci may allow spatiotemporal control of mtRNA processing. Recent high-resolution structures obtained via cryo-electron microscopy have rapidly advanced our understanding of the specialized adaptations of the mitochondrial ribosome. Production of respiratory complexes requires tight coordination between the cytoplasmic and mitochondrial translation systems.
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Posse V, Gustafsson CM. Human Mitochondrial Transcription Factor B2 Is Required for Promoter Melting during Initiation of Transcription. J Biol Chem 2017; 292:2637-2645. [PMID: 28028173 PMCID: PMC5314162 DOI: 10.1074/jbc.m116.751008] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 12/22/2016] [Indexed: 01/27/2023] Open
Abstract
The mitochondrial transcription initiation machinery in humans consists of three proteins: the RNA polymerase (POLRMT) and two accessory factors, transcription factors A and B2 (TFAM and TFB2M, respectively). This machinery is required for the expression of mitochondrial DNA and the biogenesis of the oxidative phosphorylation system. Previous experiments suggested that TFB2M is required for promoter melting, but conclusive experimental proof for this effect has not been presented. Moreover, the role of TFB2M in promoter unwinding has not been discriminated from that of TFAM. Here we used potassium permanganate footprinting, DNase I footprinting, and in vitro transcription from the mitochondrial light-strand promoter to study the role of TFB2M in transcription initiation. We demonstrate that a complex composed of TFAM and POLRMT was readily formed at the promoter but alone was insufficient for promoter melting, which only occurred when TFB2M joined the complex. We also show that mismatch bubble templates could circumvent the requirement of TFB2M, but TFAM was still required for efficient initiation. Our findings support a model in which TFAM first recruits POLRMT to the promoter, followed by TFB2M binding and induction of promoter melting.
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Affiliation(s)
- Viktor Posse
- From the Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P. O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Claes M Gustafsson
- From the Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P. O. Box 440, SE-405 30 Gothenburg, Sweden
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Shokolenko IN, Alexeyev MF. Mitochondrial transcription in mammalian cells. Front Biosci (Landmark Ed) 2017; 22:835-853. [PMID: 27814650 DOI: 10.2741/4520] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
As a consequence of recent discoveries of intimate involvement of mitochondria with key cellular processes, there has been a resurgence of interest in all aspects of mitochondrial biology, including the intricate mechanisms of mitochondrial DNA maintenance and expression. Despite four decades of research, there remains a lot to be learned about the processes that enable transcription of genetic information from mitochondrial DNA to RNA, as well as their regulation. These processes are vitally important, as evidenced by the lethality of inactivating the central components of mitochondrial transcription machinery. Here, we review the current understanding of mitochondrial transcription and its regulation in mammalian cells. We also discuss key theories in the field and highlight controversial subjects and future directions as we see them.
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Affiliation(s)
- Inna N Shokolenko
- University of South Alabama, Patt Capps Covey College of Allied Health Professions, Biomedical Sciences Department, 5721 USA Drive N, HAHN 4021, Mobile, AL 36688-0002, USA
| | - Mikhail F Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, 5851 USA Dr. North, MSB3074, Mobile, AL 36688, USA,
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40
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Indo HP, Majima HJ, Terada M, Suenaga S, Tomita K, Yamada S, Higashibata A, Ishioka N, Kanekura T, Nonaka I, Hawkins CL, Davies MJ, Clair DKS, Mukai C. Changes in mitochondrial homeostasis and redox status in astronauts following long stays in space. Sci Rep 2016; 6:39015. [PMID: 27982062 PMCID: PMC5159838 DOI: 10.1038/srep39015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 11/17/2016] [Indexed: 11/26/2022] Open
Abstract
The effects of long-term exposure to extreme space conditions on astronauts were investigated by analyzing hair samples from ten astronauts who had spent six months on the International Space Station (ISS). Two samples were collected before, during and after their stays in the ISS; hereafter, referred to as Preflight, Inflight and Postflight, respectively. The ratios of mitochondrial (mt) to nuclear (n) DNA and mtRNA to nRNA were analyzed via quantitative PCR. The combined data of Preflight, Inflight and Postflight show a significant reduction in the mtDNA/nDNA in Inflight, and significant reductions in the mtRNA/nRNA ratios in both the Inflight and Postflight samples. The mtRNA/mtDNA ratios were relatively constant, except in the Postflight samples. Using the same samples, the expression of redox and signal transduction related genes, MnSOD, CuZnSOD, Nrf2, Keap1, GPx4 and Catalase was also examined. The results of the combined data from Preflight, Inflight and Postflight show a significant decrease in the expression of all of the redox-related genes in the samples collected Postflight, with the exception of Catalase, which show no change. This decreased expression may contribute to increased oxidative stress Inflight resulting in the mitochondrial damage that is apparent Postflight.
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Affiliation(s)
- Hiroko P Indo
- Department of Oncology and Space Environmental Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima City, Kagoshima 890-8544, Japan
| | - Hideyuki J Majima
- Department of Oncology and Space Environmental Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima City, Kagoshima 890-8544, Japan
| | - Masahiro Terada
- Divison of Aerospace Medicine, The Jikei University School of Medicine, Minato-ku, Tokyo 105-8461, Japan.,Japan Aerospace Exploration Agency, Tsukuba City, Ibaraki 305-8505, Japan.,Space Biosciences Division, NASA Ames Research Center, Moffett Field, California 94035, USA
| | - Shigeaki Suenaga
- Department of Oncology and Space Environmental Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima City, Kagoshima 890-8544, Japan
| | - Kazuo Tomita
- Department of Oncology and Space Environmental Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima City, Kagoshima 890-8544, Japan
| | - Shin Yamada
- Japan Aerospace Exploration Agency, Tsukuba City, Ibaraki 305-8505, Japan
| | - Akira Higashibata
- Department of Oncology and Space Environmental Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima City, Kagoshima 890-8544, Japan.,Japan Aerospace Exploration Agency, Tsukuba City, Ibaraki 305-8505, Japan
| | - Noriaki Ishioka
- Department of Oncology and Space Environmental Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima City, Kagoshima 890-8544, Japan.,Japan Aerospace Exploration Agency, Tsukuba City, Ibaraki 305-8505, Japan.,Institute of Space and Astronautical Science, Sagamihara, Kanagawa 252-5210, Japan.,Department of Space and Astronautical Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Sagamihara, Kanagawa 252-5210, Japan
| | - Takuro Kanekura
- Department of Dermatology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima City, Kagoshima 890-8544, Japan
| | - Ikuya Nonaka
- National Center Hospital for Mental Nervous and Muscular Disorders, Kodaira, Tokyo 187-8551, Japan
| | - Clare L Hawkins
- The Heart Research Institute, 7 Eliza Street, Newtown, Sydney, 7 Eliza Street, Newtown, Sydney, NSW 2042, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Michael J Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| | - Daret K St Clair
- Department of Toxicology and Cancer Biology, University of Kentucky College of Medicine, Lexington, Kentucky 40536, USA
| | - Chiaki Mukai
- Japan Aerospace Exploration Agency, Tsukuba City, Ibaraki 305-8505, Japan.,Tokyo University of Science, Shinjuku, Tokyo 162-0825, Japan
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41
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Ramachandran A, Basu U, Sultana S, Nandakumar D, Patel SS. Human mitochondrial transcription factors TFAM and TFB2M work synergistically in promoter melting during transcription initiation. Nucleic Acids Res 2016; 45:861-874. [PMID: 27903899 PMCID: PMC5314767 DOI: 10.1093/nar/gkw1157] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 12/26/2022] Open
Abstract
Human mitochondrial DNA is transcribed by POLRMT with the help of two initiation factors, TFAM and TFB2M. The current model postulates that the role of TFAM is to recruit POLRMT and TFB2M to melt the promoter. However, we show that TFAM has ‘post-recruitment’ roles in promoter melting and RNA synthesis, which were revealed by studying the pre-initiation steps of promoter binding, bending and melting, and abortive RNA synthesis. Our 2-aminopurine mapping studies show that the LSP (Light Strand Promoter) is melted from −4 to +1 in the open complex with all three proteins and from −4 to +3 with addition of ATP. Our equilibrium binding studies show that POLRMT forms stable complexes with TFB2M or TFAM on LSP with low-nanomolar Kd values, but these two-component complexes lack the mechanism to efficiently melt the promoter. This indicates that POLRMT needs both TFB2M and TFAM to melt the promoter. Additionally, POLRMT+TFB2M makes 2-mer abortives on LSP, but longer RNAs are observed only with TFAM. These results are explained by TFAM playing a role in promoter melting and/or stabilization of the open complex on LSP. Based on our results, we propose a refined model of transcription initiation by the human mitochondrial transcription machinery.
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Affiliation(s)
- Aparna Ramachandran
- Department of Biochemistry and Molecular Biology, Rutgers, Robert Wood Johnson Medical school, Piscataway, NJ 08854, USA
| | - Urmimala Basu
- Department of Biochemistry and Molecular Biology, Rutgers, Robert Wood Johnson Medical school, Piscataway, NJ 08854, USA.,Graduate School of Biomedical Sciences, Rutgers University, Piscataway, NJ 08854, USA
| | - Shemaila Sultana
- Department of Biochemistry and Molecular Biology, Rutgers, Robert Wood Johnson Medical school, Piscataway, NJ 08854, USA
| | - Divya Nandakumar
- Department of Biochemistry and Molecular Biology, Rutgers, Robert Wood Johnson Medical school, Piscataway, NJ 08854, USA
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers, Robert Wood Johnson Medical school, Piscataway, NJ 08854, USA
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42
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Mazunin IO, Levitskii SA, Patrushev MV, Kamenski PA. Mitochondrial Matrix Processes. BIOCHEMISTRY (MOSCOW) 2016; 80:1418-28. [PMID: 26615433 DOI: 10.1134/s0006297915110036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Mitochondria possess their own genome that, despite its small size, is critically important for their functioning, as it encodes several dozens of RNAs and proteins. All biochemical processes typical for bacterial and nuclear DNA are described in mitochondrial matrix: replication, repair, recombination, and transcription. Commonly, their mechanisms are similar to those found in bacteria, but they are characterized by several unique features. In this review, we provide an overall description of mitochondrial matrix processes paying special attention to the typical features of such mechanisms.
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Affiliation(s)
- I O Mazunin
- Immanuil Kant Baltic Federal University, Institute of Chemistry and Biology, Kaliningrad, 236038, Russia.
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43
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Kühl I, Miranda M, Posse V, Milenkovic D, Mourier A, Siira SJ, Bonekamp NA, Neumann U, Filipovska A, Polosa PL, Gustafsson CM, Larsson NG. POLRMT regulates the switch between replication primer formation and gene expression of mammalian mtDNA. SCIENCE ADVANCES 2016; 2:e1600963. [PMID: 27532055 PMCID: PMC4975551 DOI: 10.1126/sciadv.1600963] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/01/2016] [Indexed: 05/27/2023]
Abstract
Mitochondria are vital in providing cellular energy via their oxidative phosphorylation system, which requires the coordinated expression of genes encoded by both the nuclear and mitochondrial genomes (mtDNA). Transcription of the circular mammalian mtDNA depends on a single mitochondrial RNA polymerase (POLRMT). Although the transcription initiation process is well understood, it is debated whether POLRMT also serves as the primase for the initiation of mtDNA replication. In the nucleus, the RNA polymerases needed for gene expression have no such role. Conditional knockout of Polrmt in the heart results in severe mitochondrial dysfunction causing dilated cardiomyopathy in young mice. We further studied the molecular consequences of different expression levels of POLRMT and found that POLRMT is essential for primer synthesis to initiate mtDNA replication in vivo. Furthermore, transcription initiation for primer formation has priority over gene expression. Surprisingly, mitochondrial transcription factor A (TFAM) exists in an mtDNA-free pool in the Polrmt knockout mice. TFAM levels remain unchanged despite strong mtDNA depletion, and TFAM is thus protected from degradation of the AAA(+) Lon protease in the absence of POLRMT. Last, we report that mitochondrial transcription elongation factor may compensate for a partial depletion of POLRMT in heterozygous Polrmt knockout mice, indicating a direct regulatory role of this factor in transcription. In conclusion, we present in vivo evidence that POLRMT has a key regulatory role in the replication of mammalian mtDNA and is part of a transcriptional mechanism that provides a switch between primer formation for mtDNA replication and mitochondrial gene expression.
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Affiliation(s)
- Inge Kühl
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Maria Miranda
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Viktor Posse
- Department of Medical Biochemistry and Cell Biology, Göteborgs Universitet, 40530 Göteborg, Sweden
| | - Dusanka Milenkovic
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Arnaud Mourier
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
- Université de Bordeaux and the Centre National de la Recherche Scientifique, Institut de Biochimie et Génétique Cellulaires UMR 5095, Saint-Saëns, F-33077 Bordeaux, France
| | - Stefan J. Siira
- Harry Perkins Institute of Medical Research, Centre for Medical Research and School of Chemistry and Biochemistry, The University of Western Australia, Perth 6009, Australia
| | - Nina A. Bonekamp
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Ulla Neumann
- Central Microscopy, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, Centre for Medical Research and School of Chemistry and Biochemistry, The University of Western Australia, Perth 6009, Australia
| | - Paola Loguercio Polosa
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari Aldo Moro, 70125 Bari, Italy
| | - Claes M. Gustafsson
- Department of Medical Biochemistry and Cell Biology, Göteborgs Universitet, 40530 Göteborg, Sweden
| | - Nils-Göran Larsson
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
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44
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Bar-Yaacov D, Hadjivasiliou Z, Levin L, Barshad G, Zarivach R, Bouskila A, Mishmar D. Mitochondrial Involvement in Vertebrate Speciation? The Case of Mito-nuclear Genetic Divergence in Chameleons. Genome Biol Evol 2015; 7:3322-36. [PMID: 26590214 PMCID: PMC4700957 DOI: 10.1093/gbe/evv226] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Compatibility between the nuclear (nDNA) and mitochondrial (mtDNA) genomes is important for organismal health. However, its significance for major evolutionary processes such as speciation is unclear, especially in vertebrates. We previously identified a sharp mtDNA-specific sequence divergence between morphologically indistinguishable chameleon populations (Chamaeleo chamaeleon recticrista) across an ancient Israeli marine barrier (Jezreel Valley). Because mtDNA introgression and gender-based dispersal were ruled out, we hypothesized that mtDNA spatial division was maintained by mito-nuclear functional compensation. Here, we studied RNA-seq generated from each of ten chameleons representing the north and south populations and identified candidate nonsynonymous substitutions (NSSs) matching the mtDNA spatial distribution. The most prominent NSS occurred in 14 nDNA-encoded mitochondrial proteins. Increased chameleon sample size (N = 70) confirmed the geographic differentiation in POLRMT, NDUFA5, ACO1, LYRM4, MARS2, and ACAD9. Structural and functionality evaluation of these NSSs revealed high functionality. Mathematical modeling suggested that this mito-nuclear spatial divergence is consistent with hybrid breakdown. We conclude that our presented evidence and mathematical model underline mito-nuclear interactions as a likely role player in incipient speciation in vertebrates.
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Affiliation(s)
- Dan Bar-Yaacov
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Zena Hadjivasiliou
- Centre for Mathematics, Physics and Engineering in the Life Sciences and Experimental Biology, UCL, London, United Kingdom Department of Genetics, Evolution and Environment, UCL, London, United Kingdom
| | - Liron Levin
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Gilad Barshad
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Amos Bouskila
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
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45
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Moustafa IM, Uchida A, Wang Y, Yennawar N, Cameron CE. Structural models of mammalian mitochondrial transcription factor B2. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:987-1002. [PMID: 26066983 DOI: 10.1016/j.bbagrm.2015.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 05/22/2015] [Accepted: 05/25/2015] [Indexed: 11/26/2022]
Abstract
Mammalian mitochondrial DNA (mtDNA) encodes 13 core proteins of oxidative phosphorylation, 12S and 16S ribosomal RNAs, and 22 transfer RNAs. Mutations and deletions of mtDNA and/or nuclear genes encoding mitochondrial proteins have been implicated in a wide range of diseases. Thus, cell survival and health of the organism require some steady-state level of the mitochondrial genome and its expression. In mammalian systems, the mitochondrial transcription factor B2 (mtTFB2 or TFB2M) is indispensable for transcription initiation. TFB2M along with two other proteins, mitochondrial RNA polymerase (mtRNAP or POLRMT) and mitochondrial transcription factor A (mtTFA or TFAM), are key components of the core mitochondrial transcription apparatus. Structural information for POLRMT and TFAM from humans is available; however, there is no available structure for TFB2M. In the present study, three-dimensional structure of TFB2M from humans was modeled using a combination of homology modeling and small-angle X-ray scattering (SAXS). The TFB2M structural model adds substantively to our understanding of TFB2M function. An explanation for the low or absent RNA methyltransferase activity is provided. A putative nucleic acid-binding site is revealed. The amino and carboxy termini, while likely lacking defined secondary structure, appear to adopt compact, globular conformations, thus "capping" the ends of the protein. Finally, sites of interaction of TFB2M with other factors, protein and/or nucleic acid, are suggested by the identification of species-specific clusters on the surface of the protein.
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Affiliation(s)
- Ibrahim M Moustafa
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Akira Uchida
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Yao Wang
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Neela Yennawar
- Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Craig E Cameron
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
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46
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Morozov YI, Parshin AV, Agaronyan K, Cheung ACM, Anikin M, Cramer P, Temiakov D. A model for transcription initiation in human mitochondria. Nucleic Acids Res 2015; 43:3726-35. [PMID: 25800739 PMCID: PMC4402542 DOI: 10.1093/nar/gkv235] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/08/2015] [Indexed: 01/10/2023] Open
Abstract
Regulation of transcription of mtDNA is thought to be crucial for maintenance of redox potential and vitality of the cell but is poorly understood at the molecular level. In this study we mapped the binding sites of the core transcription initiation factors TFAM and TFB2M on human mitochondrial RNA polymerase, and interactions of the latter with promoter DNA. This allowed us to construct a detailed structural model, which displays a remarkable level of interaction between the components of the initiation complex (IC). The architecture of the mitochondrial IC suggests mechanisms of promoter binding and recognition that are distinct from the mechanisms found in RNAPs operating in all domains of life, and illuminates strategies of transcription regulation developed at the very early stages of evolution of gene expression.
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Affiliation(s)
- Yaroslav I Morozov
- Department of Cell Biology, School of Osteopathic Medicine, Rowan University, 2 Medical Center Dr., Stratford, NJ 08084, USA
| | - Andrey V Parshin
- Department of Cell Biology, School of Osteopathic Medicine, Rowan University, 2 Medical Center Dr., Stratford, NJ 08084, USA
| | - Karen Agaronyan
- Department of Cell Biology, School of Osteopathic Medicine, Rowan University, 2 Medical Center Dr., Stratford, NJ 08084, USA
| | - Alan C M Cheung
- Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Michael Anikin
- Department of Cell Biology, School of Osteopathic Medicine, Rowan University, 2 Medical Center Dr., Stratford, NJ 08084, USA
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Gottingen, Germany
| | - Dmitry Temiakov
- Department of Cell Biology, School of Osteopathic Medicine, Rowan University, 2 Medical Center Dr., Stratford, NJ 08084, USA
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47
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Posse V, Shahzad S, Falkenberg M, Hällberg BM, Gustafsson CM. TEFM is a potent stimulator of mitochondrial transcription elongation in vitro. Nucleic Acids Res 2015; 43:2615-24. [PMID: 25690892 PMCID: PMC4357710 DOI: 10.1093/nar/gkv105] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
A single-subunit RNA polymerase, POLRMT, transcribes the mitochondrial genome in human cells. Recently, a factor termed as the mitochondrial transcription elongation factor, TEFM, was shown to stimulate transcription elongation in vivo, but its effect in vitro was relatively modest. In the current work, we have isolated active TEFM in recombinant form and used a reconstituted in vitro transcription system to characterize its activities. We show that TEFM strongly promotes POLRMT processivity as it dramatically stimulates the formation of longer transcripts. TEFM also abolishes premature transcription termination at conserved sequence block II, an event that has been linked to primer formation during initiation of mtDNA synthesis. We show that POLRMT pauses at a wide range of sites in a given DNA sequence. In the absence of TEFM, this leads to termination; however, the presence of TEFM abolishes this effect and aids POLRMT in continuation of transcription. Further, we show that TEFM substantially increases the POLRMT affinity to an elongation-like DNA:RNA template. In combination with previously published in vivo observations, our data establish TEFM as an essential component of the mitochondrial transcription machinery.
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Affiliation(s)
- Viktor Posse
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Saba Shahzad
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-17177 Stockholm, Sweden Röntgen-Ångström-Cluster, Karolinska Institutet Outstation, Centre for Structural Systems Biology, DESY-Campus, D-22603 Hamburg, Germany
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-17177 Stockholm, Sweden Röntgen-Ångström-Cluster, Karolinska Institutet Outstation, Centre for Structural Systems Biology, DESY-Campus, D-22603 Hamburg, Germany European Molecular Biology Laboratory, Hamburg Unit, D-22603 Hamburg, Germany
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, SE-40530 Gothenburg, Sweden
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Yang RF, Sun LH, Zhang R, Zhang Y, Luo YX, Zheng W, Zhang ZQ, Chen HZ, Liu DP. Suppression of Mic60 compromises mitochondrial transcription and oxidative phosphorylation. Sci Rep 2015; 5:7990. [PMID: 25612828 PMCID: PMC4303897 DOI: 10.1038/srep07990] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 12/29/2014] [Indexed: 12/12/2022] Open
Abstract
Precise regulation of mtDNA transcription and oxidative phosphorylation (OXPHOS) is crucial for human health. As a component of mitochondrial contact site and cristae organizing system (MICOS), Mic60 plays a central role in mitochondrial morphology. However, it remains unclear whether Mic60 affects mitochondrial transcription. Here, we report that Mic60 interacts with mitochondrial transcription factors TFAM and TFB2M. Furthermore, we found that Mic60 knockdown compromises mitochondrial transcription and OXPHOS activities. Importantly, Mic60 deficiency decreased TFAM binding and mitochondrial RNA polymerase (POLRMT) recruitment to the mtDNA promoters. In addition, through mtDNA immunoprecipitation (mIP)-chromatin conformation capture (3C) assays, we found that Mic60 interacted with mtDNA and was involved in the architecture of mtDNA D-loop region. Taken together, our findings reveal a previously unrecognized important role of Mic60 in mtDNA transcription.
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Affiliation(s)
- Rui-Feng Yang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100005, P.R. China
| | - Li-Hong Sun
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100005, P.R. China
| | - Ran Zhang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100005, P.R. China
| | - Yuan Zhang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100005, P.R. China
| | - Yu-Xuan Luo
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100005, P.R. China
| | - Wei Zheng
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100005, P.R. China
| | - Zhu-Qin Zhang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100005, P.R. China
| | - Hou-Zao Chen
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100005, P.R. China
| | - De-Pei Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100005, P.R. China
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49
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Levin L, Mishmar D. A Genetic View of the Mitochondrial Role in Ageing: Killing Us Softly. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 847:89-106. [DOI: 10.1007/978-1-4939-2404-2_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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50
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Levin L, Blumberg A, Barshad G, Mishmar D. Mito-nuclear co-evolution: the positive and negative sides of functional ancient mutations. Front Genet 2014; 5:448. [PMID: 25566330 PMCID: PMC4274989 DOI: 10.3389/fgene.2014.00448] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/08/2014] [Indexed: 12/31/2022] Open
Abstract
Most cell functions are carried out by interacting factors, thus underlying the functional importance of genetic interactions between genes, termed epistasis. Epistasis could be under strong selective pressures especially in conditions where the mutation rate of one of the interacting partners notably differs from the other. Accordingly, the order of magnitude higher mitochondrial DNA (mtDNA) mutation rate as compared to the nuclear DNA (nDNA) of all tested animals, should influence systems involving mitochondrial-nuclear (mito-nuclear) interactions. Such is the case of the energy producing oxidative phosphorylation (OXPHOS) and mitochondrial translational machineries which are comprised of factors encoded by both the mtDNA and the nDNA. Additionally, the mitochondrial RNA transcription and mtDNA replication systems are operated by nDNA-encoded proteins that bind mtDNA regulatory elements. As these systems are central to cell life there is strong selection toward mito-nuclear co-evolution to maintain their function. However, it is unclear whether (A) mito-nuclear co-evolution befalls only to retain mitochondrial functions during evolution or, also, (B) serves as an adaptive tool to adjust for the evolving energetic demands as species' complexity increases. As the first step to answer these questions we discuss evidence of both negative and adaptive (positive) selection acting on the mtDNA and nDNA-encoded genes and the effect of both types of selection on mito-nuclear interacting factors. Emphasis is given to the crucial role of recurrent ancient (nodal) mutations in such selective events. We apply this point-of-view to the three available types of mito-nuclear co-evolution: protein-protein (within the OXPHOS system), protein-RNA (mainly within the mitochondrial ribosome), and protein-DNA (at the mitochondrial replication and transcription machineries).
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Affiliation(s)
- Liron Levin
- Department of Life Sciences, Ben-Gurion University of the Negev Beersheba, Israel
| | - Amit Blumberg
- Department of Life Sciences, Ben-Gurion University of the Negev Beersheba, Israel
| | - Gilad Barshad
- Department of Life Sciences, Ben-Gurion University of the Negev Beersheba, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev Beersheba, Israel
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