1
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Liu Y, Liu H, Zhang F, Xu H. The initiation of mitochondrial DNA replication. Biochem Soc Trans 2024:BST20230952. [PMID: 38884788 DOI: 10.1042/bst20230952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024]
Abstract
Mitochondrial DNA replication is initiated by the transcription of mitochondrial RNA polymerase (mtRNAP), as mitochondria lack a dedicated primase. However, the mechanism determining the switch between continuous transcription and premature termination to generate RNA primers for mitochondrial DNA (mtDNA) replication remains unclear. The pentatricopeptide repeat domain of mtRNAP exhibits exoribonuclease activity, which is required for the initiation of mtDNA replication in Drosophila. In this review, we explain how this exonuclease activity contributes to primer synthesis in strand-coupled mtDNA replication, and discuss how its regulation might co-ordinate mtDNA replication and transcription in both Drosophila and mammals.
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Affiliation(s)
- Yi Liu
- Hubei Jiangxia Laboratory, Wuhan 430200, China
| | - Haibin Liu
- Hubei Jiangxia Laboratory, Wuhan 430200, China
| | - Fan Zhang
- National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, U.S.A
| | - Hong Xu
- National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, U.S.A
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2
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Goffart S, Pohjoismäki J. Analysis of Mitochondrial DNA Replication by Two-Dimensional Agarose Gel Electrophoresis. Methods Mol Biol 2023; 2615:241-266. [PMID: 36807797 DOI: 10.1007/978-1-0716-2922-2_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Two-dimensional neutral/neutral agarose gel electrophoresis (2D-AGE) has been employed for nearly two decades in the analysis of replication and maintenance processes of animal mitochondrial DNA, but the method's potential has not been fully exploited. Here, we describe the various steps involved in this technique, from DNA isolation, to two-dimensional neutral/neutral agarose gel electrophoresis (2D-AGE), Southern hybridization and interpretation. We also provide examples of the applicability of 2D-AGE to investigate the different features of mtDNA maintenance and regulation.
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Affiliation(s)
- Steffi Goffart
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland.
| | - Jaakko Pohjoismäki
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland
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3
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Sharbrough J, Bankers L, Cook E, Fields PD, Jalinsky J, McElroy KE, Neiman M, Logsdon JM, Boore JL. Single-molecule Sequencing of an Animal Mitochondrial Genome Reveals Chloroplast-like Architecture and Repeat-mediated Recombination. Mol Biol Evol 2023; 40:6980790. [PMID: 36625177 PMCID: PMC9874032 DOI: 10.1093/molbev/msad007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/28/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Recent advances in long-read sequencing technology have allowed for single-molecule sequencing of entire mitochondrial genomes, opening the door for direct investigation of the mitochondrial genome architecture and recombination. We used PacBio sequencing to reassemble mitochondrial genomes from two species of New Zealand freshwater snails, Potamopyrgus antipodarum and Potamopyrgus estuarinus. These assemblies revealed a ∼1.7 kb structure within the mitochondrial genomes of both species that was previously undetected by an assembly of short reads and likely corresponding to a large noncoding region commonly present in the mitochondrial genomes. The overall architecture of these Potamopyrgus mitochondrial genomes is reminiscent of the chloroplast genomes of land plants, harboring a large single-copy (LSC) region and a small single-copy (SSC) region separated by a pair of inverted repeats (IRa and IRb). Individual sequencing reads that spanned across the Potamopyrgus IRa-SSC-IRb structure revealed the occurrence of a "flip-flop" recombination. We also detected evidence for two distinct IR haplotypes and recombination between them in wild-caught P. estuarinus, as well as extensive intermolecular recombination between single-nucleotide polymorphisms in the LSC region. The chloroplast-like architecture and repeat-mediated mitochondrial recombination we describe here raise fundamental questions regarding the origins and commonness of inverted repeats in cytoplasmic genomes and their role in mitochondrial genome evolution.
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Affiliation(s)
| | - Laura Bankers
- Department of Biology, University of Iowa, Iowa City, IA
| | - Emily Cook
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM 87801
| | - Peter D Fields
- Zoologisches Institut, University of Basel, Basel, Switzerland
| | | | - Kyle E McElroy
- Department of Biology, University of Iowa, Iowa City, IA,Department of Ecology, Evolution, and Organismal Biology, Iowa State University, IA
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA
| | - Jeffrey L Boore
- Phenome Health and Institute for Systems Biology, Seattle, WA
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4
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Liu Y, Chen Z, Wang ZH, Delaney KM, Tang J, Pirooznia M, Lee DY, Tunc I, Li Y, Xu H. The PPR domain of mitochondrial RNA polymerase is an exoribonuclease required for mtDNA replication in Drosophila melanogaster. Nat Cell Biol 2022; 24:757-765. [PMID: 35449456 DOI: 10.1038/s41556-022-00887-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 03/08/2022] [Indexed: 11/09/2022]
Abstract
Mitochondrial DNA (mtDNA) replication and transcription are of paramount importance to cellular energy metabolism. Mitochondrial RNA polymerase is thought to be the primase for mtDNA replication. However, it is unclear how this enzyme, which normally transcribes long polycistronic RNAs, can produce short RNA oligonucleotides to initiate mtDNA replication. We show that the PPR domain of Drosophila mitochondrial RNA polymerase (PolrMT) has 3'-to-5' exoribonuclease activity, which is indispensable for PolrMT to synthesize short RNA oligonucleotides and prime DNA replication in vitro. An exoribonuclease-deficient mutant, PolrMTE423P, partially restores mitochondrial transcription but fails to support mtDNA replication when expressed in PolrMT-mutant flies, indicating that the exoribonuclease activity is necessary for mtDNA replication. In addition, overexpression of PolrMTE423P in adult flies leads to severe neuromuscular defects and a marked increase in mtDNA transcript errors, suggesting that exoribonuclease activity may contribute to the proofreading of mtDNA transcription.
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Affiliation(s)
- Yi Liu
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhe Chen
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zong-Heng Wang
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Katherine M Delaney
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Juanjie Tang
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mehdi Pirooznia
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Duck-Yeon Lee
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ilker Tunc
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yuesheng Li
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hong Xu
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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5
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So M, Stiban J, Ciesielski GL, Hovde SL, Kaguni LS. Implications of Membrane Binding by the Fe-S Cluster-Containing N-Terminal Domain in the Drosophila Mitochondrial Replicative DNA Helicase. Front Genet 2021; 12:790521. [PMID: 34950192 PMCID: PMC8688847 DOI: 10.3389/fgene.2021.790521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Recent evidence suggests that iron-sulfur clusters (ISCs) in DNA replicative proteins sense DNA-mediated charge transfer to modulate nuclear DNA replication. In the mitochondrial DNA replisome, only the replicative DNA helicase (mtDNA helicase) from Drosophila melanogaster (Dm) has been shown to contain an ISC in its N-terminal, primase-like domain (NTD). In this report, we confirm the presence of the ISC and demonstrate the importance of a metal cofactor in the structural stability of the Dm mtDNA helicase. Further, we show that the NTD also serves a role in membrane binding. We demonstrate that the NTD binds to asolectin liposomes, which mimic phospholipid membranes, through electrostatic interactions. Notably, membrane binding is more specific with increasing cardiolipin content, which is characteristically high in the mitochondrial inner membrane (MIM). We suggest that the N-terminal domain of the mtDNA helicase interacts with the MIM to recruit mtDNA and initiate mtDNA replication. Furthermore, Dm NUBPL, the known ISC donor for respiratory complex I and a putative donor for Dm mtDNA helicase, was identified as a peripheral membrane protein that is likely to execute membrane-mediated ISC delivery to its target proteins.
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Affiliation(s)
- Minyoung So
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States
| | - Johnny Stiban
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States.,Department of Biology and Biochemistry, Birzeit University, Birzeit, Palestine
| | - Grzegorz L Ciesielski
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States.,Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland.,Department of Chemistry, Auburn University at Montgomery, Montgomery, AL, United States
| | - Stacy L Hovde
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States
| | - Laurie S Kaguni
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, United States.,Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland
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6
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Leuthner TC, Meyer JN. Mitochondrial DNA Mutagenesis: Feature of and Biomarker for Environmental Exposures and Aging. Curr Environ Health Rep 2021; 8:294-308. [PMID: 34761353 PMCID: PMC8826492 DOI: 10.1007/s40572-021-00329-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2021] [Indexed: 01/12/2023]
Abstract
PURPOSE OF REVIEW Mitochondrial dysfunction is a hallmark of aging. Mitochondrial genome (mtDNA) instability contributes to mitochondrial dysfunction, and mtDNA mutagenesis may contribute to aging. However, the origin of mtDNA mutations remains somewhat controversial. The goals of this review are to introduce and review recent literature on mtDNA mutagenesis and aging, address recent animal and epidemiological evidence for the effects of chemicals on mtDNA damage and mutagenesis, propose hypotheses regarding the contribution of environmental toxicant exposure to mtDNA mutagenesis in the context of aging, and suggest future directions and approaches for environmental health researchers. RECENT FINDINGS Stressors such as pollutants, pharmaceuticals, and ultraviolet radiation can damage the mitochondrial genome or disrupt mtDNA replication, repair, and organelle homeostatic processes, potentially influencing the rate of accumulation of mtDNA mutations. Accelerated mtDNA mutagenesis could contribute to aging, diseases of aging, and sensitize individuals with pathogenic mtDNA variants to stressors. We propose three potential mechanisms of toxicant-induced effects on mtDNA mutagenesis over lifespan: (1) increased de novo mtDNA mutations, (2) altered frequencies of mtDNA mutations, or (3) both. There are remarkably few studies that have investigated the impact of environmental chemical exposures on mtDNA instability and mutagenesis, and even fewer in the context of aging. More studies are warranted because people are exposed to tens of thousands of chemicals, and are living longer. Finally, we suggest that toxicant-induced mtDNA damage and mutational signatures may be a sensitive biomarker for some exposures.
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Affiliation(s)
- Tess C Leuthner
- Nicholas School of the Environment, 9 Circuit Dr, Box 90328, Duke University, NC, 27708, USA
| | - Joel N Meyer
- Nicholas School of the Environment, 9 Circuit Dr, Box 90328, Duke University, NC, 27708, USA.
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7
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Sanchez-Contreras M, Sweetwyne MT, Kohrn BF, Tsantilas KA, Hipp MJ, Schmidt EK, Fredrickson J, Whitson JA, Campbell MD, Rabinovitch PS, Marcinek DJ, Kennedy SR. A replication-linked mutational gradient drives somatic mutation accumulation and influences germline polymorphisms and genome composition in mitochondrial DNA. Nucleic Acids Res 2021; 49:11103-11118. [PMID: 34614167 PMCID: PMC8565317 DOI: 10.1093/nar/gkab901] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/10/2021] [Accepted: 09/22/2021] [Indexed: 11/22/2022] Open
Abstract
Mutations in mitochondrial DNA (mtDNA) cause maternally inherited diseases, while somatic mutations are linked to common diseases of aging. Although mtDNA mutations impact health, the processes that give rise to them are under considerable debate. To investigate the mechanism by which de novo mutations arise, we analyzed the distribution of naturally occurring somatic mutations across the mouse and human mtDNA obtained by Duplex Sequencing. We observe distinct mutational gradients in G→A and T→C transitions delimited by the light-strand origin and the mitochondrial Control Region (mCR). The gradient increases unequally across the mtDNA with age and is lost in the absence of DNA polymerase γ proofreading activity. In addition, high-resolution analysis of the mCR shows that important regulatory elements exhibit considerable variability in mutation frequency, consistent with them being mutational ‘hot-spots’ or ‘cold-spots’. Collectively, these patterns support genome replication via a deamination prone asymmetric strand-displacement mechanism as the fundamental driver of mutagenesis in mammalian DNA. Moreover, the distribution of mtDNA single nucleotide polymorphisms in humans and the distribution of bases in the mtDNA across vertebrate species mirror this gradient, indicating that replication-linked mutations are likely the primary source of inherited polymorphisms that, over evolutionary timescales, influences genome composition during speciation.
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Affiliation(s)
- Monica Sanchez-Contreras
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Mariya T Sweetwyne
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Brendan F Kohrn
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | | | - Michael J Hipp
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth K Schmidt
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jeanne Fredrickson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jeremy A Whitson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Matthew D Campbell
- Department of Radiology, University of Washington, Seattle, WA 98195, USA
| | - Peter S Rabinovitch
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - David J Marcinek
- Department of Radiology, University of Washington, Seattle, WA 98195, USA
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
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8
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Waneka G, Svendsen JM, Havird JC, Sloan DB. Mitochondrial mutations in Caenorhabditis elegans show signatures of oxidative damage and an AT-bias. Genetics 2021; 219:6346985. [PMID: 34849888 DOI: 10.1093/genetics/iyab116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/09/2021] [Indexed: 01/25/2023] Open
Abstract
Rapid mutation rates are typical of mitochondrial genomes (mtDNAs) in animals, but it is not clear why. The difficulty of obtaining measurements of mtDNA mutation that are not biased by natural selection has stymied efforts to distinguish between competing hypotheses about the causes of high mtDNA mutation rates. Several studies which have measured mtDNA mutations in nematodes have yielded small datasets with conflicting conclusions about the relative abundance of different substitution classes (i.e., the mutation spectrum). We therefore leveraged Duplex Sequencing, a high-fidelity DNA sequencing technique, to characterize de novo mtDNA mutations in Caenorhabditis elegans. This approach detected nearly an order of magnitude more mtDNA mutations than documented in any previous nematode mutation study. Despite an existing extreme AT bias in the C. elegans mtDNA (75.6% AT), we found that a significant majority of mutations increase genomic AT content. Compared to some prior studies in nematodes and other animals, the mutation spectrum reported here contains an abundance of CG→AT transversions, supporting the hypothesis that oxidative damage may be a driver of mtDNA mutations in nematodes. Furthermore, we found an excess of G→T and C→T changes on the coding DNA strand relative to the template strand, consistent with increased exposure to oxidative damage. Analysis of the distribution of mutations across the mtDNA revealed significant variation among protein-coding genes and as well as among neighboring nucleotides. This high-resolution view of mitochondrial mutations in C. elegans highlights the value of this system for understanding relationships among oxidative damage, replication error, and mtDNA mutation.
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Affiliation(s)
- Gus Waneka
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA and
| | - Joshua M Svendsen
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA and
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA and
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9
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Lujan SA, Longley MJ, Humble MH, Lavender CA, Burkholder A, Blakely EL, Alston CL, Gorman GS, Turnbull DM, McFarland R, Taylor RW, Kunkel TA, Copeland WC. Ultrasensitive deletion detection links mitochondrial DNA replication, disease, and aging. Genome Biol 2020; 21:248. [PMID: 32943091 PMCID: PMC7500033 DOI: 10.1186/s13059-020-02138-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/07/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Acquired human mitochondrial genome (mtDNA) deletions are symptoms and drivers of focal mitochondrial respiratory deficiency, a pathological hallmark of aging and late-onset mitochondrial disease. RESULTS To decipher connections between these processes, we create LostArc, an ultrasensitive method for quantifying deletions in circular mtDNA molecules. LostArc reveals 35 million deletions (~ 470,000 unique spans) in skeletal muscle from 22 individuals with and 19 individuals without pathogenic variants in POLG. This nuclear gene encodes the catalytic subunit of replicative mitochondrial DNA polymerase γ. Ablation, the deleted mtDNA fraction, suffices to explain skeletal muscle phenotypes of aging and POLG-derived disease. Unsupervised bioinformatic analyses reveal distinct age- and disease-correlated deletion patterns. CONCLUSIONS These patterns implicate replication by DNA polymerase γ as the deletion driver and suggest little purifying selection against mtDNA deletions by mitophagy in postmitotic muscle fibers. Observed deletion patterns are best modeled as mtDNA deletions initiated by replication fork stalling during strand displacement mtDNA synthesis.
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Affiliation(s)
- Scott A Lujan
- Genome Integrity and Structural Biology Laboratory, DNA Replication Fidelity Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Matthew J Longley
- Genome Integrity and Structural Biology Laboratory, Mitochondrial DNA Replication Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Margaret H Humble
- Genome Integrity and Structural Biology Laboratory, Mitochondrial DNA Replication Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Christopher A Lavender
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Adam Burkholder
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Emma L Blakely
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK
| | - Charlotte L Alston
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK
| | - Grainne S Gorman
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Doug M Turnbull
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP, UK
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, DNA Replication Fidelity Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, Mitochondrial DNA Replication Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
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Subramanian H, Gatenby RA. Evolutionary advantage of anti-parallel strand orientation of duplex DNA. Sci Rep 2020; 10:9883. [PMID: 32555277 PMCID: PMC7303137 DOI: 10.1038/s41598-020-66705-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 05/22/2020] [Indexed: 11/09/2022] Open
Abstract
DNA in all living systems shares common properties that are remarkably well suited to its function, suggesting refinement by evolution. However, DNA also shares some counter-intuitive properties which confer no obvious benefit, such as strand directionality and anti-parallel strand orientation, which together result in the complicated lagging strand replication. The evolutionary dynamics that led to these properties of DNA remain unknown but their universality suggests that they confer as yet unknown selective advantage to DNA. In this article, we identify an evolutionary advantage of anti-parallel strand orientation of duplex DNA, within a given set of plausible premises. The advantage stems from the increased rate of replication, achieved by dividing the DNA into predictable, independently and simultaneously replicating segments, as opposed to sequentially replicating the entire DNA, thereby parallelizing the replication process. We show that anti-parallel strand orientation is essential for such a replicative organization of DNA, given our premises, the most important of which is the assumption of the presence of sequence-dependent asymmetric cooperativity in DNA.
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Affiliation(s)
| | - Robert A Gatenby
- Integrated Mathematical Oncology Department, Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, 12902, USF Magnolia Dr, Tampa, Florida, USA
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11
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Bahhir D, Yalgin C, Ots L, Järvinen S, George J, Naudí A, Krama T, Krams I, Tamm M, Andjelković A, Dufour E, González de Cózar JM, Gerards M, Parhiala M, Pamplona R, Jacobs HT, Jõers P. Manipulating mtDNA in vivo reprograms metabolism via novel response mechanisms. PLoS Genet 2019; 15:e1008410. [PMID: 31584940 PMCID: PMC6795474 DOI: 10.1371/journal.pgen.1008410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 10/16/2019] [Accepted: 09/10/2019] [Indexed: 11/18/2022] Open
Abstract
Mitochondria have been increasingly recognized as a central regulatory nexus for multiple metabolic pathways, in addition to ATP production via oxidative phosphorylation (OXPHOS). Here we show that inducing mitochondrial DNA (mtDNA) stress in Drosophila using a mitochondrially-targeted Type I restriction endonuclease (mtEcoBI) results in unexpected metabolic reprogramming in adult flies, distinct from effects on OXPHOS. Carbohydrate utilization was repressed, with catabolism shifted towards lipid oxidation, accompanied by elevated serine synthesis. Cleavage and translocation, the two modes of mtEcoBI action, repressed carbohydrate rmetabolism via two different mechanisms. DNA cleavage activity induced a type II diabetes-like phenotype involving deactivation of Akt kinase and inhibition of pyruvate dehydrogenase, whilst translocation decreased post-translational protein acetylation by cytonuclear depletion of acetyl-CoA (AcCoA). The associated decrease in the concentrations of ketogenic amino acids also produced downstream effects on physiology and behavior, attributable to decreased neurotransmitter levels. We thus provide evidence for novel signaling pathways connecting mtDNA to metabolism, distinct from its role in supporting OXPHOS. Mitochondria, subcellular compartments (organelles) found in virtually all eukaryotes, contain DNA which is believed to be a remnant of an ancestral bacterial genome. They are best known for the synthesis of the universal energy carrier ATP, but also serve as the hub of various metabolic and signalling pathways. We report here that mtDNA integrity is linked to a signaling system that influences metabolic fuel selection between fats and sugars. By disrupting mtDNA in the fruit fly we induced a strong shift towards lipid catabolism. This was caused both by a widespread decrease in post-translational acetylation of proteins, as well as specific inhibition of the machinery that transports glucose into cells across the plasma membrane. This phenomenon is very similar to the pathophysiology of diabetes, where the inability to transport glucose to cells is considered the main hallmark of the disease. Moreover, decreased protein acetylation was associated with lower levels of certain neurotransmitters, causing various effects on feeding and fertility. Our discovery reveals an unexpected role for mtDNA stability in regulating global metabolic balance and suggests that it could be instrumental in pandemic metabolic disorders such as diabetes and obesity.
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Affiliation(s)
- Diana Bahhir
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Cagri Yalgin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Liina Ots
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Sampsa Järvinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jack George
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Alba Naudí
- Experimental Medicine Department, University of Lleida-Institute for Research in Biomedicine of Lleida (UdL-IRBLLEIDA), Lleida, Spain
| | - Tatjana Krama
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Department of Plant Health, Institute of Agricultural and Environmental Sciences, Estonian University of Life Science, Tartu, Estonia
| | - Indrikis Krams
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Department of Zoology and Animal Ecology, Faculty of Biology, University of Latvia, Rīga, Latvia
- Department of Biotechnology, Daugavpils University, Daugavpils, Latvia
| | - Mairi Tamm
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Ana Andjelković
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Eric Dufour
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | - Mike Gerards
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
| | - Mikael Parhiala
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Reinald Pamplona
- Experimental Medicine Department, University of Lleida-Institute for Research in Biomedicine of Lleida (UdL-IRBLLEIDA), Lleida, Spain
| | - Howard T. Jacobs
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Priit Jõers
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- * E-mail:
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Ciesielski GL, Nadalutti CA, Oliveira MT, Jacobs HT, Griffith JD, Kaguni LS. Structural rearrangements in the mitochondrial genome of Drosophila melanogaster induced by elevated levels of the replicative DNA helicase. Nucleic Acids Res 2019; 46:3034-3046. [PMID: 29432582 PMCID: PMC5887560 DOI: 10.1093/nar/gky094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/02/2018] [Indexed: 01/10/2023] Open
Abstract
Pathological conditions impairing functions of mitochondria often lead to compensatory upregulation of the mitochondrial DNA (mtDNA) replisome machinery, and the replicative DNA helicase appears to be a key factor in regulating mtDNA copy number. Moreover, mtDNA helicase mutations have been associated with structural rearrangements of the mitochondrial genome. To evaluate the effects of elevated levels of the mtDNA helicase on the integrity and replication of the mitochondrial genome, we overexpressed the helicase in Drosophila melanogaster Schneider cells and analyzed the mtDNA by two-dimensional neutral agarose gel electrophoresis and electron microscopy. We found that elevation of mtDNA helicase levels increases the quantity of replication intermediates and alleviates pausing at the replication slow zones. Though we did not observe a concomitant alteration in mtDNA copy number, we observed deletions specific to the segment of repeated elements in the immediate vicinity of the origin of replication, and an accumulation of species characteristic of replication fork stalling. We also found elevated levels of RNA that are retained in the replication intermediates. Together, our results suggest that upregulation of mtDNA helicase promotes the process of mtDNA replication but also results in genome destabilization.
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Affiliation(s)
- Grzegorz L Ciesielski
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, USA.,Institute of Biosciences and Medical Technology, University of Tampere, FI-33014 Tampere, Finland
| | - Cristina A Nadalutti
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Marcos T Oliveira
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, USA
| | - Howard T Jacobs
- Institute of Biosciences and Medical Technology, University of Tampere, FI-33014 Tampere, Finland.,Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laurie S Kaguni
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, USA.,Institute of Biosciences and Medical Technology, University of Tampere, FI-33014 Tampere, Finland
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González de Cózar JM, Gerards M, Teeri E, George J, Dufour E, Jacobs HT, Jõers P. RNase H1 promotes replication fork progression through oppositely transcribed regions of Drosophila mitochondrial DNA. J Biol Chem 2019; 294:4331-4344. [PMID: 30635398 PMCID: PMC6433063 DOI: 10.1074/jbc.ra118.007015] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/09/2019] [Indexed: 11/12/2022] Open
Abstract
Mitochondrial DNA (mtDNA) replication uses a simple core machinery similar to those of bacterial viruses and plasmids, but its components are challenging to unravel. Here, we found that, as in mammals, the single Drosophila gene for RNase H1 (rnh1) has alternative translational start sites, resulting in two polypeptides, targeted to either mitochondria or the nucleus. RNAi-mediated rnh1 knockdown did not influence growth or viability of S2 cells, but compromised mtDNA integrity and copy number. rnh1 knockdown in intact flies also produced a phenotype of impaired mitochondrial function, characterized by respiratory chain deficiency, locomotor dysfunction, and decreased lifespan. Its overexpression in S2 cells resulted in cell lethality after 5–9 days, attributable to the nuclearly localized isoform. rnh1 knockdown and overexpression produced opposite effects on mtDNA replication intermediates. The most pronounced effects were seen in genome regions beyond the major replication pauses where the replication fork needs to progress through a gene cluster that is transcribed in the opposite direction. RNase H1 deficiency led to an accumulation of replication intermediates in these zones, abundant mtDNA molecules joined by four-way junctions, and species consistent with fork regression from the origin. These findings indicate replication stalling due to the presence of unprocessed RNA/DNA heteroduplexes, potentially leading to the degradation of collapsed forks or to replication restart by a mechanism involving strand invasion. Both mitochondrial RNA and DNA syntheses were affected by rnh1 knockdown, suggesting that RNase H1 also plays a role in integrating or coregulating these processes in Drosophila mitochondria.
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Affiliation(s)
- Jose M González de Cózar
- From the Faculty of Medicine and Health Technology and Tampere University Hospital, FI-33014 Tampere University, Finland
| | - Mike Gerards
- From the Faculty of Medicine and Health Technology and Tampere University Hospital, FI-33014 Tampere University, Finland
| | - Eveliina Teeri
- From the Faculty of Medicine and Health Technology and Tampere University Hospital, FI-33014 Tampere University, Finland
| | - Jack George
- From the Faculty of Medicine and Health Technology and Tampere University Hospital, FI-33014 Tampere University, Finland
| | - Eric Dufour
- From the Faculty of Medicine and Health Technology and Tampere University Hospital, FI-33014 Tampere University, Finland
| | - Howard T Jacobs
- From the Faculty of Medicine and Health Technology and Tampere University Hospital, FI-33014 Tampere University, Finland, .,Institute of Biotechnology, FI-00014 University of Helsinki, Finland, and
| | - Priit Jõers
- From the Faculty of Medicine and Health Technology and Tampere University Hospital, FI-33014 Tampere University, Finland.,Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
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14
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Melvin RG, Ballard JWO. Cellular and population level processes influence the rate, accumulation and observed frequency of inherited and somatic mtDNA mutations. Mutagenesis 2017; 32:323-334. [PMID: 28521046 DOI: 10.1093/mutage/gex004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mitochondria are found in all animals and have the unique feature of containing multiple copies of their own small, circular DNA genome (mtDNA). The rate and pattern of mutation accumulation in the mtDNA are influenced by molecular, cellular and population level processes. We distinguish between inherited and somatic mtDNA mutations and review evidence for the often-made assumption that mutations accumulate at a higher rate in mtDNA than in nuclear DNA (nDNA). We conclude that the whole genome mutation accumulation rate is higher for mtDNA than for nDNA but include the caveat that rates overlap considerably between the individual mtDNA- and nDNA-encoded genes. Next, we discuss the postulated causal mechanisms for the high rate of mtDNA mutation accumulation in both inheritance and in somatic cells. Perhaps unexpectedly, mtDNA is resilient to many mutagens of nDNA but is prone to errors of replication. We then consider the influence of maternal inheritance, recombination and selection on the observed accumulation pattern of inherited mtDNA mutations. Finally, we discuss environmental influences of temperature and diet on the observed frequency of inherited and somatic mtDNA mutations. We conclude that it is necessary to understand the cellular processes to fully interpret the pattern of mutations and how they influence our interpretations of evolution and disease.
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Affiliation(s)
- Richard G Melvin
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - John William O Ballard
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
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15
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Untangling Heteroplasmy, Structure, and Evolution of an Atypical Mitochondrial Genome by PacBio Sequencing. Genetics 2017; 207:269-280. [PMID: 28679546 DOI: 10.1534/genetics.117.203380] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/01/2017] [Indexed: 01/12/2023] Open
Abstract
The highly compact mitochondrial (mt) genome of terrestrial isopods (Oniscidae) presents two unusual features. First, several loci can individually encode two tRNAs, thanks to single nucleotide polymorphisms at anticodon sites. Within-individual variation (heteroplasmy) at these loci is thought to have been maintained for millions of years because individuals that do not carry all tRNA genes die, resulting in strong balancing selection. Second, the oniscid mtDNA genome comes in two conformations: a ∼14 kb linear monomer and a ∼28 kb circular dimer comprising two monomer units fused in palindrome. We hypothesized that heteroplasmy actually results from two genome units of the same dimeric molecule carrying different tRNA genes at mirrored loci. This hypothesis, however, contradicts the earlier proposition that dimeric molecules result from the replication of linear monomers-a process that should yield totally identical genome units within a dimer. To solve this contradiction, we used the SMRT (PacBio) technology to sequence mirrored tRNA loci in single dimeric molecules. We show that dimers do present different tRNA genes at mirrored loci; thus covalent linkage, rather than balancing selection, maintains vital variation at anticodons. We also leveraged unique features of the SMRT technology to detect linear monomers closed by hairpins and carrying noncomplementary bases at anticodons. These molecules contain the necessary information to encode two tRNAs at the same locus, and suggest new mechanisms of transition between linear and circular mtDNA. Overall, our analyses clarify the evolution of an atypical mt genome where dimerization counterintuitively enabled further mtDNA compaction.
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16
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Mitochondrial genotype modulates mtDNA copy number and organismal phenotype in Drosophila. Mitochondrion 2017; 34:75-83. [DOI: 10.1016/j.mito.2017.02.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 11/28/2016] [Accepted: 02/01/2017] [Indexed: 11/21/2022]
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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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18
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Abstract
Recent advances in the field of mitochondrial DNA (mtDNA) replication highlight the diversity of both the mechanisms utilized and the structural and functional organization of the proteins at mtDNA replication fork, despite the relative simplicity of the animal mtDNA genome. DNA polymerase γ, mtDNA helicase and mitochondrial single-stranded DNA-binding protein-the key replisome proteins, have evolved distinct structural features and biochemical properties. These appear to be correlated with mtDNA genomic features in different metazoan taxa and with their modes of DNA replication, although substantial integrative research is warranted to establish firmly these links. To date, several modes of mtDNA replication have been described for animals: rolling circle, theta, strand-displacement, and RITOLS/bootlace. Resolution of a continuing controversy relevant to mtDNA replication in mammals/vertebrates will have a direct impact on the mechanistic interpretation of mtDNA-related human diseases. Here we review these subjects, integrating earlier and recent data to provide a perspective on the major challenges for future research.
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Affiliation(s)
- G L Ciesielski
- Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland; Michigan State University, East Lansing, MI, United States
| | - M T Oliveira
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
| | - L S Kaguni
- Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland; Michigan State University, East Lansing, MI, United States.
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19
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Oliveira MT, Haukka J, Kaguni LS. Evolution of the metazoan mitochondrial replicase. Genome Biol Evol 2015; 7:943-59. [PMID: 25740821 PMCID: PMC4419789 DOI: 10.1093/gbe/evv042] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2015] [Indexed: 01/10/2023] Open
Abstract
The large number of complete mitochondrial DNA (mtDNA) sequences available for metazoan species makes it a good system for studying genome diversity, although little is known about the mechanisms that promote and/or are correlated with the evolution of this organellar genome. By investigating the molecular evolutionary history of the catalytic and accessory subunits of the mtDNA polymerase, pol γ, we sought to develop mechanistic insight into its function that might impact genome structure by exploring the relationships between DNA replication and animal mitochondrial genome diversity. We identified three evolutionary patterns among metazoan pol γs. First, a trend toward stabilization of both sequence and structure occurred in vertebrates, with both subunits evolving distinctly from those of other animal groups, and acquiring at least four novel structural elements, the most important of which is the HLH-3β (helix-loop-helix, 3 β-sheets) domain that allows the accessory subunit to homodimerize. Second, both subunits of arthropods and tunicates have become shorter and evolved approximately twice as rapidly as their vertebrate homologs. And third, nematodes have lost the gene for the accessory subunit, which was accompanied by the loss of its interacting domain in the catalytic subunit of pol γ, and they show the highest rate of molecular evolution among all animal taxa. These findings correlate well with the mtDNA genomic features of each group described above, and with their modes of DNA replication, although a substantive amount of biochemical work is needed to draw conclusive links regarding the latter. Describing the parallels between evolution of pol γ and metazoan mtDNA architecture may also help in understanding the processes that lead to mitochondrial dysfunction and to human disease-related phenotypes.
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Affiliation(s)
- Marcos T Oliveira
- Institute of Biosciences and Medical Technology, University of Tampere, Finland Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho," Jaboticabal, SP, Brazil
| | - Jani Haukka
- Institute of Biosciences and Medical Technology, University of Tampere, Finland
| | - Laurie S Kaguni
- Institute of Biosciences and Medical Technology, University of Tampere, Finland Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University
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20
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Lewis SC, Joers P, Willcox S, Griffith JD, Jacobs HT, Hyman BC. A rolling circle replication mechanism produces multimeric lariats of mitochondrial DNA in Caenorhabditis elegans. PLoS Genet 2015; 11:e1004985. [PMID: 25693201 PMCID: PMC4334201 DOI: 10.1371/journal.pgen.1004985] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 01/05/2015] [Indexed: 11/24/2022] Open
Abstract
Mitochondrial DNA (mtDNA) encodes respiratory complex subunits essential to almost all eukaryotes; hence respiratory competence requires faithful duplication of this molecule. However, the mechanism(s) of its synthesis remain hotly debated. Here we have developed Caenorhabditis elegans as a convenient animal model for the study of metazoan mtDNA synthesis. We demonstrate that C. elegans mtDNA replicates exclusively by a phage-like mechanism, in which multimeric molecules are synthesized from a circular template. In contrast to previous mammalian studies, we found that mtDNA synthesis in the C. elegans gonad produces branched-circular lariat structures with multimeric DNA tails; we were able to detect multimers up to four mtDNA genome unit lengths. Further, we did not detect elongation from a displacement-loop or analogue of 7S DNA, suggesting a clear difference from human mtDNA in regard to the site(s) of replication initiation. We also identified cruciform mtDNA species that are sensitive to cleavage by the resolvase RusA; we suggest these four-way junctions may have a role in concatemer-to-monomer resolution. Overall these results indicate that mtDNA synthesis in C. elegans does not conform to any previously documented metazoan mtDNA replication mechanism, but instead are strongly suggestive of rolling circle replication, as employed by bacteriophages. As several components of the metazoan mitochondrial DNA replisome are likely phage-derived, these findings raise the possibility that the rolling circle mtDNA replication mechanism may be ancestral among metazoans.
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Affiliation(s)
- Samantha C. Lewis
- Department of Biology and Interdepartmental Graduate Program in Genetics, Genomics and Bioinformatics, University of California Riverside, Riverside, California, United States of America
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
| | - Priit Joers
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
- Estonian Biocentre, Tartu, Estonia
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jack D. Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Howard T. Jacobs
- BioMediTech and Tampere University Hospital, University of Tampere, Tampere, Finland
- Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
| | - Bradley C. Hyman
- Department of Biology and Interdepartmental Graduate Program in Genetics, Genomics and Bioinformatics, University of California Riverside, Riverside, California, United States of America
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21
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Sedman T, Gaidutšik I, Villemson K, Hou Y, Sedman J. Double-stranded DNA-dependent ATPase Irc3p is directly involved in mitochondrial genome maintenance. Nucleic Acids Res 2014; 42:13214-27. [PMID: 25389272 PMCID: PMC4245962 DOI: 10.1093/nar/gku1148] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nucleic acid-dependent ATPases are involved in nearly all aspects of DNA and RNA metabolism. Previous studies have described a number of mitochondrial helicases. However, double-stranded DNA-dependent ATPases, including translocases or enzymes remodeling DNA-protein complexes, have not been identified in mitochondria of the yeast Saccharomyces cerevisae. Here, we demonstrate that Irc3p is a mitochondrial double-stranded DNA-dependent ATPase of the Superfamily II. In contrast to the other mitochondrial Superfamily II enzymes Mss116p, Suv3p and Mrh4p, which are RNA helicases, Irc3p has a direct role in mitochondrial DNA (mtDNA) maintenance. Specific Irc3p-dependent mtDNA metabolic intermediates can be detected, including high levels of double-stranded DNA breaks that accumulate in irc3Δ mutants. irc3Δ-related topology changes in rho- mtDNA can be reversed by the deletion of mitochondrial RNA polymerase RPO41, suggesting that Irc3p counterbalances adverse effects of transcription on mitochondrial genome stability.
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Affiliation(s)
- Tiina Sedman
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b, Tartu 51010, Estonia
| | - Ilja Gaidutšik
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b, Tartu 51010, Estonia
| | - Karin Villemson
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b, Tartu 51010, Estonia
| | - YingJian Hou
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b, Tartu 51010, Estonia
| | - Juhan Sedman
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23b, Tartu 51010, Estonia
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22
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Holt IJ, Jacobs HT. Unique features of DNA replication in mitochondria: a functional and evolutionary perspective. Bioessays 2014; 36:1024-31. [PMID: 25220172 DOI: 10.1002/bies.201400052] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Last year, we reported a new mechanism of DNA replication in mammals. It occurs inside mitochondria and entails the use of processed transcripts, termed bootlaces, which hybridize with the displaced parental strand as the replication fork advances. Here we discuss possible reasons why such an unusual mechanism of DNA replication might have evolved. The bootlace mechanism can minimize the occurrence and impact of single-strand breaks that would otherwise threaten genome stability. Furthermore, by providing an implicit mismatch recognition system, it should limit the occurrence of replication-dependent deletions and insertions, and defend against invading elements. Such a mechanism may also limit attempts to manipulate the mammalian mitochondrial genome.
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Affiliation(s)
- Ian J Holt
- MRC National Institute for Medical Research, London, UK
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23
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Mechanism of homologous recombination and implications for aging-related deletions in mitochondrial DNA. Microbiol Mol Biol Rev 2014; 77:476-96. [PMID: 24006472 DOI: 10.1128/mmbr.00007-13] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Homologous recombination is a universal process, conserved from bacteriophage to human, which is important for the repair of double-strand DNA breaks. Recombination in mitochondrial DNA (mtDNA) was documented more than 4 decades ago, but the underlying molecular mechanism has remained elusive. Recent studies have revealed the presence of a Rad52-type recombination system of bacteriophage origin in mitochondria, which operates by a single-strand annealing mechanism independent of the canonical RecA/Rad51-type recombinases. Increasing evidence supports the notion that, like in bacteriophages, mtDNA inheritance is a coordinated interplay between recombination, repair, and replication. These findings could have profound implications for understanding the mechanism of mtDNA inheritance and the generation of mtDNA deletions in aging cells.
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24
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Oxidative stress is not a major contributor to somatic mitochondrial DNA mutations. PLoS Genet 2014; 10:e1003974. [PMID: 24516391 PMCID: PMC3916223 DOI: 10.1371/journal.pgen.1003974] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 10/09/2013] [Indexed: 01/12/2023] Open
Abstract
The accumulation of somatic mitochondrial DNA (mtDNA) mutations is implicated in aging and common diseases of the elderly, including cancer and neurodegenerative disease. However, the mechanisms that influence the frequency of somatic mtDNA mutations are poorly understood. To develop a simple invertebrate model system to address this matter, we used the Random Mutation Capture (RMC) assay to characterize the age-dependent frequency and distribution of mtDNA mutations in the fruit fly Drosophila melanogaster. Because oxidative stress is a major suspect in the age-dependent accumulation of somatic mtDNA mutations, we also used the RMC assay to explore the influence of oxidative stress on the somatic mtDNA mutation frequency. We found that many of the features associated with mtDNA mutations in vertebrates are conserved in Drosophila, including a comparable somatic mtDNA mutation frequency (∼10(-5)), an increased frequency of mtDNA mutations with age, and a prevalence of transition mutations. Only a small fraction of the mtDNA mutations detected in young or old animals were G∶C to T∶A transversions, a signature of oxidative damage, and loss-of-function mutations in the mitochondrial superoxide dismutase, Sod2, had no detectable influence on the somatic mtDNA mutation frequency. Moreover, a loss-of-function mutation in Ogg1, which encodes a DNA repair enzyme that removes oxidatively damaged deoxyguanosine residues (8-hydroxy-2'-deoxyguanosine), did not significantly influence the somatic mtDNA mutation frequency of Sod2 mutants. Together, these findings indicate that oxidative stress is not a major cause of somatic mtDNA mutations. Our data instead suggests that somatic mtDNA mutations arise primarily from errors that occur during mtDNA replication. Further studies using Drosophila should aid in the identification of factors that influence the frequency of somatic mtDNA mutations.
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25
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Jõers P, Lewis SC, Fukuoh A, Parhiala M, Ellilä S, Holt IJ, Jacobs HT. Mitochondrial transcription terminator family members mTTF and mTerf5 have opposing roles in coordination of mtDNA synthesis. PLoS Genet 2013; 9:e1003800. [PMID: 24068965 PMCID: PMC3778013 DOI: 10.1371/journal.pgen.1003800] [Citation(s) in RCA: 16] [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: 04/04/2013] [Accepted: 07/30/2013] [Indexed: 12/19/2022] Open
Abstract
All genomes require a system for avoidance or handling of collisions between the machineries of DNA replication and transcription. We have investigated the roles in this process of the mTERF (mitochondrial transcription termination factor) family members mTTF and mTerf5 in Drosophila melanogaster. The two mTTF binding sites in Drosophila mtDNA, which also bind mTerf5, were found to coincide with major sites of replication pausing. RNAi-mediated knockdown of either factor resulted in mtDNA depletion and developmental arrest. mTTF knockdown decreased site-specific replication pausing, but led to an increase in replication stalling and fork regression in broad zones around each mTTF binding site. Lagging-strand DNA synthesis was impaired, with extended RNA/DNA hybrid segments seen in replication intermediates. This was accompanied by the accumulation of recombination intermediates and nicked/broken mtDNA species. Conversely, mTerf5 knockdown led to enhanced replication pausing at mTTF binding sites, a decrease in fragile replication intermediates containing single-stranded segments, and the disappearance of species containing segments of RNA/DNA hybrid. These findings indicate an essential and previously undescribed role for proteins of the mTERF family in the integration of transcription and DNA replication, preventing unregulated collisions and facilitating productive interactions between the two machineries that are inferred to be essential for completion of lagging-strand DNA synthesis.
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Affiliation(s)
- Priit Jõers
- Institute of Biomedical Technology and Tampere University Hospital, Tampere, Finland
- Estonian Biocentre, Tartu, Estonia
| | - Samantha C. Lewis
- Institute of Biomedical Technology and Tampere University Hospital, Tampere, Finland
- Department of Biology, University of California, Riverside, California, United States of America
| | - Atsushi Fukuoh
- Institute of Biomedical Technology and Tampere University Hospital, Tampere, Finland
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
- Department of Medical Laboratory Science, Junshin Gakuen University, Fukuoka, Japan
| | - Mikael Parhiala
- Institute of Biomedical Technology and Tampere University Hospital, Tampere, Finland
| | - Simo Ellilä
- Institute of Biomedical Technology and Tampere University Hospital, Tampere, Finland
| | - Ian J. Holt
- MRC National Institute of Medical Research, London, United Kingdom
| | - Howard T. Jacobs
- Institute of Biomedical Technology and Tampere University Hospital, Tampere, Finland
- Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
- * E-mail:
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26
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McKinney EA, Oliveira MT. Replicating animal mitochondrial DNA. Genet Mol Biol 2013; 36:308-15. [PMID: 24130435 PMCID: PMC3795181 DOI: 10.1590/s1415-47572013000300002] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Accepted: 07/11/2013] [Indexed: 11/22/2022] Open
Abstract
The field of mitochondrial DNA (mtDNA) replication has been experiencing incredible progress in recent years, and yet little is certain about the mechanism(s) used by animal cells to replicate this plasmid-like genome. The long-standing strand-displacement model of mammalian mtDNA replication (for which single-stranded DNA intermediates are a hallmark) has been intensively challenged by a new set of data, which suggests that replication proceeds via coupled leading- and lagging-strand synthesis (resembling bacterial genome replication) and/or via long stretches of RNA intermediates laid on the mtDNA lagging-strand (the so called RITOLS). The set of proteins required for mtDNA replication is small and includes the catalytic and accessory subunits of DNA polymerase γ, the mtDNA helicase Twinkle, the mitochondrial single-stranded DNA-binding protein, and the mitochondrial RNA polymerase (which most likely functions as the mtDNA primase). Mutations in the genes coding for the first three proteins are associated with human diseases and premature aging, justifying the research interest in the genetic, biochemical and structural properties of the mtDNA replication machinery. Here we summarize these properties and discuss the current models of mtDNA replication in animal cells.
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Affiliation(s)
- Emily A McKinney
- Institute of Biomedical Technology, University of Tampere, Tampere, Finland
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