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Cluett TJ, Akman G, Reyes A, Kazak L, Mitchell A, Wood SR, Spinazzola A, Spelbrink JN, Holt IJ. Transcript availability dictates the balance between strand-asynchronous and strand-coupled mitochondrial DNA replication. Nucleic Acids Res 2019; 46:10771-10781. [PMID: 30239839 PMCID: PMC6237803 DOI: 10.1093/nar/gky852] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 09/12/2018] [Indexed: 11/15/2022] Open
Abstract
Mammalian mitochondria operate multiple mechanisms of DNA replication. In many cells and tissues a strand-asynchronous mechanism predominates over coupled leading and lagging-strand DNA synthesis. However, little is known of the factors that control or influence the different mechanisms of replication, and the idea that strand-asynchronous replication entails transient incorporation of transcripts (aka bootlaces) is controversial. A firm prediction of the bootlace model is that it depends on mitochondrial transcripts. Here, we show that elevated expression of Twinkle DNA helicase in human mitochondria induces bidirectional, coupled leading and lagging-strand DNA synthesis, at the expense of strand-asynchronous replication; and this switch is accompanied by decreases in the steady-state level of some mitochondrial transcripts. However, in the so-called minor arc of mitochondrial DNA where transcript levels remain high, the strand-asynchronous replication mechanism is instated. Hence, replication switches to a strand-coupled mechanism only where transcripts are scarce, thereby establishing a direct correlation between transcript availability and the mechanism of replication. Thus, these findings support a critical role of mitochondrial transcripts in the strand-asynchronous mechanism of mitochondrial DNA replication; and, as a corollary, mitochondrial RNA availability and RNA/DNA hybrid formation offer means of regulating the mechanisms of DNA replication in the organelle.
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Affiliation(s)
- Tricia J Cluett
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB1 9SY, UK
| | | | - Aurelio Reyes
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB1 9SY, UK
| | - Lawrence Kazak
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB1 9SY, UK
| | - Alice Mitchell
- Department of Clinical Movement Neurosciences, Institute of Neurology, Royal Free Campus, University College London, London NW3 2PF, UK
| | - Stuart R Wood
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge CB1 9SY, UK
| | - Antonella Spinazzola
- Department of Clinical Movement Neurosciences, Institute of Neurology, Royal Free Campus, University College London, London NW3 2PF, UK.,MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, London, UK
| | - Johannes N Spelbrink
- Department of Pediatrics, Radboud Centre for Mitochondrial Medicine, Radboud University Medical Centre, Geert Grooteplein 10, 6500 HB, Nijmegen, The Netherlands
| | - Ian J Holt
- Department of Clinical Movement Neurosciences, Institute of Neurology, Royal Free Campus, University College London, London NW3 2PF, UK.,Biodonostia Health Research Institute, 20014 San Sebastián, Spain and IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
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Reyes A, He J, Mao CC, Bailey LJ, Di Re M, Sembongi H, Kazak L, Dzionek K, Holmes JB, Cluett TJ, Harbour ME, Fearnley IM, Crouch RJ, Conti MA, Adelstein RS, Walker JE, Holt IJ. Actin and myosin contribute to mammalian mitochondrial DNA maintenance. Nucleic Acids Res 2011; 39:5098-108. [PMID: 21398640 PMCID: PMC3130256 DOI: 10.1093/nar/gkr052] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial DNA maintenance and segregation are dependent on the actin cytoskeleton in budding yeast. We found two cytoskeletal proteins among six proteins tightly associated with rat liver mitochondrial DNA: non-muscle myosin heavy chain IIA and β-actin. In human cells, transient gene silencing of MYH9 (encoding non-muscle myosin heavy chain IIA), or the closely related MYH10 gene (encoding non-muscle myosin heavy chain IIB), altered the topology and increased the copy number of mitochondrial DNA; and the latter effect was enhanced when both genes were targeted simultaneously. In contrast, genetic ablation of non-muscle myosin IIB was associated with a 60% decrease in mitochondrial DNA copy number in mouse embryonic fibroblasts, compared to control cells. Gene silencing of β-actin also affected mitochondrial DNA copy number and organization. Protease-protection experiments and iodixanol gradient analysis suggest some β-actin and non-muscle myosin heavy chain IIA reside within human mitochondria and confirm that they are associated with mitochondrial DNA. Collectively, these results strongly implicate the actomyosin cytoskeleton in mammalian mitochondrial DNA maintenance.
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Affiliation(s)
- A Reyes
- MRC Mitochondrial Biology Unit, Cambridge, UK
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Fusté JM, Wanrooij S, Jemt E, Granycome CE, Cluett TJ, Shi Y, Atanassova N, Holt IJ, Gustafsson CM, Falkenberg M. Mitochondrial RNA polymerase is needed for activation of the origin of light-strand DNA replication. Mol Cell 2010; 37:67-78. [PMID: 20129056 DOI: 10.1016/j.molcel.2009.12.021] [Citation(s) in RCA: 148] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Revised: 07/21/2009] [Accepted: 10/14/2009] [Indexed: 11/19/2022]
Abstract
Mitochondrial DNA is replicated by a unique enzymatic machinery, which is distinct from the replication apparatus used for copying the nuclear genome. We examine here the mechanisms of origin-specific initiation of lagging-strand DNA synthesis in human mitochondria. We demonstrate that the mitochondrial RNA polymerase (POLRMT) is the primase required for initiation of DNA synthesis from the light-strand origin of DNA replication (OriL). Using only purified POLRMT and DNA replication factors, we can faithfully reconstitute OriL-dependent initiation in vitro. Leading-strand DNA synthesis is initiated from the heavy-strand origin of DNA replication and passes OriL. The single-stranded OriL is exposed and adopts a stem-loop structure. At this stage, POLRMT initiates primer synthesis from a poly-dT stretch in the single-stranded loop region. After about 25 nt, POLRMT is replaced by DNA polymerase gamma, and DNA synthesis commences. Our findings demonstrate that POLRMT can function as an origin-specific primase in mammalian mitochondria.
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Affiliation(s)
- Javier Miralles Fusté
- Division of Metabolic Diseases, Karolinska Institutet, Novum, SE-141 86 Stockholm, Sweden
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Holmes JB, Pohjoismäki JL, Yang MY, Yasukawa T, Cluett TJ, Reyes A, Goffart S, Willcox S, Rigby RE, Jackson AP, Spelbrink JN, Griffith JD, Crouch RJ, Jacobs HT, Holt IJ. 89 Analysis of extensive RNA/DNA hybrids in the replicating mammalian mitochondrial genome. Mitochondrion 2010. [DOI: 10.1016/j.mito.2009.12.082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Bailey LJ, Cluett TJ, Reyes A, Prolla TA, Poulton J, Leeuwenburgh C, Holt IJ. Mice expressing an error-prone DNA polymerase in mitochondria display elevated replication pausing and chromosomal breakage at fragile sites of mitochondrial DNA. Nucleic Acids Res 2009; 37:2327-35. [PMID: 19244310 PMCID: PMC2673436 DOI: 10.1093/nar/gkp091] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Expression of a proof-reading deficient form of mitochondrial DNA (mtDNA) polymerase γ, POLG, causes early death accompanied by features of premature ageing in mouse. However, the mechanism of cellular senescence remains unresolved. In addition to high levels of point mutations of mtDNA, the POLG mutator mouse harbours linear mtDNAs. Using one- and two-dimensional agarose gel electrophoresis, we show that the linear mtDNAs derive from replication intermediates and are indicative of replication pausing and chromosomal breakage at the accompanying fragile sites. Replication fork arrest is not random but occurs at specific sites close to two cis-elements known as OH and OL. Pausing at these sites may be enhanced in the case of exonuclease-deficient POLG owing to delayed resumption of DNA replication, or replisome instability. In either case, the mtDNA replication cycle is perturbed and this might explain the progeroid features of the POLG mutator mouse.
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Affiliation(s)
- Laura J Bailey
- MRC-Dunn Human Nutrition Unit, Wellcome Trust-MRC Building, Cambridge, UK
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Abstract
In higher vertebrates, the DNA of mitochondria takes the form of circular molecules of approximately 16 kbp. These circles are arranged in multigenomic nucleoprotein complexes or nucleoids. It is envisaged that nucleoid superstructure makes a critical contribution to the twin processes of replication and segregation of mtDNA. Replication intermediates can be isolated from cells or solid tissues and separated on agarose gels in two dimensions to reveal a wealth of data on mechanisms of DNA replication. Using this technique we have demonstrated that many molecules of replicating mtDNA have extensive regions of RNA: DNA hybrid in higher vertebrates. More recently, we have extracted mitochondrial nucleoprotein and analyzed it by the same method to derive information on the distribution of DNA-binding proteins on mitochondrial DNA. Here we describe the procedures used to isolate intact mitochondrial replication intermediates from liver and cultured cells of higher vertebrates and the process of separating DNA fragments on neutral two-dimensional agarose gels.
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Affiliation(s)
- Aurelio Reyes
- MRC Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Cambridge, UK
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Yasukawa T, Reyes A, Cluett TJ, Yang MY, Bowmaker M, Jacobs HT, Holt IJ. Replication of vertebrate mitochondrial DNA entails transient ribonucleotide incorporation throughout the lagging strand. EMBO J 2006; 25:5358-71. [PMID: 17066082 PMCID: PMC1636616 DOI: 10.1038/sj.emboj.7601392] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Accepted: 09/26/2006] [Indexed: 01/06/2023] Open
Abstract
Using two-dimensional agarose gel electrophoresis, we show that mitochondrial DNA (mtDNA) replication of birds and mammals frequently entails ribonucleotide incorporation throughout the lagging strand (RITOLS). Based on a combination of two-dimensional agarose gel electrophoretic analysis and mapping of 5' ends of DNA, initiation of RITOLS replication occurs in the major non-coding region of vertebrate mtDNA and is effectively unidirectional. In some cases, conversion of nascent RNA strands to DNA starts at defined loci, the most prominent of which maps, in mammalian mtDNA, in the vicinity of the site known as the light-strand origin.
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Affiliation(s)
| | | | | | | | | | - Howard T Jacobs
- Institute of Medical Technology and Tampere University Hospital, University of Tampere, Finland
| | - Ian J Holt
- MRC-Dunn Human Nutrition Unit, Cambridge, UK
- MRC-Dunn Human Nutrition Unit, Wellcome Trust-MRC Building, Hills Road, Cambridge CB2 2XY, UK. Tel.: +44 1223 252840; Fax: +44 1223 252845; E-mail:
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