101
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Hornig-Do HT, Günther G, Bust M, Lehnartz P, Bosio A, Wiesner RJ. Isolation of functional pure mitochondria by superparamagnetic microbeads. Anal Biochem 2009; 389:1-5. [DOI: 10.1016/j.ab.2009.02.040] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Revised: 02/06/2009] [Accepted: 02/27/2009] [Indexed: 10/21/2022]
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102
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Herpes simplex virus UL12.5 targets mitochondria through a mitochondrial localization sequence proximal to the N terminus. J Virol 2009; 83:2601-10. [PMID: 19129438 DOI: 10.1128/jvi.02087-08] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The herpes simplex virus type 1 (HSV-1) gene UL12 encodes a conserved alkaline DNase with orthologues in all herpesviruses. The HSV-1 UL12 gene gives rise to two separately promoted 3' coterminal mRNAs which encode distinct but related proteins: full-length UL12 and UL12.5, an amino-terminally truncated form that initiates at UL12 codon 127. Full-length UL12 localizes to the nucleus where it promotes the generation of mature viral genomes from larger precursors. In contrast, UL12.5 is predominantly mitochondrial and acts to trigger degradation of the mitochondrial genome early during infection. We examined the basis for these very different subcellular localization patterns. We confirmed an earlier report that the amino-terminal region of full-length UL12 is required for nuclear localization and provide evidence that multiple nuclear localization determinants are present in this region. In addition, we demonstrate that mitochondrial localization of UL12.5 relies largely on sequences located between UL12 residues 185 and 245 (UL12.5 residues 59 to 119). This region contains a sequence that resembles a typical mitochondrial matrix localization signal, and mutations that reduce the positive charge of this element severely impaired mitochondrial localization. Consistent with matrix localization, UL12.5 displayed a detergent extraction profile indistinguishable from that of the matrix protein cyclophilin D. Mitochondrial DNA depletion required the exonuclease activity of UL12.5, consistent with the idea that UL12.5 located within the matrix acts directly to destroy the mitochondrial genome. These results clarify how two highly related viral proteins are targeted to different subcellular locations with distinct functional consequences.
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103
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Ashley N, Poulton J. Mitochondrial DNA is a direct target of anti-cancer anthracycline drugs. Biochem Biophys Res Commun 2009; 378:450-5. [DOI: 10.1016/j.bbrc.2008.11.059] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Accepted: 11/14/2008] [Indexed: 10/21/2022]
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104
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Maeda-Sano K, Sato S, Ueda T, Yui R, Ito K, Hata M, Nakano A, Kita K, Murakami-Murofushi K, Sasaki N. Visualization of Mitochondrial and Apicoplast Nucleoids in the Human Malaria Parasite Plasmodium falciparum by SYBR Green I and PicoGreen Staining. CYTOLOGIA 2009. [DOI: 10.1508/cytologia.74.449] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | - Shigeharu Sato
- Division of Parasitology, MRC National Institute for Medical Research
| | - Takashi Ueda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Ryoko Yui
- Division of Biological Science, Graduate School of Science, Nagoya University
| | - Kie Ito
- Division of Biology, Faculty of Science, Ochanomizu University
- Division of Biological Science, Graduate School of Science, Nagoya University
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo
| | - Masayuki Hata
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo
| | - Akihiko Nakano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
- RIKEN Advanced Science Institute
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo
| | | | - Narie Sasaki
- Division of Biological Science, Graduate School of Science, Nagoya University
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105
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Gauthier DJ, Sobota JA, Ferraro F, Mains RE, Lazure C. Flow cytometry-assisted purification and proteomic analysis of the corticotropes dense-core secretory granules. Proteomics 2008; 8:3848-61. [PMID: 18704904 DOI: 10.1002/pmic.200700969] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The field of organellar proteomics has emerged as an attempt to minimize the complexity of the proteomics data obtained from whole cell and tissue extracts while maximizing the resolution on the protein composition of a single subcellular compartment. Standard methods involve lengthy density-based gradient and/or immunoaffinity purification steps followed by extraction, 1-DE or 2-DE, gel staining, in-gel tryptic digestion, and protein identification by MS. In this paper, we present an alternate approach to purify subcellular organelles containing a fluorescent reporter molecule. The gel-free procedure involves fluorescence-assisted sorting of the secretory granules followed by gentle extraction in a buffer compatible with tryptic digestion and MS. Once the subcellular organelle labeled, this procedure can be done in a single day, requires no major modification to any instrumentation and can be readily adapted to the study of other organelles. When applied to corticotrope secretory granules, it led to a much enriched granular fraction from which numerous proteins could be identified through MS.
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Affiliation(s)
- Daniel J Gauthier
- Neuropeptides Structure and Metabolism Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada
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106
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Ashley N, O'Rourke A, Smith C, Adams S, Gowda V, Zeviani M, Brown GK, Fratter C, Poulton J. Depletion of mitochondrial DNA in fibroblast cultures from patients with POLG1 mutations is a consequence of catalytic mutations. Hum Mol Genet 2008; 17:2496-506. [PMID: 18487244 PMCID: PMC2486441 DOI: 10.1093/hmg/ddn150] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigated clinical and cellular phenotypes of 24 children with mutations in the catalytic (alpha) subunit of the mitochondrial DNA (mtDNA) gamma polymerase (POLG1). Twenty-one had Alpers syndrome, the commonest severe POLG1 autosomal recessive phenotype, comprising hepatoencephalopathy and often mtDNA depletion. The cellular mtDNA content reflected the genotype more closely than did clinical features. Patients with tissue depletion of mtDNA all had at least one allele with either a missense mutation in a catalytic domain or a nonsense mutation. Four out of 12 patients exhibited a progressive, mosaic pattern of mtDNA depletion in cultured fibroblasts. All these patients had mutations in a catalytic domain in both POLG1 alleles, in either the polymerase or exonuclease domain or both. The tissue mtDNA content of patients who had two linker mutations was normal, and their phenotypes the mildest. Epilepsy and/or movement disorder were major features in all 21. Previous studies have implicated replication stalling as a mechanism for mtDNA depletion. The mosaic cellular depletion that we have demonstrated in cell cultures may be a manifestation of severe replication stalling. One patient with a severe cellular and clinical phenotype was a compound heterozygote with POLG1 mutations in the polymerase and exonuclease domain intrans. This suggests that POLG1 requires both polymerase and 3'-5' exonuclease activity in the same molecule. This is consistent with current functional models for eukaryotic DNA polymerases, which alternate between polymerizing and editing modes, as determined by competition between these two active sites for the 3' end of the DNA.
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Affiliation(s)
- Neil Ashley
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, The Women's Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
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107
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Mizumachi T, Muskhelishvili L, Naito A, Furusawa J, Fan CY, Siegel ER, Kadlubar FF, Kumar U, Higuchi M. Increased distributional variance of mitochondrial DNA content associated with prostate cancer cells as compared with normal prostate cells. Prostate 2008; 68:408-17. [PMID: 18196528 PMCID: PMC2268637 DOI: 10.1002/pros.20697] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Mitochondria are key organelles for apoptosis, and mitochondrial DNA (mtDNA) content can regulate cancer progression. Increases in mtDNA mutations and deletions have been reported in cancer; however, a detailed investigation of mtDNA content in cancer cells has not yet been conducted. METHODS Quantitative real-time PCR and improved extraction method were established to investigate the mtDNA content in a single prostate cell. RESULTS The heterogeneity of mtDNA content was demonstrated between the clones of prostate cancer cell line LNCaP and individual cells in each clone. To investigate whether large distributional variance of mtDNA content is associated with cancer initiation and/or progression, we first compared PZ-HPV-7, an HPV-transformed normal prostate epithelial cell line, with CA-HPV-10, transformed from prostate cancer cells derived from the same donor. We found an enhanced distributional variance of mtDNA content in CA-HPV-10. Then, we investigated mtDNA content in individual cells in laser microdisssected cancer and adjacent normal cells from prostate cancer tissue specimens using quantitative real-time PCR method. Results showed that the mtDNA content per cell follows a higher skewed distribution in cancer cells as compared in normal cells. We also observed that mtDNA content was increased in seven of nine (78%) of prostate cancers compared to normal prostate tissue. CONCLUSIONS These results indicate that prostate carcinogenesis may involve dysregulation of mtDNA content.
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Affiliation(s)
- Takatsugu Mizumachi
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Central Arkansas Veterans Health Care System, Little Rock, Arkansas
| | - Levan Muskhelishvili
- Division of Toxicologic Pathology Associates, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas
| | - Akihiro Naito
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Central Arkansas Veterans Health Care System, Little Rock, Arkansas
| | - Jun Furusawa
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Central Arkansas Veterans Health Care System, Little Rock, Arkansas
| | - Chun-Yang Fan
- Department of Pathology, University of Arkansas for Medical Sciences, Central Arkansas Veterans Health Care System, Little Rock, Arkansas
| | - Eric R. Siegel
- Department of Biostatistics, University of Arkansas for Medical Sciences, Central Arkansas Veterans Health Care System, Little Rock, Arkansas
| | - Fred F. Kadlubar
- Department of Epidemiology, University of Arkansas for Medical Sciences, Central Arkansas Veterans Health Care System, Little Rock, Arkansas
| | - Udaya Kumar
- Department of Urology, University of Arkansas for Medical Sciences, Central Arkansas Veterans Health Care System, Little Rock, Arkansas
| | - Masahiro Higuchi
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Central Arkansas Veterans Health Care System, Little Rock, Arkansas
- *Correspondence to: Masahiro Higuchi, 4301 W. Markham St., Slot 516 Little Rock, AR 72205. E-mail:
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108
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Swerdlow RH. Mitochondria in cybrids containing mtDNA from persons with mitochondriopathies. J Neurosci Res 2008; 85:3416-28. [PMID: 17243174 DOI: 10.1002/jnr.21167] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The cytoplasmic hybrid (cybrid) technique allows investigators to express selected mitochondrial DNA (mtDNA) sequences against fixed nuclear DNA (nDNA) backgrounds. Cybrids have been used to study the effects of known mtDNA mutations on mitochondrial biochemistry, mtDNA-nDNA inter-species compatibility, and mtDNA integrity in persons without mtDNA mutations defined previously. This review discusses events leading up to creation of the cybrid technique, as well as data obtained via application of the cybrid strategies listed above. Although interpreting cybrid data requires awareness of technique limitations, valuable insights into mtDNA genotype-functional phenotype relationships are suggested.
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Affiliation(s)
- Russell H Swerdlow
- Department of Neurology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
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109
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Human prohibitin 1 maintains the organization and stability of the mitochondrial nucleoids. Exp Cell Res 2008; 314:988-96. [PMID: 18258228 DOI: 10.1016/j.yexcr.2008.01.005] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2007] [Revised: 12/28/2007] [Accepted: 01/07/2008] [Indexed: 11/20/2022]
Abstract
Mitochondrial prohibitin (PHB) proteins have diverse functions, such as the regulation of apoptosis and the maintenance of mitochondrial morphology. In this study, we clarified a novel mitochondrial function of PHB1 that regulates the organization and maintenance of mitochondrial DNA (mtDNA). In PHB1-knockdown cells, we found that mtDNA is not stained by fluorescent dyes, such as ethidium bromide and PicoGreen, although the mitochondrial membrane potential still maintains. We also demonstrated that mtDNA, which is predominantly found in the NP-40-insoluble fraction when isolated from normal mitochondria, is partially released into the soluble fraction when isolated from PHB1-knockdown cells, indicating that the organization of the mitochondrial nucleoids has been altered. Furthermore, we found that PHB1 regulates copy number of mtDNA by stabilizing TFAM protein, a known protein component of the mitochondrial nucleoids. However, TFAM does not affect the organization of mtDNA as observed in PHB1-knockdown cells. Taken together, these results demonstrate that PHB1 maintains the organization and copy number of the mtDNA through both TFAM-independent and -dependent pathways.
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110
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Morten KJ, Ashley N, Wijburg F, Hadzic N, Parr J, Jayawant S, Adams S, Bindoff L, Bakker HD, Mieli-Vergani G, Zeviani M, Poulton J. Liver mtDNA content increases during development: A comparison of methods and the importance of age- and tissue-specific controls for the diagnosis of mtDNA depletion. Mitochondrion 2007; 7:386-95. [PMID: 17981517 DOI: 10.1016/j.mito.2007.09.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2007] [Revised: 08/29/2007] [Accepted: 09/04/2007] [Indexed: 11/19/2022]
Affiliation(s)
- Karl J Morten
- University of Oxford, Nuffield Department of Obstetrics and Gynaecology, The Womens Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
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111
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Navratil M, Poe BG, Arriaga EA. Quantitation of DNA copy number in individual mitochondrial particles by capillary electrophoresis. Anal Chem 2007; 79:7691-9. [PMID: 17877423 DOI: 10.1021/ac0709192] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, we present a direct method for determining mitochondrial DNA (mtDNA) copy numbers in individual mitochondrial particles, isolated from cultured cells, by means of capillary electrophoresis with laser-induced fluorescence (CE-LIF) detection. We demonstrate that this method can detect a single molecule of PicoGreen-stained mtDNA in intact DsRed2-labeled mitochondrial particles isolated from human osteosarcoma 143B cells. This ultimate limit of mtDNA detection made it possible to confirm that an individual mitochondrial nucleoid, the genetic unit of mitochondrial inheritance, can contain a single copy of mtDNA. The validation of this approach was achieved via monitoring chemically induced mtDNA depletion and comparing the CE-LIF results to those obtained by quantitative microscopy imaging and multiplex real-time PCR analysis. Owing to its sensitivity, the CE-LIF method may become a powerful tool for investigating the copy number and organization of mtDNA in mitochondrial disease and aging, and in molecular biology techniques requiring manipulation and quantitation of DNA molecules such as plasmids.
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Affiliation(s)
- Marian Navratil
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, USA
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112
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Chi C, Mikhailovsky A, Bazan GC. Design of Cationic Conjugated Polyelectrolytes for DNA Concentration Determination. J Am Chem Soc 2007; 129:11134-45. [PMID: 17705479 DOI: 10.1021/ja072471s] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cationic conjugated polyelectrolytes poly110 and poly120 were designed, synthesized, and characterized with the anticipation of function in the determination of double-stranded DNA concentration [dsDNA]. Their structures contain a pi-delocalized optically active backbone composed of phenylene-fluorene segments copolymerized with 2,1,3-benzothiadiazole (BT) units and charged pendant groups that allow excellent solubility in water. The subscript in poly1x refers to the molar percent of BT units in the chain. Addition of dsDNA to poly110 or poly120 results in a change in the color of emission from blue to green. These spectral changes can be treated to obtain the parameter delta, which can be used to generate calibration curves that indicate [dsDNA]. Analysis of photoluminescence spectra reveals that dsDNA addition gives rise to more efficient FRET from blue emitting segments to the BT sites, an increase in the BT emission quantum yield, and partial quenching of the phenylene-fluorene segments. Studies were also carried out to maximize the range of [dsDNA] determination. We find that by combining the response from two different initial concentrations of poly110, it is possible to generate calibration curves that respond with a difference in [dsDNA] of over 7 orders of magnitude.
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Affiliation(s)
- Chunyan Chi
- Department of Chemistry, Institute for Polymers and Organic Solids, University of California, Santa Barbara, California 93106, USA
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113
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Holt IJ, He J, Mao CC, Boyd-Kirkup JD, Martinsson P, Sembongi H, Reyes A, Spelbrink JN. Mammalian mitochondrial nucleoids: Organizing an independently minded genome. Mitochondrion 2007; 7:311-21. [PMID: 17698423 DOI: 10.1016/j.mito.2007.06.004] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Revised: 05/31/2007] [Accepted: 06/25/2007] [Indexed: 11/23/2022]
Abstract
Mitochondrial DNA is arranged in nucleoprotein complexes, or nucleoids. Nucleoid proteins include not only factors involved in replication and transcription but also structural proteins required for mitochondrial DNA maintenance. Although several nucleoid proteins have been identified and characterized in yeast over the course of the past decade, little was known of mammalian mitochondrial nucleoids until recently. Two publications in the past year have expanded considerably the pool of putative mammalian mitochondrial nucleoid proteins; and analysis of one of the candidates, ATAD3p, suggests that mitochondrial nucleoid formation and division are orchestrated, not random, events.
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Affiliation(s)
- Ian J Holt
- MRC-Dunn Human Nutrition Unit, Wellcome Trust-MRC Building, Hills Road, Cambridge CB2 OXY, UK.
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114
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Huang P, Yu T, Yoon Y. Mitochondrial clustering induced by overexpression of the mitochondrial fusion protein Mfn2 causes mitochondrial dysfunction and cell death. Eur J Cell Biol 2007; 86:289-302. [PMID: 17532093 DOI: 10.1016/j.ejcb.2007.04.002] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Revised: 03/15/2007] [Accepted: 04/16/2007] [Indexed: 10/23/2022] Open
Abstract
Mitochondria change their shapes dynamically mainly through fission and fusion. Dynamin-related GTPases have been shown to mediate remodeling of mitochondrial membranes during these processes. One of these GTPases, mitofusin, is anchored at the outer mitochondrial membrane and mediates fusion of the outer membrane. We found that overexpression of a mitofusin isoform, Mfn2, drastically changes mitochondrial morphology, forming mitochondrial clusters. High-resolution microscopic examination indicated that the mitochondrial clusters consisted of small fragmented mitochondria. Inhibiting mitochondrial fission prevented the cluster formation, supporting the notion that mitochondrial clusters are formed by fission-mediated mitochondrial fragmentation and aggregation. Mitochondrial clusters displayed a decreased inner membrane potential and mitochondrial function, suggesting a functional compromise of small fragmented mitochondria produced by Mfn2 overexpression; however, mitochondrial clusters still retained mitochondrial DNA. We found that cells containing clustered mitochondria lost cytochrome c from mitochondria and underwent caspase-mediated apoptosis. These results demonstrate that mitochondrial deformation impairs mitochondrial function, leading to apoptotic cell death and suggest the presence of an intricate form-function relationship in mitochondria.
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Affiliation(s)
- Pinwei Huang
- Department of Pharmacology and Physiology, University of Rochester, School of Medicine and Dentistry, 601 Elmwood Avenue, P.O. Box 604, Rochester, NY 14642, USA
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115
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Ashley N, Adams S, Slama A, Zeviani M, Suomalainen A, Andreu AL, Naviaux RK, Poulton J. Defects in maintenance of mitochondrial DNA are associated with intramitochondrial nucleotide imbalances. Hum Mol Genet 2007; 16:1400-11. [PMID: 17483096 DOI: 10.1093/hmg/ddm090] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Defects in mtDNA maintenance range from fatal multisystem childhood diseases, such as Alpers syndrome, to milder diseases in adults, including mtDNA depletion syndromes (MDS) and familial progressive external ophthalmoplegia (AdPEO). Most are associated with defects in genes involved in mitochondrial deoxynucleotide metabolism or utilization, such as mutations in thymidine kinase 2 (TK2) as well as the mtDNA replicative helicase, Twinkle and gamma polymerase (POLG). We have developed an in vitro system to measure incorporation of radiolabelled dNTPs into mitochondria of saponin permeabilized cells. We used this to compare the rates of mtDNA synthesis in cells from 12 patients with diseases of mtDNA maintenance. We observed reduced incorporation of exogenous alpha (32)P-dTTP in fibroblasts from a patient with Alpers syndrome associated with the A467T substitution in POLG, a patient with dGK mutations, and a patient with mtDNA depletion of unknown origin compared to controls. However, incorporation of alpha (32)P-dTTP relative to either cell doubling time or alpha (32)P-dCTP incorporation was increased in patients with thymidine kinase deficiency or PEO as the result of TWINKLE mutations compared with controls. The specific activity of newly synthesized mtDNA depends on the size of the endogenous pool diluting the exogenous labelled nucleotide. Our result is consistent with a deficiency in the intramitochondrial pool of dTTP relative to dCTP in cells from patients with TK2 deficiency and TWINKLE mutations. Such DNA precursor asymmetry could cause pausing of the replication complex and hence exacerbate the propensity for age-related mtDNA mutations. Because deviations from the normal concentrations of dNTPs are known to be mutagenic, we suggest that intramitochondrial nucleotide imbalance could underlie the multiple mtDNA mutations observed in these patients.
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Affiliation(s)
- Neil Ashley
- Mitochondrial Genetics Group, Nuffield Department of Obstetrics and Gynaecology, Level 3, Women's Centre,The John Radcliffe Hospital, Oxford OX3 9DU, UK
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116
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He J, Mao CC, Reyes A, Sembongi H, Di Re M, Granycome C, Clippingdale AB, Fearnley IM, Harbour M, Robinson AJ, Reichelt S, Spelbrink JN, Walker JE, Holt IJ. The AAA+ protein ATAD3 has displacement loop binding properties and is involved in mitochondrial nucleoid organization. ACTA ACUST UNITED AC 2007; 176:141-6. [PMID: 17210950 PMCID: PMC2063933 DOI: 10.1083/jcb.200609158] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Many copies of mammalian mitochondrial DNA contain a short triple-stranded region, or displacement loop (D-loop), in the major noncoding region. In the 35 years since their discovery, no function has been assigned to mitochondrial D-loops. We purified mitochondrial nucleoprotein complexes from rat liver and identified a previously uncharacterized protein, ATAD3p. Localization studies suggested that human ATAD3 is a component of many, but not all, mitochondrial nucleoids. Gene silencing of ATAD3 by RNA interference altered the structure of mitochondrial nucleoids and led to the dissociation of mitochondrial DNA fragments held together by protein, specifically, ones containing the D-loop region. In vitro, a recombinant fragment of ATAD3p bound to supercoiled DNA molecules that contained a synthetic D-loop, with a marked preference over partially relaxed molecules with a D-loop or supercoiled DNA circles. These results suggest that mitochondrial D-loops serve to recruit ATAD3p for the purpose of forming or segregating mitochondrial nucleoids.
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MESH Headings
- ATPases Associated with Diverse Cellular Activities
- Adenosine Triphosphatases
- Adenosine Triphosphate/metabolism
- Animals
- Binding Sites
- Binding, Competitive
- Cell Line, Tumor
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/metabolism
- DNA, Single-Stranded/metabolism
- DNA, Superhelical/genetics
- DNA, Superhelical/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Electrophoresis, Gel, Two-Dimensional
- Electrophoretic Mobility Shift Assay
- Humans
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- Mitochondria, Liver/metabolism
- Mitochondrial Proteins/genetics
- Mitochondrial Proteins/metabolism
- Nucleic Acid Conformation
- Nucleoproteins/genetics
- Nucleoproteins/metabolism
- Peptide Fragments/metabolism
- Plasmids/metabolism
- Protein Binding
- RNA, Small Interfering/genetics
- Rats
- Submitochondrial Particles/metabolism
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Affiliation(s)
- Jiuya He
- Medical Research Council Dunn Human Nutrition Unit, Wellcome Trust/Medical Research Council Building, Cambridge CB2 OXY, England, UK
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117
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Goffart S, Martinsson P, Malka F, Rojo M, Spelbrink JN. The mitochondria of cultured mammalian cells: II. Expression and visualization of exogenous proteins in fixed and live cells. Methods Mol Biol 2007; 372:17-32. [PMID: 18314715 DOI: 10.1007/978-1-59745-365-3_2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Mitochondria are almost ubiquitous organelles in Eukaryota. They are highly dynamic and often complex structures in the cell. The mammalian mitochondrial proteome is predicted to comprise as many as 2000-2500 different proteins. Determination of the subcellular localization of any newly identified protein is one of the first steps toward unraveling its biological function. For most mitochondrial proteins, this can now be done relatively easily by cloning a complementary deoxyribonucleic acid of interest in frame with an additional sequence for a fluorescent or nonfluorescent protein tag. Transfection and subsequent visualization, either by direct fluorescence microscopy or by indirect immunofluorescence microscopy, will give the first clue to mitochondrial localization. In combination with a fluorescent "marker" dye, the mitochondrial localization can be confirmed. This chapter describes some of the methods used in determining mitochondrial protein localization, which can also be used to study dynamics of mitochondria or individual mitochondrial proteins or protein complexes.
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Affiliation(s)
- Steffi Goffart
- FinMIT Centre of Excellence, Institute of Medical Technology and Tampere University Hospital, University of Tampere, Finland
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118
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Saffran HA, Pare JM, Corcoran JA, Weller SK, Smiley JR. Herpes simplex virus eliminates host mitochondrial DNA. EMBO Rep 2006; 8:188-93. [PMID: 17186027 PMCID: PMC1796774 DOI: 10.1038/sj.embor.7400878] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 11/08/2006] [Accepted: 11/13/2006] [Indexed: 11/08/2022] Open
Abstract
Mitochondria have crucial roles in the life and death of mammalian cells, and help to orchestrate host antiviral defences. Here, we show that the ubiquitous human pathogen herpes simplex virus (HSV) induces rapid and complete degradation of host mitochondrial DNA during productive infection of cultured mammalian cells. The depletion of mitochondrial DNA requires the viral UL12 gene, which encodes a conserved nuclease with orthologues in all herpesviruses. We show that an amino-terminally truncated UL12 isoform-UL12.5-localizes to mitochondria and triggers mitochondrial DNA depletion in the absence of other HSV gene products. By contrast, full-length UL12, a nuclear protein, has little or no effect on mitochondrial DNA levels. Our data document that HSV inflicts massive genetic damage to a crucial host organelle and show a novel mechanism of virus-induced shutoff of host functions, which is likely to contribute to the cell death and tissue damage caused by this widespread human pathogen.
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Affiliation(s)
| | - Justin M Pare
- Department of Medical Microbiology and Immunology
- Department of Cell Biology, University of Alberta, 632 Heritage Medical Research Center, Edmonton, Alberta T6G 2S2, Canada
| | | | - Sandra K Weller
- Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
| | - James R Smiley
- Department of Medical Microbiology and Immunology
- Tel: +1 780 492 4070; Fax: +1 780 492 9828; E-mail:
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119
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Khan SM, Smigrodzki RM, Swerdlow RH. Cell and animal models of mtDNA biology: progress and prospects. Am J Physiol Cell Physiol 2006; 292:C658-69. [PMID: 16899549 DOI: 10.1152/ajpcell.00224.2006] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The past two decades have witnessed an evolving understanding of the mitochondrial genome's (mtDNA) role in basic biology and disease. From the recognition that mutations in mtDNA can be responsible for human disease to recent efforts showing that mtDNA mutations accumulate over time and may be responsible for some phenotypes of aging, the field of mitochondrial genetics has greatly benefited from the creation of cell and animal models of mtDNA mutation. In this review, we critically discuss the past two decades of efforts and insights gained from cell and animal models of mtDNA mutation. We attempt to reconcile the varied and at times contradictory findings by highlighting the various methodologies employed and using human mtDNA disease as a guide to better understanding of cell and animal mtDNA models. We end with a discussion of scientific and therapeutic challenges and prospects for the future of mtDNA transfection and gene therapy.
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Affiliation(s)
- Shaharyar M Khan
- Gencia Corp., 706 B Forrest St., Charlottesville, VA 22903, USA.
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120
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Malka F, Lombès A, Rojo M. Organization, dynamics and transmission of mitochondrial DNA: focus on vertebrate nucleoids. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:463-72. [PMID: 16730385 DOI: 10.1016/j.bbamcr.2006.04.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Revised: 04/04/2006] [Accepted: 04/04/2006] [Indexed: 11/21/2022]
Abstract
Eukaryotic cells contain numerous copies of the mitochondrial genome (from 50 to 100 copies in the budding yeast to some thousands in humans) that localize to numerous intramitochondrial nucleoprotein complexes called nucleoids. The transmission of mitochondrial DNA differs significantly from that of nuclear genomes and depends on the number, molecular composition and dynamic properties of nucleoids and on the organization and dynamics of the mitochondrial compartment. While the localization, dynamics and protein composition of mitochondrial DNA nucleoids begin to be described, we are far from knowing all mechanisms and molecules mediating and/or regulating these processes. Here, we review our current knowledge on vertebrate nucleoids and discuss similarities and differences to nucleoids of other eukaryots.
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Affiliation(s)
- Florence Malka
- INSERM U582, Institut de Myologie, Groupe Hospitalier Pitié-Salpêtrière, Université Pierre et Marie Curie, IFR14, 47, boulevard de l'Hôpital, 75651 Paris cedex 13, France
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121
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Celotto AM, Frank AC, McGrath SW, Fergestad T, Van Voorhies WA, Buttle KF, Mannella CA, Palladino MJ. Mitochondrial encephalomyopathy in Drosophila. J Neurosci 2006; 26:810-20. [PMID: 16421301 PMCID: PMC6675365 DOI: 10.1523/jneurosci.4162-05.2006] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Mitochondrial encephalomyopathies are common and devastating multisystem genetic disorders characterized by neuromuscular dysfunction and tissue degeneration. Point mutations in the human mitochondrial ATP6 gene are known to cause several related mitochondrial disorders: NARP (neuropathy, ataxia, and retinitis pigmentosa), MILS (maternally inherited Leigh's syndrome), and FBSN (familial bilateral striatal necrosis). We identified a pathogenic mutation in the Drosophila mitochondrial ATP6 gene that causes progressive, adult-onset neuromuscular dysfunction and myodegeneration. Our results demonstrate ultrastructural defects in the mitochondrial innermembrane, neural dysfunction, and a marked reduction in mitochondrial ATP synthase activity associated with this mutation. This Drosophila mutant recapitulates key features of the human neuromuscular disorders enabling detailed in vivo studies of these enigmatic diseases.
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Affiliation(s)
- Alicia M Celotto
- Department of Pharmacology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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122
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Abstract
Mitochondrial DNA (mtDNA) encodes essential components of the cellular energy-producing apparatus, and lesions in mtDNA and mitochondrial dysfunction contribute to numerous human diseases. Understanding mtDNA organization and inheritance is therefore an important goal. Recent studies have revealed that mitochondria use diverse metabolic enzymes to organize and protect mtDNA, drive the segregation of the organellar genome, and couple the inheritance of mtDNA with cellular metabolism. In addition, components of a membrane-associated mtDNA segregation apparatus that might link mtDNA transmission to mitochondrial movements are beginning to be identified. These findings provide new insights into the mechanisms of mtDNA maintenance and inheritance.
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Affiliation(s)
- Xin Jie Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, Texas 75390-9148, USA
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123
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Binder DR, Dunn WH, Swerdlow RH. Molecular characterization of mtDNA depleted and repleted NT2 cell lines. Mitochondrion 2005; 5:255-65. [PMID: 16050988 DOI: 10.1016/j.mito.2005.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2005] [Revised: 04/25/2005] [Accepted: 04/26/2005] [Indexed: 10/25/2022]
Abstract
Transmitochondrial cytoplasmic hybrids (cybrids) enable functional assessment of mitochondrial DNA (mtDNA)-encoded proteins. Cybrid production often utilizes cell lines depleted of endogenous mtDNA (rho0 cells), and a number of suitable rho0 cell lines exist for this purpose. We now provide molecular data characterizing an NT2 human teratocarcinoma rho0 cell line, as well as NT2 cybrid derivatives. NT2 rho0 cells contained no detectable mtDNA on a sensitive PCR assay. Eight weeks after exogenous mtDNA transfer cybrids showed no evidence of endogenous mtDNA reversion, and heteroplasmic ratios of a single nucleotide substitution roughly reflected that of the blood samples used to repopulate their mtDNA.
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Affiliation(s)
- Daniel R Binder
- Department of Neurology, University of Virginia Health System, 1 Hospital Drive, Charlottesville, VA 22908, USA
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124
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Swerdlow RH, Redpath GT, Binder DR, Davis JN, VandenBerg SR. Mitochondrial DNA depletion analysis by pseudogene ratioing. J Neurosci Methods 2005; 150:265-71. [PMID: 16118020 DOI: 10.1016/j.jneumeth.2005.06.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2005] [Revised: 06/21/2005] [Accepted: 06/28/2005] [Indexed: 11/20/2022]
Abstract
The mitochondrial DNA (mtDNA) depletion status of rho(0) cell lines is typically assessed by hybridization or polymerase chain reaction (PCR) experiments, in which the failure to hybridize mtDNA or amplify mtDNA using mtDNA-directed primers suggests thorough mitochondrial genome removal. Here, we report the use of an mtDNA pseudogene ratioing technique for the additional confirmation of rho0 status. Total genomic DNA from a U251 human glioma cell line treated with ethidium bromide was amplified using primers designed to anneal either mtDNA or a previously described nuclear DNA-embedded mtDNA pseudogene (mtDNApsi). The resultant PCR product was used to generate plasmid clones. Sixty-two plasmid clones were genotyped, and all arose from mtDNApsi template. These data allowed us to determine with 95% confidence that the resultant mtDNA-depleted cell line contains less than one copy of mtDNA per 10 cells. Unlike previous hybridization or PCR-based analyses of mtDNA depletion, this mtDNApsi ratioing technique does not rely on interpretation of a negative result, and may prove useful as an adjunct for the determination of rho0 status or mtDNA copy number.
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Affiliation(s)
- Russell H Swerdlow
- Department of Neurology, University of Virginia Health System, Box 394, Charlottesville, VA 22908, USA.
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