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Recent Advances in Detecting Mitochondrial DNA Heteroplasmic Variations. Molecules 2018; 23:molecules23020323. [PMID: 29401641 PMCID: PMC6017848 DOI: 10.3390/molecules23020323] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 01/27/2018] [Accepted: 01/31/2018] [Indexed: 12/31/2022] Open
Abstract
The co-existence of wild-type and mutated mitochondrial DNA (mtDNA) molecules termed heteroplasmy becomes a research hot point of mitochondria. In this review, we listed several methods of mtDNA heteroplasmy research, including the enrichment of mtDNA and the way of calling heteroplasmic variations. At the present, while calling the novel ultra-low level heteroplasmy, high-throughput sequencing method is dominant while the detection limit of recorded mutations is accurate to 0.01% using the other quantitative approaches. In the future, the studies of mtDNA heteroplasmy may pay more attention to the single-cell level and focus on the linkage of mutations.
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McKenzie M, Chiotis M, Hroudová J, Lopez Sanchez MIG, Lim SC, Cook MJ, McKelvie P, Cotton RGH, Murphy M, St John JC, Trounce IA. Capture of somatic mtDNA point mutations with severe effects on oxidative phosphorylation in synaptosome cybrid clones from human brain. Hum Mutat 2015; 35:1476-84. [PMID: 25219341 DOI: 10.1002/humu.22694] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 09/03/2014] [Indexed: 01/13/2023]
Abstract
Mitochondrial DNA (mtDNA) is replicated throughout life in postmitotic cells, resulting in higher levels of somatic mutation than in nuclear genes. However, controversy remains as to the importance of low-level mtDNA somatic mutants in cancerous and normal human tissues. To capture somatic mtDNA mutations for functional analysis, we generated synaptosome cybrids from synaptic endings isolated from fresh hippocampus and cortex brain biopsies. We analyzed the whole mtDNA genome from 120 cybrid clones derived from four individual donors by chemical cleavage of mismatch and Sanger sequencing, scanning around two million base pairs. Seventeen different somatic point mutations were identified, including eight coding region mutations, four of which result in frameshifts. Examination of one cybrid clone with a novel m.2949_2953delCTATT mutation in MT-RNR2 (which encodes mitochondrial 16S rRNA) revealed a severe disruption of mtDNA-encoded protein translation. We also performed functional studies on a homoplasmic nonsense mutation in MT-ND1, previously reported in oncocytomas, and show that both ATP generation and the stability of oxidative phosphorylation complex I are disrupted. As the mtDNA remains locked against direct genetic manipulation, we demonstrate that the synaptosome cybrid approach can capture biologically relevant mtDNA mutants in vitro to study effects on mitochondrial respiratory chain function.
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Affiliation(s)
- Matthew McKenzie
- Centre for Genetic Diseases, MIMR-PHI Institute of Medical Research, Monash University, Clayton, Victoria, 3168, Australia; Monash University, Clayton, Victoria, 3168, Australia
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Naue J, Hörer S, Sänger T, Strobl C, Hatzer-Grubwieser P, Parson W, Lutz-Bonengel S. Evidence for frequent and tissue-specific sequence heteroplasmy in human mitochondrial DNA. Mitochondrion 2014; 20:82-94. [PMID: 25526677 DOI: 10.1016/j.mito.2014.12.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 12/02/2014] [Accepted: 12/09/2014] [Indexed: 10/24/2022]
Abstract
Mitochondrial point heteroplasmy is a common event observed not only in patients with mitochondrial diseases but also in healthy individuals. We here report a comprehensive investigation of heteroplasmy occurrence in human including the whole mitochondrial control region from nine different tissue types of 100 individuals. Sanger sequencing was used as a standard method and results were supported by cloning, minisequencing, and massively parallel sequencing. Only 12% of all individuals showed no heteroplasmy, whereas 88% showed at least one heteroplasmic position within the investigated tissues. In 66% of individuals up to 8 positions were affected. The highest relative number of heteroplasmies was detected in muscle and liver (79%, 69%), followed by brain, hair, and heart (36.7%-30.2%). Lower percentages were observed in bone, blood, lung, and buccal cells (19.8%-16.2%). Accumulation of position-specific heteroplasmies was found in muscle (positions 64, 72, 73, 189, and 408), liver (position 72) and brain (partial deletion at position 71). Deeper analysis of these specific positions in muscle revealed a non-random appearance and position-specific dependency on age. MtDNA heteroplasmy frequency and its potential functional importance have been underestimated in the past and its occurrence is ubiquitous and dependent at least on age, tissue, and position-specific mutation rates.
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Affiliation(s)
- Jana Naue
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstrasse 9, D-79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg, Germany.
| | - Steffen Hörer
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstrasse 9, D-79104 Freiburg, Germany.
| | - Timo Sänger
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstrasse 9, D-79104 Freiburg, Germany.
| | - Christina Strobl
- Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, A-6020 Innsbruck, Austria.
| | - Petra Hatzer-Grubwieser
- Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, A-6020 Innsbruck, Austria.
| | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, A-6020 Innsbruck, Austria; Penn State Eberly College of Science, University Park, PA, USA.
| | - Sabine Lutz-Bonengel
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstrasse 9, D-79104 Freiburg, Germany.
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Li M, Schönberg A, Schaefer M, Schroeder R, Nasidze I, Stoneking M. Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes. Am J Hum Genet 2010; 87:237-49. [PMID: 20696290 PMCID: PMC2917713 DOI: 10.1016/j.ajhg.2010.07.014] [Citation(s) in RCA: 226] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 07/21/2010] [Accepted: 07/22/2010] [Indexed: 11/29/2022] Open
Abstract
Heteroplasmy, the existence of multiple mtDNA types within an individual, has been previously detected by using mostly indirect methods and focusing largely on just the hypervariable segments of the control region. Next-generation sequencing technologies should enable studies of heteroplasmy across the entire mtDNA genome at much higher resolution, because many independent reads are generated for each position. However, the higher error rate associated with these technologies must be taken into consideration to avoid false detection of heteroplasmy. We used simulations and phiX174 sequence data to design criteria for accurate detection of heteroplasmy with the Illumina Genome Analyzer platform, and we used artificial mixtures and replicate data to test and refine the criteria. We then applied these criteria to mtDNA sequence reads for 131 individuals from five Eurasian populations that had been generated via a parallel tagged approach. We identified 37 heteroplasmies at 10% frequency or higher at 34 sites in 32 individuals. The mutational spectrum does not differ between heteroplasmic mutations and polymorphisms in the same individuals, but the relative mutation rate at heteroplasmic mutations is significantly higher than that estimated for all mutable sites in the human mtDNA genome. Moreover, there is also a significant excess of nonsynonymous mutations observed among heteroplasmies, compared to polymorphism data from the same individuals. Both mutation-drift and negative selection influence the fate of heteroplasmies to determine the polymorphism spectrum in humans. With appropriate criteria for avoiding false positives due to sequencing errors, next-generation technologies can provide novel insights into genome-wide aspects of mtDNA heteroplasmy.
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Affiliation(s)
- Mingkun Li
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany
| | - Anna Schönberg
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany
| | - Michael Schaefer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany
| | - Roland Schroeder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany
| | - Ivane Nasidze
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany
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5
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Lutz-Bonengel S, Sänger T, Parson W, Müller H, Ellwart JW, Follo M, Bonengel B, Niederstätter H, Heinrich M, Schmidt U. Single lymphocytes from two healthy individuals with mitochondrial point heteroplasmy are mainly homoplasmic. Int J Legal Med 2007; 122:189-97. [PMID: 17922134 DOI: 10.1007/s00414-007-0190-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Accepted: 07/26/2007] [Indexed: 11/26/2022]
Abstract
The nature of mitochondrial DNA heteroplasmy is still unclear. It could either be caused by two mitochondrial DNA (mtDNA) haplotypes coexisting within a single cell or by an admixture of homoplasmic cells, each of which contains only one type of mtDNA molecule. To address this question, single lymphocytes were separated by flow cytometry assisted cell sorting and analyzed by cycle sequencing or minisequencing. To attain the required PCR sensitivity, the reactions were carried out on the surface of chemically structured glass slides in a reaction volume of 1-2 microl. In this study, blood samples from two healthy donors showing mitochondrial point heteroplasmy in direct sequencing (195Y and 234R, respectively) were analyzed. Nearly 96% of single lymphocytes tested were found to be in a homoplasmic state, but heteroplasmic cells were also detected. These results suggest that mitochondrial point heteroplasmy in blood may well be mainly due to the mixture of homoplasmic cells.
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Affiliation(s)
- Sabine Lutz-Bonengel
- Institute of Legal Medicine, Albert Ludwig University Freiburg, Albertstrasse 9, 79104 Freiburg, Germany.
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Lo MC, Lee HM, Lin MW, Tzen CY. Analysis of Heteroplasmy in Hypervariable Region II of Mitochondrial DNA in Maternally Related Individuals. Ann N Y Acad Sci 2006; 1042:130-5. [PMID: 15965054 DOI: 10.1196/annals.1338.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Mitochondrial DNA sequences have been widely employed for identity investigation. However, the presence of a heteroplasmic site may complicate sequence analysis for forensic purposes when two samples are compared. To study this potential problem, we analyzed the hypervariable region of the displacement loop in five maternally related individuals, that is, grandmother, mother, one son, and two daughters. The results showed that three of them had a heteroplasmic site at nucleotide position (np) 204, located in the hypervariable region II. By using Bayesian inference to assess the significance of the mother-offspring pairs, a likelihood ratio of 1.78 x 10(5) was obtained. Therefore, Bayesian inference does not place the prior odds into the context of the two different likelihood ratios derived from the DNA evidence. On the other hand, the chromatogram of the denaturing high-performance liquid chromatography system proved that the single peak in a sequencing chromatogram at np 204 was, in fact, heteroplasmic in nature. This study demonstrated that heteroplasmy is a common occurrence in tissue from normal individuals and should be taken into account in forensic investigation when samples appear to differ at a single nucleotide position by direct sequencing.
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Affiliation(s)
- Mei-Chen Lo
- Graduate Institute of Cell & Molecular Biology, Taipei Medical University, Taiwan, ROC
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Hancock DK, Tully LA, Levin BC. A Standard Reference Material to determine the sensitivity of techniques for detecting low-frequency mutations, SNPs, and heteroplasmies in mitochondrial DNA. Genomics 2006; 86:446-61. [PMID: 16024219 DOI: 10.1016/j.ygeno.2005.06.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2005] [Revised: 05/10/2005] [Accepted: 06/11/2005] [Indexed: 10/25/2022]
Abstract
Human mitochondrial DNA (mtDNA) mutations are important for forensic identifications and mitochondrial disease diagnostics. Low-frequency mutations, heteroplasmies, or SNPs scattered throughout the DNA in the presence of a majority of mtDNA with the Cambridge Reference Sequence (CRS) are almost impossible to detect. Therefore, the National Institute of Science and Technology has developed heteroplasmic human mtDNA Standard Reference Material (SRM) 2394 to allow scientists to determine their sensitivity in detecting such differences. SRM 2394 is composed of mixtures ranging from 1/99 to 50/50 of two 285-bp PCR products from two cell lines that differ at one nucleotide position. Twelve laboratories using various mutation detection methods participated in a blind interlaboratory evaluation of a prototype of SRM 2394. Most of these procedures were unable to detect the mutation when present below 20%, an indication that, in many real-life cases, low-frequency mutations remain undetected and that more sensitive mutation detection techniques are urgently needed.
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Affiliation(s)
- Diane K Hancock
- Biotechnology Division, National Institute of Science and Technology, 100 Bureau Drive, MS 8311, Gaithersburg, MD 20899-8311, USA
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Sekiguchi K, Kasai K, Levin BC. Inter- and intragenerational transmission of a human mitochondrial DNA heteroplasmy among 13 maternally-related individuals and differences between and within tissues in two family members. Mitochondrion 2005; 2:401-14. [PMID: 16120336 DOI: 10.1016/s1567-7249(03)00028-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2002] [Revised: 02/05/2003] [Accepted: 02/11/2003] [Indexed: 11/27/2022]
Abstract
The transmission of a C16,291C/T heteroplasmy in the HV1 region of human mitochondrial DNA (mtDNA) was examined in buccal cells from 13 maternally-related individuals across three generations and in additional tissues (hair, blood, or finger nails) from three members of this family. The ratio of C:T at nucleotide position (np) 16,291 showed wide intra- and intergenerational variation as well as tissue variation within individuals. Our results demonstrate that one or two sequence differences between samples in the mtDNA does not warrant an exclusion. To avoid false exclusions especially when comparing mtDNA from hair samples, we recommend the analysis of as many samples as possible in order to minimize the possibility that the detection of a rare polymorphism in a single sample would be considered an exclusion when it is really a match. The observation that the transmission of a mtDNA heteroplasmy from one individual to her offspring is likely to differ among the first-generation offspring and between that generation and subsequent generations lends further credence to the bottleneck theory of inheritance of human mtDNA.
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Affiliation(s)
- Kazumasa Sekiguchi
- Biotechnology Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8311, Gaithersburg, MD 20899-8311, USA
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9
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Bannwarth S, Procaccio V, Paquis-Flucklinger V. Surveyor™ Nuclease: A new strategy for a rapid identification of heteroplasmic mitochondrial DNA mutations in patients with respiratory chain defects. Hum Mutat 2005; 25:575-82. [PMID: 15880407 DOI: 10.1002/humu.20177] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular analysis of mitochondrial DNA (mtDNA) is a critical step in diagnosis and genetic counseling of respiratory chain defects. No fast method is currently available for the identification of unknown mtDNA point mutations. We have developed a new strategy based on complete mtDNA PCR amplification followed by digestion with a mismatch-specific DNA endonuclease, Surveyor Nuclease. This enzyme, a member of the CEL nuclease family of plant DNA endonucleases, cleaves double-strand DNA at any mismatch site including base substitutions and small insertions/deletions. After digestion, cleavage products are separated and analyzed by agarose gel electrophoresis. The size of the digestion products indicates the location of the mutation, which is then confirmed and characterized by sequencing. Although this method allows the analysis of 2 kb mtDNA amplicons and the detection of multiple mutations within the same fragment, it does not lead to the identification of homoplasmic base substitutions. Homoplasmic pathogenic mutations have been described. Nevertheless, most homoplasmic base substitutions are neutral polymorphisms while deleterious mutations are typically heteroplasmic. Here, we report that this method can be used to detect mtDNA mutations such as m.3243A>G tRNA(Leu) and m.14709T>C tRNA(Glu) even when they are present at levels as low as 3% in DNA samples derived from patients with respiratory chain defects. Then, we tested five patients suffering from a mitochondrial respiratory chain defect and we identified a variant (m.16189T>C) in two of them, which was previously associated with susceptibility to diabetes and cardiomyopathy. In conclusion, this method can be effectively used to rapidly and completely screen the entire human mitochondrial genome for heteroplasmic mutations and in this context represents an important advance for the diagnosis of mitochondrial diseases.
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Affiliation(s)
- Sylvie Bannwarth
- Department of Medical Genetics, Hopital Archet 2, CHU Nice, France
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10
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Moraes CT, Atencio DP, Oca-Cossio J, Diaz F. Techniques and pitfalls in the detection of pathogenic mitochondrial DNA mutations. J Mol Diagn 2004; 5:197-208. [PMID: 14573777 PMCID: PMC1907336 DOI: 10.1016/s1525-1578(10)60474-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mutations in the mitochondrial DNA (mtDNA) are now recognized as major contributors to human pathologies and possibly to normal aging. A large number of rearrangements and point mutations in protein coding and tRNA genes have been identified in patients with mitochondrial disorders. In this review, we discuss genotype-phenotype correlations in mitochondrial diseases and common techniques used to identify pathogenic mtDNA mutations in human tissues. Although most of these approaches employ standard molecular biology tools, the co-existence of wild-type and mutated mtDNA (mtDNA heteroplasmy) in diseased tissues complicates both the detection and accurate determination of the size of the mutated fractions. To address these problems, novel approaches were developed and are discussed in this review.
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Affiliation(s)
- Carlos T Moraes
- Department of Neurology, University of Miami School of Medicine, Miami, Florida 33136, USA.
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11
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Budowle B, Allard MW, Wilson MR, Chakraborty R. FORENSICS ANDMITOCHONDRIALDNA: Applications, Debates, and Foundations. Annu Rev Genomics Hum Genet 2003; 4:119-41. [PMID: 14527299 DOI: 10.1146/annurev.genom.4.070802.110352] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Debate on the validity and reliability of scientific methods often arises in the courtroom. When the government (i.e., the prosecution) is the proponent of evidence, the defense is obliged to challenge its admissibility. Regardless, those who seek to use DNA typing methodologies to analyze forensic biological evidence have a responsibility to understand the technology and its applications so a proper foundation(s) for its use can be laid. Mitochondrial DNA (mtDNA), an extranuclear genome, has certain features that make it desirable for forensics, namely, high copy number, lack of recombination, and matrilineal inheritance. mtDNA typing has become routine in forensic biology and is used to analyze old bones, teeth, hair shafts, and other biological samples where nuclear DNA content is low. To evaluate results obtained by sequencing the two hypervariable regions of the control region of the human mtDNA genome, one must consider the genetically related issues of nomenclature, reference population databases, heteroplasmy, paternal leakage, recombination, and, of course, interpretation of results. We describe the approaches, the impact some issues may have on interpretation of mtDNA analyses, and some issues raised in the courtroom.
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Affiliation(s)
- Bruce Budowle
- Laboratory Division, FBI, Washington, DC 20535, USA.
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12
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Khaidakov M, Heflich RH, Manjanatha MG, Myers MB, Aidoo A. Accumulation of point mutations in mitochondrial DNA of aging mice. Mutat Res 2003; 526:1-7. [PMID: 12714177 DOI: 10.1016/s0027-5107(03)00010-1] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Mitochondrial DNA (mtDNA) exists in a highly genotoxic environment created by exposure to reactive oxygen species, somewhat deficient DNA repair, and the relatively low fidelity of polymerase gamma. Given the severity of the environment, it was anticipated that mutation accumulation in the mtDNA of aging animals should exceed that of nuclear genes by several orders of magnitude. We have analyzed fragments amplified from the D-loop region of mtDNA from 2 to 22-month-old mice. The amplified 432 bp fragments were cloned into plasmid vectors, and plasmid DNAs from individual clones were purified and sequenced. None of 110 fragments from young mice contained a mutation, while 9 of 87 clones originating from old animals contained base substitutions (chi square = 11.9, P<0.001). The estimated mutation frequency in mtDNA from old mice was 11.6+/-2.7 or 25.4+/-7.8 per 10(5) nucleotides (depending on assumptions of clonality), which exceeds existing estimates for mutation frequencies for nuclear genes by approximately 1000-fold. Our data suggest that at 22 months of age, which roughly corresponds to 3/4 of the mouse natural life span, most mtDNA molecules carry multiple point mutations.
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Affiliation(s)
- Magomed Khaidakov
- Division of Genetic and Reproductive Toxicology, US FDA National Center for Toxicological Research, 3900 NCTR Road, Jefferson, AR 72079, USA
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13
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Kraytsberg Y, Nekhaeva E, Bodyak NB, Khrapko K. Mutation and intracellular clonal expansion of mitochondrial genomes: two synergistic components of the aging process? Mech Ageing Dev 2003; 124:49-53. [PMID: 12618006 DOI: 10.1016/s0047-6374(02)00169-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The foundations of the Mitochondrial mutational theory of aging include two assumptions: the high abundance of mitochondrial mutations and their ability to clonally expand within individual cells. The up-to-date data pertinent to these assumptions is reviewed and semi-quantitative estimates of the frequencies of mutants and intracellular expansions are offered. The incidence of mutations in various aged tissues may be on the order of one mutant per mitochondrial genome copy, and most of the cells are likely to be affected by intracellular clonal expansions of mitochondrial genomes. Thus aged tissue may be considered a mosaic of cells with different mutant mitochondrial genotypes. Interestingly, independent studies show that a wide range of aged tissues presents with a mosaic of cells with different mitochondrial phenotypes. The necessary methodologies are available to explore whether the two mosaics are causally related. The answer apparently is positive in muscle; other tissues, brain in particular, await exploration.
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Affiliation(s)
- Yevgenya Kraytsberg
- Beth Israel Deaconess Medical Center and Harvard Medical School, Rm. 921, 77 Ave. L. Pasteur, Boston, MA 02215, USA
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Ono T, Isobe K, Nakada K, Hayashi JI. Human cells are protected from mitochondrial dysfunction by complementation of DNA products in fused mitochondria. Nat Genet 2001; 28:272-5. [PMID: 11431699 DOI: 10.1038/90116] [Citation(s) in RCA: 319] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Extensive complementation between fused mitochondria is indicated by recombination of 'parental' mitochondrial (mt) DNA (ref. 1,2) of yeast and plant cells. It has been difficult, however, to demonstrate the occurrence of complementation between fused mitochondria in mammalian species through the presence of recombinant mtDNA molecules, because sequence of mtDNA throughout an individual tends to be uniform owing to its strictly maternal inheritance. We isolated two types of respiration-deficient cell lines, with pathogenic mutations in mitochondrial tRNAIle or tRNALeu(UUR) genes from patients with mitochondrial diseases. The coexistence of their mitochondria within hybrids restored their normal morphology and respiratory enzyme activity by 10-14 days after fusion, indicating the presence of an extensive and continuous exchange of genetic contents between the mitochondria. This complementation between fused mitochondria may represent a defence of highly oxidative organelles against mitochondrial dysfunction caused by the accumulation of mtDNA lesions with age.
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Affiliation(s)
- T Ono
- Institute of Biological Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
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15
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Affiliation(s)
- L A Tully
- Biotechnology Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8311, Gaithersburg, MD 20899-8311, USA
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16
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Abstract
The mitochondrial DNA encodes only a few gene products compared to the nuclear DNA. These products, however, play a decisive role in determining cell function. Should this DNA mutate spontaneously or be damaged by free radicals the functionality of the gene products will be compromised. A number of mitochondrial genetic diseases have been identified. Some of these are quite serious and involve the central nervous system as well as muscle, heart, liver and kidney. Aging has been characterized by a gradual increase in base deletions in this DNA. This increase in deletion mutation has been suggested to be the cumulative result of exposure to free radicals.
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Affiliation(s)
- C D Berdanier
- Department of Foods and Nutrition, University of Georgia, 30602, Athens, GA, USA.
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17
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Abstract
Diabetes mellitus is the most common genetic disease in the Western world today. It is the phenotype for >150 genotypes. Each of these genotypes is characterized by impaired glucose tolerance and impaired control of intermediary metabolism. There are many strains of mice and rats that can be used to study diabetes in its various forms. One of these is the BHE/Cdb rat, which mimics the human phenotype with a mutation in the mitochondrial (mt) DNA. The result of such mutation is a loss in metabolic control with respect to the role of the mitochondria in this control. This review addresses those aspects of control that are exerted by mt oxidative phosphorylation (OXPHOS). Diet can have both genomic and nongenomic effects on OXPHOS. The type of dietary fat influences the fluidity of the mt membranes and hence, mt function. The dietary fat effect depends on the genetic background of the consumer. Diabetes-prone BHE/Cdb rats with base substitutions in the mt ATPase 6 gene are more likely to be influenced by the diet effect on mt membrane fluidity than are normal rats. Vitamin A also affects mt function through an effect on mt gene expression. BHE/Cdb rats have a greater need for vitamin A than normal rats and supplemental vitamin A appears to influence OXPHOS.
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Affiliation(s)
- C D Berdanier
- Department of Foods and Nutrition, University of Georgia, Athens, GA 30602, USA
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Shitara H, Kaneda H, Sato A, Inoue K, Ogura A, Yonekawa H, Hayashi JI. Selective and continuous elimination of mitochondria microinjected into mouse eggs from spermatids, but not from liver cells, occurs throughout embryogenesis. Genetics 2000; 156:1277-84. [PMID: 11063701 PMCID: PMC1461340 DOI: 10.1093/genetics/156.3.1277] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Exclusion of paternal mitochondria in fertilized mammalian eggs is very stringent and ensures strictly maternal mtDNA inheritance. In this study, to examine whether elimination was specific to sperm mitochondria, we microinjected spermatid or liver mitochondria into mouse embryos. Congenic B6-mt(spr) strain mice, which are different from C57BL/6J (B6) strain mice (Mus musculus domesticus) only in possessing M. spretus mtDNA, were used as mitochondrial donors. B6-mt(spr) mice and a quantitative PCR method enabled selective estimation of the amount of M. spretus mtDNA introduced even in the presence of host M. m. domesticus mtDNA and monitoring subsequent changes of its amount during embryogenesis. Results showed that M. spretus mtDNA in spermatid mitochondria was not eliminated by the blastocyst stage, probably due to the introduction of a larger amount of spermatid mtDNA than of sperm mtDNA into embryos on fertilization. However, spermatid-derived M. spretus mtDNA was eliminated by the time of birth, whereas liver-derived M. spretus mtDNA was still present in most newborn mice, even though its amount introduced was significantly less than that of spermatid mtDNA. These observations suggest that mitochondria from spermatids but not from liver have specific factors that ensure their selective elimination and resultant elimination of mtDNA in them, and that the occurrence of elimination is not limited to early stage embryos, but continues throughout embryogenesis.
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Affiliation(s)
- H Shitara
- Department of Laboratory Animal Science, Tokyo Metropolitan Institute of Medical Science, Tokyo 113-8613, Japan.
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Tully LA, Parsons TJ, Steighner RJ, Holland MM, Marino MA, Prenger VL. A sensitive denaturing gradient-Gel electrophoresis assay reveals a high frequency of heteroplasmy in hypervariable region 1 of the human mtDNA control region. Am J Hum Genet 2000; 67:432-43. [PMID: 10873789 PMCID: PMC1287188 DOI: 10.1086/302996] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2000] [Accepted: 06/09/2000] [Indexed: 11/03/2022] Open
Abstract
A population study of heteroplasmy in the hypervariable region 1 (HV1) portion of the human mtDNA control region was performed. Blood samples from 253 randomly chosen individuals were examined using a sensitive denaturing gradient-gel electrophoresis (DGGE) system. This method is capable of detecting heteroplasmic proportions as low as 1% and virtually all heteroplasmy where the minor component is > or = 5%. Heteroplasmy was observed in 35 individuals (13.8%; 95% confidence interval [CI] 9.6-18.0). Of these individuals, 33 were heteroplasmic at one nucleotide position, whereas 2 were heteroplasmic at two different positions (a condition known as "triplasmy"). Although heteroplasmy occurred at a total of 16 different positions throughout HV1, it was most frequently observed at positions 16093 (n=13) and 16129 (n=6). In addition, the majority of heteroplasmic variants occurred at low proportions and could not be detected by direct sequencing of PCR products. This study indicates that low-level heteroplasmy in HV1 is relatively common and that it occurs at a broad spectrum of sites. Our results corroborate those of other recent reports indicating that heteroplasmy in the control region is more common than was previously believed-a finding that is of potential importance to evolutionary studies and forensic applications that are based on mtDNA variation.
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Affiliation(s)
- L A Tully
- University of Maryland, School of Medicine, Division of Human Genetics, Baltimore, MD, USA.
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20
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Calloway CD, Reynolds RL, Herrin GL, Anderson WW. The frequency of heteroplasmy in the HVII region of mtDNA differs across tissue types and increases with age. Am J Hum Genet 2000; 66:1384-97. [PMID: 10739761 PMCID: PMC1288202 DOI: 10.1086/302844] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/1999] [Accepted: 01/25/2000] [Indexed: 11/03/2022] Open
Abstract
An immobilized sequence-specific oligonucleotide (SSO) probe system consisting of 16 SSO probes that detect sequence polymorphisms within five regions of the mtDNA control region was used to investigate the frequency of heteroplasmy in human mtDNA. Five regions of hypervariable region II (HVII) of the control region were studied in blood-, muscle-, heart-, and brain-tissue samples collected from 43 individuals during autopsy. An initial search for heteroplasmy was conducted by use of the SSO probe system. Samples in which multiple probe signals were detected within a region were sequenced for the HVII region, to verify the typing-strip results. The frequency of heteroplasmy was 5 of 43 individuals, or 11.6%. The frequency of heteroplasmy differed across tissue types, being higher in muscle tissue. The difference in the frequency of heteroplasmy across different age groups was statistically significant, which suggests that heteroplasmy increases with age. As a test for contamination and to confirm heteroplasmy, the samples were sequenced for the HVI region and were typed by use of a panel of five polymorphic nuclear markers. Portions of the tissues that appeared to be heteroplasmic were extracted at least one additional time; all gave identical results. The results from these tests indicate that the multiple sequences present in individual samples result from heteroplasmy and not from contamination.
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Affiliation(s)
- C D Calloway
- Roche Molecular Systems, Alameda, CA, 94501, USA. Sandy.
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21
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Abstract
For many years it has been assumed that the vast majority of mitochondrial genomes of a single individual are identical, both in the same tissue and within different tissues. Incidences of heteroplasmy (i.e., the occurrence of two or more codominating types of molecules within the mitochondrial DNA population of the same individual) were thought to be extremely rare. This study strongly supports the thesis that heteroplasmy is a principle, rather than an exception, in mitochondrial DNA genetics. During direct sequencing of the first hypervariable segment of the human mitochondrial control region (HV1) in 100 single hair roots obtained from 35 individuals, 24 different heteroplasmic positions were identified. Unusually high levels of heteroplasmy (up to six positions in the HV1 region) were encountered in two individuals. Two individuals related in maternal lineage shared the same heteroplasmic positions. Moreover, highly variable levels of heteroplasmy were observed even among roots from the same individual. The most probable mechanisms involved in generating so many mismatches are mutations occurring presumably in the female germline, followed by differential segregation of mitotypes during the development of individual hairs. Generally, heteroplasmy complicates sequence comparisons in mitochondrial DNA testing performed for forensic purposes, but in some cases it can substantially increase the discriminating power of the analysis.
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Affiliation(s)
- T Grzybowski
- The Ludwik Rydygier University School of Medical Sciences, Forensic Medicine Institute, Bydgoszcz, Poland.
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22
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Chen JZ, Hebert PD. Terminal branch haplotype analysis: a novel approach to investigate newly arisen variants of mitochondrial DNA in natural populations. Mutat Res 1999; 434:219-31. [PMID: 10486593 DOI: 10.1016/s0921-8777(99)00030-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The discrimination of recent mutational derivatives from ancestral variation is a critical antecedent to any effort which aims to identify the factors modulating the rates of origin and persistence of new mutants. We propose that newly arisen mtDNA variants, which we designate as terminal branch haplotypes (TBHs), can be recognized by joint sequencing and phylogenetic analysis. This study examined mtDNA diversity in natural populations of the brown bullhead (Ameiurus nebulosus) from four heavily contaminated sites and three relatively pristine locations. While sequence analysis of the mtDNA D-loop region revealed that TBHs were prevalent in these populations, contaminant exposure appeared to play a minor role in their generation. Instead, most TBHs likely arose due to spontaneous mutations with variation in their incidence among sites reflecting the impact of demographic factors.
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Affiliation(s)
- J Z Chen
- Department of Zoology, University of Guelph, ON, Canada.
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23
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Chen JZ, Hebert PD. Intraindividual sequence diversity and a hierarchical approach to the study of mitochondrial DNA mutations. Mutat Res 1999; 434:205-17. [PMID: 10486592 DOI: 10.1016/s0921-8777(99)00029-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Investigations of intraindividual sequence diversity in mtDNA are a key step in exploring the linkage between somatic mutations in mtDNA and mitochondrial genome evolution. This paper reports a directional cloning procedure enabling the isolation of multiple copies of the D-loop region of the mitochondrial genome from the fish Ameiurus nebulosus. Sequence analysis of 708 D-loop molecules revealed eight mutants, an average intraindividual mutation frequency of 1.12%. Three different types of mutations were detected but each derived from a single mutational event. By contrasting the spectrum of nucleotide variation at multiple biological levels, one can investigate the effects of spontaneous mutations on genome evolution. Such hierarchical analysis suggested shifts in the type and distribution of mtDNA (mitochondrial DNA) mutations at different biological levels, indicating the need to recognize three different rates of mtDNA sequence change from the cellular to population level.
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Affiliation(s)
- J Z Chen
- Department of Zoology, University of Guelph, Ontario, Canada.
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24
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Takai D, Isobe K, Hayashi J. Transcomplementation between different types of respiration-deficient mitochondria with different pathogenic mutant mitochondrial DNAs. J Biol Chem 1999; 274:11199-202. [PMID: 10196206 DOI: 10.1074/jbc.274.16.11199] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two cell lines were used for determination of whether interaction occurred between different types of respiration-deficient mitochondria. One was a respiration-deficient rho- cell line having mutant mitochondrial DNA (mtDNA) with a 5,196-base pair deletion including five tRNA genes (tRNAGly, Arg, Ser(AGY), Leu(CUN), His), DeltamtDNA5196, causing Kearns-Sayre syndrome. The other was a respiration-deficient syn- cell line having mutant mtDNA with an A to G substitution at 4,269 in the tRNAIle gene, mtDNA4269, causing fatal cardiomyopathy. The occurrence of mitochondrial interaction was examined by determining whether cybrids constructed by fusion of enucleated rho- cells with syn- cells became respiration competent by exchanging their tRNAs. No cybrids were isolated in selection medium, where only respiration-competent cells could survive, suggesting that no interaction occurred, or that it occurred so slowly that sufficient recovery of mitochondrial respiratory function was not attained by the time of selection. The latter possibility was confirmed by the observations that heteroplasmic cybrids with both mutant mtDNA4269 and DeltamtDNA5196 isolated without selection showed restored mitochondrial respiration activity. This demonstration of transcomplementation between different respiration-deficient mitochondria will help in understanding the relationship between somatic mutant mtDNAs and the roles of such mutations in aging processes.
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Affiliation(s)
- D Takai
- Institute of Biological Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
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25
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Shitara H, Hayashi JI, Takahama S, Kaneda H, Yonekawa H. Maternal inheritance of mouse mtDNA in interspecific hybrids: segregation of the leaked paternal mtDNA followed by the prevention of subsequent paternal leakage. Genetics 1998; 148:851-7. [PMID: 9504930 PMCID: PMC1459812 DOI: 10.1093/genetics/148.2.851] [Citation(s) in RCA: 136] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The transmission profiles of sperm mtDNA introduced into fertilized eggs were examined in detail in F1 hybrids of mouse interspecific crosses by addressing three aspects. The first is whether the leaked paternal mtDNA in fertilized eggs produced by interspecific crosses was distributed stably to all tissues after the eggs' development to adults. The second is whether the leaked paternal mtDNA was transmitted to the subsequent generations. The third is whether paternal mtDNA continuously leaks in subsequent backcrosses. For identification of the leaked paternal mtDNA, we prepared total DNA samples directly from tissues or embryos and used PCR techniques that can detect a few molecules of paternal mtDNA even in the presence of 10(8)-fold excess of maternal mtDNA. The results showed that the leaked paternal mtDNA was not distributed to all tissues in the F1 hybrids or transmitted to the following generations through the female germ line. Moreover, the paternal mtDNA leakage was limited to the first generation of an interspecific cross and did not occur in progeny from subsequent backcrosses. These observations suggest that species-specific exclusion of sperm mtDNA in mammalian fertilized eggs is extremely stringent, ensuring strictly maternal inheritance of mtDNA.
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Affiliation(s)
- H Shitara
- Institute of Biological Sciences, University of Tsukuba, Ibaraki, Japan
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26
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Takai D, Inoue K, Goto YI, Nonaka I, Hayashi JI. The interorganellar interaction between distinct human mitochondria with deletion mutant mtDNA from a patient with mitochondrial disease and with HeLa mtDNA. J Biol Chem 1997; 272:6028-33. [PMID: 9038225 DOI: 10.1074/jbc.272.9.6028] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
For the examination of possible intermitochondrial interaction of human mitochondria from different cells, cybrids were constructed by introducing HeLa mitochondria into cells with respiration-deficient (rho-) mitochondria. Respiration deficiency was due to the predominance of mutant mtDNA with a 5,196-base pair deletion including five tRNA genes (DeltamtDNA5196). The HeLa mtDNA and DeltamtDNA5196 encoded chloramphenicol-resistant (CAPr) and chloramphenicol-sensitive (CAPs) 16 S rRNA, respectively. The first evidence for the interaction was that polypeptides exclusively encoded by DeltamtDNA5196 were translated on the introduction of HeLa mitochondria, suggesting supplementation of the missing tRNAs by rho- mitochondria from HeLa mitochondria. Second, the exchange of mitochondrial rRNAs was observed; even in the presence of CAP, CAPs DeltamtDNA5196-specific polypeptides as well as those encoded by CAPr HeLa mtDNA were translated in the cybrids. These phenomena can be explained assuming that the translation in rho- mitochondria was restored by tRNAs and CAPr 16 S rRNA supplied from HeLa mitochondria, unambiguously indicating interorganellar interaction. These observations introduce a new concept of the dynamics of the mitochondrial genetic system and help in understanding the relationship among mtDNA mutations and expression of human mitochondrial diseases and aging.
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Affiliation(s)
- D Takai
- Institute of Biological Sciences, University of Tsukuba, Ibaraki 305, Japan
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27
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Lutz S, Weisser HJ, Heizmann J, Pollak S. mtDNA as a tool for identification of human remains. Identification using mtDNA. Int J Legal Med 1996; 109:205-9. [PMID: 9007636 DOI: 10.1007/bf01225519] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Two cases are presented in order to emphasize the importance of mitochondrial DNA in forensic medicine. The first case involved a charred body which could not be identified by morphological means because of severe destruction of all tissues. The parallel use of PCR methods using genomic DNA and sequencing of the mitochondrial d-loop region produced unequivocal and reproducible results. In the second case, various parts of a highly decomposed body were investigated. The application of standard PCR methods for genomic DNA proved unsuitable to answer the question whether the body parts belonged to the same body. However, when sequencing of mitochondrial DNA segments amplified from tissue and bone samples was performed, clearly interpretable results were obtained.
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Affiliation(s)
- S Lutz
- Institut für Rechtsmedizin, Klinikum der Universität Freiburg, Germany
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28
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Kawai H, Akaike M, Yokoi K, Nishida Y, Kunishige M, Mine H, Saito S. Mitochondrial encephalomyopathy with autosomal dominant inheritance: a clinical and genetic entity of mitochondrial diseases. Muscle Nerve 1995; 18:753-60. [PMID: 7783765 DOI: 10.1002/mus.880180712] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We report a Japanese family with chronic progressive external ophthalmoplegia (CPEO) with autosomal dominant inheritance, and review 54 reported CPEO patients in seven families (including the present family) with autosomal dominant inheritance and mtDNA deletions in the skeletal muscle. Mean age at onset in the CPEO was 26 years, which is older than that in published solitary cases. In addition to blepharoptosis and external opthalmoplegia, proximal muscle atrophy and weakness were found in 62%, hearing loss in 25%, and ataxia in 17% of the patients. Retinal degeneration was not found, and cardiac involvement was very rare. mtDNA deletions in the muscle were multiple and large scale, and all such deletions were located in the non-D-loop region. Autosomal dominant CPEO has unique clinical features which differ from those of solitary CPEO, and is associated with multiple large-scale mtDNA deletions. Thus, autosomal dominant CPEO can be considered a clinical and genetic entity of mitochondrial diseases.
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Affiliation(s)
- H Kawai
- First Department of Internal Medicine, School of Medicine, University of Tokushima, Japan
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29
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Nuclear but not mitochondrial genome involvement in human age-related mitochondrial dysfunction. Functional integrity of mitochondrial DNA from aged subjects. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)37457-4] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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30
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Gadaleta MN, Rainaldi G, Lezza AM, Milella F, Fracasso F, Cantatore P. Mitochondrial DNA copy number and mitochondrial DNA deletion in adult and senescent rats. Mutat Res 1992; 275:181-93. [PMID: 1383760 DOI: 10.1016/0921-8734(92)90022-h] [Citation(s) in RCA: 170] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In order to understand the cause of the reduced mitochondrial DNA transcription in heart and brain of senescent rat previously reported, we focused our attention on the content and structure of rat mitochondrial DNA in adult and senescent rats. The estimate of the mtDNA copy number in liver, heart and brain of adult and senescent rats showed that in all organs examined the senescent individuals have a mtDNA content higher than the adult counterparts. The analysis of mtDNA structural changes involved the search for point mutations and large deletions. As for the first case, the determination of the nucleotide sequence of many independent clones containing two mtDNA restriction fragments isolated from rat cerebral hemispheres did not show any sequence difference between adult and senescent individuals. However, analysis of mtDNA deletions by the polymerase chain reaction in liver and brain of adult and senescent rats identified a small population of mtDNA molecules harboring a deletion of 4834 bp. The estimate of the proportion of deleted molecules in the liver showed that they represent 0.02% and 0.0005% of total mtDNA in senescent and adult rat liver respectively. Therefore, a mtDNA deletion also accumulates in the rat during aging. This result supports the hypothesis of the accumulation of deleted mtDNA molecules in aging. However, the low percentage of deleted mtDNA molecules already found and the reversibility of the reduced mitochondrial DNA transcription in senescent rat raise doubts on the primary role of the irreversibly damaged mtDNA molecules in aging. Deleted mtDNA molecules along with changes caused by lipid peroxidation of mitochondrial membranes might contribute to the overall decline of mitochondrial function.
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Affiliation(s)
- M N Gadaleta
- Dipartimento di Biochimica e Biologia Molecolare, Università di Bari, Italy
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31
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Sullivan KM, Hopgood R, Gill P. Identification of human remains by amplification and automated sequencing of mitochondrial DNA. Int J Legal Med 1992; 105:83-6. [PMID: 1520642 DOI: 10.1007/bf02340829] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The highly decomposed remains of a corpse were identified by the amplification and direct sequencing of mitochondrial (mt) DNA. Degraded DNA was extracted from bone fragments and a necrotic skin sample and amplified at 2 hypervariable segments within the mitochondrial non-coding region using 2 rounds of nested PCR. Both strands of the amplified regions were sequenced and compared with each other to ensure fidelity of the data. Sequences from the bone and skin were found to be identical and matched data generated from a blood sample provided by a presumptive sister of the deceased. Thus, this evidence was consistent with the sister and the deceased being related.
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Affiliation(s)
- K M Sullivan
- Central Research and Support Establishment, Forensic Science Service, Reading, Berkshire, UK
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32
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Bodenteich A, Mitchell LG, Merril CR. A lifetime of retinal light exposure does not appear to increase mitochondrial mutations. Gene 1991; 108:305-9. [PMID: 1660842 DOI: 10.1016/0378-1119(91)90451-g] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Recently, there have been a number of reports of an accumulation of mutations in the mitochondrial (mt) genome with age. Such mutations may be due in part to the mt oxidative metabolic pathways which provide most of the cell's energy, but also generate free radicals. In addition, the mt genome in some tissues, such as the retina, may also accumulate mutations from the effects of ultraviolet light. To obtain information concerning the possible accumulation of retinal mt mutations with age, we cloned retinal mt DNA from a 71-year-old person. Thirty-two kilobases of sequence from 83 independently isolated clones representing two regions, a coding and a noncoding region, of the mt genome were obtained. Three polymorphisms between these sequences and the standard 'Anderson sequence' were discovered. Only one heteroplasmic mutation was found. These results confirm the low somatic mutation rate found in prior studies utilizing different types of human tissues. In addition, these results suggest that there is little if any accumulated damage to the mt DNA of the retina during normal aging.
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Affiliation(s)
- A Bodenteich
- Laboratory of Biochemical Genetics, National Institute of Mental Health, Washington, DC 20032
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33
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Pikó L, Hougham AJ, Bulpitt KJ. Studies of sequence heterogeneity of mitochondrial DNA from rat and mouse tissues: evidence for an increased frequency of deletions/additions with aging. Mech Ageing Dev 1988; 43:279-93. [PMID: 2849701 DOI: 10.1016/0047-6374(88)90037-1] [Citation(s) in RCA: 135] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
To obtain information on the extent of random nucleotide changes in mitochondrial DNA (mtDNA) from different organs of young adult and senescent Fischer 344 rats, the temperature of thermal denaturation (tm) was measured in (1) the native mtDNA cut at a single SstI site and (2) the reannealed duplexes formed after the initial melting of the mtDNA sample. No change was found between the two tm values in either young or senescent mtDNA, suggesting that the overall mismatch in nucleotide sequence in these samples was below the resolution of the method estimated at about 0.2%. In another experiment, mtDNA samples from young adult or senescent BALB/c mouse liver were digested with EcoRI, denatured and allowed to reanneal. The duplexes formed by the 14-kb EcoRI fragment were analyzed in randomly taken electron micrographs for the occurrence of mismatched segments. About 1.8% of reconstituted duplexes in adult mtDNA and 11% of those in senescent mtDNA contained small loops or knobs suggestive of deletions/additions of about 400 +/- 150 nucleotides. These data correspond to about 1% of the native mtDNA population in adult liver and about 5% in senescent liver having deleted/inserted segments. Although deletions/insertions may occur at variable sites, their distribution appears to be non-random. These findings suggest that small sequence rearrangements, which have been observed previously in unicircular dimers of mouse and human mtDNA, occur also in monomeric mtDNA from normal tissues and accumulate with aging.
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Affiliation(s)
- L Pikó
- Developmental Biology Laboratory, Veterans Administration Medical Center, Sepulveda, CA 91343
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34
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Mita S, Monnat RJ, Loeb LA. Direct selection of mutations in the human mitochondrial tRNAThr gene: reversion of an 'uncloneable' phenotype. Mutat Res 1988; 199:183-90. [PMID: 3362158 DOI: 10.1016/0027-5107(88)90244-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Several regions of the human mitochondrial genome are refractory to cloning in plasmid and bacteriophage DNA vectors. For example, recovery of recombinant M13 clones containing a 462 basepair MboI-Kpn I restriction fragment that spans nucleotide positions 15591 to 16053 of HeLa cell mitochondrial DNA was as much as 100-fold lower than the recovery of M13 clones containing other regions of the human mitochondrial genome. All of 50 recombinant M13 clones containing this 'uncloneable' fragment had one or more changes in nucleotide sequence. Each clone contained at least one alteration in two nucleotide positions within the tRNAThr gene that encode portions of the anticodon loop and D-stem of the HeLa mitochondrial tRNAThr. These results imply that the HeLa mitochondrial tRNAThr gene is responsible for the 'uncloneable' phenotype of this region of human mitochondrial (mt) DNA. A total of 61 nucleotide sequence alterations were identified in 50 independent clones containing the HeLa mt tRNAThr gene. 56 mutations were single-base substitutions; 5 were deletions. Approximately 80% of the base substitution mutations were A:T----G:C transitions. A preference for A:T----G:C transition mutations also characterizes polymorphic base substitution variants in the mitochondrial DNA of unrelated individuals. This similarity suggests that human mitochondrial DNA sequence variation within and between individuals may have a common origin.
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Affiliation(s)
- S Mita
- Joseph Gottstein Memorial Cancer Research Laboratory, Department of Pathology SM-30, University of Washington, Seattle 98195
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35
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