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PubMed1998

A False-Positive Diagnosis for the Common MELAS (A3243G) Mutation Caused by a Novel Variant (A3426G) in the ND1 Gene of Mitochondria DNA.

Background: Several mutations in mitochondrial DNA (mtDNA) are associated with the syndrome of mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS). The "common" MELAS mutation, A3243G in the tRNA leucine (UUR) gene, affects approximately 80% of cases and is associated with respiratory chain complex I deficiency. Methods and Results: The A3243G mutation creates an ApaI restriction endonuclease site and can be detected by polymerase chain reaction (PCR) amplification of a region of mtDNA containing nt 3243, followed by ApaI digestion and electrophoretic analysis of the resulting fragments. Analysis of mtDNA from a child with complex I deficiency indicated the presence of the mutation homoplasmically in heart, liver, and skeletal muscle. Sequencing revealed only normal tRNA leucine (UUR) sequence, and a novel variant at nt 3426 in the ND1 subunit of complex I, which creates an ApaI site. ApaI digestion results in fragments of similar size to those found in patients with the A3243G mutation. Conclusions: A novel variant at nt 3426 of mtDNA creates an ApaI site and can potentially cause a false-positive result for the presence of the A3243G mutation. Given the highly polymorphic nature of mtDNA, care must be exercised in choosing primers for restriction endonuclease-based diagnostic tests for point mutations, and confirmation of a mutation by an independent method is recommended.

Journal Article↗

PubMed2002

Recommendations for consistent treatment of length variants in the human mitochondrial DNA control region.

Human mitochondrial DNA (mtDNA) analysis is a valuable forensic tool, useful in cases where the amount of extracted DNA is low or highly degraded. Population databases are used to determine the relative rarity of a particular profile obtained in a forensic case. Rather than full DNA sequence information, sequence profiles are compared to a reference sequence, and the differences from the reference are recorded in forensic databases. A standard method is proposed for characterizing length variants, and examples are described using actual human control region mtDNA profiles. Consistency in alignment and nomenclature avoids inadvertently describing two sequences as different when in fact they are the same.

Base Sequence↗

PubMed2001

Mitochondrial theory of aging matures--roles of mtDNA mutation and oxidative stress in human aging.

Mitochondrial theory of aging, a variant of free radical theory of aging, proposes that accumulation of damage to mitochondria and mitochondrial DNA (mtDNA) leads to aging of humans and animals. It has been supported by the observation that mitochondrial function declines and mtDNA mutation increases in tissue cells in an age-dependent manner. Age-related impairment in the respiratory enzymes not only decreases ATP synthesis but also enhances production of reactive oxygen species (ROS) through increased electron leakage in the respiratory chain. Human mtDNA, which is not protected by histones and yet is exposed to high levels of ROS and free radicals in the matrix of mitochondria, is susceptible to oxidative damage and mutation in tissue cells. In the past decade, more than one hundred mtDNA mutations have been found in patients with mitochondrial disease, and some of them also occur in aging human tissues. The incidence and abundance of these mutant mtDNAs are increased with age, particularly in tissues with great demand for energy. On the other hand, recent studies have revealed that the ability of the human cell to cope with oxidative stress is compromised in aging. Comparative analysis of gene expression by microarray technology has shown that a number of genes related to oxidative stress response are altered in aging animals. We discovered that the transcripts of early growth response protein-1, growth arrest and DNA damage-inducible proteins and glutathione S-transferase genes are increased in response to oxidative stress in human skin fibroblasts. Moreover, the activities of Cu,Zn-SOD, catalase and glutathione peroxidase decrease with age, whereas Mn-SOD activity increases with age up to 65 years and slightly declines thereafter in skin fibroblasts. Such an imbalance in the function of antioxidant enzymes may result in excess production of damaging ROS in the cell. This notion is supported by the observation that intracellular levels of H2O2 and oxidative damage to DNA and lipids are significantly increased with age of the fibroblast donor. Furthermore, the mitochondrial pool of reduced glutathione declines and DNA damage is enhanced in aging tissues. Taken together, these observations and our previous findings that mtDNA mutations and oxidative damage are increased in aging human tissues suggest that mitochondrial theory of aging is mature.

Aging↗

PubMed1993

Latitudinal differences in sex chromosome inversions, sex linked allozymes, and mitochondrial DNA variation in Drosophila subobscura.

Mitochondrial DNA, sex linked allozymes, and chromosome A gene arrangement data, from eight European natural populations of Drosophila subobscura, were analyzed to determine the existence of latitudinal clines. Strong north-south correlations with latitude were found for gene arrangements and for the Hbdh and 6Pgdh allozymes. Gametic associations between the A2 gene arrangement, the Hbdh96 and the 6Pgdh96 alleles, point out some kind of epistatic interaction. At mtDNA level, the Hae III, A variant did not show a previously found north-south clinal variation.

Alleles↗

PubMed2000

Human mtDNA sublimons resemble rearranged mitochondrial genoms found in pathological states.

Sublimons, originally identified in plant mitochondria, are defined as rearranged mtDNA molecules present at very low levels. We have analysed the primary structures of sublimons found in human cells and tissues and estimated their abundance. Each tissue of a given individual contains a wide range of different sublimons and the most abundant species differ between tissues in a substantially systematic manner. Sublimons are undetectable in rho(0) cells, indicating that they are bona fide derivatives of mtDNA. They are most prominent in post-mitotic tissue subject to oxidative stress. Rearrangement break-points, often defined by short direct repeats, are scattered, but hotspot regions are clearly identifiable, notably near the end of the D-loop. The region between the replication origins is therefore frequently eliminated. One other hotspot region is located adjacent to a known site of protein binding, suggesting that recombination may be facilitated by protein-protein interactions. For a given primary rearrangement, both deleted and partially duplicated species can be detected. Although each sublimon is typically present at a low level, at most a few copies per cell, sublimon abundance in a given tissue can vary over three orders of magnitude between healthy individuals. Collectively, therefore, they can represent a non-negligible fraction of total mtDNA. Their structures are very similar to those of the rearranged molecules found in pathological states, such as adPEO and MNGIE; therefore, we propose that, as in plants, human mtDNA sublimons represent a pool of variant molecules that can become amplified under pathological conditions, thus contributing to cellular dysfunction.

Adult↗

PubMed1997

The 'common deletion' is not increased in parkinsonian substantia nigra as shown by competitive polymerase chain reaction.

Previous studies have estimated levels of mitochondrial DNA (mtDNA) carrying the 4,977-base-pair 'common deletion' in tissues from patients with Parkinson's disease (PD) by using semiquantitative techniques. The role of this deleted mtDNA species in the pathogenesis of PD has remained controversial. We have applied competitive polymerase chain reaction to achieve exact quantitation of deleted mtDNA in the substantia nigra and additional brain regions of cases with neuropathologically confirmed Lewy-body parkinsonism. In addition, genotyping was carried out for CYP2D6G1,934A and CYP2D6C2,938T alleles and the mitochondrial ND2 (nucleotide 5,460) and transfer RNA for glutamine (nucleotide 4,336) sequence variants. Parkinsonian brains showed 1-3% deleted mtDNA in the substantia nigra, that is, deletion levels were not higher than in age-matched controls. Our findings suggest that the defect in complex I of the respiratory chain observed in PD is not primarily due to the 'common deletion.'

Aged↗

PubMed2026

Precision ID mtDNA Whole Genome Panel and sequencing of telogen hairs - perspectives for validation and implementation in casework.

Shed hair is a commonly encountered type of forensic evidence. Shed telogen hairs generally contain insufficient or highly degraded nuclear DNA for STR profiling; however, mtDNA analysis of telogen hair and hair shafts remains possible. We validated whole mitochondrial genome (mtGenome) sequencing using the Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific) and subsequently implemented the panel for the analysis of telogen hair, buccal, and casework samples. We analysed 90 diluted DNA samples containing 3-3,600 mtDNA copies, shed telogen hairs and their corresponding mtDNA from buccal swabs from 91 individuals, and 11 archived DNA extracts from hair samples in criminal cases. Complete mtGenome sequences were consistently recovered in 99% of samples across DNA dilution series at DNA input levels as low as 47 mtDNA copies, demonstrating the assay's robustness under low-template conditions. We obtained complete and reproducible mtGenome sequences with ≥ 327 mtDNA copies/µL from telogen hair samples. After applying ISFG recommendations and excluding low-confidence discrepancies associated with high-strand bias, heteroplasmic variants and sequencing artifacts, mtGenome sequence concordance increased from 93.4% to 100%. None of the 16 negative controls produced complete mtDNA sequences. Six negative controls showed low-level mtDNA signal (2-8 variants), consisting predominantly of common polymorphisms. These samples did not yield complete mtGenome sequences and showed no correspondence to any of the analysed samples. Finally, archived telogen hair samples from criminal cases presented complete mtGenome sequences with an average read depth of 1,037x.Our findings highlight the reliability of mtDNA analysis of telogen hairs using the Precision ID mtDNA Whole Genome Panel for implementation in forensic casework.

Forensic casework↗

PubMed2005

Contribution of mitochondrial DNA repair to cell resistance from oxidative stress.

Numerous studies have revealed that a part of the cellular response to chronic oxidative stress involves increased antioxidant capacity. However, another defense mechanism that has received less attention is DNA repair. Because of the important homeostatic role of mitochondria and the exquisite sensitivity of mitochondrial DNA (mtDNA) to oxidative damage, we hypothesized that mtDNA repair plays an important role in the protection against oxidative stress. To test this hypothesis mtDNA damage and repair was evaluated in normal HA1 Chinese hamster fibroblasts and oxidative stress-resistant variants isolated following chronic exposure to H2O2 or 95% O2. Reactive oxygen species were generated enzymatically using xanthine oxidase and hypoxanthine. When treated with xanthine oxidase reduced levels of initial mtDNA damage and enhanced mtDNA repair were observed in the cells from the oxidative stress-resistant variants, relative to the parental cell line. This enhanced mtDNA repair correlated with an increase in mitochondrial apurinic/apyrimidinic endonuclease activity in both H2O2- and O2-resistant HA1 variants. This is the first report showing enhanced mtDNA repair in the cellular response to chronic oxidative stress. These results provide further evidence for the crucial role that mtDNA repair pathways play in protecting cells against the deleterious effects of reactive oxygen species.

Animals↗

PubMed1991

Congenital hypoplastic anemia, diabetes, and severe renal tubular dysfunction associated with a mitochondrial DNA deletion.

Mitochondrial DNA (mtDNA) deletion is associated with a variety of clinical entities. In addition to progressive external ophthalmoplegia and Kearns-Sayre syndrome, mtDNA deletions have been demonstrated in Pearson's syndrome. We report an mtDNA deletion in an infant with a variant of Pearson's syndrome. Not only does she have congenital anemia, severe tubulopathy, and exocrine pancreas insufficiency, but she also has diabetes and cerebral atrophy. However, there are no signs of gut or liver involvement. Bone marrow improved while new tissues were involved, thus showing variability in progression of the disease. Decreased respiratory chain enzyme activities were demonstrated in muscle, and an mtDNA deletion was demonstrated in muscle, kidney, leukocytes, and fibroblasts.

Child, Preschool↗

PubMed1986

An approach to yeast classification by mapping mitochondrial DNA from Dekkera/Brettanomyces and Eeniella genera.

Sequences hybridizing to mitochondrial DNA probes from Saccharomyces cerevisiae have been mapped in six mitochondrial genomes from the Dekkera/Brettanomyces yeasts and in mtDNA from the closely related Eeniella nana. Sequence order for the 34.5 kbp mtDNA of E. nana is identical to that for mtDNAs from B. custersianus (28.5 kbp) and B. naardenensis (41.7 kbp) thereby suggesting that the former yeast is affiliated with the latter two species. A closer relationship is suggested for D. intermedia and D. bruxellensis as mtDNAs from these yeasts, 73.2 and 85.0 kbp respectively, have the same sequence order and mostly common restriction endonuclease sites. Differences between the two molecules are reminiscent of those found in mtDNA polymorphisms of S. cerevisiae strains thereby suggesting that the two Dekkera yeasts are variants of a single species. An unusual feature of the Dekkera species mtDNA is an inversion of the cytochrome b hybridizable region relative to the LrRNA sequence. Likewise mtDNA from B. anomalus (57.7 kbp) has an inversion of the cytochrome oxidase subunit 1 sequence with respect to the LrRNA sequence. By contrast the largest mtDNA (101.1 kbp) from B. custersii has the cytochrome b and LrRNA sequences in the same orientation. In addition hybridizable regions in this mtDNA are found in three clusters that are separated by several thousand base pairs of sequence deficient in restriction endonuclease sites. This observation together with the low guanine and cytosine content of the mtDNA suggests that the regions separating the sequence clusters are mostly adenine and thymine residues.

Chromosome Mapping↗

PubMed2005

Infantile onset spinocerebellar ataxia is caused by recessive mutations in mitochondrial proteins Twinkle and Twinky.

Infantile onset spinocerebellar ataxia (IOSCA) (MIM 271245) is a severe autosomal recessively inherited neurodegenerative disorder characterized by progressive atrophy of the cerebellum, brain stem and spinal cord and sensory axonal neuropathy. We report here the molecular background of this disease based on the positional cloning/candidate approach of the defective gene. Having established the linkage to chromosome 10q24, we restricted the critical DNA region using single nucleotide polymorphism-based haplotypes. After analyzing all positional candidate transcripts, we identified two point mutations in the gene C10orf2 encoding Twinkle, a mitochondrial deoxyribonucleic acid (mtDNA)-specific helicase, and a rarer splice variant Twinky, underlying IOSCA. The founder IOSCA mutation, homozygous in all but one of the patients, leads to a Y508C amino acid change in the polypeptides. One patient, heterozygous for Y508C, carries a silent coding region cytosine to thymine transition mutation in his paternal disease chromosome. This allele is expressed at a reduced level, causing the preponderance of messenger RNAs encoding Y508C polypeptides and thus leads to the IOSCA disease phenotype. Previously, we have shown that different mutations in this same gene cause autosomal dominant progressive external ophthalmoplegia (adPEO) with multiple mtDNA deletions (MIM 606075), a neuromuscular disorder sharing a spectrum of symptoms with IOSCA. IOSCA phenotype is the first recessive one due to Twinkle and Twinky mutations, the dominant PEO mutations affecting mtDNA maintenance, but in IOSCA, mtDNA stays intact. The severe neurological phenotype observed in IOSCA, a result of only a single amino acid substitution in Twinkle and Twinky, suggests that these proteins play a crucial role in the maintenance and/or function of specific affected neuronal subpopulations.

Age of Onset↗

PubMed2000

Mitochondrial DNA sequence diversity in bipolar affective disorder.

OBJECTIVE: Point mutations in mitochondrial DNA (mtDNA) are one mechanism that could explain the apparent excess maternal transmission of bipolar affective disorder observed in some families. The authors sequenced the mtDNA from probands with bipolar disorder and tested nucleotide variants for association with the disorder. METHOD: The entire 16.5 kilobase mitochondrial genome was sequenced in nine unrelated probands selected from large pedigrees with exclusively maternal transmission of bipolar affective disorder. Compared to a reference sequence, variants were detected at 107 nucleotide positions. Fifteen variants of possible pathogenic significance were selected for further study. These variants were assayed in 93 unrelated probands with bipolar I, bipolar II, or schizoaffective-manic disorder and 63 comparison subjects, all of whom were classified into the major groups comprising the European mtDNA haplotype structure (haplogroups). RESULTS: The major European haplogroups were represented at the expected frequencies among both probands and comparison subjects. There was no significant difference between probands and comparison subjects in the frequency of any variant, although odds ratios >2 or <0.5 were observed for four variants. Frequencies of these four variants were similar in probands and haplogroup-matched comparison subjects. The results of all comparisons were essentially unchanged when probands from families with an apparently paternal transmission pattern were excluded. CONCLUSIONS: The results demonstrate that bipolar affective disorder occurs across all of the major European mtDNA haplogroups but do not reveal any point mutations that explain excess maternal transmission of the disorder.

Adolescent↗

PubMed2026

Pathogenic human mitochondrial tRNA variants impair RNA processing by compromising 5' leader removal.

Human mitochondrial genome (mtDNA) encodes multiple proteins in the oxidative phosphorylation complexes as well as the ribosomal and transfer RNAs (tRNAs) needed for in situ translation. These genes are transcribed from only three promoters, producing polycistronic transcripts that are co-transcriptionally cleaved by mitochondrial RNase enzymes to release majority of individual gene products. tRNAs separate many of these genes and are thought to serve as "punctuation" marks that enable RNase recognition, binding, and hydrolysis of the 5' "leader" and 3' "trailer" sequences flanking the tRNA. Mutations in the tRNA genes dominate the mtDNA-linked mitochondrial pathologies; yet a systematic study of the impact of tRNA sequence variation on the RNase-catalyzed processing is lacking. Here, we employed human mitochondrial tRNATyr as a model system to dissect the effect of tRNA variants on the in vitro 5' leader and 3' trailer hydrolysis. We found that nucleotide variations located near the catalytic interfaces - particularly within or near the tRNA acceptor stem - showed the strongest defects in 5' processing and prevented release of the downstream tRNA in a tRNA cluster where multiple tRNAs are transcribed in tandem. This work provides mechanistic insight into how mutations disrupt coordinated mitochondrial tRNA processing and establish a framework for predicting variant effects based on their structural position relative to the processing enzymes.

Journal Article↗

PubMed2003

Familial optic atrophy with white matter changes.

We report two brothers who suffer from infantile onset optic atrophy and blindness. MRI of the brain demonstrated periventricular white matter changes in both children. Neurological and developmental examination are normal. Extensive laboratory investigations rule out metabolic disorders that can be associated with optic atrophy. No mutations associated with Leber hereditary optic neuropathy (LHON) were found and sequencing of the mitochondrially encoded complex 1 subunits was normal. We suggest that this family represents either an atypical variant of LHON with a yet undescribed mtDNA mutation or a new syndrome.

Adolescent↗

PubMed1986

Mitochondrial plasmids of Neurospora: integration into mitochondrial DNA and evidence for reverse transcription in mitochondria.

The Mauriceville (3.6 kb) and Varkud (3.8 kb) mitochondrial plasmids of Neurospora are closely related, closed circular DNAs whose nucleotide sequences and genetic organization suggest relationships to mitochondrial introns and retrotransposons. Here we isolated mutants whose growth is impaired as a result of malevolent behavior of these plasmids. All 12 mutants contain variant plasmids that are suppressive relative to mtDNA, and ten also contain defective mtDNAs. All the suppressive plasmids contain small insertions, generally including a mitochondrial tRNA sequence, at or near the major 5' RNA start site. The structure of the suppressive plasmids suggests that they were generated via an RNA intermediate and a reverse transcription step. At least three of the mutants contain defective mtDNAs into which mitochondrial plasmid sequences have integrated. Sequences at the plasmid-mtDNA junctions are also consistent with integration via an RNA intermediate.

Chromosome Mapping↗

PubMed1978

EcoRI cleavage site variants of mitochondrial DNA molecules from rats.

The mitochondrial DNA (mtDNA) molecules of some rats obtained from the SASCO colony contain six EcoRI-sensitive sites while the mtDNA molecules of other rats obtained from the same source contain only four EcoRI sites. By mapping the positions of the EcoRI sites on the molecules relative to the D-loop it was determined that mtDNA molecules from all rats have four EcoRI sites in common, but all the mtDNA molecules of some rats have two extra EcoRI sites. EcoRI sensitivity of mtDNA molecules was shown to be maternally inherited. Construction of heteroduplex molecules failed to reveal evidence of gross nucleotide sequence changes associated with differences in EcoRI sensitivity.

Animals↗

PubMed1987

Mitochondrial DNA variation and genetic structure in populations of Drosophila melanogaster.

The understanding of the genetic structure of a species can be improved by considering together data from different types of genetic markers. In the past, a number of worldwide populations of Drosophila melanogaster have been extensively studied for several such markers, including allozymes, chromosomal inversions, and quantitative characters. Here we present results from a study of restriction-fragment-length polymorphisms of mitochondrial DNA (mtDNA) in 92 isofemale lines from many of the same geographic populations of D. melanogaster. Eleven restriction enzymes were used, of which four revealed restriction-site polymorphism. A total of 24 different haplotypes were observed, of which 18 were unique to single populations. In many populations, the unique haplotypes have reached high frequency without being observed in neighboring populations. A Wagner parsimony tree reveals that mutationally close variants show geographical clumping, suggesting local differentiation of mtDNA in populations. The Old-World and the New-World populations are differentiated, with the predominant Old-World haplotype being virtually absent from the New World. These results contrast with those for the nuclear genes, in which many loci show parallel clines in different continents, and suggest a common origin of D. melanogaster populations in North America.

Animals↗

PubMed2001

[T4336C variant--a marker of mitochondrial subgroup H1, a common component of the Russian and German gene pool].

Analysis of mitochondrial DNA (mtDNA) restriction polymorphism carried out in a sample of Russians from Magadan (n = 150) showed that the frequency of the +4332AvaII variant (a T-C transition at nucleotide position 4336) in this population was 4.7%. All +4332AvaII types of mtDNA belonged to the mitochondrial group H. They were characterized by a back of the AluI restriction endonuclease site at position 7025. According to hypervariable segment 1 sequencing data, they contained the 16304C variant, and thus belong to the subgroup H1. Thus, the +4332AvaII (T4336C) variant is a marker of the mitochondrial subgroup H1, chiefly occurring in German-speaking populations. Utilization of the H1-mtDNA markers for the investigation of the genetic history and the origin of Slavs is discussed.

DNA, Mitochondrial↗