Large-scale Mitochondrial DNA Deletions Research Articles

Comparative mapping of the POLG gene to cattle chromosome 21q17→q22 by FISH and confirmation by RH mapping

The DNA directed polymerase gamma gene (POLG), known to be located on human chromosome (HSA) 15q25 (Walker et al., 1997), encodes the only DNA polymerase responsible for mitochondrial DNA (mtDNA) replication. Mutations in human POLG have been identified in affected families with progressive external ophthalmoplegia (PEO) characterized by accumulation of large-scale mitochondrial DNA deletions (OMIM #157640; Van Goethem et al., 2001). This gene was identified as candidate gene for congenital bilateral convergent strabismus with exophthalmus (BCSE) in cattle (OMIA 000353; Distl, 1993; Distl and Gerst, 2000). This monogenic autosomal dominant inherited phenotype in cattle shows similarities to the heterogeneous dominant and recessive forms of PEO in man, e.g. eye muscle biopsies of affected humans and cattle demonstrated the presence of ragged red fibers and many mtDNA deletions (Li et al., 1999). Application of a comparative approach, using a human cDNA to screen a bovine BAC library revealed a POLG-containing bovine BAC clone. To facilitate future linkage studies we report the physical mapping of the bovine POLG gene to cattle chromosome (BTA) 21q17→q22 by FISH and RH mapping.

Mutation of POLG is associated with progressive external ophthalmoplegia characterized by mtDNA deletions.

Progressive external ophthalmoplegias (PEO) characterized by accumulation of large-scale mitochondrial DNA (mtDNA) deletions are rare human diseases. We mapped a new locus for dominant PEO at 15q22-q26 in a Belgian pedigree and identified a heterozygous mutation (Y955C) in the polymerase motif B of the mtDNA polymerase gamma (POLG). We identified three additional POLG missense mutations compatible with recessive PEO In two nuclear families. POLG is the only DNA polymerase responsible for mtDNA replication.

Large-scale mitochondrial DNA deletions in skeletal muscle of patients with end-stage renal disease

End-stage renal disease (ESRD) is associated with enhanced oxidative stress. This disease state provides a unique system for investigating the deleterious effect of exogenous sources of free radicals and reactive oxygen species (ROS) on mitochondrial DNA (mtDNA). To test the hypothesis that uremic milieu might cause more severe damage to mtDNA, we investigated the prevalence and abundance of mtDNA deletions in the skeletal muscles of ESRD patients. The results showed that the frequencies of occurrence of the 4977 bp and 7436 bp deletions of mtDNA in the muscle tissues of the older ESRD patients were higher than those of the younger patients. The frequency of occurrence of the 4977 bp-deleted mtDNA in the muscle was 33.3% for the patients in the age group of < 40 years, 66.6% in the 41–60-year-old group, 100% in the 61–80-year-old group, and 100% in patients >80 years of age, respectively. Only 22% of the normal aged controls carried the 4977 bp mtDNA deletion, whereas 77% (17/22) of the ESRD patients exhibited the mtDNA deletion. Using a semiquantitative PCR method, we determined the proportion of the 4977 bp-deleted mtDNA from the muscles that had been confirmed to harbor the deletion. We found that the proportions of the 4977 bp-deleted mtDNA in the muscle were significantly higher than those of the aged matched controls. Using long-range PCR techniques, a distinctive array of mtDNA deletions was demonstrated in the muscle of uremic patients. In summary, we found diverse and multiple mtDNA deletions in the skeletal muscles of ESRD patients. These deletions are more prevalent and abundant in ESRD patients than those found in normal populations. Accumulation of uremic toxins and impaired free radical scavenging systems may be responsible for the increased oxidative stress in ESRD patients. Such stress may result in oxidative damage and aging-associated mutation of the mitochondrial genome.

Role of adenine nucleotide translocator 1 in mtDNA maintenance.

Autosomal dominant progressive external ophthalmoplegia is a rare human disease that shows a Mendelian inheritance pattern, but is characterized by large-scale mitochondrial DNA (mtDNA) deletions. We have identified two heterozygous missense mutations in the nuclear gene encoding the heart/skeletal muscle isoform of the adenine nucleotide translocator (ANT1) in five families and one sporadic patient. The familial mutation substitutes a proline for a highly conserved alanine at position 114 in the ANT1 protein. The analogous mutation in yeast caused a respiratory defect. These results indicate that ANT has a role in mtDNA maintenance and that a mitochondrial disease can be caused by a dominant mechanism.

34] Photoaging-associated large-scale deletions of mitochondrial DNA

Heteroplasmy, replicative segregation, low copy numbers of mtDNA, and selection mechanisms at the molecular and cellular level are all factors that determine requirements toward the experimental design for the detection and the quantification of mtDNA mutations. The short half-life and low stability of ROS further increase the technical demands. However, the continuous improvement of techniques has given us more insight into the interactions between ROS and mtDNA, both at the level of endogenous ROS produced by the normal mitochondrial metabolism and exogenous sources of ROS, such as singlet oxygen, which can result from treatments such as UVA exposure.

Cellular and molecular studies in muscle and cultures from patients with multiple mitochondrial DNA deletions.

In the last decade, several mitochondrial encephalomyopathies have been pathogenically associated with large-scale mitochondrial DNA deletions that are sporadic, or with point mutations that are maternally inherited. The mutations were also demonstrated in cultures of muscle satellite cells obtained from the patients. Subsequently, multiple deletions in mitochondrial DNA were found in several families. The affected members had progressive external ophthalmoplegia, cataracts and limb weakness, inherited as an autosomal dominant trait, or progressive external ophthalmoplegia with neurogastrointestinal encephalomyopathy or with cardiomyopathy, inherited as an autosomal recessive trait. To better understand the developmental pathobiology and localization of the multiple deletions, we performed comparative molecular genetic studies in muscle and cultures from patients. Whereas multiple deletions were found in muscle fragments from which muscle satellite cells were removed by enzymatic digestion, no deletions were found in the satellite cells or their cultured progeny. Our results suggest that multiple mitochondrial DNA deletions arise as somatic mutations during later stages of muscle development, or in terminally differentiated myofibers.

Acute exercise causes mitochondrial DNA deletion in rat skeletal muscle.

The present study was conducted to determine the effects of acute overload exercise on mitochondrial DNA and the structure of skeletal muscles. Rats were forced to run for 20 min until reaching complete exhaustion. We detected the large-scale deletion (7052 bp) of mitochondrial DNA by the nested polymerase chain reaction, and also observed mitochondrial ultrastructural changes in the soleus muscle.

Deletions of mitochondrial DNA in Kearns-Sayre syndrome. 1988.

We have identified large-scale deletions in muscle mitochondrial DNA (mtDNA) in seven of seven patients with Kearns-Sayre syndrome (KSS). We found no detectable deletions in the mtDNA of ten non-KSS patients with other mitochondrial myopathies or encephalomyopathies, or three normal controls. The deletions ranged in size from 2.0 to 7.0 kb, and did not localize to any single region of the mitochondrial genome. The proportion of mutated genomes in each KSS patient ranged from 45% to 75% of total mtDNA. There was no correlation between the size or site of the deletion, biochemical abnormality of mitochondrial enzymes, or clinical severity. The data bolster arguments that KSS is a unique disorder and genetic in origin.

Two co-existing mechanisms account for the large-scale deletions of mitochondrial DNA in Podospora anserina that involve the 5' border of a group-II intron.

A degenerative syndrome associated with the accumulation of site-specific deletions within mitochondrial chromosomes occurs in strains of Podospora anserina carrying the AS1-4 nuclear mutation. The site-specific deletion event has been assumed to result from the transposition of a group-II intron (intron alpha) behind an IBS motif, followed by recombination between the two intron repeats. We show here that a number of distinct deletions can accumulate in AS1-4 strains. Most of them are present in low amounts in wild-type cells where they are only detectable in PCR experiments. The deletions can be divided into two classes. In class I, intron alpha is joined to an IBS motif. In class II, the intron is not joined to an IBS site, it can be truncated or contain a few upstream exonic nucleotides; some junctions carry non-templated nucleotides. These results indicate that at least two mechanisms are involved in the generation of large-scale mitochondrial deletions in Podospora. One of them seems to be based on the transposition properties of the group-II alpha intron, the other one on illegitimate recombination. We propose that these two mechanisms use DNA double-strand breaks occurring within the 5' region of intron alpha.

PRIMARY AND SECONDARY DEFICIENCIES OF THE MITOCHONDRIAL RESPIRATORY CHAIN

The first observation of mitochondrial respiratory chain dysfunction was made in 1959 with the report of a biochemical defect in the skeletal muscle of a euthyroid patient with hypermetabolism. Since then, numerous disorders have been found to be associated with mitochondrial respiratory chain dysfunction, the nervous system being particularly affected. In 1988, the discovery of large-scale deletions of mitochondrial DNA (mtDNA) in mitochondrial myopathies and a point mutation associated with Leber's hereditary optic neuropathy marked the beginning of a new era of mitochondrial research with the identification of many more pathogenic mutations. More recently, there has been great interest in the role of mitochondrial dysfunction in neurodegenerative diseases and aging. In this review, we discuss inborn and acquired mitochondrial abnormalities and the relationship of mitochondrial respiratory chain dysfunction to neurological disorders.

AT-rich sequences flanking the 5′-end breakpoint of the 4977-bp deletion of human mitochondrial DNA are located between two bent-inducing DNA sequences that assume distorted structure in organello

The 4977-bp deletion is the most common deletion among more than 90 large-scale deletions of human mitochondrial DNA (mtDNA) that are associated with aging and mitochondrial myopathies. The reason why the frequency of occurrence of this common deletion is so high in aged and myopathic human tissues is not clear. Since several studies proved that unusual DNA structures play very important roles in a number of recombination events, we hypothesized that some kind of unusual DNA structure may flank the breakpoints of the 4977-bp mtDNA deletion. We used two-dimensional (2-D) gel electrophoresis to assess the mobility abnormalities of the PCR-amplified DNA fragments encompassing the sequences of nucleotide position (np) 7901 to 9058 of human mtDNA. The results showed that the sequences of np 7901–8732 and np 8251–9058 exhibited retarded and increased mobilities, respectively, and the sequence of np 8285–8676 showed normal mobility in the 2-D gel. This indicates that the 5′-end breakpoint of the 4977-bp deletion is located within the junction site of two flanking bent-inducting DNA sequences. We confirmed this notion by using osmium tetroxide (OsO 4) to probe mtDNA in organello. The results showed that the two AT-rich sequences flanking the 5′-end breakpoint of the 4977-bp deletion are susceptible to OsO 4 modification. These findings suggest that the DNA sequences of the 5′-end breakpoint of the common mtDNA deletion are rendered to assume a more distorted structure than B-DNA by these two flanking bent-inducing DNA sequences in organello and thereby render this region to be more vulnerable to attack by reactive oxygen species and free radicals.

Co-existence of high levels of a cytochrome b mutation and of a tandem 200 bp duplication in the D-loop of muscle human mitochondrial DNA

Previous studies have suggested that some patients with large-scale mitochondrial DNA (mtDNA) deletions also presented a heteroplasmic 260 bp tandem duplication in the mtDNA D-loop region. Such duplications were observed not only in patients with mitochondrial pathology but also in aged subjects. However, the percentage of duplicated mtDNA did not exceed a few per cent of the total mtDNA, except in one example where it reached 30%. We report here another type of 200 bp duplication in the mtDNA D-loop region that, instead of being associated with a large-scale deletion, is correlated to the presence of a point mutation in the cytochrome b gene. The 200 bp duplication concerned up to 95% of the total mtDNA of some muscle mitochondria and was absent from the patient lymphocyte DNA. The percentages of the 200 bp duplication and that of the cytochrome b mutation were relatively close in whole muscle as well as in single muscle fibres, suggesting a correlation between the mutation and the duplication. This duplication could also be detected by PCR in two other patients with mitochondrial disorders but without known deletion or mtDNA mutation. These data suggest that the accumulation of these small duplications in the mtDNA D-loop could be indicative of the presence of other defects of the mtDNA which would damage the respiratory chain function. These deficiencies would induce the generation of small duplications in the D-loop.

1-29-16 Large-scale mitochondrial DNA deletions in patients with CPEO syndrome in Taiwan

1-29-16 Large-scale mitochondrial DNA deletions in patients with CPEO syndrome in Taiwan

Hypokinesia Causes Oxidative Damage and Mitochondrial DNA Deletion in Rat Skeletal Muscle.

The present study was conducted to determine effects of oxidative stress on mitochondrial genome caused by disuse atrophy of skeletal muscles by hindlimbs suspension. We used rats as subjects, and produced hypokinesia by hindlimbs’ (tail) suspension. With electron microscopy, confirming previous results, we found mitochondrial swelling, accompanied by blurred matrix changes in the soleus muscle. Surprisingly, in these muscles, we were able to detect two types of large-scale deletions (about 3.9 and 5.2 kb) of mitochondrial DNA (mtDNA) by the polymerase chain reaction. Our study showed that hypokinesia for two weeks caused not only oxidative damage to the histology of skeletal muscular mitochondoria and but also deletion of mtDNA. Situated close to the energy-generating system, mtDNA is susceptible to oxidative stress and is likely to generate mutations.

Clonal expansion of mitochondrial DNA with multiple deletions in autosomal dominant progressive external ophthalmoplegia.

Sporadic progressive external ophthalmoplegia and Kearns-Sayre syndrome are usually associated with single large-scale mitochondrial DNA deletions in muscle. In progressive external ophthalmoplegia with autosomal dominant inheritance, multiple mitochondrial DNA deletions have been reported. We studied several members of a Swedish family with autosomal dominant progressive external ophthalmoplegia and multiple mitochondrial DNA deletions by polymerase chain reaction analysis of single muscle fibers and by in situ hybridization, combined with enzyme histochemical analysis. Muscle fiber segments with deficiency of cytochrome c oxidase, which is partially encoded by mitochondrial DNA, had accumulated mitochondrial DNA with deletions and showed reduced levels of wild-type mitochondrial DNA. The deletions varied between individual muscle fibers. There was one predominant deletion in each cytochrome c oxidase-deficient muscle fiber segment. Sequencing of the deletion breakpoints showed that most but not all of the deletions were flanked by direct repeats. Young, clinically affected individuals of this family without limb muscle symptoms did not show mitochondrial DNA deletions or cytochrome c oxidase-deficient muscle fibers. Our results indicate that a nuclear factor predisposes to the development of somatic multiple mitochondrial DNA deletions. Mitochondrial DNA with multiple different deletions shows clonal expansion, which leads to mitochondrial myopathy with ragged-red fibers and muscle weakness.

The unusual structures of the hot-regions flanking large-scale deletions in human mitochondrial DNA.

Large-scale deletions of mitochondrial DNA (mtDNA) are common events that have been found to occur in human ageing and in patients with mitochondrial myopathies. The mechanisms by which these deletions occur remain unclear, but several mechanisms have been proposed, such as slipped-mispairing, illegitimate recombination, and oxidative reactions elicited by free radicals. In addition, the DNA topological stress and local DNA structures have been suggested as the important factors in eliciting the recombinational events. Upon examination of 128 breakpoints of human mtDNA deletions that have been published in the past 8 years, we found that these large-scale deletions often occur at some 'hot-regions'. We thus hypothesized that there exist unusual structures in these regions of human mtDNA that are important for eliciting the deletions. To test this hypothesis, we used PCR techniques to amplify the sequences of the so-called hot-regions and analysed the PCR products by two-dimensional gel electrophoresis. We found that the sequences of nucleotide position (np) 5221-5988, np 6928-7493, np 7901-8732 and np 15327-16228 exhibited retarded mobilities like bent DNA structures; np 5989-6750, np 13282-13653 and np 13282-14850 showed increased mobilities like anti-bent DNA structures. Moreover, except for the sequences of np 1175-1766 found in 12 S and 16 S rRNA genes exhibiting abnormal mobility like bent DNA structures, we did not observe significant mobility abnormalities in the np 499-5545 region where deletions rarely occurred. We thus conclude that these hot-regions assume some kinds of unusual DNA structures, which may render these regions more sensitive to the attack of free radicals or serve as recognition motifs for certain recombination machinery that is involved in the large-scale deletions of human mtDNA.

Mitochondrial DNA deletion in a patient with mitochondrial myopathy, lactic acidosis, and stroke-like episodes (MELAS) and Fanconi's syndrome

Large-scale mitochondrial DNA deletion was found in a 5-year-old girl with mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) and Fanconi's syndrome. Muscle biopsy disclosed ragged-red fibers and cytochrome c oxidase negative fibers. Respiratory chain studies were normal. Southern blot analysis demonstrated a 10.5-Kb heteroplasmic deletion in both muscle and blood. Deleted genomes represented 40% of total mitochondrial DNA in muscle and 63% in blood. There was no evidence of point mutations characteristic of MELAS. We suggest that not only patients with progressive external ophthalmoplegia syndromes, but also those with defined syndromes [e.g., MELAS or myoclonic epilepsy and ragged-red fibers (MERRF)] without characteristic point mutations, be screened for mitochondrial DNA deletions.

Phenotype-genotype correlations in skeletal muscle of patients with mtDNA deletions.

Large-scale deletions of mitochondrial DNA (mtDNA) have been associated with a subgroup of mitochondrial encephalomyopathies, usually characterized by progressive external ophthalmoplegia (PEO) and mitochondrial proliferation in muscle fibers. We and others have shown that muscle from patients with mtDNA deletions have variable cytochrome c oxidase (COX) deficiency and reduction of mitochondrially-synthesized polypeptides in affected muscle fibers. The present work summarizes the phenotype-genotype correlations observed in patients' muscle. In situ hybridization revealed that, while most COX-deficient fibers had increased levels of mutant mtDNA, they almost invariably had reduced levels of normal mtDNA. PCR quantitation of both deleted and wild-type mtDNAs in normal and respiration-deficient muscle fibers from patients with the "common deletion" showed that deleted mtDNAs were present in normal fibers (31 +/- 26%), but their percentages were much higher in affected fibers (95% +/- 2%). Absolute levels of deleted mtDNA were also increased in affected fibers, whereas absolute levels of wild-type mtDNA were significantly reduced. Taken together, our results suggest that although a specific ratio between mutant and wild-type mitochondrial genomes is probably the major determinant of the respiratory chain deficiency associated with mtDNA deletions, the reduction in the absolute amounts of wild-type mtDNA may also play a significant pathogenetic role.

Diffuse leukodystrophy with a large-scale mitochondrial DNA deletion

An 8-year-old girl with progressive ataxia and bulbar palsy showed diffuse white-matter lesions in the occipital to parietal lobes on magnetic resonance imaging. Since she had slightly elevated lactate in the cerebrospinal fluid, a muscle biopsy was done which revealed scattered ragged-red fibres and focal cytochrome c oxidase deficiency. Southern blot and polymerase-chain-reaction analyses revealed a large-scale mitochondrial DNA deletion, which was 6990 base-pairs in length with 6 base-pair (-TCATCG-) direct repeats at the junctions. Mitochondrial DNA mutation should be considered as one of the candidate causes for diffuse leukodystrophy in children.

Deletion screening of mitochondrial DNA via multiprimer DNA amplification

We report an application of multiprimed polymerase chain reaction (PCR) which allows a rapid, non-radioactive detection of deletions mitochondrial DNA using EDTA-blood and muscle samples. The use of two primer sets consisting of three forward and five reverse primers, respectively, allows a competitive PCR resulting in significant amplification products only in the presence of deletion-harbouring DNA species. Under the conditions described, deletions causing Kearns-Sayre syndrome (KSS) and progressive external ophthalmoplegia (PEO) have been successfully detected. The location of the primers on mitochondrial DNA used in this study should allow identification and localization of most of the large-scale deletions (i.e. more than 1 kb) of mitochondrial DNA reported so far.