SEARCH · PubMed Health

Results for “mtDNA variants”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 343 records · Page 19Linked to original sources

PubMed1995

Phenotypic expression of mitochondrial genotypes in cultured skin fibroblasts and in Epstein-Barr virus-transformed lymphocytes in Pearson syndrome.

Pearson syndrome is a fatal disorder involving the hematopoietic system and exocrine pancreas. Mitochondrial respiratory chain deficiencies and/or rearrangements of the mitochondrial DNA were consistently observed in all patients. We report here on the variant phenotypic expression of mitochondrial genotypes in cultured cells from a patient with Pearson syndrome. Skin fibroblasts and lymphocytes harbored, respectively, 60% and 80% of deleted mtDNA molecules initially and displayed defective respiratory chain activities. In both cases, there was a progressive recovery of respiratory chain activities during in vitro cell proliferation due to the loss of deleted mtDNA molecules in cultured skin fibroblasts and to an increase in the mtRNA translation efficiency in Epstein-Barr virus-transformed lymphocytes. The present study suggests that various cellular responses to abnormal mitochondrial genotypes might contribute to the tissue-specific expression of mitochondrial disorders in vivo.

Anemia, Sideroblastic↗

PubMed1985

Insertion of a foreign nucleotide sequence into mitochondrial DNA causes senescence in Neurospora intermedia.

The kalilo variants of Neurospora contain a cytoplasmic genetic factor that causes senescence. This factor is a 9.0 kb transposable element (kalDNA) that lacks nucleotide sequence homology with mtDNA and is inserted into the mitochondrial chromosome, often at sites located within the open reading frame in the intron-DNA of the mitochondrial 25S-rRNA gene. Genomes containing the "foreign" DNA insert accumulate during growth, and death occurs as the cells become deficient in functional large and small subunits of mitochondrial ribosomes. The kalDNA transposon may be an "activator" element that causes breaks in mtDNA. Nonsenescing [+] strains of Neurospora do not contain kalDNA.

Base Sequence↗

PubMed2003

Biochemical genetic variability in brown hares (Lepus europaeus) from Greece.

Allozyme variability of 91 brown hares (Lepus europaeus) from seven regions in Greece was compared to existing data of Bulgarian populations to test the hypothesis of the occurrence ofspecific alleles in Greece, likely stemming from an isolated Late Pleistocene refugial population in the southern Balkans. This hypothesis is particularly suggested by some subfossil Late Pleistocene hare remains in Greece and the reported high mtDNA diversity in Greek hares. Allozymic diversity could be higher in Greek hares than in hares from neighboring regions as a result of the accumulation of variants in a long-lasting Pleistocene refugium. Conversely, Greek hares could exhibit reduced genetic diversity because of long-lasting low effective population sizes during the Late Glacial Maximum and a lower chance of postglacial gene flow from other populations into this rather marginal part in the southern Balkans. Horizontal starch gel electrophoresis of proteins from 35 loci revealed three alleles (Es-1(-162), Pep-2(114), Mpi(88)) at low frequencies, which were not found in Bulgarian or any other brown hare population. In contrast, some alleles from the populations from Bulgaria and other regions of Europe were absent in the Greek samples. Population genetic statistics indicated only a slight tendency of increased gene pool diversity in Greek hares, little substructuring in Greek and Bulgarian populations, respectively, as well as an only slightly lower level of gene flow between the two neighboring regions, as compared to the gene flow within each region. The results conform to the hypothesis of a Late Pleistocene refugial population in the southern Balkans, with some few specific nuclear gene pool characteristics, but little effect on the overall genetic differentiation between Greek and Bulgarian hares.

Alleles↗

PubMed1994

Genetic variants of ribosomal DNA and mitochondrial DNA between swamp and river buffaloes.

To clarify the genetic relationship between Swamp and River buffaloes, the restriction fragment length polymorphisms (RFLPs) of nuclear genomic ribosomal DNA (rDNA) and cytoplasmic mitochondrial DNA (mtDNA) were analysed. Blood or liver samples from 73 Swamp and three River buffaloes were collected in East and South-east Asian countries. DNA samples from cattle, goats and sheep were used for comparisons. The analysis of rDNA allowed water buffaloes, cattle, goats and sheep to be characterized by four distinct repeat-types. However, swamp and river buffaloes showed the same repeat-type. Divergence of water buffalo and cattle is considered to have occurred approximately four to six million years ago. The RFLPs for mtDNA divided water buffaloes into three haplotypes, swamp-1, swamp-2 and river types. Swamp-1 accounted for 91% of all swamp buffaloes while swamp-2 was observed only in water buffaloes from Thailand (9%). All river buffaloes were of the same haplotype. No differences were observed between swamp and river buffaloes at the rDNA level. In contrast, a few distinct differences between them were found at the mtDNA level. Therefore, mtDNA polymorphisms provide an adequate means for classifying water buffaloes into either swamp or river buffaloes.

Animals↗

PubMed2002

Are substitutions in the first hypervariable region of the mitochondrial DNA displacement-loop in sudden infant death syndrome due to maternal inheritance?

AIM: To investigate whether all substitutions in the first hypervariable region (HVR1) in sudden infant death syndrome (SIDS) can be recovered along the maternal line of the family (inherited), or whether SIDS victims have new substitutions compared to maternal relatives (somatic mutations) that may be related to environmental factors. METHODS: Seventy-one SIDS/mother pairs, including 11 families with SIDS, mother and mother's relatives and/or SIDS siblings, were studied. The HVR1 sequence was recorded in the base-pair range 16056-16400. The recorded HVR1 sequence was compared with the Cambridge sequence, and differences were recorded as substitutions. The substitution pattern in the SIDS victims was compared with the pattern found in family members along the maternal line. RESULTS: All the substitutions found in SIDS victims could be traced in the maternal line of the family; in 5 cases this was observed through three generations, and in 3 cases through four generations. DISCUSSION: In patients with known mitochondrial (mt) DNA disease, a large number of sequence variants have been found in the D-loop region. Substitutions in the D-loop may be part of a haplotype with mutations elsewhere in the mtDNA. CONCLUSION: HVR1 substitutions in SIDS victims are hereditary and not due to somatic mutations.

Adult↗

PubMed2025

Structural diversity and evolutionary constraints of oxidative phosphorylation.

The oxidative phosphorylation (OxPhos) system is central to metabolism. The more than 90 structural subunits are encoded by different chromosome categories (autosomal, X, and mtDNA). The system is envisioned as an invariant structure between cells and individuals. However, a comprehensive analysis of the 1,000 Genomes Project data reveals unexpected genetic intra-individual variability resulting from the heterozygosity of diploid autosomal genes, while diversity at the population level is generated by variability in mtDNA. We characterized the different levels of structural constriction at evolutionary and population levels for all OxPhos protein residues. To support this analysis, we developed ConScore, a conservation-based predictor of variant impact within OxPhos proteins (area under the receiver operating characteristic curve [ROC-AUC] = 0.97; area under the precision-recall curve [PR-AUC] = 0.94). Notably, for the nuclear-encoded subunits, we found mechanisms limiting individual variability as allelic imbalance or homozygosity bias. Integrating structural, functional, and genetic data, we highlight the significance of each OxPhos protein position, expanding insights into its role in speciation and disease.

Oxidative Phosphorylation↗

PubMed2006

Post-glacial recolonization of the Great Lakes region by the common gartersnake (Thamnophis sirtalis) inferred from mtDNA sequences.

Pleistocene events played an important role in the differentiation of North American vertebrate populations. Michigan, in particular, and the Great Lakes region, in general, were greatly influenced by the last glaciation. While several hypotheses regarding the recolonization of this region have been advanced, none have been strongly supported. We generated 148 complete ND2 mitochondrial DNA (mtDNA) sequences from common gartersnake (Thamnophis sirtalis) populations throughout the Great Lakes region to evaluate phylogeographic patterns and population structure and to determine whether the distribution of haplotypic variants is related to the post-Pleistocene retreat of the Wisconsinan glacier. The common gartersnake was utilized, as it is believed to have been one of the primary vertebrate invaders of the Great Lakes region following the most recent period of glacial retreat and because it has been a model species for a variety of evolutionary, ecological, behavioral, and physiological studies. Several genetically distinct evolutionary lineages were supported by both genealogical and molecular population genetic analyses, although to different degrees. The geographic distribution of the majority of these lineages is interpreted as reflecting post-glacial recolonization dynamics during the late Pleistocene. These findings generally support previous hypotheses of range expansion in this region.

Animals↗

PubMed2003

Mitochondrial DNA mutations in human colonic crypt stem cells.

The mitochondrial genome encodes 13 essential subunits of the respiratory chain and has remarkable genetics based on uniparental inheritance. Within human populations, the mitochondrial genome has a high rate of sequence divergence with multiple polymorphic variants and thus has played a major role in examining the evolutionary history of our species. In recent years it has also become apparent that pathogenic mitochondrial DNA (mtDNA) mutations play an important role in neurological and other diseases. Patients harbor many different mtDNA mutations, some of which are mtDNA mutations, some of which are inherited, but others that seem to be sporadic. It has also been suggested that mtDNA mutations play a role in aging and cancer, but the evidence for a causative role in these conditions is less clear. The accumulated data would suggest, however, that mtDNA mutations occur on a frequent basis. In this article we describe a new phenomenon: the accumulation of mtDNA mutations in human colonic crypt stem cells that result in a significant biochemical defect in their progeny. These studies have important consequences not only for understanding of the finding of mtDNA mutations in aging tissues and tumors, but also for determining the frequency of mtDNA mutations within a cell.

Aged↗

PubMed1995

Length heteroplasmy in the first hypervariable segment of the human mtDNA control region.

The first hypervariable segment of the human mtDNA control region contains a homopolymeric tract of cytosines between nt 16184 and 16193, interrupted at position 16189 by a thymine, according to the Cambridge reference sequence. A variant commonly found in population screening is a T-to-C transition at nt 16189, resulting in an uninterrupted homopolymeric tract. Direct sequencing of individuals with this variant produces a characteristic blurred sequence in nucleotides beyond the tract. Sequencing clones from these individuals revealed that this is caused by high levels of length heteroplasmy in the homopolymeric tract and low levels of length heteroplasmy in the four adenines following the tract. We have developed a rapid method involving densitometry of sequencing gels to quantify the relative proportions of different length variants present in an individual. We have used this to study the proportions of length variants in individuals from three twin pairs and two maternal lineages. While unrelated individuals usually have different proportions of length variants, all maternally related individuals studied have the same proportions, even if they are only distantly related. It is not obvious how identical heteroplasmic profiles are maintained in maternally related individuals, but some possible mechanisms are suggested.

Base Sequence↗

PubMed2002

Sequence analysis of the entire mitochondrial genome in Parkinson's disease.

The pathogenesis of Parkinson's disease (PD) is largely unknown. Indirect evidence suggests that mutations in mitochondrial DNA (mtDNA) might play a role, but previous studies have not consistently associated any specific mutations with PD. However, these studies have generally been confined to limited areas of the mitochondrial genome. We therefore sequenced the entire mitochondrial genome from substantia nigra of 8 PD and 9 control subjects. Several sequence variants were distributed differently between PD and control subjects, but all were previously reported polymorphisms. Several secondary LHON mutations were found, as well as a number of novel missense mutations, but all were rare and did not differ between PD and control subjects. Finally, PD and control subjects did not differ in the total number of all mutations, nor the total number of missense mutations. Thus, mtDNA involvement in PD, if any, is likely to be complex and should be reconsidered carefully.

Amino Acid Substitution↗

PubMed2006

[A search for Y-chromosomal species-specific markers and their use for hybridization analysis in ground squirrels].

In four ground squirrel species from the Volga region-yellow (Spermophilus fulvus), russet (S. major), little (S. pygmaeus), and speckled (S. suslicus)--four hybridization variants (major/fulvus, major/pygmaeus, major/suslicus, and pygmaeus/suslicus) have been reliably described. Earlier we have shown that populations of S. major from the Volga region were characterized by wide introgression of mtDNA from S. fulvus and S. pygmaeus, which probably, resulted from ancient hybridization. In this study, the same populations were used to analyze the introgression of the Y chromosome, which (unlike mtDNA) is paternally inherited. Three genes, ZfY, SRY, and SmcY were tested as Y-chromosomal candidate markers. It was demonstrated that Y chromosome of ground squirrels lacked the ZfY gene, while its homologous structure, ZfY(X), was presumably linked to the X chromosome. The SRY region examined was rather conservative. In particular, the sequences determined in S. major and S. fulvus were identical, while three out of four substitutions found in S. pygmaeus were located in the coding region. The SmcY gene was found to be the most suitable marker, providing distinguishing of all of the four ground squirrel species by nine nucleotide substitutions. Introgression at the Y chromosome was observed only in two cases: in one S. major individual (out of 51 phenotypically pure animals) caught in the major/fulvus sympatry zone, and in four (one litter) out of fourteen S. fulvus individuals caught in close vicinity of the sympatry zone of these two species. Among 28 S. pymaeus and 9 S. suslicus individuals, no foreign SmcY genes were detected. Two colonies of the "hybrid accumulation" type were examined with eight major/suslicus hybrids analyzed in the first and seventeen major/fulvus hybrids in the second colony. The prevalence of the S. major paternal lineages was observed in both colonies (87.5 and 82.4%, respectively). The data obtained suggest that compared to wide mtDNA introgression, introgression of Y chromosome in the Volga region ground squirrels is statistically significantly less frequent event.

Animals↗

PubMed2026

Differential contributions of mt-Tr and Cs variants to developmental cochlear defects and mitochondrial dysfunction in A/J mice.

A/J mice exhibit early-onset hearing loss linked to Cdh23, mitochondrial tRNA-Arg (mt-Tr), and citrate synthase (Cs) variants. Although developmental cochlear defects have been identified in juvenile A/J mice, the hierarchical contributions of mt-Tr versus Cs remain unclear. Using reciprocal intercross-derived strains to decouple mitochondrial haplotypes from nuclear factors, we demonstrate that the mitochondrial background is the primary determinant of auditory dysfunction. Mice with A/J mtDNA (AXB strains) displayed significantly higher ABR thresholds, accelerated hair cell attrition, and severe stereocilia dysmorphology compared to those with B6 mtDNA (BXA strains), occurring largely independently of the Cs genotype. While the Cs mutation exacerbated hearing loss, its impact was secondary to that of the dominant mitochondrial background. Systemic behavioral assessments and mitochondrial assays confirmed that A/J mitochondria exert a more profound metabolic impact than the Cs mutation. Our findings establish that the mitochondrial genomic background, with the mt-Tr locus as a prominent candidate variant, serves as the principal driver of developmental cochlear defects and early-onset hearing loss in A/J mice, while the nuclear Cs mutation acts as a synergistic modifier. This study underscores the critical role of mitonuclear crosstalk in inner ear maturation and provides new insights into the etiology of hereditary hearing loss.

Animals↗

PubMed1989

Cytochrome c oxidase deficiency in Leigh's syndrome: genetic evidence for a nuclear DNA-encoded mutation.

Although an apparently generalized defect of cytochrome c oxidase (COX) occurs in many patients with subacute necrotizing encephalomyelopathy (Leigh's syndrome), the mode of inheritance in this disorder is not known. We transformed COX-deficient fibroblasts from a child with Leigh's syndrome with simian virus 40 to obtain cells with an infinite life span. These cells were still COX-deficient, grew normally in HAT medium, and were ouabain-sensitive. We fused these cells with a HAT-sensitive, ouabain-resistant variant of HeLa cells (HeLacot) and isolated surviving hybrid clones in ouabain-containing HAT medium. Prolonged cultivation of the hybrids was accompanied by preferential loss of HeLacot mitochondrial DNA (mtDNA), as determined by mtDNA restriction patterns of parental and hybrid cell DNA with the restriction endonuclease HaeII. COX activity was normal or higher than normal in hybrids, including the progeny of cell clones that had lost almost all the HeLacot mtDNA. These data demonstrate that COX deficiency in this Leigh's syndrome patient's cells was corrected by a nuclear DNA-encoded factor from the HeLacot parent and ruled out an mtDNA mutation as the basis for COX deficiency. This system can be used to determine whether different generalized mitochondrial disorders are due to mutations of nuclear or mtDNA.

Brain Diseases, Metabolic↗

PubMed1994

Maternally inherited hypertrophic cardiomyopathy due to a novel T-to-C transition at nucleotide 9997 in the mitochondrial tRNA(glycine) gene.

We report a unique heteroplasmic T-to-C transition at nucleotide 9997 in the mitochondrial tRNA(glycine) gene in a multiplex family who manifested nonobstructive cardiomyopathy. The degree of mtDNA heteroplasmy generally correlated with the severity of the symptoms. This T-to-C transition disrupts hydrogen bonding in the region adjacent to the acceptor stem of the tRNA molecule. The thymine residue at position 9997 is highly conserved in mammals, as well as in various vertebrates and invertebrates. A PCR diagnostic test for the presence of the 9997 T-to-C transition revealed that the base change was always present in high proportion in affected family members, not present in unaffected family members, and never present in control subjects from various ethnic groups (25 groups sampled, 42 individuals), thus ruling out the possibility that this change represents a polymorphic variant in the general population. The degree of heteroplasmy in lymphoblast cultures also correlated with the level of enzyme activity present for cytochrome c oxidase (complex IV) and succinate cytochrome c oxidoreductase (complexes II and III). The absence of previously reported mtDNA mutations associated with hypertrophic cardiomyopathy was verified by both PCR diagnostic procedures and sequence analysis. All mitochondrial tRNA genes, as well as genes encoding ATPase subunits 6 and 8, were sequenced and found not to possess base changes consistent with the clinical profile. More detailed biochemical and molecular biological investigations are discussed.

Adenosine Triphosphatases↗

PubMed1979

Evolutionary aspects of variant types of rat mitochondrial DNA'S.

Mitochondrial DNA's (mtDNAs) were prepared from various kinds of individual Norway rats, Rattus norvegicus, and from three types of individual black rats, Rattus rattus, (Asian type, Ceylon type, and Oceanian type). Intra- and interspecies divergence of their mtDNA sequences were calculated based on changes in restriction endonuclease cleavage sites. The extent of intraspecies divergence of black rats (about 8%) is much larger than that of Norway rats (1%) and the mtDNA of Asian-type black rats resembles the mtDNA of Norway rats more closely than it resembles the mtDNA of other types of black rats. These results strongly suggest that during the course of intraspecies differentiation of black rats, probably long after the separation of the three types of black rats, some Asian-type black rats were isolated sexually and formed a new species, Norway rats. On the basis of our observations we propose a hypothetical process to explain the evolution of animal mtDNA.

Animals↗

PubMed2002

Cryptic lineages in a small frog: the post-glacial history of the spring peeper, Pseudacris crucifer (Anura: Hylidae).

The spring peeper (Pseudacris crucifer) is believed to have been a primary herpetological invader of eastern North America following the most recent period of glacial retreat. We examined the phylogeographic pattern and population structure of P. crucifer to determine whether the distribution of haplotypic variants reflect post-Pleistocene recolonization dynamics. A number of geographically isolated evolutionary lineages were supported by both maximum parsimony and neighbor-joining analyses, and by coalescence approaches applied to mtDNA. South-western Ontario represents a high level of genotypic diversity (pi) due to the presence of two divergent lineages. The geographic distribution of these lineages are interpreted as reflecting post-glacial recolonization dynamics from separate, isolated refugia during the late Pleistocene that have come into secondary contact in SW Ontario. The phylogenetic placement of haplotypes from the range of P. crucifer bartramiana (Florida and South Carolina) does not allow for monophyly of P. crucifer crucifer, and therefore the bartramiana subspecies designation does not reflect a separate evolutionary lineage.

Animals↗

PubMed2006

Study on tandem repeat sequence variation in sheep mtDNA D-loop region.

The 75-nt-long tandem repeat sequence in the control region of mtDNA of 77 individuals, of which 69 were from different indigenous sheep breeds in China and 8 were from imported breeds, was sequenced and analyzed to investigate the origin and differentiation of Chinese indigenous sheep breeds and also the genetic diversities and relationships among them. A total of 28 variable sites were detected within 309 repeated sequences, among which 7 sites were singleton variable sites with two variants, 1 site was a singleton variable site with three variants, and 20 sites were parsimony informative sites with two variants. A total of 63 haplotypes were sorted from 28 polymorphic sites, among which two main and basic haplotypes, namely, Hap 1 and Hap 3 were present at a much higher proportion, at 12.94% and 30.42%, respectively. It could be inferred that Chinese indigenous sheep breeds originated from two maternal ancestors because of the maternal inheritance characteristics of the mtDNA. Altay sheep and Kazakstan sheep are closely related and do not differentiate significantly. Mongolian sheep and Ujumuqin sheep also share a close relationship. Tibetan sheep, Mongolian sheep, and Ujumuqin sheep have lower genetic diversity than Altay sheep and Kazakstan sheep.

Animals↗

PubMed1998

[Mitochondrial myopathy, deafness and type 2 diabetes mellitus with tRNALeu(UUR) point mutation in mitochondrial DNA].

BACKGROUND: A heteroplasmic A3243G point mutation in tRNALeu(UUR) gene of mitochondrial DNA (mtDNA) is found in patients with MELAS syndrome (Mitochondrial Encephalomyopathy, Lactic Acidosis and Stroke-like episodes), less frequently in patients with other dominating clinical features, such as deafness, diabetes mellitus type 2, hypertrophic cardiomyopathy, renal problems or inborn development defects. Present report describes histochemical, enzymatic and molecular biology studies of the family with clinical variant of meals syndrome. METHODS AND RESULTS: A 45-year-old woman with progressive muscle weakness, external ophtalmoplegia, perceptive deafness, ischemic heart disease, diabetes mellitus type 2 and hyperlactacidemia was metabolically investigated because the multiorgan problems indicated mitochondrial origin of the disease. Muscle biopsy revealed pronounced myopathic changes, ragged red fibers and decreased activity of respiratory chain enzymes - succinate cytochrome c reductase (< 5% control) and cytochrome c oxidase (< 10% control). Restriction fragment analysis of mtDNA from muscle, blood and hair follicles detected heteroplasmic A -> G mutation in the position 3243 of the tRNALeu(UUR) gene, which was more pronounced in muscle (28% of total mtDNA) than in blood (12%) or in hair follicles (10%). No mutation was found in blood and hair follicles of patient's mother and daughter. CONCLUSIONS: Diagnostics of mitochondrial diseases require close collaboration of clinicians with specialised laboratories. Treatment of mitochondrial disorders is only symptomatic, however, early diagnosis of the molecular defect is important for genetic counselling.

DNA, Mitochondrial↗