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PubMed2003

The mitochondrial genome of the tapeworm Taenia solium: a finding of the abbreviated stop codon U.

The complete nucleotide sequence of the tapeworm Taenia solium mitochondrial DNA (mtDNA) has been determined. The sequence is 13,709 base pairs in length and contains 36 genes (12 for proteins involved in oxidative phosphorylation, 2 for ribosomal RNAs, and 22 for transfer RNAs). The gene content and organization of the T. solium mtDNA are identical to those of other taeniid mtDNAs. All genes are transcribed in the same direction, and all protein-coding genes appear to initiate with the AUG or GUG codon. In a gene for NADH dehydrogenase subunit 1, the abbreviated stop codon U was confirmed for the first time in flatworm mtDNAs.

Animals↗
PubMed2001

Chromosome races with Pliocene origins: evidence from mtDNA.

There are eight distinct chromosomal races of the New Zealand weta Hemideina thoracica. We used mtDNA sequence data to test the hypothesis that these races originated on islands during the early Pliocene (7--4 million years ago). Nine major mitochondrial lineages were identified from 65 cytochrome oxidase I sequences. Phylogenetic analysis of these lineages suggests that they arose at approximately the same time. The geographical distribution of some lineages coincides with areas that were islands during the Pliocene. Overall, hierarchical AMOVA analysis shows that chromosomal races and Pliocene islands describe only 28% and 24%, respectively, of the total current mtDNA variation. However, removing one widespread (A) and one putatively introgressed (F) lineage increases these estimates to 65% and 80%, respectively. Intraspecific sequence divergence was very high, reaching a maximum of 9.5% (uncorrected distance) and GC content was high compared to other insect mtDNA sequences. Average corrected distance among mtDNA lineages supports the Pliocene origins of this level of genetic diversity. In the southern part of the species range there is reduced mtDNA variation, probably related to local extinction of H. thoracica populations from recent volcanic activity and subsequent re-colonization from a leading edge. In contrast, in this southern part there are five chromosome races, suggesting that chromosome races here may be younger than those in the north.

Animals↗
PubMedDate not supplied

[Dibromoethylacetate - a new agent for fixing the unwound regions of DNA. Denaturation maps of mitochondrial DNA from the rat liver].

On the basis of the reaction of dibromoethylacetate with adenine and cytosine at the uncoiled regions of DNA it was possible to fix these molten regions (the degree of denaturation was about 16%) for rat liver mitochondrial DNA. Modification of all accessible adenine and cytosine residues in 0.14 M Na-acetate, pH 5.65, was completed at 70-80 degrees C in 15-20 min. Using the computer orientation for the set of fixed BamHI-fragments and the linear molecules of full length the denaturation map of mtDNA was constructed, the GC-content of the molten regions was about 28%. The dibromoethylacetate is a perspective agent for screening DNA with a low content of destabilizing regions (for instance, DNA of malignant cells).

Adenine↗
PubMed1983

Variance of ploidy in mitochondrial nucleus during spherulation in Physarum polycephalum.

In Physarum polycephalum, microplasmodia differentiated into spherules when cultures were aged for 8-10 days. Respiration rates of the microplasmodia decreased rapidly with ageing to a 90% decrease in oxygen consumption over 9 days. We studied this phenomena by isolating and characterizing mitochondria from microplasmodia and spherules at different stages of spherulation. Oxygen uptake by the isolated mitochondria decreased with spherulation. Morphological and biochemical analyses showed that mitochondrial differentiation to inactive state was characterized by a decrease not only in dimension but also of content (DNA, RNA and protein). Diminutive mitochondria contained small particle-shaped mitochondrial nuclei. The DNA content, measured by microscopic fluorometry, was about 1.15 and 0.58 X 10(-10) g, which corresponded to about 16 and 8 genome copies, respectively (e.g., 32 genome copies per mitochondrion at mitochondrial G1). Restriction endonuclease analysis showed that the physical structure and methylation pattern of the mtDNA had not changed although the DNA content per mitochondrion had decreased remarkably with spherulation. This showed that changes in the ploidy level of the mitochondrial nucleus during spherulation were due to reduction in the number of whole mitochondrial genomes.

Cell Fractionation↗
PubMed2006

Extensive variation in nuclear mitochondrial DNA content between the genomes of Phytophthora sojae and Phytophthora ramorum.

Fragments of mitochondrial DNA (mtDNA) transferred to the nuclear genome are called nuclear mitochondrial DNAs (NUMTs). We report here a comparison of NUMT content between genomes from two species of the same genus. Analysis of the genomes of Phytophthora sojae and P. ramorum revealed large differences in the NUMT content of the two genomes: 16.27 x 10(-3) and 2.28 x 10(-3)% of each genome, respectively. Substantial differences also exist between the two species in the sizes of the NUMTs found in each genome, with ranges of 20 to 405 bp for P. sojae and 19 to 137 bp for P. ramorum. Furthermore, in P. sojae, fragments from the mitochondrial genes rns, rnl, coxl, and nad (various subunits) are found most frequently, whereas P. ramorum NUMTs most often originate from the cox3, rpsl4, nad4, and nad5 genes. The large differences in the presumptive mtDNA insertions suggest that the insertions occurred subsequent to the divergence of the two species, and this is supported by sequence comparisons among the NUMTs and the mtDNA sequences of the two species. P. sojae mtDNA sequences inserted in the nuclear genome appear to have been altered as a result of insertions, deletions, inversions, and translocations and provide insights into active mechanisms of sequence divergence in this plant pathogen. No clear examples were found of NUMTs forming functional nuclear genes or of NUMTs inserted into exons or introns of any nuclear gene.

Cell Nucleus↗
PubMed2000

Complete sequence of the mitochondrial genome of Tetrahymena pyriformis and comparison with Paramecium aurelia mitochondrial DNA.

We report the complete nucleotide sequence of the Tetrahymena pyriformis mitochondrial genome and a comparison of its gene content and organization with that of Paramecium aurelia mtDNA. T. pyriformis mtDNA is a linear molecule of 47,172 bp (78.7 % A+T) excluding telomeric sequences (identical tandem repeats of 31 bp at each end of the genome). In addition to genes encoding the previously described bipartite small and large subunit rRNAs, the T. pyriformis mitochondrial genome contains 21 protein-coding genes that are clearly homologous to genes of defined function in other mtDNAs, including one (yejR) that specifies a component of a cytochrome c biogenesis pathway. As well, T. pyriformis mtDNA contains 22 open reading frames of unknown function larger than 60 codons, potentially specifying proteins ranging in size from 74 to 1386 amino acid residues. A total of 13 of these open reading frames ("ciliate-specific") are found in P. aurelia mtDNA, whereas the remaining nine appear to be unique to T. pyriformis; however, of the latter, five are positionally equivalent and of similar size in the two ciliate mitochondrial genomes, suggesting they may also be homologous, even though this is not evident from sequence comparisons. Only eight tRNA genes encoding seven distinct tRNAs are found in T. pyriformis mtDNA, formally confirming a long-standing proposal that most T. pyriformis mitochondrial tRNAs are nucleus-encoded species imported from the cytosol. Atypical features of mitochondrial gene organization and expression in T. pyriformis mtDNA include split and rearranged large subunit rRNA genes, as well as a split nad1 gene (encoding subunit 1 of NADH dehydrogenase of respiratory complex I) whose two segments are located on and transcribed from opposite strands, as is also the case in P. aurelia. Gene content and arrangement are very similar in T. pyriformis and P. aurelia mtDNAs, the two differing by a limited number of duplication, inversion and rearrangement events. Phylogenetic analyses using concatenated sequences of several mtDNA-encoded proteins provide high bootstrap support for the monophyly of alveolates (ciliates, dinoflagellates and apicomplexans) and slime molds.

Animals↗
PubMed1998

Genome structure and gene content in protist mitochondrial DNAs.

Although the collection of completely sequenced mitochondrial genomes is expanding rapidly, only recently has a phylogenetically broad representation of mtDNA sequences from protists (mostly unicellular eukaryotes) become available. This review surveys the 23 complete protist mtDNA sequences that have been determined to date, commenting on such aspects as mitochondrial genome structure, gene content, ribosomal RNA, introns, transfer RNAs and the genetic code and phylogenetic implications. We also illustrate the utility of a comparative genomics approach to gene identification by providing evidence that orfB in plant and protist mtDNAs is the homolog of atp8 , the gene in animal and fungal mtDNA that encodes subunit 8 of the F0portion of mitochondrial ATP synthase. Although several protist mtDNAs, like those of animals and most fungi, are seen to be highly derived, others appear to be have retained a number of features of the ancestral, proto-mitochondrial genome. Some of these ancestral features are also shared with plant mtDNA, although the latter have evidently expanded considerably in size, if not in gene content, in the course of evolution. Comparative analysis of protist mtDNAs is providing a new perspective on mtDNA evolution: how the original mitochondrial genome was organized, what genes it contained, and in what ways it must have changed in different eukaryotic phyla.

Amino Acid Sequence↗
PubMed1998

Alteration of mitochondrial DNA and RNA level in human fibroblasts with impaired vitamin B12 coenzyme synthesis.

Alterations of mitochondrial (mt) nucleic acid metabolism in methylmalonic aciduria (MMA) were studied in two cell lines from skin fibroblasts of patients with mitochondrial (GM00595) or cytosolic (GM10011) defects in the biosynthesis pathways of cobalamin coenzymes. The mtDNA level increased two-fold in GM00595 cells, which carry a mt defect in the adenosylcobalamin synthesis, whereas no appreciable change was found in GM10011 cells. The content of the two rRNAs 16S and 12S mtRNAs, normalized for the mtDNA copy number, decreased by 70% and 50% in GM00595 and GM10011, respectively. The normalized content of ND1, ND2 and CO I mRNAs decreased in GM00595, but was unchanged in GM10011. Respiratory chain complex activities measured in these two cell lines were not different from control activities. These data suggest that the maintenance of the mt function is due to doubling of mtDNA and that this compensatory response takes place only in those cells in which the greater reduction of the level of rRNA might have brought the content of these transcripts below the threshold value for optimal expression of the mt genome.

Amino Acid Metabolism, Inborn Errors↗
PubMed2004

GUG is an efficient initiation codon to translate the human mitochondrial ATP6 gene.

A maternally inherited and practically homoplasmic mitochondrial (mtDNA) mutation, 8527A>G, changing the initiation codon AUG into GUG, normally coding for a valine, was observed in the ATP6 gene encoding the ATPase subunit a. No alternate Met codon could replace the normal translational initiator. The patient harboring this mutation exhibited clinical symptoms suggesting a mitochondrial disease but his mother who carried the same mtDNA mutation was healthy. The mutation was absent from 100 controls and occurred once amongst 44 patients suspected of Leber Hereditary Optic Neuropathy (LHON) but devoid of typical LHON mutations. In patient fibroblasts, no effect of 8527A>G mutation could be demonstrated on the biosynthesis of mtDNA-encoded proteins, on size and the content of ATPase subunit a, on ATP hydrolysis and on mitochondrial membrane potential. In addition, ATP synthesis was barely decreased. Therefore, GUG is a functional initiation codon for the human ATP6 gene.

Adenosine Triphosphatases↗
PubMed2003

Acetylation and level of mitochondrial transcription factor A in several organs of young and old rats.

To gain further information on the role of mitochondrial transcription factor A (TFAM) in mitochondrial biogenesis, we studied the post-translational modifications of the protein in 6- and 28-month-old rat liver. Mass spectrometry and immunoblot analysis revealed that TFAM was acetylated at a single lysine residue and that the level of acetylation did not change with age. The measurement of the content of TFAM and of mitochondrial DNA (mtDNA) in several organs (cerebellum, heart, kidney, and liver) of young and old rats showed an age-related increase of mtDNA and TFAM in all the organs analyzed, except in heart. These data are discussed in the light of the multiple roles of TFAM in mitochondrial biogenesis and of the age-related change of the mitochondrial transcription.

Acetylation↗
PubMed1998

Increased mitochondrial DNA deletion in the brain of SAMP8, a mouse model for spontaneous oxidative stress brain.

Oxidative stress is considered to be closely correlated with degenerative brain abnormalities. In this study, the plausibility of a SAMP8 strain mouse showing memory deterioration and short life span as an oxidative stress brain model was evaluated. Mitochondrial DNA deletions were detected using polymerase chain reaction (PCR) as cumulative spontaneous oxidative stress. In the 4-8-week-old SAMP8 brain, multiple mitochondrial DNA (mtDNA) deletions were already found and the contents were significantly higher than those of SAMR1 or ddY controls. Enzyme activity studies indicated that electron transport was disturbed at the lower site of the chain and the electronegativity of the upper site might be increased, a cause of radical production and therefore oxidative stress.

Aging↗
PubMed1998

Complete sequence of the mitochondrial DNA of Chlamydomonas eugametos.

The complete nucleotide sequence of the Chlamydomonas eugametos (Chlamydomonadales, Chlorophyceae, sensu Mattox and Stewart) mitochondrial genome has been determined (22,897 bp, 34.6% G + C). The genes identified in this circular-mapping genome include those for apocytochrome b, subunit 1 of the cytochrome oxidase complex, subunits 1, 2, 4, 5, and 6 of the NADH dehydrogenase complex, discontinuous large and small subunit ribosomal rRNAs and three tRNAs whose anticodons CAU, CCA and UUG are specific for methionine, tryptophan and glutamine, respectively. The C. eugametos mitochondrial DNA (mtDNA), therefore, shares almost the same reduced set of coding functions and similar unusual features of rRNA gene organization with the linear 15.8 kb mtDNA of Chlamydomonas reinhardtii, the only other completely sequenced chlamydomonadalean mtDNA. However, sequence analysis of the C. eugametos mtDNA has revealed the following distinguishing features relative to those of C. reinhardtii: (1) the absence of a reverse transcriptase-like gene homologue, (2) the presence of an additional gene for tRNA(met) that may be a pseudogene, (3) a completely different gene order, (4) transcription of all genes from the same mtDNA strand, (5) a lower G + C content, (6) less pronounced bias in codon usage, and (7) nine group I introns, several of which contain open reading frames coding for potential maturases/endonucleases and two have a nucleotide at the 5' or 3' splice site of the deduced precursor RNAs that deviates from highly conserved nucleotides reported in other group I introns. The features of mitochondrial genome organization and gene content shared by C. eugametos and C. reinhardtii contrast with those of other green algal mtDNAs that have been characterized in detail. The deep evolutionary divergence between these two Chlamydomonas taxa within the Chlamydomonadales suggests that their shared features of mitochondrial genome organization evolved prior to the origin of this group.

Animals↗
PubMed1989

Content of mitochondrial DNA and of three mitochondrial RNAs in developing and adult rat cerebellum.

The content of DNA and of 16S rRNA and of two mRNAs, i.e., the mRNA for the cytochrome c oxidase subunit I and the mRNA for one subunit of the NADH dehydrogenase (ND4), in free (nonsynaptic) mitochondria of developing and adult rat cerebellum has been determined. During postnatal development, DNA content of free (nonsynaptic) mitochondria increases 10 times from 1 to 30 days of age whereas, in adult rats, it is about 60% compared to that found in 30-day-old rats. The total content of each RNA species studied also increases during development. However, when the content of each RNA is expressed per mtDNA molecule, rRNAs and mRNAs behave differently: 16S rRNA level does not change during development and it is not significantly different from that of the adult rat, whereas the level of mRNAs is higher during development than in the adult rat and changes with age. These results are discussed in light of mitochondrial biogenesis in rat cerebellum during development and of the regulation of the mitochondrial DNA transcription process.

Animals↗
PubMed1998

[Mitochondrial DNA and Parkinson disease. Methodologic review].

UNLABELLED: Parkinson's disease (PD), a disorder of unknown etiology, is associated with the degeneration of dopaminergic neurons in nigro-striatal pathways. MPTP, a meperidine analog, causes parkinsonism in human and nonhuman primates. MPP+, the active metabolite of MPTP, inhibits the activity of respiratory chain complex I. In patients with PD, a reduced complex I activity was found in substantia nigra, skeletal muscle, and platelets. Because complex I is partially encoded by the mitochondrial genome, several studies have searched for mitochondrial (mt) DNA abnormalities in patients with PD. Our aim was to answer the following questions: (1) are there some abnormalities of mtDNA in PD? (2) if there are some, what are these abnormalities? and (3) what is the pathogenic role of these abnormalities? METHODS: The literature review was performed using Medline [National Library of Medicine, Washington] and Current Contents [Institute for Scientific Information, Philadelphia] databases. Periods screened were 1966-March, 1998 (Medline) and March 17, 1997-March 9, 1998 (Current Contents). Keywords were: "Parkinson" or "Parkinson's", and "mitochondrial DNA" or "mtDNA". We limited our research to articles in English and French. RESULTS: Medline search provided 59 articles. Current Contents search provided 22 articles. Twelve articles were found in both databases. Thirty-eight of the 69 articles were either reviews about mitochondrial diseases (19 articles) or original articles not related to mtDNA (19 articles). Our final selection included the remaining 31 articles.

1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine↗
PubMed1999

Oxidative damage to mitochondrial DNA and its relationship to diabetic complications.

Increased oxidative stress induced by hyperglycemia may contribute to the pathogenesis of diabetic complications. Oxidative stress is known to increase the conversion of deoxyguanosine (dG) to 8-hydroxydeoxyguanosine (8-OHdG) in DNA, which is linked to increased mitochondrial DNA (mtDNA) deletions. We investigated mtDNA deletions and 8-OHdG in the muscle DNA of non-insulin-dependent diabetes mellitus (NIDDM) patients. mtDNA deletion of 4977 bp (delta mtDNA4977) and the content of 8-OHdG in the muscle DNA of the NIDDM patients were much higher than those of the control subjects. There was a significant correlation between delta mtDNA4977 and the 8-OHdG content (P < 0.0001). Both delta mtDNA4977 and the 8-OHdG content were also correlated with the duration of diabetes. Delta mtDNA4977 and the 8-OHdG content in muscle DNA increased in proportion to the severity of diabetic nephropathy and retinopathy. This is the first report that an increase in delta mtDNA4977 and 8-OHdG is proportional to the severity of diabetic complications. Oxidative mtDNA damage is speculated to contribute to the pathogenesis of diabetic complications though a defect in mitochondrial oxidative phosphorylation or other mechanisms. 8-OHdG and delta mtDNA4977 are useful markers to evaluate oxidative mtDNA damage in the diabetic patients.

8-Hydroxy-2'-Deoxyguanosine↗
PubMed2004

Impact of mitochondrial DNA on radiation sensitivity of transformed human fibroblast cells: clonogenic survival, micronucleus formation and cellular ATP level.

The purpose of this study was to evaluate the impact of mitochondrial DNA (mtDNA) on the radiation sensitivity of transformed human fibroblast cells. The p+ and p0 human fibroblast cell lines were used, which carry wild-type mtDNA and no mtDNA, respectively. Clonogenic radiosensitivity was evaluated by colony formation assay and micronucleus (MN) formation assay. The ATP assay was then used to address the discrepancy between the results of the former two assays. Despite the lack of a significant difference in survival in the colony formation assay, p+ and p0 cells exhibited high and low radiosensitivities, respectively, in the MN formation assay (P < 0.003). This difference in MN formation correlated with high and low levels of cellular ATP content in p+ and p0 cells (P = 0.004). The addition of antimycin A suppressed differences in both MN formation and cellular ATP content. In the transformed human fibroblast cells we used, mtDNA played an important role in radiation-induced MN formation that was correlated with the levels of cellular ATP content. These results may imply the presence of an MN expression pathway that is dependent on the intrinsic ATP level and that may be compensated and lead to an equivalent level of clonogenic survival.

Adenosine Triphosphate↗
PubMed2004

[An experimental study on large fragment deletion of rat myocardial mitochondrial DNA during early postburn stage].

OBJECTIVE: To investigate the influence of peroxidative injury in rat myocardium on the mitochondrial DNA (mtDNA) during early postburn stage. METHODS: Thirty-six Sprague-Dawley (SD) rats were employed in the study and were randomly divided into sham scald (SS) and scald groups. The rats in scald groups were inflicted with 30% TBSA III degree scalding and were further divided into 1, 3, 6, 12 and 24 post-scald hour (PSH) groups. The mtDNA deletion was determined by semi-quantitative PCR. The rat myocardial tissue samples were harvested and homogenized and the contents of superoxide dismutase (SOD) and malondialdehyde (MDA) were determined. RESULTS: There was no mtDNA deletion in the rat myocardium in SS group. Partial or complete large fragment (4.8 kb) mtDNA deletion in the rat myocardium was identified at 1, 3 and 24 PSHs (P < 0.05 or 0.01). The SOD activity in the rat myocardium significantly decreased at 1 PSH, reaching the lowest level (76.90 +/- 8.30 U/mg) at 6 PSH, but the MDA content increased evidently at 1 PSH, peaking [(3.17 +/- 0.80) nmol/mg] at 6 PSH (P < 0.05). CONCLUSION: Peroxidative injury to the rat myocardium during early postburn stage might be the principal cause of the 4834 bp deletion of mtDNA in rat myocardium.

Animals↗
PubMed2001

Brief communication: paleoanthropology and the population genetics of ancient genes.

The Mezmaiskaya cave mtDNA is similar in many ways to the Feldhofer cave Neandertal sequence and the more recently obtained Vindija cave sequence. If we accept the contention that the Mezmaiskaya cave specimen is a Neandertal infant, its mtDNA provides no new information about the fate of the European Neandertals. However, there is reason to believe that the Mezmaiskaya cave infant is not a Neandertal, and this places its importance in another light, because it delimits the possible hypotheses of Neandertal and recent human genetic relationships. One possibility is a that the pattern found in ancient mtDNA results from the replacement of an isolated gene pool (Neandertals) by one of its contemporaries (modern humans). A second possibility is natural selection expressed as the substitution of an advantageous mtDNA variant within a single large species, including both Neandertals and modern humans. The geologic, archaeological, and dating evidence shows the Mezmaiskaya cave infant to be a burial from a level even more recent than the Upper Paleolithic preserved at the site, and its anatomy does not contradict the assessment that the Mezmaiskaya cave infant is not a Neandertal. Therefore, the second pattern can be favored over the first.

Animals↗