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Early-onset fatal encephalomyopathy associated with severe mtDNA depletion.

UNLABELLED: We studied a 3-month-old girl who was admitted to hospital because of respiratory distress. The clinical course was characterized by a rapidly progressive generalized hypotonia with lactic acidosis and she died at 4 months of age. A muscle biopsy showed few ragged-red fibres and lack of histochemical cytochrome c oxidase reaction in all fibres. Enzyme activities of the respiratory chain complexes containing subunits encoded by the mitochondrial DNA (mtDNA) were markedly decreased. A quantitative Southern blot analysis revealed 99% depletion of mtDNA in muscle and normal amounts in blood. There was no family history and the dizygotic twin sister of the patient was no symptomatic. CONCLUSION: This new case confirms the rapidly fatal evolution associated with severe depletion of muscle mtDNA.

Acidosis, Lactic↗

A phylogenetic study of the origin of the domestic pig estimated from the near-complete mtDNA genome.

The near-complete pig mtDNA genome sequence (15,997 bp) was determined from two domestic pigs (one Chinese Meishan and one Swedish Landrace) and two European wild boars. The sequences were analyzed together with a previously published sequence representing a Swedish domestic pig. The sequences formed three distinct clades, denoted A, E1, and E2, with considerable sequence divergence between them (0.8-1.2%). The results confirm our previous study (based on the sequence of the cytochrome B gene and the control region only) and provide compelling evidence that domestication of pigs must have occurred from both an Asian and a European subspecies of the wild boar. We estimated the time since the divergence of clade A (found in Chinese Meishan pigs) and E1 (found in European domestic pigs) at about 900,000 years before present, long before domestication about 9,000 years ago. The pattern of nucleotide substitutions among the sequences was in good agreement with previous interspecific comparisons of mammalian mtDNA; the lowest substitution rates were observed at nonsynonymous sites in protein-coding genes, in the tRNA and rRNA genes, while the highest rates were observed at synonymous sites and in the control region. The presence of Asian clade A in some major European breeds (Large White and Landrace) most likely reflects the documented introgression of Asian germplasm into European stocks during the 18th and 19th centuries. The coexistence of such divergent mtDNA haplotypes for 100+ generations is expected to lead to the presence of recombinant haplotypes if paternal transmission and recombination occur at a low frequency. We found no evidence of such recombination events in the limited sample studied so far.

Amino Acid Sequence↗

Brassica nap cytoplasmic male sterility is associated with expression of a mtDNA region containing a chimeric gene similar to the pol CMS-associated orf224 gene.

Two different cytoplasmic male-sterility (CMS) systems, nap and pol, are found in the oilseed rape (canola) species Brassica napus. Physical mapping studies have previously shown that organizational differences between the sterile pol and fertile cam mitochondrial genomes are restricted to a relatively small region immediately upstream of the atp6 gene. An approximately 4.5-kb pol mtDNA segment containing a chimeric open reading frame (orf224) co-transcribed with atp6 is missing from cam mtDNA and located at a different site on nap mtDNA; expression of the orf224/atp6 gene region is highly correlated with the pol CMS trait. Sequence analysis now shows that the transposed nap segment contains an open reading frame (ORF) related to, but distinct from, pol orf224. This open reading frame (orf222) potentially encodes a protein of 222 amino acids possessing 79% sequence similarity to the predicted product of the pol orf224 gene. nap orf222 is co-transcribed with the third exon of the trans-spliced nad5 gene and another ORF. orf222 transcripts are several times more abundant in nap CMS than in fertility restored nap-cytoplasm plants and qualitative transcript differences for the region between CMS and restored plants are found as well. Expression of the orf222/nad5c/orf139 region is specifically correlated with nap CMS: of 21 mitochondrial gene regions examined, including all the sites of rearrangement between the nap and fertile cam mitochondrial genomes and 22 known genes, only the orf222/nad5c/orf139 region detected transcript differences between maintainer cam cytoplasm, nap CMS- and fertility restored nap cytoplasm-plants. Our results suggest that expression of the orf222/nad5c/orf139 region may be associated with nap CMS, and, more generally, that different forms of CMS may be associated with genes encoding structurally similar proteins.

Amino Acid Sequence↗

Pleomorphic mitochondrial and different filamentous inclusions in inflammatory myopathies associated with mtDNA deletions.

Mitochondrial changes are frequently observed in muscle fibers of patients with inclusion body myositis (IBM) and polymyositis (PM), suggesting that mitochondrial function may be especially impaired in these forms of inflammatory myopathies. Intranuclear and cytoplasmic tubulofilamentous inclusions are characteristic, although not totally specific for IBM. In the present cases, the inclusions were strikingly pleomorphic when chloroquine had been given for long periods. The nuclear inclusions were always tubular, whereas the cytoplasmic filaments had either a tubular, a helical, or a cross-striated structure with different diameters and arrangements in association with myelin-like figures, and vacuoles. Abnormal mitochondria containing paracrystalline, globoid, and other inclusions, noted in IBM, were occasionally also seen in PM or vasculitis. By contrast, in the latter, no intranuclear or cytoplasmic tubulofilamentous inclusions were apparent in muscle fibers. This study reports for the first time the presence of membrane-bound crystalloid inclusions in a muscle fiber with numerous abnormal mitochondria; similar structures have thus far only been observed in macrophages. The identity and function of these inclusions remains unknown. Using PCR analysis we detected different mtDNA deletions not only in IBM, but also in PM and vasculitis, indicating at least some degree of association between the structural mitochondrial abnormalities and the mtDNA mutations. There was no topographical correlation between the presence of tubular or helical filaments and the mitochondrial abnormalities. As already noted by others, the mitochondrial changes in IBM were more frequent than expected in this age group. It is suggested that the presence of the mtDNA deletions in IBM and PM are not primary, but rather the result of the underlying, presumably immunological disorder causing nuclear and secondary or simultaneous mitochondrial changes.

Adult↗

Continental and subcontinental distributions of mtDNA control region types.

When the mtDNA profile of a crime scene matches that of a suspect, it is necessary to determine the probability of a chance match by consulting the frequencies of the identified allele in a "reference population". The ceiling principle suggests that that population should be chosen in which the allele of the suspect is found at the highest frequency, in order to give the suspect the maximum benefit of doubt. Recently, we advocated the use of a worldwide mitochondrial database combined with a geographical information system to identify the regions of the world with the highest frequencies of matching mtDNA types. Here, we demonstrate that the alternative approach of defining a ceiling reference population on the basis of continent or phenotype (race) is too coarse for a non-negligible percentage of mtDNA control region types.

DNA, Mitochondrial↗

Forensic mass screening using mtDNA.

At the forensic autopsy of a sexual murder victim, some trace hairs, possibly belonging to the perpetrator, were saved. Initially, the analysis of a pubic hair shaft only revealed the presence of the mitochondrial (mt) DNA haplotype profile consisting of the (CA)(6) allele and the complete hypervariable region 1 (HV1) and 2 (HV2) sequence. Later, typing of some further telogene trace hairs, which had been stored for several years, yielded a nuclear short tandem repeat (STR) profile. We used both the mtDNA haplotype and the STR profile to start a DNA mass screening project involving 2,335 male citizens of the relevant communities. MtDNA screening was carried out by using the CA repeat amplification in combination with an SNP typing procedure based on the restriction site analysis of amplified d-loop sequences. The aim of our paper is to put mass screening with mtDNA up for discussion.

Alleles↗

Hungarian mtDNA population databases from Budapest and the Baranya county Roma.

To facilitate forensic mtDNA testing in Hungary, we have generated control region databases for two Hungarian populations: 211 individuals were sampled from the urban Budapest population and 208 individuals were sampled from a Romani ("gypsy") population in Baranya county. Sequences were generated using a highly redundant approach to minimize potential database errors. The Budapest population had high sequence diversity with 180 lineages, 183 polymorphic positions, and a random match probability of 1%. In contrast, the Romani population exhibited low sequence diversity, with only 56 lineages, 109 segregating sites, and a random match probability of 8.8%. The mtDNA haplogroup compositions of the two populations were also distinct, with the large proportion of haplogroup M samples (35%) in the Roma the most obvious difference between the two populations. These factors highlight the importance of considering population structure when generating reference databases for forensic testing purposes. Comparisons between our Romani population sample and other published data indicate the need for heightened caution when sampling and using mtDNA databases of small endogamous populations. The Romani populations that we compared showed significant departures from genetic uniformity.

DNA, Mitochondrial↗

Striking differentiation of sub-populations within a genetically homogeneous isolate (Ogliastra) in Sardinia as revealed by mtDNA analysis.

Since the reduced genetic diversity found in isolates should simplify the study of complex traits, analyses of patterns of homogeneity within populations are of particular interest. We analysed the mtDNA haplogroups and hypervariable segment I (HVS-I) sequences of 475 individuals from a geographically restricted and isolated area (Ogliastra) within Sardinia, comprehending 175 random samples from 20 out of 23 villages. The remaining 300 subjects were chosen from the other three villages, Talana, Urzulei and Perdasdefogu, by sampling all maternal lineages. A comparison with other European populations reveals that Ogliastra ranks among the most genetically homogenous population and that it has been small and isolated throughout its history. The lack of variation and the high genetic homogeneity indicate that an important founder event and a demographic expansion took place during the Neolithic (approximately 7700 years before present) in Ogliastra's mtDNA gene pool. We present highly resolved phylogenetic networks for Ogliastra and for the three sub-isolates. MtDNA differentiation in the sub-populations versus Ogliastra is revealed by a strong demarcation in their genetic pools due to distinctive founder effects and genetic drift. We found that genetic homogeneity strictly depends on a scale factor in population size and on sampling methodology. The outstanding homogeneity and the reduced female gene pool observed in Ogliastra, in the European context, hide an extremely marked differentiation in sub-isolates originated from the same archaic population. Although Ogliastra can be considered a genetically homogeneous isolate, small villages' divergent genetic histories underline the importance of more systematic analysis of DNA variation between and within populations.

DNA↗

Evolutionary history of the mtDNA 9-bp deletion in Chinese populations and its relevance to the peopling of east and southeast Asia.

In total, 1218 Chinese from twelve ethnic groups and nine Han geographic groups were screened for the mtDNA 9-bp deletion motif. The frequency of the 9-bp deletion in all samples was 14.7% but ranged from 0% to 32% in the various ethnic groups. Three individuals had a triplication of the 9-bp segment. Phylogenetic and demographic analyses of the mtDNA hypervariable segment 1 (HVS 1) sequences suggest that the 9-bp deletion occurred more than once in China. The majority of the Chinese deletion haplotypes (about 90%) have a common origin as a mutational event following an initial expansion of modern humans in eastern Asia. Other deletion haplotypes and the three haplotypes with a 9-bp triplication may have arisen independently in the Chinese, presumably by replication error. HVS1 haplotype analysis suggests two possible migration routes of the 9-bp deletion in east and southeast Asia. Both migrations originated in China with one route leading to the Pacific Islands via Taiwan, the other to southeast Asia and possibly the Nicobar Islands. Along both routes of peopling, a decrease in HVSI diversity of the mtDNA haplotypes is observed. The "Polynesian motif (16217T/C, 16247A/G, and 16261C/T)" and the 16140T/C, 16266C/A, or C/G polymorphisms appear specific to each migration route.

Asia↗

Haplotype-matched controls as a tool to discriminate polymorphisms from pathogenic mutations in mtDNA.

We have studied the pathogenic role of 10044A-->G, a heteroplasmic mitochondrial DNA (mtDNA) mutation that has been suggested to be pathogenic in one family with severe pediatric morbidity. We found the mutation at an average frequency of 1.9% among 259 individuals including healthy controls. The mutation appeared to be heteroplasmic by restriction fragment analysis but analysis of subcloned polymerase chain reaction fragments confirmed homoplasmy. The polymorphic nature of 10044A-->G was verified by demonstrating exclusive association with a rare mtDNA haplotype within haplogroup H. We suggest that the evaluation of putatively pathogenic mutations in mtDNA should include the analysis of a sufficient number of haplotype-matched control samples and that the heteroplasmy should be verified by cloning.

Case-Control Studies↗

Human mtDNA hypervariable regions, HVR I and II, hint at deep common maternal founder and subsequent maternal gene flow in Indian population groups.

We have analysed the hypervariable regions (HVR I and II) of human mitochondrial DNA (mtDNA) in individuals from Uttar Pradesh (UP), Bihar (BI) and Punjab (PUNJ), belonging to the Indo-European linguistic group, and from South India (SI), that have their linguistic roots in Dravidian language. Our analysis revealed the presence of known and novel mutations in both hypervariable regions in the studied population groups. Median joining network analyses based on mtDNA showed extensive overlap in mtDNA lineages despite the extensive cultural and linguistic diversity. MDS plot analysis based on Fst distances suggested increased maternal genetic proximity for the studied population groups compared with other world populations. Mismatch distribution curves, respective neighbour joining trees and other statistical analyses showed that there were significant expansions. The study revealed an ancient common ancestry for the studied population groups, most probably through common founder female lineage(s), and also indicated that human migrations occurred (maybe across and within the Indian subcontinent) even after the initial phase of female migration to India.

DNA, Mitochondrial↗

De novo COX2 mutation in a LHON family of Caucasian origin: implication for the role of mtDNA polymorphism in human pathology.

Recent studies suggest that certain mutations with phylogeographic importance as haplogroup markers may also influence the phenotypic expression of particular mitochondrial disorders. One such disorder, Leber's hereditary optic neuropathy (LHON), demonstrates a clear expression bias in mtDNAs belonging to haplogroup J, a West Eurasian maternal lineage defined by polymorphic markers that have been called 'secondary' disease mutations. In this report, we present evidence for a de novo heteroplasmic COX2 mutation associated with a LHON clinical phenotype. This particular mutation-at nucleotide position 7,598-occurs in West Eurasian haplogroup H, the most common maternal lineage among individuals of European descent, whereas previous studies have detected this mutation only in East Eurasian haplogroup E. A review of the available mtDNA sequence data indicates that the COX2 7598 mutation occurs as a homoplasic event at the tips of these phylogenetic branches, suggesting that it could be a variant that is rapidly eliminated by selection. This finding points to the potential background influence of polymorphisms on the expression of mild deleterious mutations such as LHON mtDNA defects and further highlights the difficulties in distinguishing deleterious mtDNA changes from neutral polymorphisms and their significance in the development of mitochondriopathies.

Adult↗

Sequence polymorphisms of the mtDNA control region in a human isolate: the Georgians from Swanetia.

In this work, we analyzed the sequence diversity of the mtDNA control region (HVI and HVII) in a sample of 48 individuals from Swanetia (Georgia), using direct fluorescent-based sequencing methods. We identified 43 different mtDNA haplotypes resulting from 78 polymorphic sites (46 in HVI and 32 in HVII). Most of the variable positions identified in both HVI and HVII were transitions (82.6 and 71.9%, respectively). The frequency of length heteroplasmy in the homopolymeric C-stretch regions was the same for both segments (10.4%). The sequence diversity increased markedly when both hypervariable regions were analyzed jointly (HVI: 0.985, HVII: 0.975, HVI+HVII: 0.994). Accordingly, the probability of two randomly selected sequences matching (random match probability, RMP) decreased from 3.4% (HVI) to 2.6% (HVI+HVII), despite which the RMP values in Georgians remained higher than estimated in most Europeans. This suggests that the variability of maternal lineages tends to be lower in traditional human isolates and, therefore, the potential of discrimination of mtDNA in forensic analysis is more limited in this type of population. The incorporation of HVII data also contributed to the refinement of results regarding the genetic relationships among the samples included in the analyses, which stress the importance of considering HVII in both population and forensic genetics.

Base Sequence↗

Phylogeographic analysis of mtDNA variation in four ethnic populations from Yunnan Province: new data and a reappraisal.

Two sets of mitochondrial DNA (mtDNA) hypervariable segment I (HVS-I) data from four ethnic populations (Tibetan, Va, Dai, and Lahu) from Yunnan Province, China, were analyzed here by using phylogeographic methods. The results suggest that more attention should be paid to sampling methodology when addressing the genetic relationship and affinity among ethnic populations. Comparison of related data from different labs may serve as a check for the credibility of the data and will help discern the origin of the ethnic populations. Generally, Tibetan populations have more north-prevalent haplogroups (clades of the mtDNA phylogeny), while Dai and Lahu populations have high frequencies of south-prevalent haplogroups. The Vas, although autochthonous according to historical records, show signs of gene admixtures from northern and southern populations, for they harbor high frequencies of the south-prevalent haplogroup F and the north-prevalent haplogroup D as well as other northern mtDNA lineages such as M9 and G2a. The consanguineous marriage customs of the Lahu, together with possible genetic drift during this group's historical migration, left a conspicuous genetic imprint on its current gene pool.

Asian People↗

Distribution of Assamese macaques (Macaca assamensis) in the inner Himalayan region of Bhutan and their mtDNA diversity.

The distributions of Assamese macaques (Macaca assamensis) and rhesus macaques (M. mulatta) in Bhutan have been only partially documented. In order to investigate the distribution patterns of these species, we conducted field observation and genetic assessment with mitochondrial DNA (mtDNA) typing of macaques in the Inner Himalayas of Bhutan. There were 24 sightings of macaque groups, and all were visually identified as Assamese macaques. No groups of rhesus macaques were sighted in this survey area, in contrast with the survey results in the Nepalese Himalayas. Molecular phylogenetic analysis revealed that the Bhutan macaques are closer in proximity to their counterparts in the Indo-Chinese region (Thailand and Laos) than to rhesus macaques in China, Laos and India. However, clustering results suggested the marked differentiation of the macaques in Bhutan from the Assamese macaques in Indo-China. We tentatively conclude that the macaques of the Inner Himalayan regions in Bhutan are Assamese macaques and that they appear to be of a lineage distinct from Assamese macaques in the Indo-Chinese region (subspecies M. a. assamensis). The degree of mtDNA diversity suggests that the Assamese macaques in Bhutan are of a more ancient ancestry than M. a. assamensis, thereby supporting the speciation hypothesis of the expansion of a sinica-group of macaques from South Asia to Southeast and then to East Asia (Fooden; Fieldiana Zool 45:1-44, 1988). Assignment of Assamese macaques in Bhutan to M. a. pelops is premature due to the lack of molecular data and recent taxonomic controversy. The mtDNA diversity of Assamese macaques was greater than that of rhesus macaques, suggesting the earlier speciation of Assamese macaques. The significance of the ecogeographic segregation model of macaque distribution is discussed in relation to the evolutionary range expansion into the Himalayan regions in South Asia.

Animals↗

Regulation of the expression of mitochondrial proteins: relationship between mtDNA copy number and cytochrome-c oxidase activity in human cells and tissues.

The relationship between the relative amounts of nuclear and mitochondrial genes for cytochrome-c oxidase subunits and their transcripts and cytochrome-c oxidase activity was investigated in several human tissues and cell lines to get more insight into the regulation of the expression of this mitochondrial enzyme complex. The results show: (1) a wide range of mtDNA copy numbers; (2) constant ratios between the steady-state levels of the transcripts for the various cytochrome-c oxidase subunits, and (3) large variations in cytochrome-c oxidase activity in different tissues and cell lines that could not be related to the differences in mtDNA copy number. We conclude that the transcription of genes for both mitochondrial and nuclear cytochrome-c oxidase subunits is regulated coordinatedly, but also that the mtDNA copy number plays a minor role in determining differences in cytochrome-c oxidase activity between different cell and tissue types.

Cell Nucleus↗

Identification of transcription promoter regions from rat mtDNA that are utilized in vivo by the bacterial RNA polymerase.

We have used a prokaryotic promoter-identification vector, pKO-1, to isolate rat mitochondrial DNA (mtDNA) sequences that can act as bacterial transcription promoters. Three putative promoter-containing clones that hydridized to mtDNA probes were identified. The strength of the promoters was quantitated by measuring galactokinase activity. The three promoters mapped to three distinct regions of the mtDNA - one within the 5' half of the 16S rRNA gene, one within the ATPase subunit 6 gene, and the last at the carboxy terminal end of the cytochrome oxidase subunit I gene.

Adenosine Triphosphatases↗

No genetic differences between affected and unaffected members of a German family with Leber's hereditary optic neuropathy (LHON) with respect to ten mtDNA point mutations associated with LHON.

In order to investigate possible synergistic influences of different mtDNA mutations on penetrance and severity of Leber's hereditary optic neuropathy (LHON), a large German LHON pedigree is characterized with respect to 10 different mutations associated with LHON. All members of the family carry three different mtDNA mutations (at nucleotide 4,216, 11,778 and 13,708) in a homoplasmic form, regardless of whether or not they are clinically affected. Testing for another 7 mutations reveals negative results in all family members. Hence, the variable disease expression of the family members cannot be explained by varying combinations of LHON-associated mtDNA mutations.

Base Sequence↗