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[Spectrum of pathogenic mtDNA mutations in Leber hereditary optic neuropathy families from Siberia].

The results of clinical, genealogical and molecular investigation of eighteen families with Leber hereditary optic neuropathy (LHON), identified on the territory of Siberia during the period from 1997 to 2005, are presented. Comprehensive analysis of mitochondrial genome variations in probands and their matrilineal relatives revealed the presence of relatively frequent (G11778A, G3460A, and T14484C), as well as rare and new mutations with the established or presumptive pathological effect (T10663C, G363A, C4640T, and A14619G). The G11778A mutation was detected in nine pedigrees (50%), mostly in the families of ethnic Russians. In eight of these families G11778A was found in preferred association with the coding-region substitutions, typical of western Eurasian mtDNA lineage (haplogroup) TJ. On the contrary, the G3460A mutation was detected in the three families belonging to the indigenous Siberian populations (Tuvinians, Altaians, and Buryats). It was associated with clearly different haplotypes of eastern Eurasian haplogroups, C3, D5, and D8. Unexpectedly, the G3460A de novo mutation was found in a large Tuvinian pedigree. At the same time, in eleven out of fourteen families of Caucasoid origin pathogenic mutations in the ND genes were associated with the T4216C and C1542A coding-region mutations, marking the root motif of haplogoup TJ. It is suggested that phylogenetically ancient mutations could have provided their carriers with the adaptive advantages upon the development of Central and Northern Europe at the end of the last glaciation (10 000 to 9 000 years ago), thereby, contributing to the preservation of weekly pathogenic LHON mutations, appearing at specific genetic background.

Adolescent↗

mtDNA polymorphism in two communities of Jews.

Twenty-one types of mtDNA were found in a survey of 39 Israeli Jews, of whom 18 were Sephardic and 21 Ashkenazic. The survey was made with six restriction enzymes that together recognize an average of 600 bp/genome. The differences among the types appear to be due to base substitution at 19 cleavage sites, one deletion, and one conformational mutation. The numbers of differences imply that these modern Jews stem from a minimum of 21 maternal lineages that were already distinct from one another 4,000-5,000 years ago. In three of the four cases where a type was found in more than one person, it occurred in both Ashkenazic and Sephardic populations. The diversity of types in the combined sample of two Jewish populations is lower than both that in a sample from various parts of Africa and that in a sample from various parts of East Asia. Nevertheless, it is as high as that in a sample from diverse parts of New Guinea, an area much larger than that in Israel to which the Jewish population traces back.

Base Composition↗

A new mtDNA mutation associated with Leber hereditary optic neuroretinopathy.

A single base mutation at nucleotide position 3460 (nt 3460) in the ND1 gene in human mtDNA was found to be associated with Leber hereditary optic neuroretinopathy (LHON). The G-to-A mutation converts an alanine to a threonine at the 52d codon of the gene. The mutation also abolishes an AhaII restriction site and thus can be detected easily by RFLP analysis. The mutation was found in three independent Finnish LHON families but in none of the 60 controls. None of the families with the nt 3460 mutation in ND1 had the previously reported nt 11778 mutation in the ND4 gene. The G-to-A change at nt 3460 is the second mutation so far detected in LHON.

Animals↗

[PCR-RFLP analysis of the mtDNA Cytb gene in three different horse breeds].

Restriction endonucleases, namely BamH I, Taq I, Hae III, Rsa I and Hinc II, were used to analyze the polymorphism of partial mtDNA Cytb gene sequences from 256 horses 6 types (Thoroughbred, Sanhe, Wuzhumuqin, Xinihe, Wushen and Pony) including the imported breed, cultivated breed and local breed. The products of endonuclease digestion were run on 8% non-denaturing polyacrylamide gel electrophoresis and detected by silver staining. Results indicated BamH I and Taq I polymorphism. In all 7 restriction patterns were defected that could be sorted into 3 haplotypes, of which haplotypes I and III were the basic haplotypes. We infer that these horses came from one female ancestor through the analysis thorough one pattern, namely BamH I-B.

Animals↗

[The genetic relation of four ethnic populations in China's Guizhou is revealed by sequence variations of mtDNA D-loop].

OBJECTIVE: Through maternal inheritance, to explore the genetic structures and relationships of Dong, Gelao, Tujia and Yi ethnic population in Guizhou of China. METHODS: The mtDNA D-loop hypervariable segment I (HVS I ) in 108 samples of four ethnic populations were sequenced. Then, the nucleotide diversity was estimated and a phylogenetic tree was constructed by Neighbor-Joining method. RESULTS: In the detected 497 bp fragments, 86 polymorphic sites were found, and 82 different haplotypes were identified. The phylogenetic tree of four ethnic populations showed: Yi, Tujia and Gelao clustered more closely than Dong did. CONCLUSION: Yi and Tujia population are very closely related, the reason may be that they either originate from a common ancestry or frequently undergo the gene exchanges and admixtures. The genetic relationship between Tujia and Gelao population is nearer, perhaps because they have settled in the adjacent regions. Dong and Yi population show the farthest genetic relationship, this is probably due to their different historical origins and geographic segregation.

Base Sequence↗

Rapid detection of the A----G(8344) mutation of mtDNA in Italian families with myoclonus epilepsy and ragged-red fibers (MERRF).

We devised a rapid PCR-based method to screen for an A----G transition at nucleotide 8344 of the human mitochondrial tRNA(Lys) gene, which was recently reported, by Shoffner and co-workers, to be associated with myoclonus epilepsy and ragged-red fibers (MERRF), a maternally transmitted mitochondrial encephalomyopathy (Shoffner et al. 1990). We confirmed this association in five of seven Italian MERRF pedigrees. The mutation was specific for the MERRF trait, because it was never found in mtDNA of non-MERRF individuals, including 14 normal and 110 diseased controls. Our study corroborates the idea that the A----G(8344) mutation is the most frequent and widespread genetic cause of MERRF.

Base Sequence↗

Markedly different ATP requirements for rRNA synthesis and mtDNA light strand transcription versus mRNA synthesis in isolated human mitochondria.

In isolated mitochondria from HeLa cells, the ATP requirements for mitochondral DNA (mtDNA) transcription and RNA processing can be satisfied by either endogenous synthesis, mainly through oxidative-phosphorylation, or by exogenous supply. The pattern of RNA synthesis changes dramatically depending upon the level of ATP available. At the low intramitochondrial ATP levels produced from endogenous ADP in the presence of an oxidizable substrate and phosphate, the mRNA species are labeled to a substantial extent, whereas there is only a marginal labeling of the rRNA species and light (L) strand transcripts. By contrast, high ATP levels, either provided exogenously or produced endogenously in the presence of an oxidizable substrate, phosphate, and exogenous ADP, strongly stimulate rRNA synthesis (about 10-fold) and light (L) strand transcription (greater than 10-fold), with only a slight increase in mRNA synthesis.

Adenosine Triphosphate↗

Expression of the "split gene" COB in yeast mtDNA. Translation of intervening sequences in mutant strains.

This study deals with the effects that mutations in the COB region of yeast mtDNA have on the expression of mitochondrially made polypeptides. Based on the detection of two series of polypeptide chain-terminating mutations, we conclude that two proteins are specified by this region, apocytochrome b (Mr = 30,000) and a polypeptide of Mr = 42,000. One series of mutations generates new polypeptides ranging in size from 8,000 to 29,000 daltons; all of them are precipitated by serum direct against apocytochrome b. These mutations are located in five distinct segments of the COB region, the sequences alpha to epsilon coding for apocytochrome b. The second series of mutations, generating new polypeptides ranging in size from 17,000 to 41,000 daltons, is located within the first intervening sequence (alpha/beta) of the split gene for apocytochrome b. These mutations cause premature chain termination in the COOH-terminal part of a 42,000-dalton polypeptide. Its NH2-terminal part is likely to be specified by sequence alpha and thus to be homologous to that of apocytochrome b. We conclude that the 42,000-dalton polypeptide is translated on a processing intermediate of th COB transcript by reading through sequence alpha into sequence alpha/beta. We discuss the hypothesis that this polypeptide has a function in the expression of the COB region, possibly at the level of transcript processing.

DNA, Mitochondrial↗

Rat mitochondrial mtDNA-binding proteins to inter-specifically conserved sequences in the displacement loop region of vertebrate mtDNAs.

We describe two new inter-specifically conserved sequences named Mt5 and Mt6 elements which are around the termination associated sequence (TAS) at the 3' end of the displacement loop (D-loop) region of vertebrate mtDNAs. We employed gel mobility shift assay to search for D-loop-binding proteins using partially purified rat mitochondrial mtDNA-binding proteins and 10 human DNA fragments covering the entire D-loop region as probe DNAs. Competition binding assays indicated the presence of four different rat mitochondrial D-loop-binding proteins. Each of the rat proteins bound, in a sequence-specific manner, to a probe DNA containing an inter-specifically conserved sequence; TAS, Mt5, B block, and a A+T-rich sequence overlapping the conserved sequence block I.

Animals↗

MtDNA polymorphisms in a sample of Czechoslovaks and in two groups of Italians.

Mitochondrial DNA (mtDNA) variation was investigated in a group of 185 unrelated individuals (64 Czechoslovaks, 99 Northern and 28 Central Italians) using total blood DNA and the six restriction enzymes HpaI, BamHI, HaeII, MspI, AvaII and HincII. Among the 25 patterns (morphs) found, two morphs for HaeII, one for MspI and one for AvaII were new and each was represented by a single individual from Northern Italy. They account for four of the five new types encountered in this survey, being the fifth type characterized by the presence of the very rare morph HaeII-13. The populations analysed confirm the Caucasoid characteristics of certain polymorphisms. A review of the European data available so far is reported.

Czechoslovakia↗

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↗

Demographic history of India and mtDNA-sequence diversity.

The demographic history of India was examined by comparing mtDNA sequences obtained from members of three culturally divergent Indian subpopulations (endogamous caste groups). While an inferred tree revealed some clustering according to caste affiliation, there was no clear separation into three genetically distinct groups along caste lines. Comparison of pairwise nucleotide difference distributions, however, did indicate a difference in growth patterns between two of the castes. The Brahmin population appears to have undergone either a rapid expansion or steady growth. The low-ranking Mukri caste, however, may have either maintained a roughly constant population size or undergone multiple bottlenecks during that period. Comparison of the Indian sequences to those obtained from other populations, using a tree, revealed that the Indian sequences, along with all other non-African samples, form a starlike cluster. This cluster may represent a major expansion, possibly originating in southern Asia, taking place at some point after modern humans initially left Africa.

Base Sequence↗

[Gene pool of residents of northeastern Eurasia in light of data on polymorphism of mitochondrial DNA. I. New data on polymorphism of restriction sites of the D-loop of mtDNA in aboriginal populations of the Caucasus and Siberia].

New data about eleven polymorphic sites of restriction in the D-loop of mtDNA revealed with the Ava II, BamH I, EcoR V, Hae III, Kpn I, Rsa I, and Sau3A I restriction enzymes in native populations of the Caucasus (N = 40) and Siberia (N = 44) are presented. A comparison of these groups with each other and with common data for western and eastern Europe as well as for central and eastern Asia reveals a large similarity of all the population groups of Eurasia in respect to the frequency of each polymorphic site separately. The interpopulation differentiation of frequency of polymorphic restriction sites in Eurasia is low and identical at such different hierarchical levels of population structure as ethnic group and extended regional population group. An analysis of differences between sites in the frequency of the presence of restriction sites for BamH I, EcoR V, Hae III, and Sau3A I and the absence of sites for Ava II, Kpn I, and Rsa I at definite loci of the nucleotide chain allowed determination of the region of equilibrium between direct, site-generating, and reverse mutations to be 0.43q. Among eleven polymorphic restriction sites analyzed here, only polymorphism in the Hae III site at the position 16,517 in the population of Eurasia was characterized with frequencies close to equilibrium that determined the extremely large evolutionary age of this polymorphism.

Base Sequence↗

mtDNA sequences suggest a recent evolutionary divergence for Beringian and northern North American populations.

Conventional descriptions of the pattern and process of human entry into the New World from Asia are incomplete and controversial. In order to gain an evolutionary insight into this process, we have sequenced the control region of mtDNA in samples of contemporary tribal populations of eastern Siberia, Alaska, and Greenland and have compared them with those of Amerind speakers of the Pacific Northwest and with those of the Altai of central Siberia. Specifically, we have analyzed sequence diversity in 33 mitochondrial lineages identified in 90 individuals belonging to five Circumpolar populations of Beringia, North America, and Greenland: Chukchi from Siberia, Inupiaq Eskimos and Athapaskans from Alaska, Eskimos from West Greenland, and Haida from Canada. Hereafter, we refer to these five populations as "Circumarctic peoples." These data were then compared with the sequence diversity in 47 mitochondrial lineages identified in a sample of 145 individuals from three Amerind-speaking tribes (Bella Coola, Nuu-Chah-Nulth, and Yakima) of the Pacific Northwest, plus 16 mitochondrial lineages identified in a sample of 17 Altai from central Siberia. Sequence diversity within and among Circumarctic populations is considerably less than the sequence diversity observed within and among the three Amerind tribes. The similarity of sequences found among the geographically dispersed Circumarctic groups, plus the small values of mean pairwise sequence differences within Circumarctic populations, suggest a recent and rapid evolutionary radiation of these populations. In addition, Circumarctic populations lack the 9-bp deletion which has been used to trace various migrations out of Asia, while populations of southeastern Siberia possess this deletion. On the basis of these observations, while the evolutionary affinities of Native Americans extend west to the Circumarctic populations of eastern Siberia, they do not include the Altai of central Siberia.

Alaska↗

Autosomal recessive Wolfram syndrome associated with an 8.5-kb mtDNA single deletion.

Wolfram syndrome (MIM 222300) is characterized by optic atrophy, diabetes mellitus, diabetes insipidus, neurosensory hearing loss, urinary tract abnormalities, and neurological dysfunction. The association of clinical manifestations in tissues and organs unrelated functionally or embryologically suggested the possibility of a mitochondrial implication in the disease, which has been demonstrated in two sporadic cases. Nonetheless, familial studies suggested an autosomal recessive mode of transmission, and recent data demonstrated linkage with markers on the short arm of human chromosome 4. The patient reported here, as well as her parents and unaffected sister, carried a heteroplasmic 8.5-kb deletion in mtDNA. The deletion accounted for 23% of mitochondrial genomes in lymphocytes from the patient and approximately 5% in the tissues studied from members of her family. The presence of the deletion in the patient in a proportion higher than in her unaffected parents suggests a putative defect in a nuclear gene that acts at the mitochondrial level.

Base Sequence↗

mtDNA variation indicates Mongolia may have been the source for the founding population for the New World.

mtDNA RFLP variation was analyzed in 42 Mongolians from Ulan Bator. All four founding lineage types (A [4.76%], B [2.38%], C [11.9%], and D [19.04%]) identified by Torroni and colleagues were detected. Seven of the nine founding lineage types proposed by Bailliet and colleagues and Merriwether and Ferrell were detected (A2 [4.76%], B [2.38%], C1 [11.9%], D1 [7.14%], D2 [11.9%], X6 [16.7%], and X7 [9.5%]). Sixty-four percent of these 42 individuals had "Amerindian founding lineage" haplotypes. A survey of 24 restriction sites yielded 16 polymorphic sites and 21 different haplotypes. The presence of all four of the founding lineages identified by the Torroni group (and seven of Merriwether and Ferrell's nine founding lineages), combined with Mongolia's location with respect to the Bering Strait, indicates that Mongolia is a potential location for the origin of the founders of the New World. Since lineage B, which is widely distributed in the New World, is absent in Siberia, we conclude that Mongolia or a geographic location common to both contemporary Mongolians and American aboriginals is the more likely origin of the founders of the New World.

DNA, Mitochondrial↗

mtDNA polymorphism in East Asian Populations, with special reference to the peopling of Japan.

Nucleotide sequences of the major noncoding (D-loop) region of human mtDNA from five East Asian populations including mainland Japanese, Ainu, Ryukyuans, Koreans, and Chinese were analyzed. On the basis of a comparison of 482-bp sequences in 293 East Asians, 207 different sequence types were observed. Of these, 189 were unique to their respective populations, whereas 18 were shared between two or three populations. Among the shared types, eight were found in common between the mainland Japanese and Koreans, which is the largest number in the comparison. The intergenic COII/tRNA(Lys) 9-bp deletion was observed in every East Asian population with varying frequencies. The D-loop sequence variation suggests that the deletion event occurred only once in the ancestry of East Asians. Phylogenetic analysis revealed that East Asian lineages were classified into at least 18 monophyletic clusters, though lineages from the five populations were completely intermingled in the phylogenetic tree. However, we assigned 14 of the 18 clusters for their specificity on the basis of the population from which the maximum number of individuals in each cluster was derived. Of note is the finding that 50% of the mainland Japanese had continental specificity in which Chinese or Koreans were dominant, while < 20% of either Ryukyuans or Ainu possessed continental specificity. Phylogenetic analysis of the entire human population revealed the closest genetic affinity between the mainland Japanese and Koreans. Thus, the results of this study are compatible with the hybridization model on the origin of modern Japanese. It is suggested that approximately 65% of the gene pool in mainland Japanese was derived from the continental gene flow after the Yayoi Age.

Asian People↗

mtDNA sequence diversity in Africa.

mtDNA sequences were determined from 241 individuals from nine ethnic groups in Africa. When they were compared with published data from other groups, it was found that the !Kung, Mbuti, and Biaka show on the order of 10 times more sequence differences between the three groups, as well as between those and the other groups (the Fulbe, Hausa, Tuareg, Songhai, Kanuri, Yoruba, Mandenka, Somali, Tukana, and Kikuyu), than these other groups do between one other. Furthermore, the pairwise sequence distributions, patterns of coalescence events, and numbers of variable positions relative to the mean sequence difference indicate that the former three groups have been of constant size over time, whereas the latter have expanded in size. We suggest that this reflects subsistence patterns in that the populations that have expanded in size are food producers whereas those that have not are hunters and gatherers.

Agriculture↗