Extensive amino acid sequence homologies between animal lectins.

We have established the amino acid sequence of the beta-D-galactoside binding lectin from the electric eel and the sequences of several peptides from a similar lectin isolated from human placenta. These sequences were compared with the published sequences of peptides derived from the beta-D-galactoside binding lectin from human lung and with sequences deduced from cDNAs assigned to the beta-D-galactoside binding lectins from chicken embryo skin and human hepatomas. Significant homologies were observed. One of the highly conserved regions that contains a tryptophan residue and two glutamic acid residues is probably part of the beta-D-galactoside binding site, which, on the basis of spectroscopic studies of the electric eel lectin, is expected to contain such residues. The similarity of the hydropathy profiles and the predicted secondary structure of the lectins from chicken skin and electric eel, in spite of differences in their amino acid sequences, strongly suggests that these proteins have maintained structural homologies during evolution and together with the other beta-D-galactoside binding lectins were derived from a common ancestor gene.     

Inverted repeats in chloroplast DNA from higher plants

The circular chloroplast DNAs from spinach, lettuce, and corn plants have been examined by electron microscopy and shown to contain a large sequence repeated one time in reverse polarity. The inverted sequence in spinach and lettuce chloroplast DNA has been found to be 24,400 base pairs long. The inverted sequence in the corn chloroplast DNA is 22,500 base pairs long. Denaturation mapping studies have shown that the structure of the inverted sequence is highly conserved in these three plants. Pea chloroplast DNA does not contain an inverted repeat. All of the circular dimers of pea chloroplast DNA are found to be in a head-to-tail confirmation. Circular dimers of spinach and lettuce were also found to have head-to-tail conformation. However, approximately 70-80% of the circular dimers in preparations of lettuce and spinach chloroplast DNA were found to be in a head-to-head conformation. We propose that the head-to-head circular dimers are formed by a recombination event between two circular monomers in the inverted sequence.     

Extensive polymorphism in the mitochondrial DNA of apes.

Ape species are 2-10 times more variable than the human species with respect to the nucleotide sequence of mtDNA, even though ape populations have been smaller than the human population for at least 10,000 years. This finding was made by comparing purified mtDNAs from 27 individuals with the aid of 25 restriction endonucleases; for an additional 59 individuals, comparisons were made with fewer enzymes by using the blot hybridization method. The amount of intraspecific sequence divergence was greatest between orangutans of Borneo and Sumatra. Among common chimpanzees, a large component of the variation is due to two highly distinct forms of mtDNA that may reflect a major geographic subdivision. The least amount of sequence variation occurred among lowland gorillas, which exhibit only twice as much sequence variation as humans. The large intraspecific differences among apes, together with the geological and protein evidence, leads us to propose that each ape species is the remnant of an ancient and widespread population that became subdivided geographically and reduced in size and range, perhaps by hominid competition. The low variation among human mtDNAs is consistent with geological evidence that the human species is young. The distribution of site changes within the mitochondrial genome was also examined. Comparison of closely related mtDNAs shows that the ribosomal RNA genes have diverged more slowly than the rest of the genome.     

Sequence homologies among bacterial and mitochondrial superoxide dismutases

Superoxide dismutase from chicken-liver mitochondria (manganese enzyme) and the two dismutases from Escherichia coli (manganese and iron enzymes) were analyzed through 29 cycles of automated Edman degradations. The high degree of homology among the amino-terminal sequences of these three dismutases corroborates their known similarity of structural and functional properties, and serves as further evidence for the endosymbiotic origin of mitochondria. In contrast, these three sequences exhibit no significant homology with the amino-terminal sequence of bovine-erythrocyte superoxide dismutase, which is consistent with the classification of eukaryotic copper-zinc dismutases as a family distinct from the manganese enzymes in stability and catalytic properties.     

Extensive variation and heteroplasmy in size of mitochondrial DNA among geographic populations of Drosophila melanogaster

Size variation and heteroplasmy in mitochondrial DNA (mtDNA) are relatively common in natural populations of Drosophila melanogaster. Of 92 isofemale lines of flies obtained from various geographic regions throughout the world, 75 lines were homoplasmic and showed a total of 12 different mtDNA size classes. The remaining 17 lines were heteroplasmic, each line carrying two different mtDNAs, and, in all but one case, the mtDNAs in these heteroplasmic lines differed in size; a total of nine size classes was represented among them. In cases where one type was predominant within an individual, it was usually the smaller mtDNA. This finding parallels what was observed in homoplasmic lines, in that the smaller mtDNAs were much more common than the larger variants in most populations. The data suggest a high rate of mutational occurrence of mtDNA size variants and some natural selection against them.     

Mariner-like transposases are widespread and diverse in flowering plants

Complete and partial sequences of mariner-like elements (MLEs) have been reported for hundreds of species of animals, but only two have been identified in plants. On the basis of these two plant MLEs and several related sequences identified by database searches, plant-specific degenerate primers were derived and used to amplify a conserved region of MLE transposase genes from a variety of plant genomes. Positive products were obtained for 6 dicots and 31 monocots of 54 plant species tested. Phylogenetic analysis of 68 distinct MLE transposase sequences from 25 grass species is consistent with vertical transmission and rapid diversification of multiple lineages of transposases. Surprisingly, the evolution of MLEs in grasses was accompanied by repeated and independent acquisition of introns in a localized region of the transposase gene.     

Extensive sequence homology in the DNA coding for elongation factor Tu from Escherichia coli and the Chlamydomonas reinhardtii chloroplast.

Considerable DNA sequence homology can be detected between the Escherichia coli genes coding for translational components and Chlamydomonas reinhardtii chloroplast DNA. Labeled chloroplast DNA was found to hybridize to restriction fragments of the transducing phage lambda fus3 that code for elongation factor Tu. The chloroplast probe also reacts with fragments coding for ribosomal proteins carried by this phage. The region homologous to the elongation factor genes was located on the physical map of the chloroplast genome by probing restriction fragments of chloroplast DNA with cloned fragments, labeled in vitro, carrying the E. coli elongation factor Tu genes.     

线粒体转运RNA基因突变与原发性高血压的相关研究

目的探究线粒体转运RNA(tRNA)基因突变与母系遗传原发性高血压(EH)的关联性。方法依据EH诊断和母系遗传判别标准,筛选2015年1月至2018年12月解放军总医院心血管内科收治的母系遗传EH患者17例(A组)、非母系遗传EH患者65例(B组)。选取同期来院进行健康体检的正常对照人群33名(C组)。对全线粒体DNA(mtDNA)进行测序并与线粒体基因文库MitoMap的修正剑桥序列进行比对,分析3组受试者线粒体tRNA基因突变率差异及其与母系遗传EH发生的关系。应用SPSS 19.0软件对数据进行分析。结果纳入人群中母系遗传EH占总EH 20.7%(17/82)。mtDNA序列对比分析发现,与C组(0.04%)比较,A组(0.28%,P=0.024)及B组(0.12%,P=0.046)患者线粒体tRNA基因总变异率明显升高,但A与B组间比较差异无统计学意义(P=0.076)。对A组患者进一步分析显示,仅有1个线粒体tRNA基因位点突变的先证者A06、A11和A13所在3个家系分别发生mtDNA A5823G、mtDNA T4386C与mtDNA C15910T突变,三个家系母系成员EH发病率分别为53.8%(7/13)、87.5%(7/8)和75.0%(9/12),发病率均较高,提示这3个位点突变可能与母系遗传EH发生密切关联。另外,mtDNA 5597缺失在A组(4例,23.5%)、B组(14例,21.5%)和C组(1例,3.0%)均出现。与C组比较,A组(P=0.002)与B组(P=0.002)患者mtDNA 5597缺失率均显著升高,但A组与B组间比较差异无统计学意义(P=0.127)。结论 mtDNA A5823G、mtDNA T4386C与mtDNA C15910T突变与母系遗传EH有较好的关联性,但mtDNA 5597缺失与母系遗传EH关系不大。     

Altering the balance between healthy and mutated mitochondrial DNA

Pathogenic mutations of the mitochondrial genome are frequently found to co-exist with wild-type mtDNA molecules, a state known as heteroplasmy. In most disease cases, the mutation is recessive with manifestation of a clinical phenotype occurring when the proportion of mutated mtDNA exceeds a high threshold. The concept of increasing the ratio of healthy to mutated mtDNA as a means to correcting the biochemical defect has received much attention. A number of strategies are highlighted in this article, including manipulation of the mitochondrial genome by antigenomic drugs or restriction endonucleases, zinc finger peptide-targeted nucleases and exercise-induced gene shifting. The feasibility of these approaches has been demonstrated in a number of models, however more work is necessary before use in human patients.     

DNA phosphorothioation is widespread and quantized in bacterial genomes

Phosphorothioate (PT) modification of DNA, with sulfur replacing a nonbridging phosphate oxygen, was recently discovered as a product of the dnd genes found in bacteria and archaea. Given our limited understanding of the biological function of PT modifications, including sequence context, genomic frequencies, and relationships to the diversity of dnd gene clusters, we undertook a quantitative study of PT modifications in prokaryotic genomes using a liquid chromatography-coupled tandem quadrupole mass spectrometry approach. The results revealed a diversity of unique PT sequence contexts and three discrete genomic frequencies in a wide range of bacteria. Metagenomic analyses of PT modifications revealed unique ecological distributions, and a phylogenetic comparison of dnd genes and PT sequence contexts strongly supports the horizontal transfer of dnd genes. These results are consistent with the involvement of PT modifications in a type of restriction-modification system with wide distribution in prokaryotes.     

Extensive pathogenicity of mitochondrial heteroplasmy in healthy human individuals

A majority of mitochondrial DNA (mtDNA) mutations reported to be implicated in diseases are heteroplasmic, a status with coexisting mtDNA variants in a single cell. Quantifying the prevalence of mitochondrial heteroplasmy and its pathogenic effect in healthy individuals could further our understanding of its possible roles in various diseases. A total of 1,085 human individuals from 14 global populations have been sequenced by the 1000 Genomes Project to a mean coverage of ∼2,000× on mtDNA. Using a combination of stringent thresholds and a maximum-likelihood method to define heteroplasmy, we demonstrated that ∼90% of the individuals carry at least one heteroplasmy. At least 20% of individuals harbor heteroplasmies reported to be implicated in disease. Mitochondrial heteroplasmy tend to show high pathogenicity, and is significantly overrepresented in disease-associated loci. Consistent with their deleterious effect, heteroplasmies with derived allele frequency larger than 60% within an individual show a significant reduction in pathogenicity, indicating the action of purifying selection. Purifying selection on heteroplasmies can also be inferred from nonsynonymous and synonymous heteroplasmy comparison and the unfolded site frequency spectra for different functional sites in mtDNA. Nevertheless, in comparison with population polymorphic mtDNA mutations, the purifying selection is much less efficient in removing heteroplasmic mutations. The prevalence of mitochondrial heteroplasmy with high pathogenic potential in healthy individuals, along with the possibility of these mutations drifting to high frequency inside a subpopulation of cells across lifespan, emphasizes the importance of managing mitochondrial heteroplasmy to prevent disease progression.Hundreds to thousands of copies of mitochondrial DNA (mtDNA) are present in each single human cell, in contrast to only two copies of nuclear DNAs. These mtDNAs can differ from each other as a result of inherited or somatic mutations. The coexistence of multiple mtDNA variants in a single cell or among cells within an individual is called heteroplasmy (1). Mitochondrial heteroplasmy has been shown to be implicated in a large spectrum of human diseases. Besides classical mitochondrial diseases such as mitochondrial myopathy, myoclonic epilepsy with ragged red fibers, and mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes, mitochondrial heteroplasmy also plays roles in complex disorders, including type 2 diabetes mellitus, aging, cancer, and late-onset neurodegenerative diseases (1–7). Of the over 500 mtDNA point mutations reported so far that are implicated in disease, ∼55% were observed at known heteroplasmic sites (7). The coexistence of mutant and wild-type mtDNAs requires the pathogenic mutation to reach a frequency threshold before it could evince itself as clinical phenotypes (mitochondrial threshold effect) (4, 8).Mitochondrial heteroplasmy is common in healthy human populations. Before the application of next-generation sequencing (NGS) technologies, most studies focused on the mtDNA control region and revealed that 6∼11.6% of the population carry heteroplasmy in this region (9–11). The advent of NGS technologies enables the inquiry of mitochondrial heteroplasmy at the genome-wide scale. Several studies using these approaches allowed detection of medium- and high-frequency heteroplasmy with minor allele frequency (MAF) higher than 9%, and it was found that 25∼65% of the general population have at least one heteroplasmy across the entire mitochondrial genome (12–14). However, deeper sequencing depth at the order of thousands is required for confident identification of low-frequency heteroplasmy (MAF in the range of 1%∼10%) (15, 16). Without considering these low-frequency heteroplasmy, the population prevalence of mitochondrial heteroplasmy is underestimated (12–14). Moreover, a preliminary study with ultra-deep sequencing (4,158∼20,803×) of two ∼300-bp mtDNA regions was able to find heteroplasmies with very low frequency (>0.2%) in all tested healthy samples (17). Further investigation with a large sample size and deep sequencing coverage across the whole mitochondrial genome is needed to reveal the universal prevalence of mtDNA heteroplasmy in healthy human populations.Despite the widespread presence of heteroplasmy in the healthy population, its pathogenic potential has not been well characterized, and the population prevalence of pathogenic heteroplasmy might be underestimated. It has been recognized that mitochondrial heteroplasmy across the genome increases with age (9, 18–20) and acquires unique patterns in tumors (21, 22). A recent epidemiological study indicates that pathogenic mtDNA mutations might be more common in the general population than previously appreciated (23). This study investigated 10 common pathogenic mtDNA mutations in over 3,000 healthy individuals and revealed that at least 1 in 200 individuals harbors a mutation that could potentially cause disease (23); this is much higher than epidemiological estimates of the prevalence of mtDNA diseases, which is only ∼1 in 5,000 (24). This discrepancy is likely due to the mitochondrial threshold effect, because most of the pathogenic mutations exist as heteroplasmy and are compensated by the wild-type mtDNA (4, 23). The population prevalence of pathogenic mtDNA mutations should be much higher if more reported pathogenic mutations are examined in a large sample.Characterizing the pathogenic potential of mitochondrial heteroplasmy in healthy individuals and its underlying evolutionary forces will further our understanding of the roles of mtDNA variations in aging, tumorigenic, and neurodegenerative processes. In this study, we addressed this issue by analyzing deep sequencing data of mtDNA for 1,085 healthy individuals sampled from 14 global populations in the 1000 Human Genomes Project (25). First, we quantified the prevalence of mitochondrial heteroplasmy, especially disease-associated heteroplasmy, in this healthy cohort. We further characterized the pathogenicity of mitochondrial heteroplasmy with computationally predicted and experimentally reported pathogenic effects. Moreover, we scrutinized the patterns of genomic distribution and site-frequency spectrum for mitochondrial heteroplasmy and elucidated the major evolutionary forces underlying these patterns. We demonstrated that pathogenic mitochondrial heteroplasmy is prevalent in healthy individuals, likely due to insufficient purifying selection in removing them. The implication of our results in health management was also discussed.     

Association between mitochondrial DNA haplogroup variation and coronary artery disease

Background and aimsMitochondrial DNA (mtDNA) haplogroups have been associated with the development of coronary artery disease (CAD) in European populations. However, the specific mtDNA haplogroups associated with CAD have not been investigated in Chinese populations.Methods and resultsHere, we carried out a case–control study including 1036 and 481 CAD patients and 973 and 511 geographically matched asymptomatic control subjects in southern and northern China, respectively. After adjusting for age and gender, our results indicated that mtDNA haplogroups are not associated with the occurrence of CAD and its subcategories, acute coronary syndromes and stable coronary heart disease, in both southern and northern Chinese populations. By focusing on the southern Chinese population, we further revealed that mtDNA haplogroups are not associated with CAD severity.Type 2 diabetes (T2D) and hypertension are two key driving factors for the development of CAD, nonetheless, we found that the frequencies of the 12 studied mtDNA haplogroups did not differ between patients with and without T2D or hypertension.ConclusionmtDNA haplogroups are not associated with the occurrence of CAD or its subcategories in Chinese populations. Other factors such as environment and nuclear genetic background may contribute to the occurrence of CAD.     

Correlation between clinical characteristics and mitochondrial D-loop DNA mutations in hepatocellular carcinoma

Background Mitochondrial DNA (mtDNA) mutations are found in many kinds of human cancer. The aim of this study was to evaluate the relationship between mtDNA mutations in the liver and human hepatocarcinogenesis.Methods Direct sequencing of mtDNA was done in 54 hepatocellular carcinomas (HCCs) and 47 surrounding liver tissue samples, obtained from 54 patients with HCC, and in 5 liver samples without inflammation, obtained from 5 patients with metastatic liver tumors. We also examined p53 mutations in the 54 HCCs to examine the correlation between nuclear DNA mutations and mtDNA mutations.Results Mutations of mtDNA in the D-loop region were found in both HCC and noncancerous liver tissue. In normal liver without chronic inflammation, no mtDNA mutation was detected. In every case, the number of mtDNA mutations in HCC correlated with that in noncancerous liver tissue. Twelve of 52 mutation sites in the D-loop region of mtDNA were specific for HCC. The mean number of mtDNA mutations was 1.7 in well-differentiated HCC, as compared with 4.5 in moderately differentiated HCC and 4.6 in poorly differentiated HCC. The frequency of mtDNA mutations was thus higher in less differentiated HCC. We detected p53 mutations in 15 (28%) of 54 HCCs. The mean number of mtDNA mutations was 5.3 in HCC with p53 mutations and 3.8 in HCC with wild-type p53 (P = 0.024).Conclusions A higher frequency of mtDNA mutations was found in less differentiated HCCs, and it is also possible that mtDNA mutations are related to nuclear DNA mutations in HCC. The accumulation of mtDNA mutations is a useful predictor of hepatocarcinogenesis.     

Transmission of mitochondrial and chloroplast genomes in crosses of Chlamydomonas.

Physical differences between organelle genomes of the interfertile species Chlamydomonas reinhardtii and Chlamydomonas smithii have been used to demonstrate that sexual zygotes transmit chloroplast and mitochondrial DNA from opposite mating types. Processes responsible can be separated functionally and genetically, although both are controlled by mating type. In vegetative diploids, chloroplast and mitochondrial genomes are transmitted biparentally, but a 1-kilobase insert present in the C. smithii mitochondrial genome spreads unidirectionally to all C. reinhardtii genomes in a manner reminiscent of the intron found in the mitochondrial 21S rRNA gene of omega + strains of yeast.     

Fine-scale mergers of chloroplast and mitochondrial genes create functional,transcompartmentally chimeric mitochondrial genes

The mitochondrial genomes of flowering plants possess a promiscuous proclivity for taking up sequences from the chloroplast genome. All characterized chloroplast integrants exist apart from native mitochondrial genes, and only a few, involving chloroplast tRNA genes that have functionally supplanted their mitochondrial counterparts, appear to be of functional consequence. We developed a novel computational approach to search for homologous recombination (gene conversion) in a large number of sequences and applied it to 22 mitochondrial and chloroplast gene pairs, which last shared common ancestry some 2 billion years ago. We found evidence of recurrent conversion of short patches of mitochondrial genes by chloroplast homologs during angiosperm evolution, but no evidence of gene conversion in the opposite direction. All 9 putative conversion events involve the atp1/atpA gene encoding the alpha subunit of ATP synthase, which is unusually well conserved between the 2 organelles and the only shared gene that is widely sequenced across plant mitochondria. Moreover, all conversions were limited to the 2 regions of greatest nucleotide and amino acid conservation of atp1/atpA. These observations probably reflect constraints operating on both the occurrence and fixation of recombination between ancient homologs. These findings indicate that recombination between anciently related sequences is more frequent than previously appreciated and creates functional mitochondrial genes of chimeric origin. These results also have implications for the widespread use of mitochondrial atp1 in phylogeny reconstruction.     

Inheritance of chloroplast DNA in Chlamydomonas reinhardtii

Two symmetrically located deletions of approximately 100 base pairs each have been identified in chloroplast DNA of Chlamydomonas reinhardtii. Although present in a mutant strain that requires acetate for growth, both deletions have been shown to be distinct from the nonphotosynthetic phenotype of this strain. These physical markers in the chloroplast genome and maternally inherited genetic markers showed strict cotransmission in reciprocal crosses. Thus, our results are consistent with the location of the well-characterized maternally inherited genetic markers in chloroplast DNA of C. reinhardtii.     

Perturbation of chloroplast DNA amounts and chloroplast gene transmission in Chlamydomonas reinhardtii by 5-fluorodeoxyuridine

5-Fluorodeoxyuridine selectively decreases the rate of chloroplast DNA replication in Chlamydomonas resulting after several generations of growth in equilibrium levels as low as one-seventh of normal. When the maternal parent is treated prior to mating, the decrease of chloroplast DNA appears to perturb the normal maternal transmission of chloroplast genes, dramatically increasing the proportion of exceptional zygotes transmitting chloroplast genes from the paternal parent.     

The relation between D-galactose injection and mitochondrial DNA 4834 bp deletion mutation

Since,D-galactose (D-gal) overload model has been used as a premature aging model, we hypothesized that it may also lead to accelerated aging in the inner ear. Furthermore, though the mitochondrial DNA (mtDNA) 4834 bp deletion mutation has been considered as the marker of aging, there is no information available in the literature concerning the mtDNA 4834 bp deletion mutation condition of the D-gal induced premature aging model. We investigate the changes in inner ear enzymatic activity, the occurring of mtDNA 4834 bp deletion in inner ear and other tissues and the relating hearing thresholds after the administration of high dosage (150 mg/kg per day) and low dosage (50 mg/kg per day) of D-gal to rats. Furthermore, the incidence of the mtDNA 4834 bp deletion in different tissues as well as in blood sample was compared. The results showed that daily subcutaneous injections of D-gal into rats for 8 weeks could lead to the biochemical defects and mtDNA 4834 bp deletion in the inner ear tissue and other tissues, which represent the typical aging animals, but the relating hearing threshold shifts (TS) were nearly identical in the three groups. This study also indicates that using of blood samples to detect mtDNA 4834 bp deletion in clinical research might lead to a 'false negative' result. A higher sensitive result could be gained using tissue biopsy to examine mtDNA 4834 bp deletion.