Polymorphism of the Gene for Subunit 6 of the NADH Dehydrogenase Complex in Ethnic Russians of Russia

A sample of ethnic Russians of Russia was tested for polymorphism of the NADH dehydrogenase subunit 6 (ND6) gene mapping to the mtDNA region 14,170–14,569. Genetic diversity of ND6 haplotypes was estimated at 0.406, and probability of haplotype random match, at 0.598. Combined with typing the mtDNA control region, analysis of the ND6 gene polymorphism was assumed to improve the reliability of forensic identification. Several point substitutions in the ND6 gene region proved to be associated with particular transitions in the mtDNA control region; the association was characterized with the coefficient.     

Mitochondrial ATPase subunit 6 and cytochrome B gene polymorphisms in young obese adults.

We hypothesized that the mutational strand asymmetry is more strongly exerted upon the mitochondrial cytochrome b (Cytb) gene, which is distant from the origin of the light-strand replication (Ori(L)), than upon the ATPase subunit 6 (ATP6) gene, which is close to the Ori(L). To test this hypothesis, we determined the sequences of these two genes in 96 Japanese young obese adults. The frequency of G-->A transitions was significantly higher than that of C-->T transitions in the Cytb gene, whereas the frequencies of G-->A and C-->T transitions were not significantly different in the ATP6 gene. The marked mutational strand asymmetry in the Cytb gene can be explained by the deamination of C to uracil in the long single-stranded state of the heavy strand during replication. The ratio of the nonsynonymous substitutions at the second codon positions to those at the first codon positions was significantly lower in the Cytb gene than in the ATP6 gene. The physicochemical differences between the standard and the replaced amino acid residues were significantly smaller in the Cytb gene than in ATP6 one. The present study indicates that amino acid sequences are less variable for Cytb than for ATP6 in spite of the strong mutational strand asymmetry for the Cytb gene.     

水稻液泡ATPaseB亚基基因的克隆及其在低磷胁迫下的表达特征分析(英)

利用抑制性扣除杂交 (SSH)技术构建水稻 (OryzasativaL .)根系磷饥饿诱导cDNA文库 ,获得编码液泡ATPase (V_ATPase)B亚基的克隆 ,通过反转录PCR方法获得该基因的完整序列。该基因编码 4 87个氨基酸 ,含有一个保守的ATP结合位点 ,其蛋白分子量为 5 4 .0 6kD ,等电点为 4 .99。Southern印迹表明 ,V_ATPaseB亚基基因在水稻基因组中以单拷贝形式存在。氨基酸同源性分析发现 ,V_ATPaseB亚基是一个较为保守的蛋白亚基 ,其序列变化伴随生物的进化过程同步进行。Northern印迹表明 ,V_ATPaseB亚基在水稻根系中受到磷饥饿诱导表达 ,磷饥饿 6～ 12h出现表达高峰 ,而在叶片中表达高峰有所滞后 (2 4～ 4 8h)。在缺磷环境条件下 ,ATPaseB亚基可能通过提高其表达量 ,进而提高质子转运活性 ,形成跨膜的电化学梯度 ,为体内储备磷跨液泡膜运输提供能量 ,从而提高植物体内磷的利用效率及其耐低磷的能力。     

Universal Primers for Amplification of Mitochondrial Small Subunit Ribosomal RNA-Encoding Gene in Scleractinian Corals

We describe the construction of polymerase chain reaction primers designed to amplify a portion of the mitochondrial (mt) small subunit ribosomal (SSU) RNA-encoding genes in scleractinian corals. Combinations of cloning and sequencing show that the amplified fragments are between 694 and 896 bp in length. Alignment of the amplified DNA sequences to the published mt SSU rRNA genes of Metridium senile and Sarcophyton glaucum indicates several conserved regions among actiniarian, corallimorpharian, octocorallian, and scleractinians, suggesting this primer set can successfully amplify over 80% of the mt SSU rDNA region of scleractinian corals. Surveys of sequence variation and estimation of the rate of evolution show an extremely slow divergence of the SSU rRNA gene in the family Acroporidae. Received June 11, 1999; accepted October 4, 1999.     

Similarity of the edited sequences of Leishmania kinetoplast geneMURF4 (ATPase6)

The primary structure of the edited part of theMURF4 (ATPase6) gene was compared for seven species of flagellateLeishmania. The length of this region in all cases was identical and the sequences proved to be highly homologous. The observed differences appear to correspond to the taxonomic position of the species, which belong to three subgenera,Sauroleishmania, Leishmania, andViannia.     

Reduction of the edited domain of the mitochondrial A6 gene for ATPase subunit 6 in Trypanosomatidae

The sequence of mitochondrial A6 (MURF4) was compared for several trypanosomatids in order to assess the reduction of the edited domain (ED). The association between the ED reduction and the phylogenetic position of a species proved to be less tight than believed earlier. Compared with digenetic species, monogenetic ones more often displayed ED reduction and had smaller ED.     

从ATPase8-6基因研究杂交多倍体鱼线粒体母性遗传

异源四倍体鲫鲤是世界上首例人工培育的两性可育并形成群体的且能自然繁殖的四倍体鱼。本文采用质粒克隆测序法测定了红鲫、异源四倍体鲫鲤、三倍体湘云鲫和三倍体湘云鲤的ATPase8和ATPase6基因全序列 ,结合鲤鱼、日本白鲫和斑马鱼的同源序列 ,对不同倍性水平鲤科鱼类的ATPase8和ATPase6基因进行了比较 ,分析了碱基组成、变异情况以及核苷酸和氨基酸序列差异。红鲫、鲤鱼、异源四倍体鲫鲤、日本白鲫、三倍体湘云鲫和三倍体湘云鲤之间的序列差异为 0 0 % - 1 3 4 % ,它们与外群斑马鱼之间的序列差异为 2 7 9% -31 0 %。用MEGA软件中的MP法、ME法、NJ法和UPGMA法构建分子系统树 ,得到了相似的拓扑结构。结果分析表明 ,人工杂交多倍体异源四倍体鲫鲤、三倍体湘云鲫和三倍体湘云鲤在线粒体ATPase8和ATPase6基因上具有严格的母性遗传特征。值得注意的是 ,异源四倍体鲫鲤经过 1 1代的繁育后 ,与其原始母本红鲫仍然保持了非常高的同源性 ,说明了新的异源四倍体基因库在线粒体ATPase8和ATPase6基因上拥有稳定的遗传特性。对不同倍性鲤科鱼类线粒体ATPase8和ATPase6基因的研究表明 ,ATPase8和ATPase6基因是杂交鱼后代遗传变异研究的一个很好的分子标记     

脊椎动物线粒体DNA的基因重排

将GenBank上已公布的321种脊椎动物mtDNA全序列,按纲整理归类,绘制基因排布图并进行比对。比对结果表明：81个物种的mtDNA中观察到基因重排现象,涉及脊椎动物各纲,其中9个物种同时存在基因顺序变化和基因倒置现象,所有的基因重排都涉及tRNA的变化。脊椎动物mtDNA基因顺序变化可分为3类：1)邻接的基因或片段的位置交换;2)接近于控制序列或轻链起始位点的基因或片段的位置变化,有时还伴随着控制序列的倍增;3)I-Q-M区域的变化。所有鸟类、蛇类、鳄类和有袋类的mtDNA具有各自独特的基因排列顺序。基因倒置现象常见于鱼类和哺乳类,且多表现为tRNA从轻链往重链上迁移。本文就这些基因重排现象、发生重排的机制和mtDNA基因重排在系统发生研究中的应用做一简要概述。     

Covariation of Mitochondrial Genome Size with Gene Lengths: Evidence for Gene Length Reduction During Mitochondrial Evolution

Reduction of genome size and gene shortening have been observed in a number of parasitic and mutualistic intracellular symbionts. Reduction of coding capacity is also a unifying principle in the evolutionary history of mitochondria, but little is known about the evolution of gene length in mitochondria. The genes for cytochrome c oxidase subunits I–III, cytochrome b, and the large and small subunit rRNAs are, with very few exceptions, always found on the mitochondrial genome. These resident mitochondrial genes can therefore be used to test whether the reduction in gene lengths observed in a number of intracellular symbionts is also seen in mitochondria. Here we show that resident mitochondrial gene products are shorter than their corresponding counterparts in -proteobacteria and, furthermore, that the reduction of mitochondrial genome size is correlated with a reduction in the length of the corresponding resident gene products. We show that relative genomic AT content, which has been identified as a factor influencing gene lengths in other systems, cannot explain gene length/genome size covariance observed in mitochondria. Our data are therefore in agreement with the idea that gene length evolves as a consequence of selection for smaller genomes, either to avoid accumulation of deleterious mutations or triggered by selection for a replication advantage.     

栽培大豆中一个线粒体atp6基因的分离与鉴定(英文)

线粒体ATP酶 (mtATPase)复合体在高等植物生命活动中起重要作用。从栽培大豆 (Glycinemax (L .)Merr.)中分离鉴定了一个新的mtATPase第六亚基 (EC 3.6 .1.34 )基因 (atp6 ) ,它编码具 2 2 3个氨基酸的ATP6亚基 ,是所有已克隆的atp6基因中最短的一个 ,并把它命名为atp6copy3(atp6_3)。通过对 9种栽培大豆的PCR分析及序列分析表明atp6_3广泛存在于栽培大豆中。以atp6_3为探针对大豆重组近交系的RFLP分析初步表明栽培大豆线粒体有父性遗传的可能性。水杨酸处理明显抑制atp6的表达 ,并对其可能作用进行了讨论     

Mitochondrial Ribosomal Protein L11 Gene of Dictyostelium discoideum Resides not in the Nuclear Genome but in the Mitochondrial Genome

During the course of analysis of the mitochondrial genome ofthe cellular slime mold, Dictyostelium discoideum, we founda gene (rpl11) for mitochondrial ribosomal protein L11 (RPL11),having 172 amino acid residues. Southern blot analysis revealedthat the gene resided in the mitochondrial DNA as a singlecopybut not in the nuclear DNA. From Northern blot experiments,one major mRNA (about 27 kb) and two minor mRNAs (about 4 and5 kb) for the gene were detected in the mitochondria. This isthe first report showing that the active gene for RPL11 stillresides in the mitochondrial genome and has not been transferredto the nuclear genome in D. discoideum.     

A Genome-Wide Map of Mitochondrial DNA Recombination in Yeast

In eukaryotic cells, the production of cellular energy requires close interplay between nuclear and mitochondrial genomes. The mitochondrial genome is essential in that it encodes several genes involved in oxidative phosphorylation. Each cell contains several mitochondrial genome copies and mitochondrial DNA recombination is a widespread process occurring in plants, fungi, protists, and invertebrates. Saccharomyces cerevisiae has proved to be an excellent model to dissect mitochondrial biology. Several studies have focused on DNA recombination in this organelle, yet mostly relied on reporter genes or artificial systems. However, no complete mitochondrial recombination map has been released for any eukaryote so far. In the present work, we sequenced pools of diploids originating from a cross between two different S. cerevisiae strains to detect recombination events. This strategy allowed us to generate the first genome-wide map of recombination for yeast mitochondrial DNA. We demonstrated that recombination events are enriched in specific hotspots preferentially localized in non-protein-coding regions. Additionally, comparison of the recombination profiles of two different crosses showed that the genetic background affects hotspot localization and recombination rates. Finally, to gain insights into the mechanisms involved in mitochondrial recombination, we assessed the impact of individual depletion of four genes previously associated with this process. Deletion of NTG1 and MGT1 did not substantially influence the recombination landscape, alluding to the potential presence of additional regulatory factors. Our findings also revealed the loss of large mitochondrial DNA regions in the absence of MHR1, suggesting a pivotal role for Mhr1 in mitochondrial genome maintenance during mating. This study provides a comprehensive overview of mitochondrial DNA recombination in yeast and thus paves the way for future mechanistic studies of mitochondrial recombination and genome maintenance.     

Apparent Selection Intensity for the Cytochrome Oxidase Subunit I Gene Varies with Mode of Reproduction in Echinoderms

When most amino acid substitutions in protein-coding genes are slightly deleterious rather than selectively neutral, life history differences can potentially modify the effective population size or the selective regime, resulting in altered ratios of non-synonymous to synonymous substitutions among taxa. We studied substitution patterns for the mitochondrial cytochrome oxidase subunit I (COI) gene in a sea star genus (Leptasterias spp.) with an obligate brood-protecting mode of reproduction and small-scale population genetic subdivision, and compared the results to available COI sequences in nine other genera of echinoderms with pelagic larvae: three sea stars, five sea urchins and one brittle star. We predicted that this life history difference would be associated with differences in the ratio of non-synonymous (dN) to synonymous (dS) substitution rates. Leptasterias had a significantly greater dN/dS ratio (both between species and within species), a significantly smaller transition/transversion rate ratio, and a significantly lower average nucleotide diversity within species, than did the non-brooding genera. Other explanations for the results, such as altered mutation rates or selective sweeps, were not supported by the data analysis. These findings highlight the potential influence of reproductive traits and other life history factors on patterns of nucleotide substitution within and between species.     

Subunit f of the Yeast Mitochondrial ATP Synthase: Topological and Functional Studies

Modified versions of subunit f were produced by mutagenesis of theATP17 gene of Saccharomyces cerevisiae. A version of subunit f devoid of thelast 28 amino acid residues including the unique transmembranous domaincomplemented the oxidative phosphorylation of the null mutant. However, atwo-fold decrease in the specific ATP synthase activity was measured andattributed to a decrease in the stability of the mutant ATP synthase complexas shown by the low oligomycin-sensitive ATPase activity at alkaline pH. Themodification or not by non-permeant maleimide reagents of cysteine residuesintroduced at the N and C termini of subunit f indicated aN_in-C_out orientation. From the C terminus of subunit fit was possible to cross-link subunit 4 (also called subunit b), which isanother component of the F₀ sector and which also displays a shorthydrophilic segment exposed to the intermembrane space.     

Effect of the protonmotive force on ATP-linked processes and mobilization of the bound natural ATPase inhibitor in beef heart submitochondrial particles

In an attempt to determine whether the natural ATPase inhibitor (IF₁) plays a role in oxidative phosphorylation, the time course of ATP synthesis and ATP hydrolysis in inside-out submitochondrial particles from beef heart mitochondria either possessing IF₁ (Mg-ATP particles) or devoid of IF₁ (AS particles) was investigated and compared to movements of IF₁, as assessed by an isotopic assay. The responses of the above reactions to preincubation of the particles in aerobiosis with NADH or succinate were as follows: (1) The few seconds lag that preceded the steady-rate phase of ATP synthesis was shortened and even abolished both in Mg-ATP particles and AS particles. The rate of ATP synthesis in the steady state was independent of the length of the lag. (2) ATPase was slowly activated, maximal activation being obtained after a 50-min preincubation; there was no direct link between the development of the protonmotive force (maximal within 1 sec) and ATPase activation. (3) Bound IF₁ was slowly released; the release of bound IF₁ as a function of the preincubation period was parallel to the enhancement of ATPase activity; the maximal amount of IF₁ released was a small fraction of the total IF₁ bound to the particles (less than 20%). (4) The double reciprocal plots of the rates of ATP and ITP hydrolysis vs. substrate concentrations that were curvilinear in the absence of preincubation with a respiratory substrate became linear after aerobic preincubation with the substrate. The data conclusively show that only ATPase activity in submitochondrial particles is correlated with the release of IF₁, and that the total extent of IF₁ release induced by respiration is limited. On the other hand, the kinetics of ATPase in control and activated particles are consistent with the existence of two conformations of the membrane-bound F₁-ATPase, directed to ATP synthesis or ATP hydrolysis and distinguishable by their affinity for IF₁.     

Molecular Phylogeny of the Chipmunk Genus Tamias Based on the Mitochondrial Cytochrome Oxidase Subunit II Gene

Complete sequences of the mitochondrial cytochrome oxidase subunit II gene were used to construct a phylogeny for 21 of the 25 currently recognized chipmunk species. Phylogenetic analyses indicate that T. striatus (subgenus Tamias, eastern United States) and T. sibiricus (subgenus Eutamias, Asia) are distantly related to the other species (subgenus Neotamias), which constitute a western North American radiation. We discuss and compare our molecular phylogeny to previous taxonomies and present a suggested classification of the species groups for the subgenus Neotamias.     

Domain Characterization and Interaction of the Yeast Vacuolar ATPase Subunit C with the Peripheral Stator Stalk Subunits E and G

The proton pumping activity of the eukaryotic vacuolar ATPase (V-ATPase) is regulated by a unique mechanism that involves reversible enzyme dissociation. In yeast, under conditions of nutrient depletion, the soluble catalytic V₁ sector disengages from the membrane integral V_o, and at the same time, both functional units are silenced. Notably, during enzyme dissociation, a single V₁ subunit, C, is released into the cytosol. The affinities of the other V₁ and V_o subunits for subunit C are therefore of particular interest. The C subunit crystal structure shows that the subunit is elongated and dumbbell-shaped with two globular domains (C_head and C_foot) separated by a flexible helical neck region (Drory, O., Frolow, F., and Nelson, N. (2004) EMBO Rep. 5, 1148–1152). We have recently shown that subunit C is bound in the V₁-V_o interface where the subunit is in contact with two of the three peripheral stators (subunit EG heterodimers): one via C_head and one via C_foot (Zhang, Z., Zheng, Y., Mazon, H., Milgrom, E., Kitagawa, N., Kish-Trier, E., Heck, A. J., Kane, P. M., and Wilkens, S. (2008) J. Biol. Chem. 283, 35983–35995). In vitro, however, subunit C binds only one EG heterodimer (Féthière, J., Venzke, D., Madden, D. R., and Böttcher, B. (2005) Biochemistry 44, 15906–15914), implying that EG has different affinities for the two domains of the C subunit. To determine which subunit C domain binds EG with high affinity, we have generated C_head and C_foot and characterized their interaction with subunit EG heterodimer. Our findings indicate that the high affinity site for EGC interaction is C_head. In addition, we provide evidence that the EGC_head interaction greatly stabilizes EG heterodimer.