Deletion bias in avian introns over evolutionary timescales

The role that introns play in the function and evolution of nuclear genomes is not fully understood. Recent models of intron evolution suggest that selection and drift may interact to maintain introns in multicellular organisms. In addition, deletion mutations are more likely to become fixed than insertion mutations. Examination of indel substitutions over macroevolutionary timescales in pigeons and doves (Aves: Columbiformes) reveals that deletion substitutions outnumber insertion substitutions by over six times. The length of indel events is variable.     

Bioenergetics in human evolution and disease: implications for the origins of biological complexity and the missing genetic variation of common diseases

Two major inconsistencies exist in the current neo-Darwinian evolutionary theory that random chromosomal mutations acted on by natural selection generate new species. First, natural selection does not require the evolution of ever increasing complexity, yet this is the hallmark of biology. Second, human chromosomal DNA sequence variation is predominantly either neutral or deleterious and is insufficient to provide the variation required for speciation or for predilection to common diseases. Complexity is explained by the continuous flow of energy through the biosphere that drives the accumulation of nucleic acids and information. Information then encodes complex forms. In animals, energy flow is primarily mediated by mitochondria whose maternally inherited mitochondrial DNA (mtDNA) codes for key genes for energy metabolism. In mammals, the mtDNA has a very high mutation rate, but the deleterious mutations are removed by an ovarian selection system. Hence, new mutations that subtly alter energy metabolism are continuously introduced into the species, permitting adaptation to regional differences in energy environments. Therefore, the most phenotypically significant gene variants arise in the mtDNA, are regional, and permit animals to occupy peripheral energy environments where rarer nuclear DNA (nDNA) variants can accumulate, leading to speciation. The neutralist–selectionist debate is then a consequence of mammals having two different evolutionary strategies: a fast mtDNA strategy for intra-specific radiation and a slow nDNA strategy for speciation. Furthermore, the missing genetic variation for common human diseases is primarily mtDNA variation plus regional nDNA variants, both of which have been missed by large, inter-population association studies.     

基于线粒体控制区的滇金丝猴群体遗传学研究

滇金丝猴（Rhinopithecus bieti）是我国著名的濒危保护动物。迄今为止,关于滇金丝猴并基于DNA序列的的群体遗传学研究还没有报道。 本文测定了来自于云南省维西县滇金丝猴群体样本的线粒体控制区全序列以及部分个体的细胞色素b全序列。在排除了核线粒体假基因存在的可能性之后,滇金丝猴维西群体内部被确认存在着两个序列分歧较大的分枝。 即使如此,如果考虑到群体结构和迁移的影响,维西群体的遗传多样性水平可能并不高。

     

对虾白斑综合征病毒中国地方株变异区基因的比较

对虾白斑综合征病毒(White spot syndromevirus,WSSV)是对虾养殖的主要病原之一,它是目前发现的基因组最大的动物病毒,为环状双链DNA病毒[1,2],全基因组序列分析结果显示,对虾白斑综合征病毒和其他杆状病毒相差甚远,最新病毒分类报告已将该病毒划归新建立的线头病毒科(Nima-viridae)白斑病毒属(Whispovirus)[3,4]。目前Gen-Bank公布有3个版本的WSSV全序列[1,2],其基因组大小的测定结果相差较大。不同的WSSV毒株可能在形态结构、理化性质上无法区分,但病毒基因组限制酶切片段长度多态性(RFLP)可以将之区分开来,Marks等[6,7]通过计…     

玉米S组细胞质雄性不育线粒体R区序列与多型性分析

玉米Ｓ组细胞难性不育（ＣＭＳ）可能与线粒体基因组中的Ｒ区域有关。对不同核背景下唐徐、双２种Ｓ胞质的线粒体ＤＮＡ以Ｒ区特异探针的Ｓｏｕｔｈｅｒｎ分析发现均有６．７ｋｂ、４．５ｋｂ、１．８ｋｂ的３条谱带,分别对应于２种位于线粒体基因组中间的类型和１个线性末端,并且核背景对这３种不同形式的Ｒ区域的量有影响。对Ｍｏ１７和７７核背景下Ｎ、Ｔ、Ｃ４种胞质１７种材料的玉米线粒体基因组中Ｒ区的Ｓｏｕｔｈｅｒｎ分析     

线粒体的分子进化与氧效应

线粒体通常被认为是消耗氧气产生ATP的细胞器.但自然界有多种生物具有厌氧型线粒体,其厌氧生物化学和遗传学研究表明,线粒体可能来源于兼性厌氧的α-蛋白细菌,在有氧环境中,起始共生体的厌氧功能丧失或被改变而进化成为经典的线粒体,但在厌氧环境中,有氧呼吸功能丧失了进化.厌氧型线粒体为了完成能量的转化,改变了呼吸链的组成,表现出产能模式的多样性.而经典线粒体在利用氧化反应获得能量的同时,也通过电子漏产生了自由基,对生命体本身构成了威胁.事实上,生命体呼吸链的进化是沿着不断加强对氧的利用效率和不断克服氧毒性的方向发展的.     

鱼类线粒体DNA研究新进展

线粒体DNA是分子生物学研究中的一个热门领域,已成为鱼类进化生物学和群体遗传学研究的重要分子遗传标记。本文对鱼类线粒体DNA分子生物学的最新研究进展进行了较详细的阐述。重点介绍鱼类线粒体DNA全序列的研究进展、组成及特征,鱼类线粒体DNA非编码区结构研究进展,鱼类线粒体DNA多态性及其主要的检测方法;综述了最近有关鱼类线粒体DNA在鱼类系统学、种间杂交渐渗、种群识别、起源和进化、地理分化等研究中的应用情况。     

线粒体蛋白质组及蛋白质量控制

线粒体是哺乳动物细胞内重要细胞器,不仅通过氧化磷酸化产生ATP为细胞提供能量,也参与调节钙离子稳态、活性氧(reactive oxygen species,ROS)的产生、细胞应激反应和细胞死亡等过程,其功能障碍不仅导致多种人类疾病的发生,而且也能降低动物卵母细胞质量和早期胚胎发育能力.大量证据表明,线粒体的功能依赖于...     

广东地区汉族群体线粒体DNA 9bp序列缺失频率研究

旨在研究中国广东省部分地区汉族人群线粒体DNA RegionⅤ9bp序列缺失情况.采用PCR-PAGE和直接测序法对3个群体144份样本mtDNA RegionⅤ进行序列分析.结果只检测到标准型和短型(即9 bp缺失)两种多态.广东汉族人群的平均缺失频率为21.5%,广州、东莞和湛江汉族人群的缺失频率依次为20.8%、19.2%和25.0%.由此得出,广东汉族人群mtDNA 9 bp缺失频率较高,与其它地区汉族群体存在一定的差异.     

突变在基因组进化中的意义

在漫长的进化历史中,各物种间和物种内基因组的差异是如何形成、积累乃至保留下来的,不仅是进化生物学中需要解决的核心问题,也是整个生命科学面临的基本问题之一。对该问题的探求必然要通过对突变的深入了解,因为突变不仅是基因组进化的重要驱动力,还是基因 组进化研究的基础。文章围绕突变的性质及其在基因组进化中的深远意义,系统介绍了国际上相关研究的发展历程,所获得的成果和最新动向。     

Mitochondrial diseases preferentially involve proteins with prokaryote homologues

The comparison of each of the 393 nuclear-encoded human mitochondrial proteins annotated in the SwissProt databank with 256,953 proteins from 94 prokaryote species showed that two thirds of the mitochondrial proteome were homologous with prokaryotic proteins, whereas one third was not. Prokaryotic mitochondrial proteins differ markedly from eukaryotic proteins, particularly in regard to their size, localization, function, and mitochondrial-targeting N-terminal sequence. Remarkably, the majority of nuclear genes implicated in respiratory chain mitochondrial diseases were found to be of prokaryotic ancestry. Our study indicates that the investigation of the co-evolution of eukaryotic and prokaryotic mitochondrial proteins should lead to a better understanding of mitochondrial diseases.     

Molecular phylogeny and plumage evolution in gulls (Larini)

We used DNA sequence data of the mitochondrial control region and cytochrome b gene to assess phylogenetic relationships among 32 gull species and two outgroup representatives. We tentatively estimated divergence times from transversional substitutions calibrated against DNA–DNA hybridization data. Several strongly supported species groups are identified, but the relationships between these species groups and the rooting of the gull tree remain unresolved. Geographical range extension appears as a factor of speciation, but several related, well‐differentiated species seem to have evolved within comparatively restricted areas. Some plumage characters used in the past for delimiting species groups appear inappropriate. The dark hooded species, for instance, do not constitute a natural assemblage. Molecular data also allowed the identification of several striking plumage convergences that had obscured the true relationships between gull species until now. For example, the dark tropical gulls analysed here each belong to totally different clades and are independent examples of convergent plumage evolution under common environmental constraints. The reverse situation also happened, with two arctic‐distributed species, the ivory gull (Pagophila eburnea) and the Sabine’s gull (Xema sabini), appearing as sister taxa despite completely different plumage features. Molecular data have thus significantly improved our understanding of gull evolution.     

基于转录组分析的染色体大片段缺失及其对井冈霉素高产菌株的影响

【目的】测试大片段删减低转录区域对菌体生长和井冈霉素产量的影响。【方法】通过转录组分析,选择染色体上连续的基因低转录区域进行大片段缺失,通过Cre-loxP位点特异性重组得到1.2 Mb片段缺失突变株LCY-4。HPLC检测缺失株井冈霉素产量的变化,并测定干重绘制生长曲线。【结果】通过转录组分析,我们在井冈霉素高产菌株TL01染色体左侧末端发现了1.9 Mb的连续基因低转录区,使用Cre-loxP系统对其中的1.2 Mb区域进行大片段缺失,成功得到了1.2 Mb缺失突变株LCY-4。和出发菌株TL01相比,缺失突变株LCY-4中井冈霉素发酵产量基本保持不变,生物量有显著提高,最高增幅达到44%。【结论】1.2 Mb区域的成功缺失,意味着基于转录组分析寻找连续的基因低转录区域并加以缺失的策略的可行性。1.2 Mb片段缺失对菌体生物量积累具有明显促进作用,为后续将其开发成氨基环醇类药物异源表达的通用高产宿主奠定了基础。     

Hydrogenosomes: convergent adaptations of mitochondria to anaerobic environments

Hydrogenosomes are membrane-bound organelles that compartmentalise the final steps of energy metabolism in a number of anaerobic eukaryotes. They produce hydrogen and ATP. Here we will review the data, which are relevant for the questions: how did the hydrogenosomes originate, and what was their ancestor? Notably, there is strong evidence that hydrogenosomes evolved several times as adaptations to anaerobic environments. Most likely, hydrogenosomes and mitochondria share a common ancestor, but an unequivocal proof for this hypothesis is difficult because hydrogenosomes lack an organelle genome - with one remarkable exception (Nyctotherus ovalis). In particular, the diversity of extant hydrogenosomes hampers a straightforward analysis of their origins. Nevertheless, it is conceivable to postulate that the common ancestor of mitochondria and hydrogenosomes was a facultative anaerobic organelle that participated in the early radiation of unicellular eukaryotes. Consequently, it is reasonable to assume that both, hydrogenosomes and mitochondria are evolutionary adaptations to anaerobic or aerobic environments, respectively.     

Tom22', an 8-kDa trans-site receptor in plants and protozoans, is a conserved feature of the TOM complex that appeared early in the evolution of eukaryotes

One of the earliest events in the evolution of mitochondriawas the development a means to translocate proteins made inthe cytosol into the "protomitochondrion." How this was achievedremains uncertain, and the nature of the earliest version ofthe protein translocation machinery is not known. Comparativesequence analysis suggests three subunits, Tom40, Tom7, andTom22 as common elements of the protein translocase in the mitochondrialouter membrane in diverse extant eukaryotes. Tom22, the 22-kDasubunit, plays a critical role in the function of this complexin fungi and animals, and we show that an 8-kDa subunit of theplant translocase is a truncated form of Tom22. It has a singletransmembrane segment conforming in sequence to the same regionof Tom22 from other eukaryotic lineages and a short carboxy-terminaltrans domain located in the mitochondrial intermembrane space.The trans domain from the Arabidopsis thaliana protein functionsin yeast lacking their own Tom22 by complementing protein importdefects and restoring cell growth. Moreover, we have identifiedorthologs of Tom22, Tom7, and Tom40 in diverse eukaryotes suchas the diatom Phaeodactylum tricornutum, the amoebic slime Dictyosteliumdiscoideum, and the protozoan parasite Plasmodium falciparum.This finding strongly suggests these subunits as the core ofthe protein translocase in the earliest mitochondria.