线粒体基因组靶向编辑研究进展

线粒体作为细胞中重要的细胞器,其携带有自身的基因组。线粒体基因组发生突变后,可能导致人类疾病。开发靶向线粒体基因组的新型基因编辑工具在疾病治疗和疾病模型构建中具有重要意义。该文总结了线粒体基因编辑领域的进展,特别是近期以DdCBE和TALED为代表的重大进展;同时,也指出目前线粒体基因编辑工具仍然有一些缺点。该文拟为新型线粒体基因编辑工具的研发提供参考。     

后生动物线粒体基因组:起源、大小和基因排列进化

由于受到强烈的进化约束,后生动物线粒体基因组在大小和基因含量上一直保持稳定,相比之下核基因组则发生了巨大的改变。后生动物线粒体基因组结构的可塑性在一定程度上归功于可能由tRNA基因介导的基因重排事件,虽然亲缘关系密切的物种间也可能出现基因重排,但同门内的线粒体基因组仍趋向于具有类似的结构特征。我们对后生动物线粒体基因组的起源、大小和基因排列进化方面的特点进行了介绍。     

线粒体基因组的遗传与进化研究进展

线粒体基因组是当前生命科学的热门话题之一。文章根据国内外有关线粒体DNA的结构、表达过程和遗传特征方面的最新研究成果,重点介绍线粒体基因组与核基因组关系、线粒体遗传密码及基因组的进货线索等问题,并简要说明了线粒体基因组遗传分析的要点。     

基因组时代线粒体基因组拼装策略及软件应用现状

随着测序技术的不断发展,越来越多物种的全基因组数据被测定和广泛应用。在二代基因组数据爆发式增长的同时,除了核基因组数据,线粒体基因组数据也非常重要。高通量测序的全基因组序列中除了核基因组序列也包括线粒体基因组序列,如何从海量的全基因组数据中提取和拼装线粒体基因组序列并加以应用成为线粒体基因组在分子生物学、遗传学和医学等方面的研究方向之一。基于此,从全基因组数据中提取线粒体基因组序列的策略及相关的软件不断发展。根据从全基因组数据中锚定线粒体reads的方式和后续拼装策略的不同,可以分为有参考序列拼装方法和从头拼装方法,不同拼装策略及软件也表现出各自的优势和局限性。本文总结并比较了当前从全基因组数据中获得线粒体基因组数据的策略和软件应用,并对使用者在使用不同策略和相关软件方面给予建议,以期为线粒体基因组在生命科学的相关研究中提供方法上的参考。     

哺乳类线粒体基因组

作为真核细胞的一种重要细胞器的线粒体含有独立的并自主复制和转录的DNA基因组。虽然线粒体蛋白质的大部分系核DNA编码,但有一小部分是线粒体DNA(mt DNA)编码,并由线粒体的蛋白质合成系统合成。线粒体蛋白质合成系统中的rRNA和tRNA也是mt DNA编码。mt DNA的复制、转录以及蛋白质合成系统均有其本身特点,既与非线粒体真核系统有所不同,又有别于原核细胞中者。因此,线粒体基因组的研究在生物学上有重要意义。此外,线粒体的起源和进化是许多生物学家所感兴趣的和长期争论的问题,而mt DNA的进化比较     

哺乳类线粒体基因组

作为真核细胞的一种重要细胞器的线粒体含有独立的并自主复制和转录的DNA基因组。虽然线粒体蛋白质的大部分系核DNA编码,但有一小部分是线粒体DNA(mt DNA)编码,并由线粒体的蛋白质合成系统合成。线粒体蛋白质合成系统中的rRNA和tRNA也是mt DNA编码。mt DNA的复制、转录以及蛋白质合成系统均有其本身特点,既与非线粒体真核系统有所不同,又有别于原核细胞中者。因此,线粒体基因组的研究在生物学上有重要意义。此外,线粒体的起源和进化是许多生物学家所感兴趣的和长期争论的问题,而mt DNA的进化比较     

双斑萤叶甲基因组调研及线粒体基因组分析

双斑萤叶甲Monolepta hieroglyphica为杂食性鞘翅目害虫。近年来,该虫对我国农业的为害呈加重趋势,本文对双斑萤叶甲基因组进行调研及对线粒体基因组进行分析,为进一步的全基因组测序提供参考,并为双斑萤叶甲线粒体研究提供基础资料。本文采用Illumina Hiseq 2000测序平台对单只雌性双斑萤叶甲进行双末端测序,测序结果表明:双斑萤叶甲基因组大小约为2.4 Gb,重复序列含量约为52.61%,杂合率为0.67%,GC含量为30.29%。双斑萤叶甲基因组较大,但其基因组的杂合率和GC含量较低。利用基因组测序原始数据,借助NOVOPlasty软件直接提取基因组中线粒体基因组序列并进行组装,获得16 299 bp的双斑萤叶甲线粒体基因组。通过MITOS软件对线粒体基因组进行注释,斑萤叶甲线粒体基因组共有37个基因,包括13蛋白编码基因、22个转运RNA及2个核糖体RNA基因,以及1个非编码的控制区。其线粒体基因组基因排列方式与果蝇的模式排列相同,并未发生基因重排。进一步利用线粒体COX1蛋白构建的系统进化树,为双斑萤叶甲隶属于鞘翅目、多食亚目、叶甲科、萤叶甲亚科的分类地位提供了分子依据。并初步发现鞘翅目内各个物种遗传距离相对于昆虫纲下其它目的各个物种之间遗传距离较远。     

线粒体基因组:结构特点和基因含量进化

线粒体具有其自身的遗传系统——一个来自内共生的α-变形细菌祖先的基因组。线粒体基因组的生物学功能非常保守,仅涉及与线粒体有关的5个方面的过程:呼吸和氧化磷酸化、翻译、转录、RNA成熟和蛋白运输。真核生物线粒体基因含量的变化异常显著,在包括被子植物在内的各种真核生物相对频繁地发生线粒体基因丢失的同时,动物和某些植物类群的线粒体基因含量相对来说则比较稳定。tRNA基因含量的变化反映了线粒体对来自核的tRNA在使用上的差异,而蛋白基因含量的变化主要是由于功能性的基因转移到核所造成的。对线粒体基因组学领域中有关基因组起源、结构和基因含量进化方面的研究进行综述。     

蛹虫草线粒体DNA与细胞核DNA进化关系的比较

【目的】分析蛹虫草是否存在核内线粒体DNA片段,比较蛹虫草线粒体DNA与细胞核DNA的碱基变异程度及所反映的菌株间的系统发育关系。【方法】通过本地BLAST或LAST对蛹虫草线粒体基因组和核基因组进行序列相似性搜索;从10个已知线粒体基因组的蛹虫草菌株中分别扩增7个细胞核蛋白编码基因片段,并与其在14个线粒体蛋白编码基因上的碱基变异情况进行比较。【结果】蛹虫草核基因组中存在5处较短的核内线粒体DNA片段,总长只有278bp。蛹虫草核DNA的变异频率整体上高于线粒体DNA。核DNA和线粒体DNA所反映的蛹虫草菌株间的系统发育关系存在显著差异。【结论】蛹虫草线粒体DNA与核DNA间不存在长片段的基因交流,二者变异频率不同,所反映的蛹虫草菌株间的系统发育关系也有差异。本研究增加了对蛹虫草线粒体与细胞核DNA进化关系的认识。     

线粒体自噬的研究进展

由于线粒体在生物氧化和能量转换过程中会产生活性氧,线粒体DNA又比核DNA更容易发生突变,因此线粒体是一种比较容易受到损伤的细胞器.及时清除细胞内受损的线粒体对细胞维持正常的状态具有重要的作用.细胞主要通过自噬来清除损伤线粒体,维持细胞稳态.越来越多的研究表明,线粒体自噬是一种特异性的过程,线粒体通透性孔道通透性的改变在这个过程中起着重要的作用.线粒体自噬在维持细胞内线粒体的正常功能和基因组稳定性上起着重要作用,但是线粒体发生自噬的信号通路及其调控机制还有待进一步深入研究.     

线粒体DNA靶向治疗

线粒体(mitochondrion)是真核生物细胞中的一种非常重要的细胞器,含有独立于细胞核染色体外的遗传物质,通过氧化磷酸化产生ATP,是细胞的能量工厂,与细胞分化、信号转导、代谢稳态等过程密切联系。线粒体功能的紊乱与癌症、神经退行性疾病、糖尿病等许多疾病的发生、发展及治疗息息相关。线粒体在细胞命运中扮演的关键角色,使对线粒体这一特殊细胞器的探索成为生命科学研究热点之一。人线粒体DNA(mitochondrial DNA, mtDNA)是一相对保守且仅16 kb的环状双链DNA分子,只含37个基因,但这些基因都是维持线粒体功能稳定必不可少的部分。随着对线粒体功能认识的不断深入,研究人员发现mtDNA突变,会导致活性氧自由基过量产生,从而引起细胞衰老,甚至引发诸多疾病,例如遗传性视神经病变、线粒体脑肌病伴高乳酸血症和卒中样发作综合征等。但是,目前针对这些线粒体基因疾病尚无非常有效的治疗手段。为了进一步了解这一关键细胞器,研究人员开发了一些有效的方法来突破线粒体的复杂屏障。本文将重点介绍并讨论近几年靶向mtDNA的研究进展,主要从药物修饰、材料递送、基因编辑等方面进行了总结,希望能为推动线粒体的研究提供一些新的思路。     

Metabolic maps and functions of the Plasmodium mitochondrion

The mitochondrion of Plasmodium species is a validated drug target. However, very little is known about the functions of this organelle. In this review, we utilize data available from the Plasmodium falciparum genome sequencing project to piece together putative metabolic pathways that occur in the parasite, comparing this with the existing biochemical and cell biological knowledge. The Plasmodium mitochondrion contains both conserved and unusual features, including an active electron transport chain and many of the necessary enzymes for coenzyme Q and iron-sulphur cluster biosynthesis. It also plays an important role in pyrimidine metabolism. The mitochondrion participates in an unusual hybrid haem biosynthesis pathway, with enzymes localizing in both the mitochondrion and plastid organelles. The function of the tricarboxylic acid cycle in the mitochondrion is unclear. We discuss directions for future research into this fascinating, yet enigmatic, organelle.     

Organization of heterogeneous mitochondrial DNA molecules in mitochondrial nuclei of cultured tobacco cells

Summary The molecular size of mitochondrial DNA (mtDNA) molecules and the number of copies of mtDNA per mitochondrion were evaluated from cultured cells of the tobacco BY-2 line derived fromNicotiana tabacum L. cv. Bright Yellow-2. To determine the DNA content per mitochondrion, protoplasts of cultured cells were stained with 4,6-diamidino-2-phenylindole (DAPI), and the intensity of the fluorescence emitted from the mitochondrial nuclei (mt-nuclei) was measured with a video-intensified photon counting microscope system (VIM system). Each mitochondrion except for those undergoing a division contained one mt-nucleus. The most frequently measured size of the DNA in the mitochondria was between 120 and 200 kilobase pairs (kbp) throughout the course of culture of the tobacco cells. Mitochondria containing more than 200 kbp of DNA increased significantly in number 24 h after transfer of the cells into fresh medium but their number fell as the culture continued. Because division of mitochondria began soon after transfer of the cells into fresh medium and continued for 3 days, the change of the DNA content per mitochondrion during the culture must correspond to DNA synthesis of mitochondria in the course of mitochondrial division. By contrast, the analyses of products of digestion by restriction endonucleases indicated that the genome size of the mtDNA was at least 270 kbp. Electron microscopy revealed that mtDNAs were circular molecules and their length ranged from 1 to 35 m, and 60% of them ranged from 7 to 11 rn. These results indicate that the mitochondrial genome in tobacco cells consists of multiple species of mtDNA molecules, and mitochondria do not contain all the mtDNA species. Therefore, mitochondria are heterogeneous in mtDNA composition.Abbreviations DAPI 4, 6-diamidino-2-phenylindole - mtDNA mitochondrial DNA - mt-genome mitochondrial genome - mt-nucleus mitochondrial nucleus - ptDNA proplastid DNA - pt-nucleus proplastid nucleus - VIM system video-intensified photon counting microscope system     

在小鼠发育过程中线粒体基因组新型R环的表达

本实验室在成年小鼠线粒体DNA(mtDNA)D环上发现了一个新颖的轻链RNA转录本,这个RNA能够同DNA双链结合,形成一个稳定的DNA-RNA杂合结构(R环)。在此基础上,利用RT-PCR和Northern印迹法检测了小鼠线粒体基因组中R环的时空表达的特点。发现R环在小鼠不同组织、不同发育阶段中的表达水平有差异,其表达模式具有分化的位相性和时序性,提示R环有可能作为参与调控线粒体基因表达的分子,因而具有重要意义。     

重构胚中线粒体命运的研究进展

线粒体是哺乳动物细胞中最为重要的细胞器之一,是除细胞核外惟一含有功能性基因组的细胞器,通过氧化磷酸化产生维持细胞正常生理功能的ATP。重构胚中线粒体的命运及线粒体与供体核间的互作关系已越来越成为研究的焦点,综述了同种、异种核移植,ICSI,卵胞质移植及异源线粒体注射后,重构胚中线粒体的命运。     

Sequencing of the Dutch Elm Disease Fungus Genome Using the Roche/454 GS-FLX Titanium System in a Comparison of Multiple Genomics Core Facilities

As part of the DNA Sequencing Research Group of the Association of Biomolecular Resource Facilities, we have tested the reproducibility of the Roche/454 GS-FLX Titanium System at five core facilities. Experience with the Roche/454 system ranged from <10 to >340 sequencing runs performed. All participating sites were supplied with an aliquot of a common DNA preparation and were requested to conduct sequencing at a common loading condition. The evaluation of sequencing yield and accuracy metrics was assessed at a single site. The study was conducted using a laboratory strain of the Dutch elm disease fungus Ophiostoma novo-ulmi strain H327, an ascomycete, vegetatively haploid fungus with an estimated genome size of 30–50 Mb. We show that the Titanium System is reproducible, with some variation detected in loading conditions, sequencing yield, and homopolymer length accuracy. We demonstrate that reads shorter than the theoretical minimum length are of lower overall quality and not simply truncated reads. The O. novo-ulmi H327 genome assembly is 31.8 Mb and is comprised of eight chromosome-length linear scaffolds, a circular mitochondrial conti of 66.4 kb, and a putative 4.2-kb linear plasmid. We estimate that the nuclear genome encodes 8613 protein coding genes, and the mitochondrion encodes 15 genes and 26 tRNAs.     

The mitochondrial gene encoding ribosomal protein S12 has been translocated to the nuclear genome in Oenothera.

The Oenothera mitochondrial genome contains only a gene fragment for ribosomal protein S12 (rps12), while other plants encode a functional gene in the mitochondrion. The complete Oenothera rps12 gene is located in the nucleus. The transit sequence necessary to target this protein to the mitochondrion is encoded by a 5'-extension of the open reading frame. Comparison of the amino acid sequence encoded by the nuclear gene with the polypeptides encoded by edited mitochondrial cDNA and genomic sequences of other plants suggests that gene transfer between mitochondrion and nucleus started from edited mitochondrial RNA molecules. Mechanisms and requirements of gene transfer and activation are discussed.     

Sperm Mitochondria in Reproduction： Good or Bad and Where Do They Go？

The mitochondrion is the major energy provider to power sperm motility. In mammals, aside from the nuclear genome, mitochondrial DNA （mtDNA） also contributes to oxidative phosphorylation to impact production of ATP by coding 13 polypeptides. However, the role of sperm mitochondria in fertilization and its final fate after fertilization are still controversial. The viewpoints that sperm bearing more mtDNA will have a better fertilizing capability and that sperm mtDNA is actively eliminated during early embryogenesis are widely accepted. However, this may be not true for several mammalian species, including mice and humans. Here, we review the sperm mitochondria and their mtDNA in sperm functions, and the mechanisms of maternal mitochondrial inheritance in mammals.     

一种棉花线粒体DNA的提取方法

线粒体是重要的细胞器,它有自身的基因组。其基因组DNA与细胞核基因组DNA相比,含量较低。棉花当中富含棉酚、丹宁等物质,这对提取DNA有很大的影响。因此我们根据棉花自身的特点,找到了一种提取棉花线粒体DNA经济有效的方法,其质量可以满足限制性酶切、PCR、分子杂交等实验的要求。