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。     

The Relationship Between the Rate of Molecular Evolution and the Rate of Genome Rearrangement in Animal Mitochondrial Genomes

Evolution of mitochondrial genes is far from clock-like. The substitution rate varies considerably between species, and there are many species that have a significantly increased rate with respect to their close relatives. There is also considerable variation among species in the rate of gene order rearrangement. Using a set of 55 complete arthropod mitochondrial genomes, we estimate the evolutionary distance from the common ancestor to each species using protein sequences, tRNA sequences, and breakpoint distances (a measure of the degree of genome rearrangement). All these distance measures are correlated. We use relative rate tests to compare pairs of related species in several animal phyla. In the majority of cases, the species with the more highly rearranged genome also has a significantly higher rate of sequence evolution. Species with higher amino acid substitution rates in mitochondria also have more variable amino acid composition in response to mutation pressure. We discuss the possible causes of variation in rates of sequence evolution and gene rearrangement among species and the possible reasons for the observed correlation between the two rates. [Reviewing Editor: Dr. David Pollock]     

植物抗旱基因及其在草坪草中的应用

从植物抗旱的生物学原理、渗透调节物质、清除活性氧、保护生物大分子及其膜结构的蛋白质、转录因子及其他酶类的基因工程等方面综述了目前抗旱基因研究的进展以及存在的一些问题。     

石蜡包埋组织的DNA提取及其在免疫球蛋白基因重排分析中的应用

基因重排分析在淋巴瘤诊断中具有重要意义.文章应用改良DNA提取方法,从30例淋巴增生性病变石蜡包埋组织获得的DNA虽有不同程度的降解,但适于PCR扩增Ig重链基因重排分析;约1/3病例提出高分子量DNA,可用于DNA印迹杂交.因此,石蜡包埋组织同样可为某些疾患,如淋巴瘤疑难和罕见病例的回顾性分子病理学研究提供基因诊断的DNA来源.     

Plant Mitochondrial Genome Evolution and Cytoplasmic Male Sterility

Mitochondria are responsible for providing energy currency to life processes in the molecular form of ATP and are therefore typically referred to as the power factories of cells. Plant mitochondria are also relevant to the common phenomenon of cytoplasmic male sterility, which is agronomically important in various crop species. Cytoplasmic male sterility (CMS) is a complex trait that may be influenced by patterns of mitochondrial genome evolution, and by intergenomic gene transfer among the organellar and nuclear compartments of plant cells. Here, we review patterns and processes that shape plant mitochondrial genomes, some relevant interactions between organelles, and the general features shared by the majority of cytoplasmic male-sterile genes in plants to further the goal of understanding CMS.     

草鱼生肌因子5基因的克隆及其组织表达谱分析

目的:获得草鱼生肌因子5(Myf-5)基因序列,分析其在草鱼不同组织和不同发育阶段中的表达规律。方法:根据鲤鱼Myf-5基因序列设计引物,用草鱼肌肉组织总RNA,经RT-PCR扩增其Myf-5基因序列;利用半定量RT-PCR分析草鱼Myf-5基因在草鱼不同组织和不同发育阶段的mRNA表达特性。结果:获得了草鱼Myf-5基因开放读框序列723 bp,GenBank登录号为GU290227;该基因编码由240个氨基酸残基组成的蛋白,具有MyoD家族基因的典型性碱性螺旋-环-螺旋(bHLH)结构,其氨基酸序列与斑马鱼、鲤鱼、虹鳟、大西洋鲑等的同源性较高(74%~97%),与哺乳动物和禽类如人、小鼠、大鼠、猪、牛和鸡的同源性较低(56%~60%);在草鱼红肌、白肌、肝胰脏、肾脏、脑和肠中均检测到Myf-5基因的表达,红肌、白肌和脑组织中Myf-5基因mRNA的表达量显著高于其他组织(P<0.05);草鱼Myf-5基因的表达随着其生长发育呈下降趋势,在较大规格试验鱼(500 g)中的表达显著低于其他2种规格(50~60 g、120~130 g)的试验鱼(P<0.05)。结论:获得了草鱼Myf-5基因序列,其在红肌、白肌和脑组织中的表达量显著高于其他组织,并随生长发育呈下降趋势,为研究Myf-5在草鱼肌肉发育过程中的作用提供了基础资料。     

基于支持向量机的细菌基因组水平转移基因预测

随着各种生物基因组序列测定工作的完成,大量的DNA序列数据涌现出来,为研究在基因组中寻找水平转移基因提供了极大的便利.将基因序列特征分析和支持向量机技术结合起来,通过分析基因序列的特征差异发现水平转移基因.依据以前研究工作的基础,选取了绝对密码子使用频率(FCU)作为序列特征,主要因为它既包含了基因密码子使用偏性的信息,也包含了基因所编码蛋白的氨基酸组成信息,支持向量机利用这些信息进行水平转移基因分析和预测,可以提高预测的准确性.另外,提出了基于分链的水平转移基因预测新方法,即将细菌基因组前导链和滞后链上的基因区别对待,分别进行水平转移基因预测.结果显示,基本预测方法要优于目前预测结果最好的Tsirigos等提出的基于八联核苷酸频率的打分算法,命中率的相对提高率最高达31.47%,而基于分链的方法对水平转移基因的预测取得了更好的结果.     

草鱼连续两代的雌核发育群体及湘江流域群体基因组DNA的微卫星比较分析

对湘江流域草鱼群体,一代及连续两代极体型人工诱导雌核发育草鱼群体基因组DNA的微卫星引物统计分析结果表明:湘江流域草鱼群体存在一定程度的遗传多态性;大多数被检测的微卫星位点上存在两个以上的等位基因,但遗传多样性程度较低。一代人工诱导雌核发育草鱼群体中个体的基因位点已基本纯合,但就整个群体而言,个体之间的基因型还不完全一致,表现出一定的多态性。连续两代人工诱导雌核发育草鱼群体中不仅所检测个体的基因位点已完全纯合,并且各个体的基因型也完全相同。这些观察结果说明所检测的两代人工诱导雌核发育草鱼群体是纯合的,经连续两代人工诱导雌核发育可能建立起草鱼纯系。该实验结果还发现不仅草鱼的微卫星位点上存在等位基因的多态性,而且微卫星位点本身也存在多态性;在人工诱导草鱼雌核发育的过程中不仅存在微卫星等位基因快速丢失的现象,而且也存在微卫星位点丢失的现象。因此,加强对自然水体中草鱼种质资源多样性的保护和利用各种现代生物学技术纯化、筛选和组合优良性状基因,是草鱼遗传育种中同样重要和不可或缺的两个方面。     

Bacterial Protein Interaction Networks: Connectivity is Ruled by Gene Conservation,Essentiality and Function

BackgroundProtein-protein interaction (PPI) networks are the backbone of all processes in living cells. In this work, we relate conservation, essentiality and functional repertoire of a gene to the connectivity k (i.e. the number of interactions, links) of the corresponding protein in the PPI network.MethodsOn a set of 42 bacterial genomes of different sizes, and with reasonably separated evolutionary trajectories, we investigate three issues: i) whether the distribution of connectivities changes between PPI subnetworks of essential and nonessential genes; ii) how gene conservation, measured both by the evolutionary retention index (ERI) and by evolutionary pressures, is related to the connectivity of the corresponding protein; iii) how PPI connectivities are modulated by evolutionary and functional relationships, as represented by the Clusters of Orthologous Genes (COGs).ResultsWe show that conservation, essentiality and functional specialisation of genes constrain the connectivity of the corresponding proteins in bacterial PPI networks. In particular, we isolated a core of highly connected proteins (connectivities k≥40), which is ubiquitous among the species considered here, though mostly visible in the degree distributions of bacteria with small genomes (less than 1000 genes).ConclusionThe genes that support this highly connected core are conserved, essential and, in most cases, belong to the COG cluster J, related to ribosomal functions and the processing of genetic information.     

苏云金芽孢杆菌vip3A基因的检测及保守性分析

Vip3A蛋白是苏云金芽孢杆菌(Bacillus thuringiensis,Bt)在营养期分泌的一类新型杀虫蛋白。用PCR方法从114个Bl菌株和41个Bl标准菌株中筛选到39株即约25％的菌株含有vip3A基因。利用所制备的Vip3A蛋白的多克隆抗体对以上含有vip3A基因的Bt菌株进行Western印迹分析,发现多数PCR反应为阳性的菌株都产生89kD大小的蛋白,其中有4株没有Vip3A蛋白的表达。从以上菌株中挑选2个对夜蛾科害虫具有较高和较低毒力的菌株,即S101和6ll,并分别进行vip3A基因的克隆和测序,再与GenBank上所登录的其它6个全长vip3A基因和2个已报道的但未登录GenBank的vip3A基因进行核苷酸和氨基酸序列比较,结果表明,vip3A是一个极其保守的基因。将以上所克隆的2个却3A基因即vip3A—S101和vip3A-611分别插入表达载体pQE30构建了表达质粒pOTP-S101和pOTP-6ll,转化到大肠杆菌M15,经lmmol／L IPTG诱导后均表达89kD大小的Vip3A蛋白。蛋白可溶性试验表明,Vip3A-S101和Vip3A-611分别有48％和35％的蛋白是可溶的。将Vip3A-S101和Vip3A-6ll蛋白和已报道的Vip3A—S184蛋白对初孵斜纹夜蛾(Spodoptera litura)幼虫进行生物测定,结果表明,3个Vip3A蛋白对斜纹夜蛾幼虫毒力没有显著性差异,这说明了Vip3A个别氨基酸的变化对蛋白的杀虫活性没有影响。     

Base Composition Skews, Replication Orientation, and Gene Orientation in 12 Prokaryote Genomes

Variation in GC content, GC skew and AT skew along genomic regions was examined at third codon positions in completely sequenced prokaryotes. Eight out of nine eubacteria studied show GC and AT skews that change sign at the origin of replication. The leading strand in DNA replication is G-T rich at codon position 3 in six eubacteria, but C-T rich in two Mycoplasma species. In M. genitalium the AT and GC skews are symmetrical around the origin and terminus of replication, whereas its GC content variation has been shown to have a centre of symmetry elsewhere in the genome. Borrelia burgdorferi and Treponema pallidum show extraordinary extents of base composition skew correlated with direction of DNA replication. Base composition skews measured at third codon positions probably reflect mutational biases, whereas those measured over all bases in a sequence (or at codon positions 1 and 2) can be strongly affected by protein considerations due to the tendency in some bacteria for genes to be transcribed in the same direction that they are replicated. Consequently in some species the direction of skew for total genomic DNA is opposite to that for codon position 3. Received: 2 February 1998 / Accepted: 15 June 1998     

Conservation and Periodicity of DNA Bend Sites in Eukaryotic Genomes

DNA bend sites appear every 680 bp on average in the human -and ß-globin gene regions. Although most of theirmolecular nature has not been unraveled, a potential bend coresequence A₂N₈A₂N₈A₂ (A/A/A) and its complementary T₂N₈T₂N₈T₂(T/T/T) appeared preferentially either in or very close to mostof the bend sites, whereas other combinations of A₂ and T₂ dinucleotides,A/T/T + A/A/T, T/T/A + T/A/A and A/T/A + T/A/T, did not. Thedistances between any two of the core sequences in the entireß-globin locus showed a strong bias to a length of701–800 bp and multiples thereof, suggesting that thereis periodicity throughout the locus. This bias was not foundfor other combinations of A₂ and T₂. Again, this periodicitywas identified in many eukaryotic genes, whereas the tendencywas absent in mRNAs and prokaryotic as well as viral genomes.     

Pervasiveness of Gene Conservation and Persistence of Duplicates in Cellular Genomes

In this work detailed statistics on ancestral gene duplication and gene conservation in completely sequenced cellular genomes are presented. Analysis of open reading frame (ORF) products having simultaneous matches in several distinct organisms showed a significant correlation between duplication and conservation. Systematic comparisons of predicted proteomes of 23 organisms (including 20 that have been completely sequenced), have allowed us to quantify the degree of ancestral duplication within each genome and the level of conservation between genomes, using threshold values calculated for individual organisms. Statistical analysis of various gene proportions revealed interesting trends in gene structure and evolution, such as that (a) more than one-quarter (25%–66%) of the predicted ORF products of the surveyed organisms are not unique, indicating a high level of ancestral duplications; (b) levels of exclusive conservation within Bacteria are higher than those within the eukaryal or archaeal domains; and (c) at least one-half (47–99%) of the total predicted ORF products in the surveyed genomes have one or several highly significant matches in another genome. Significant matches are based on simulations taking into account the mean size of ORF products and the composition of each target organism's proteome. The methodology we have developed ensures stability and comparability of our results as the number of completely sequenced genomes increases. Received: 4 May 1998 / Accepted: 28 September 1998     

动物中microRNA 的保守性和进化历程

microRNA 是一类长度约为22 个核苷酸的内源性非编码单链RNA, 在后生动物中普遍存在, 在转录后过程调控基因表达. miRNA 在个体发育过程中发挥着各种功能, 如发育时序调控和细胞分化、神经发育等. miRNA 在各种后生动物中具有保守性, 而且多个关键类群的出现皆伴随着大量新miRNA 的产生, 这些现象都表明miRNA 与动物的系统发生密切相关. 本文从miRNA 的产生和作用机制、在后生动物中的分布格局及其在个体发育中的调控功能3 个方面论述了miRNA 的保守性, 并结合miRNA 的发生和发展历程, 探讨了miRNA 在动物进化中起到的重要作用.     

酿酒酵母进级进化过程中的基因丢失现象初探

酿酒酵母进级进化过程中的基因丢失问题很少被研究．利用现有的蛋白质数据库，通过设定判断标准，预期可以获得更多这方面的案例以便进行相关问题的研究．利用SMART蛋白质域家族数据库，根据在已完成测序的7种真核生物蛋白质域家族成员中存在或不存在酿酒酵母蛋白质域信号，判断是否发生了基因丢失．通过这种方法，共有6个酿酒酵母基因判断为在进级进化过程中发生了丢失，还探讨了这些基因发生丢失的可能机制．     

东北地区抗肌营养不良蛋白基因缺失的研究及应用

为了解东北地区Duchenne／Becker型肌营养不良症患者基因缺失的分布及进行产前基因诊断,用12对引物以多重PCR法检测120例DMD／BMD患者,并分析缺失型患者dystrophin基因的断裂点分布及各引物优化组合,并将高危男性胎儿行缺失检测。结果表明,缺失检出率为49．2％,66．4％的断裂点位于内含子44～52内,以内含子50为最多(14．8％),4对外显子引物的优化组合为外显子48、51、45和8,总检出率为41．7％;29例高危胎儿中9例男性胎儿为缺失型,缺失位点与先证者相同。通过首次对我国东北地区DMD／BMD患者筛查缺失发现dystrophin基因缺失主要分布于两个热区内,与国内其他地区比较外显子8附近区域可能是该地区缺失断裂的高发区;内含子44～52高度不稳定,其中内含子44的稳定性要高于中央缺失热区的稳定性,内含子50的不稳定性存在地区及种族差异;引物优化组合为检测患者及产前基因诊断提供了捷径,尤其是对散发家系是可行的并且有其优越性。     

人癌胚抗原与新城疫病毒HN基因共表达载体的构建及表达

注射肿瘤疫苗 ,诱发机体产生特异性抗肿瘤免疫 ,是肿瘤生物治疗及手术后预防肿瘤复发、转移的重要手段之一。肿瘤核酸疫苗较重组蛋白或多肽疫苗来说 ,具有无可比拟的优点 ,它可同时诱导体液免疫和细胞免疫 ,后者在肿瘤免疫中起关键作用。传统的肿瘤疫苗是经各种方法灭活后的自体瘤苗 ,它虽可以诱导细胞免疫 ,但仍存在着灭活不彻底 ,导致人为瘤细胞种植的潜在危险 ,况且从操作性方面也较为繁琐、复杂。肿瘤抗原往往抗原性较弱 ,尤其是相关抗原 ,在某些正常组织中也有微量的表达 ,这容易使机体免疫系统对它产生免疫耐受 ,因此在激发肿瘤特异性…