昆虫水平基因转移及其研究进展

水平基因转移(horizontal gene transfer, HGT)是生物体获得遗传信息的方式之一,对生物体进化起重要作用。近年来,越来越多昆虫中的水平基因转移现象被报道,如在鳞翅目(如家蚕、甜菜夜蛾、小菜蛾、斜纹夜蛾)、半翅目(如柑橘粉蚧、烟粉虱)、鞘翅目(如咖啡果小蠹、米象、光肩星天牛)、膜翅目(如金小蜂)、双翅目(如果蝇、白纹伊蚊)等昆虫中广泛存在水平转移基因,且不同的水平转移基因对昆虫的营养合成与共生、吸收与消化、毒素产生与解毒、生长和发育、体色改变等方面有着重要作用。本文结合国内外专家学者的相关报道,就HGT的研究步骤与技术方法、评判HGT发生的方法、昆虫HGT的供体与功能几个方面进行了总结和讨论,以期更加深入地了解水平基因转移现象,为探究水平基因转移的作用机制、理解昆虫的进化、遗传和行为、并将水平基因转移应用到农业生产中为农业害虫的绿色防治提供更多思路。     

基因水平转移的评判方法和转移方式研究进展

基因水平转移是不同物种之间或细胞器间基因的交流。基因水平转移现象在原核生物中普遍存在, 在真核生物中近年来也发现了众多例证, 说明水平转移是生物界的普遍现象。文章着重对基因水平转移的概念、评判基因水平转移的标准, 水平转移的特点和转移方式, 以及基因水平转移对基因组进化的作用等方面的研究进展进行了综述。在已有的基因水平转移研究中进化树分析法、碱基组成分析法、选择压力分析法、内含子分析法、特殊序列分析法和核苷酸组成偏向性分析法等几种是常用的方法; 转座序列是生物中最易于发生水平转移的基因类型;原核生物基因水平转移的主要方式有转化、接合和转导, 真核生物中水平转移发生方式尚不清楚。基因水平转移在基因、基因组和生物进化中有着其独特的作用。     

家蚕chi、gluE和fruA基因与微生物相应基因的同源性及基因水平转移初探

通过对家蚕(Bombyxm mori)大规模EST的分析,发现家蚕的chi、gluE和fruA基因分别与微生物的相应基因存在高度的氨基酸序列同源性,且进化关系很近,但与线虫(Caenorhabditis elegans)、果蝇(Drosophila melanogaster)、按蚊(Anopheles gamble)以及家蚕近缘昆虫的类似基因之间的相似性却非常低。这表明它们可能分别与微生物的同源基因具有共同的祖先,即微生物的基因水平转移给了家蚕,进化途径不属于垂直遗传。     

植菌昆虫及共生真菌共生机制

大约4-6千万年前,3种昆虫类群：白蚁、蚂蚁及食菌甲虫独立进化了培植真菌作为食物的能力,完成了从收集、捕获到主动种植真菌作为食物的生活方式的转变。“耕种”的生活方式最终使得这些昆虫占据重要的生态位。这3类昆虫种植真菌的过程具有明确的人类农业的特点,包括接种、培育、收获以及对培养物的营养依赖。围绕这些环节,昆虫适应不同的功能而进行分工合作,同时通过与一类放线菌共生,利用其产生抗生素来保护菌圃。切叶蚁（attine ant）及其共生真菌、白蚁（termite）及其共生蚁巢伞、食菌甲虫（ambrosia beetles）及其共生真菌是典型的被广泛研究的真菌和昆虫共生体系。而这种培植真菌的能力并不仅仅存在于以上3类昆虫中。植菌卷叶象甲Euops chinensis精心制作叶苞并接种储菌器真菌;蜥蜴甲虫Doubledaya bucculenta以及树蜂Sirex spp.也存在接种共生真菌作物的行为。从本质上讲,昆虫的真菌培植体系与人类的农业体系非常类似,因此对于种植真菌昆虫的系统研究能够为应对全球粮食短缺和农业持续高产提供一些有价值的参考。     

水平基因转移

简要介绍了水平基因转移（horizontal gene transfer,HGT）的基本概念以及进行转移的主要方式：由质粒或病毒等介导的水平基因转移和基因的“直接”水平转移。并结合基因组序列分析,重点阐述远缘生物之间发生的广泛的基因交流,以及其与进化、系统发育和基因工程生物安全性问题的探讨。 Abstract:In this paper the conception of horizontal gene transfer (HGT) was introduced,and main mode of HGT was also enumerated as follows:HGT by medium such as plasmid and virus etc.and the HGT without any medium.The transfer of genes from one species to another especially between remote species was emphasized by the information from genome sequencing.The problems about evolution phylogenies and safety of GEMs (gene engineered microorganisms) for HGT were discussed.     

动物类群中水平基因转移的研究进展

水平基因转移(horizontal gene transfer,HGT)是指遗传物质在种间通过非垂直传递方式的移动。HGT可能造成种群的快速协同进化、不同物种间的趋同进化、获得新遗传性状等,是物种进化的重要驱动力之一。过去对HGT的研究主要集中在原核生物和植物方面,但近年来动物方面的HGT现象逐渐受到关注。为进一步了解动物类群中HGT的研究概况,列举了近年来动物类群中HGT的实例和相关证据,评估了证据的可靠性,同时简要介绍了HGT的验证方法,以期更好地理解HGT在动物进化中的重要意义。     

植菌昆虫与其共生真菌协同进化分子机制

昆虫菌业（fungiculture）是一种类似于人类种植业的昆虫种植体系,包括种植、耕作、收获和营养依赖4个过程,可分为高级的社会性昆虫如切叶蚂蚁、白蚁等和低级的非社会性昆虫如食菌小蠹虫、卷叶象甲、蜥蜴甲虫、树蜂等,它们均能种植并取食真菌。近年来随着组学及微生物组技术的发展,植菌昆虫与其共生真菌协同进化的分子机制研究方面取得了重要进展。系统发育分析阐明了植菌昆虫的起源与进化历程,并显示出与共生真菌系统发育的一致性;共生真菌细胞核数量也从双核增加到最多17个核,而染色体倍型也从单倍体增加为二倍体甚至多倍体;组学分析则揭示了植菌昆虫与其共生真菌在精氨酸、碳水化合物、木质素及几丁质合成或降解等方面显示出了高度的协同进化。本文系统综述了植菌昆虫及其共生真菌的系统进化、核进化及基因组进化进展,并探讨这种协同进化机制的生物学意义。     

影响果蝇味觉感受及寄主植物的选择的基因

在漫长的进化过程中，果蝇这个家族中的Dros—ophila sechellia演变成了一种专食性昆虫，它的寄主植物是诺丽（Morinda citrifolia，又名Tahitian noni）。这种植物含有己酸（HA）和辛酸（OA）。其它的果蝇都排斥这2种物质因而对诺丽避之唯恐不及，而偏偏D．sechellia受其吸引而对诺丽“情有独钟”。这到底是为什么呢？     

昆虫内共生菌研究概况

内共生菌与昆虫形成互惠共生关系,在宿主昆虫的生长、生殖、传播植物病害以及探讨生命起源与进化等等方面都有很重要的意义。从昆虫内共生菌的特点、内共生菌在昆虫体内的分布、对昆虫的影响、获得少或缺内共生菌的方法及其研究内共生菌的潜在意义等方面进行了综述。     

昆虫细胞中的基因转移

在组织培养协会第36届年会的“昆虫细胞中的基因表达”专题会上展示了以DNA为媒介的基因转移(转染)的最新进展。 已开发了二个用作评价转染率与研究转染基因调节的总系统(General system),其中之一是依赖干插入DNA的短期(暂时)表达系统;与一个则包括了从在细胞分裂时转染DNA已经复制的细胞个体中的克隆选择。     

Phylogeny vs genome reshuffling: horizontal gene transfer

The evolutionary events in organisms can be tracked to the transfer of genetic material. The inheritance of genetic material among closely related organisms is a slow evolutionary process. On the other hand, the movement of genes among distantly related species can account for rapid evolution. The later process has been quite evident in the appearance of antibiotic resistance genes among human and animal pathogens. Phylogenetic trees based on such genes and those involved in metabolic activities reflect the incongruencies in comparison to the 16S rDNA gene, generally used for taxonomic relationships. Such discrepancies in gene inheritance have been termed as horizontal gene transfer (HGT) events. In the post-genomic era, the explosion of known sequences through large-scale sequencing projects has unraveled the weakness of traditional 16S rDNA gene tree based evolutionary model. Various methods to scrutinize HGT events include atypical composition, abnormal sequence similarity, anomalous phylogenetic distribution, unusual phyletic patterns, etc. Since HGT generates greater genetic diversity, it is likely to increase resource use and ecosystem resilience.     

Eukaryotic origin of a metabolic pathway in virus by horizontal gene transfer

Horizontal gene transfer, the movement of genetic materials across the normal mating barriers between organisms occurs frequently and contributes significantly to the evolution of both eukaryotic and prokaryotic genomes. However, few concurrent transfers of functionally related genes implemented in a pathway from eukaryotes to prokaryotes are observed. Here, we did phylogenetic analyses to support that the genes, i.e. dihydrofolate reductase, glycine hydroxymethyltransferase, and thymidylate synthase involved in thymidylate metabolism, in Hz-1 virus were obtained from insect genome recently by independent horizontal gene transfers. In addition, five other related genes in nucleotide metabolism show evidences of horizontal gene transfers. These genes demonstrate similar expression pattern, and they may have formatted a functionally related pathway (e.g. thymidylate synthesis, and DNA replication) in Hz-1 virus. In conclusion, we provide an example of horizontal gene transfer of functionally related genes in a pathway to prokaryote from eukaryote.     

A likelihood framework to measure horizontal gene transfer

We suggest a likelihood-based approach to estimate an overall rate of horizontal gene transfer (HGT) in a simplified setting. To this end, we assume that the number of occurring HGT events within a given time interval follows a Poisson process. To obtain estimates for the rate of HGT, we simulate the distribution of tree topologies for different numbers of HGT events on a clocklike species tree. Using these simulated distributions, we estimate an HGT rate for a collection of gene trees representing a set of taxa. As an illustrative example, we use the "Clusters of Orthologous Groups of proteins" (COGs). We also perform a correction of the estimated rate taking into account the inaccuracies due to gene tree reconstructions. The results suggest a corrected HGT rate of about 0.36 per gene and unit time, in other words 11 HGT events have occurred on average among the 44 taxa of the COG species tree. A software package to estimate an HGT rate is available online (http://www.cibiv.at/software/hgt/).     

A naturally occurring horizontal gene transfer from a eukaryote to a prokaryote

Summary Naturally occurring horizontal gene transfers between nonviral organisms are difficult to prove. Only with the availability of sequence data from a wide variety of organisms can a convincing case be made. In the case of putative gene transfers between prokaryotes and eukaryotes, the minimum requirements for inferring such an event include (1) sequences of the transferred gene or its product from several appropriately divergent eukaryotes and several prokaryotes, and (2) a similar set of sequences from the same (or closely related organisms) for another gene or genes. Given these criteria, we believe that a strong case can be made forEscherichia coli having acquired a second glyceraldehyde-3-phosphate dehydrogenase gene from some eukaryotic host. Ancillary observations on the general rate of change and the time of the prokaryote-eukaryote divergence support the notion.     

Phylogenetic analysis of the isopenicillin-N-synthetase horizontal gene transfer

A phylogenetic study of the isopenicillin-N-synthetase (IPNS) gene sequence from prokaryotic and lower eukaryotic producers of β-lactam antibiotics by means of a maximum-likelihood approach has been carried out. After performing an extensive search, rather than invoking a global molecular clock, the results obtained are best explained by a model with three rates of evolution. Grouped in decreasing order, these correspond toA. nidulans and then to the rest of the eukaryotes and prokaryotes, respectively. The estimated branching date between prokaryotic and fungal IPNS sequences (852 ±106 MY) strongly supports the hypothesis that the IPNS gene was horizontally transferred from bacterial β-lactam producers to filamentous fungi. Correspondence to: A. Moya     

Natural transformation as a mechanism of horizontal gene transfer among environmental Aeromonas species

Aeromonas species are common inhabitants of aquatic environments and relevant as human pathogens. Their potential as pathogens may be related in part to lateral transfer of genes associated with toxin production, biofilm formation, antibiotic resistance, and other virulence determinants. Natural transformation has not been characterized in aeromonads. DNA from wild-type, prototrophic strains that had been isolated from environmental sources was used as donor DNA in transformation assays with auxotrophs as the recipients. Competence was induced in 20% nutrient broth during the stationary phase of growth. Optimal transformation assay conditions for one chosen isolate were in Tris buffer with magnesium or calcium, pH 5–8, and a saturating concentration of 0.5 μg of DNA per assay (3.3 ng of DNA μl⁻¹) at 30 °C. Sodium was also required and could not be replaced with ammonium, potassium, or lithium. The maximal transformation frequency observed was 1.95 × 10⁻³ transformants (recipient cell)⁻¹. A survey of environmental Aeromonas auxotrophic recipients (n = 37), assayed with donor DNA from other wild-type environmental aeromonads under optimal assay conditions, demonstrated that 73% were able to act as recipients, and 100% were able to act as donors to at least some other aeromonads. Three different transformation groups were identified based on each isolates’ ability to transform other strains with its DNA. The transformation groups roughly corresponded to phylogenetic groups. These results demonstrate that natural transformation is a general property of Aeromonas environmental isolates with implications for the genetic structures of coincident Aeromonas populations.     

基因转移因子———一类在海洋中广泛存在的介导水平基因转移的新型生物因子

基因转移因子(Gene Transfer Agent,GTA)是一种由细菌释放的、形态和有尾病毒类似的生物颗粒。GTA颗粒携带的遗传物质是宿主基因组的随机小片段而不包含编码GTA自身的基因或病毒基因组。根据4个模式菌株释放的GTA的研究,GTA具有高效的,种间介导基因水平转移的功能。近年来大规模细菌基因组测序,发现编码GTA的基因簇广泛存在于海洋细菌基因组上,GTA是在海洋环境中发生水平基因转移的重要模式。本文在总结4个模式菌株释放的GTA的认识的基础上,着重描述海洋主要类群的细菌释放的GTA的特征,讨论在海洋生态系统中,GTA对水平基因转移的贡献,并对未来的研究进行了展望。     

On surrogate methods for detecting lateral gene transfer

Surrogate methods for detecting lateral gene transfer are those that do not require inference of phylogenetic trees. Herein I apply four such methods to identify open reading frames (ORFs) in the genome of Escherichia coli K12 that may have arisen by lateral gene transfer. Only two of these methods detect the same ORFs more frequently than expected by chance, whereas several intersections contain many fewer ORFs than expected. Each of the four methods detects a different non-random set of ORFs. The methods may detect lateral ORFs of different relative ages; testing this hypothesis will require rigorous inference of trees.     

Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer

The mitochondrial genome of grape (Vitis vinifera), the largestorganelle genome sequenced so far, is presented. The genomeis 773,279 nt long and has the highest coding capacity amongknown angiosperm mitochondrial DNAs (mtDNAs). The proportionof promiscuous DNA of plastid origin in the genome is also thelargest ever reported for an angiosperm mtDNA, both in absoluteand relative terms. In all, 42.4% of chloroplast genome of Vitishas been incorporated into its mitochondrial genome. In orderto test if horizontal gene transfer (HGT) has also contributedto the gene content of the grape mtDNA, we built phylogenetictrees with the coding sequences of mitochondrial genes of grapeand their homologs from plant mitochondrial genomes. Many incongruentgene tree topologies were obtained. However, the extent of incongruencebetween these gene trees is not significantly greater than thatobserved among optimal trees for chloroplast genes, the commonancestry of which has never been in doubt. In both cases, weattribute this incongruence to artifacts of tree reconstruction,insufficient numbers of characters, and gene paralogy. Thisfinding leads us to question the recent phylogenetic interpretationof Bergthorsson et al. (2003, 2004) and Richardson and Palmer(2007) that rampant HGT into the mtDNA of Amborella best explainsphylogenetic incongruence between mitochondrial gene trees forangiosperms. The only evidence for HGT into the Vitis mtDNAfound involves fragments of two coding sequences stemming fromtwo closteroviruses that cause the leaf roll disease of thisplant. We also report that analysis of sequences shared by bothchloroplast and mitochondrial genomes provides evidence fora previously unknown gene transfer route from the mitochondrionto the chloroplast.