植物中的水平基因转移

水平基因转移是不通过生殖而进行的遗传物质交流, 在原核生物和单细胞真核生物的进化中起着重要作用。然而, 水平基因转移在多细胞真核生物之间的发生频率以及对多细胞真核生物进化的影响尚不明确。近期的一些研究显示, 水平基因转移在高等植物之间以及高等植物和其它生物之间普遍存在。该文将对高等植物中已发现的一些水平基因转移现象进行综述, 并尝试解析植物之间水平基因转移可能的机制及其重要意义。     

真核生物中原核生物基因的来源被揭示

<正>多年来,人们一直认为真核生物基因组中所见的原核生物基因是在一个原核细胞器的内共生之后到达那里的。但最近的研究证据表明,在真核生物之间以及在原核生物和真核生物之间也存在实质性的横向基因转移。对细菌、古菌和真核生物基因组所做的这项分析,没有发现连续横向基因转移对真核基因内容的演化具有可以检测得到的累积影响的证据。相反,真核生物是在广泛的差异基因(differential gene)丢失之后、在相对于线粒体和质体起源的两次"演化涌入"事件中获得其原核生物基因的。     

纤毛虫中的编程性翻译移码

编程性翻译移码现象存在于病毒、原核生物和真核生物中。单细胞真核生物游仆虫基因组中含有的编程性翻译移码基因远远高于其他真核生物基因组。游仆虫中已经报道的编程性翻译移码基因的滑动序列特征为AAA-UAR-V,其上游都有SD(Shine-Dalgarno sequence)相似序列CAAGAA。同时,编程性移码的发生受肽链释放因子eRF1和tRNALys的影响。     

逆转座子和逆向遗传信息流

一、引言 遗传信息可以从基因组的一个位点转移到另一个位点,转移的信息或是由DNA所携带,或是由RNA所携带。DNA介导的转位作用在原核生物和真核生物中都能发生;RNA介导的转位作用目前仅发现于真核生物。逆转位作用的遗传因子则称     

Ⅰ-E型CRISPR/Cas系统介导适应性免疫分子机制研究进展北大核心CSCD

为了更好地适应环境,原核生物可通过水平基因转移的方式获取外源基因(来自噬菌体、质粒或其他物种基因组)。在获取外源基因的同时,原核生物也面临着"自私基因"入侵的风险。因此,原核生物需建立相应的机制选择性地摄取或降解外源DNA,从而防范基因转移带来的潜在危害。近年来,人们在原核生物中发现了由小RNA介导降解DNA的防御外源基因入侵的适应性免疫。在免疫防御过程中,首先外源DNA部分片段整合至细胞自身基因组上成簇出现的重复序列(CRISPR)上;然后表达并加工成熟的CRISPR RNA和相关Cas蛋白形成CRISPR/Cas复合体降解再次入侵的外源DNA。本文在简介CRISPR/Cas系统的基础上,重点探讨近年来关于大肠杆菌中I-E型CRISPR/Cas系统作用机制和调控机制的研究进展。     

原核生物eno基因在系统进化中应用及水平转移分析

多基因系统发育研究方法是系统发育分析中的一个重要手段,基因树冲突已成为分子系统发育研究中日益突出的问题。烯醇化酶基因(eno)及其编码的蛋白广泛存在于五界系统中,烯醇化酶为糖酵解途径中重要酶类。文章选取原核生物已注释的eno基因序列进行了系统发育分析。对其中的138个模式菌株的eno基因序列进行系统发育分析和同源性搜索,发现19个模式菌株的eno基因是通过水平转移而来;并通过核苷酸组成、密码子偏好性和基因排列等基因特征分析,进一步验证了水平转移基因的外源性。结果表明:原核生物eno序列具有较高保守性,其大小适中,是研究原核生物系统发育的良好材料。文章在对基因水平转移的供体和受体菌株生活习性、进化历史以及烯醇化酶的结构和功能的研究过程中提供重要参考价值。     

功能基因中的微卫星序列

微卫星序列广泛存在真核生物和一些原核生物的基因组中,它在基因组中的分布并不是随机的。不同重复拷贝类别在基因组中存在种属间和碱基组成的特异性,各种优势的重复序列类型不同。此外,基因中在编码区和非编码区的分布也表现出种属和碱基组成差异。这种差异显示了微卫星序列起源进化的复杂性,也反映了基因中微卫星序列的生物学功能。功能基因为遗传学工作者提供了一个联系表型和基因型的手段,研究功能基因中的微卫星序列不仅在绘制精细遗传图谱、筛选重要农艺性状基因、物种进化等问题上都有着重要的作用,而且在疾病治疗有潜在的应用价值。本文主要阐述了微卫星序列的形成机制、基因中微卫星序列的分布以及功能基因中微卫星序列的生物学作用,并指出了目前实践中的一些问题。     

DNA聚合酶X家族的起源与进化分析

随着DNA聚合酶X家族成员数量的增加,家族内部的系统发育需要重新检查。来自病毒和细胞的DNA聚合酶X家族成员序列第一次被汇编在一起,进行系统发育分析。分析显示：真核生物DNA聚合酶bcta(polβ)是这个家族的祖先基因,可能与昆虫痘病毒(EPv)之间发生过基因的水平转移;DNA聚合酶mu(polμ)基因仅存在于哺乳动物基因组中,是脱氧核苦酸末端转移酶(TdT)的重复基因;这个家族在低等真核生物的种系进化过程中发生了基因丢失。     

串联重复序列的物种差异及其生物功能

串联重复序列是指1-200个碱基左右的核心重复单位,以头尾相串联的方式重复多次所组成的重 复序列。它广泛存在于真核生物和一些原核生物的基因组中,并表现出种属、碱基组成等的特异性。在基因组 整体水平上,各种优势的重复序列类型不同。即使在同一重复序列类型内部,不同重复拷贝类别(如AT、AC 等)在基因组中的存在也表现出很大的差异。同时,这些重复序列类型和各重复拷贝类别在同一物种的不同染 色体间,以及基因的编码区和非编码区间也表现种属和碱基组成差异。这些差异显示了重复序列起源和进化的 复杂性,可能涉及到多种机制和因素,并与生物功能密切相关。另外,由于重复序列分析软件和统计标准还存 在算法、重复长度、完美性等问题,需要进一步探讨。此外,串联重复序列的自身进化关系、全基因组水平上 的进化地位、在基因组中的生物功能、重复序列数据库建立和应用研究等,将是今后研究的主要课题。     

内含子Ⅱ的作用机制和演化

内含子是广泛存在于原核生物的叶绿体、线粒体以及真核生物基因组中的非编码DNA序列,但其含有的调控元件却常常影响基因的表达效率。内含子的自我剪接在mRNA的成熟过程中起着重要作用,内含子也可利用逆转录剪接作用插入到同源或异源DNA中,同时也常常通过“外显子改组”来促进基因进化。文章重点介绍了近年来在内含子Ⅱ作用机制及演化方面研究的最新进展。     

Frequent,independent transfers of a catabolic gene from bacteria to contrasted filamentous eukaryotes

Even genetically distant prokaryotes can exchange genes between them, and these horizontal gene transfer events play a central role in adaptation and evolution. While this was long thought to be restricted to prokaryotes, certain eukaryotes have acquired genes of bacterial origin. However, gene acquisitions in eukaryotes are thought to be much less important in magnitude than in prokaryotes. Here, we describe the complex evolutionary history of a bacterial catabolic gene that has been transferred repeatedly from different bacterial phyla to stramenopiles and fungi. Indeed, phylogenomic analysis pointed to multiple acquisitions of the gene in these filamentous eukaryotes—as many as 15 different events for 65 microeukaryotes. Furthermore, once transferred, this gene acquired introns and was found expressed in mRNA databases for most recipients. Our results show that effective inter-domain transfers and subsequent adaptation of a prokaryotic gene in eukaryotic cells can happen at an unprecedented magnitude.     

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 genomic timescale for the origin of eukaryotes

Background  

Genomic sequence analyses have shown that horizontal gene transfer occurred during the origin of eukaryotes as a consequence of symbiosis. However, details of the timing and number of symbiotic events are unclear. A timescale for the early evolution of eukaryotes would help to better understand the relationship between these biological events and changes in Earth's environment, such as the rise in oxygen. We used refined methods of sequence alignment, site selection, and time estimation to address these questions with protein sequences from complete genomes of prokaryotes and eukaryotes.     

Distant horizontal gene transfer is rare for multiple families of prokaryotic insertion sequences

Horizontal gene transfer in prokaryotes is rampant on short and intermediate evolutionary time scales. It poses a fundamental problem to our ability to reconstruct the evolutionary tree of life. Is it also frequent over long evolutionary distances? To address this question, we analyzed the evolution of 2,091 insertion sequences from all 20 major families in 438 completely sequenced prokaryotic genomes. Specifically, we mapped insertion sequence occurrence on a 16S rDNA tree of the genomes we analyzed, and we also constructed phylogenetic trees of the insertion sequence transposase coding sequences. We found only 30 cases of likely horizontal transfer among distantly related prokaryotic clades. Most of these horizontal transfer events are ancient. Only seven events are recent. Almost all of these transfer events occur between pairs of human pathogens or commensals. If true also for other, non-mobile DNA, the rarity of distant horizontal transfer increases the odds of reliable phylogenetic inference from sequence data.     

The molecular evolution of catalatic hydroperoxidases: evidence for multiple lateral transfer of genes between prokaryota and from bacteria into eukaryota

The past decade has produced an increasing number of reports on horizontal gene transfer between prokaryotic organisms. Only recently, with the flood of available whole genome sequence data and a renewed intensity of the debate about the universal tree of life, a very few reports on lateral gene transfer (LGT) from prokaryotes into the Eukaryota have been published. We have investigated and report here on the molecular evolution of the gene families that encode catalatic hydroperoxidases. We have found that this process included not only frequent horizontal gene transfer among prokaryotes but also several lateral gene transfer events between bacteria and fungi and between bacteria and the protistan ancestor of the alga/plant lineage.     

Horizontal gene transfer in eukaryotic evolution

Horizontal gene transfer (HGT; also known as lateral gene transfer) has had an important role in eukaryotic genome evolution, but its importance is often overshadowed by the greater prevalence and our more advanced understanding of gene transfer in prokaryotes. Recurrent endosymbioses and the generally poor sampling of most nuclear genes from diverse lineages have also complicated the search for transferred genes. Nevertheless, the number of well-supported cases of transfer from both prokaryotes and eukaryotes, many with significant functional implications, is now expanding rapidly. Major recent trends include the important role of HGT in adaptation to certain specialized niches and the highly variable impact of HGT in different lineages.     

Alternative characterizations of Fitch’s xenology relation

Journal of Mathematical Biology - Horizontal gene transfer (HGT) is an important factor for the evolution of prokaryotes as well as eukaryotes. According to Walter M. Fitch, two genes are xenologs...     

The p-type ATPase superfamily

P-type ATPases function to provide homeostasis in higher eukaryotes, but they are essentially ubiquitous, being found in all domains of life. Thever and Saier [J Memb Biol 2009;229:115-130] recently reported analyses of eukaryotic P-type ATPases, dividing them into nine functionally characterized and 13 functionally uncharacterized (FUPA) families. In this report, we analyze P-type ATPases in all major prokaryotic phyla for which complete genome sequence data are available, and we compare the results with those for eukaryotic P-type ATPases. Topological type I (heavy metal) P-type ATPases predominate in prokaryotes (approx. tenfold) while type II ATPases (specific for Na(+),K(+), H(+) Ca(2+), Mg(2+) and phospholipids) predominate in eukaryotes (approx. twofold). Many P-type ATPase families are found exclusively in prokaryotes (e.g. Kdp-type K(+) uptake ATPases (type III) and all ten prokaryotic FUPA familes), while others are restricted to eukaryotes (e.g. phospholipid flippases and all 13 eukaryotic FUPA families). Horizontal gene transfer has occurred frequently among bacteria and archaea, which have similar distributions of these enzymes, but rarely between most eukaryotic kingdoms, and even more rarely between eukaryotes and prokaryotes. In some bacterial phyla (e.g. Bacteroidetes, Flavobacteria and Fusobacteria), ATPase gene gain and loss as well as horizontal transfer occurred seldom in contrast to most other bacterial phyla. Some families (i.e. Kdp-type ATPases) underwent far less horizontal gene transfer than other prokaryotic families, possibly due to their multisubunit characteristics. Functional motifs are better conserved across family lines than across organismal lines, and these motifs can be family specific, facilitating functional predictions. In some cases, gene fusion events created P-type ATPases covalently linked to regulatory catalytic enzymes. In one family (FUPA Family 24), a type I ATPase gene (N-terminal) is fused to a type II ATPase gene (C-terminal) with retention of function only for the latter. Several pseudogene-encoded nonfunctional ATPases were identified. Genome minimalization led to preferential loss of P-type ATPase genes. We suggest that in prokaryotes and some unicellular eukaryotes, the primary function of P-type ATPases is protection from extreme environmental stress conditions. The classification of P-type ATPases of unknown function into phylogenetic families provides guides for future molecular biological studies.     

Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes

The presence of shared conserved insertion or deletions (indels) in protein sequences is a special type of signature sequence that shows considerable promise for phylogenetic inference. An alternative model of microbial evolution based on the use of indels of conserved proteins and the morphological features of prokaryotic organisms is proposed. In this model, extant archaebacteria and gram-positive bacteria, which have a simple, single-layered cell wall structure, are termed monoderm prokaryotes. They are believed to be descended from the most primitive organisms. Evidence from indels supports the view that the archaebacteria probably evolved from gram-positive bacteria, and I suggest that this evolution occurred in response to antibiotic selection pressures. Evidence is presented that diderm prokaryotes (i.e., gram-negative bacteria), which have a bilayered cell wall, are derived from monoderm prokaryotes. Signature sequences in different proteins provide a means to define a number of different taxa within prokaryotes (namely, low G+C and high G+C gram-positive, Deinococcus-Thermus, cyanobacteria, chlamydia-cytophaga related, and two different groups of Proteobacteria) and to indicate how they evolved from a common ancestor. Based on phylogenetic information from indels in different protein sequences, it is hypothesized that all eukaryotes, including amitochondriate and aplastidic organisms, received major gene contributions from both an archaebacterium and a gram-negative eubacterium. In this model, the ancestral eukaryotic cell is a chimera that resulted from a unique fusion event between the two separate groups of prokaryotes followed by integration of their genomes.