Origin and evolution of a novel DnaA-like plasmid replication type in Rhodobacterales

Large extrachromosomal elements are widespread among Alphaproteobacteria, but it is unclear how up to a dozen low-copy plasmids can stably coexist within the same cell. We systematically analyzed the distribution of different replicons in about 40 completely sequenced genomes of the Roseobacter clade (Rhodobacterales) and surprisingly identified a novel plasmid replicon type. The conserved replication module comprises the characteristic partitioning operon (parAB) and a hitherto unknown replicase. The latter shows a weak homology to the chromosomal replication initiator DnaA and was accordingly named "DnaA-like." Phylogenetic analyses of the adjacent parAB genes document a common ancestry with repA- and repB-type plasmids and moreover indicate the presence of two dnaA-like compatibility groups. This conclusion is supported by conserved palindrome sequences within the replication module that probably represent crucial centromeric anchors for plasmid partitioning. The functionality of dnaA-like replicons was proven by transformation experiments in Phaeobacter gallaeciensis BS107 (DSM 17395). This Roseobacter strain furthermore allows the phenotypical monitoring of plasmid incompatibility, based on a 262-kb dnaA-like replicon required for the brown pigmentation of the bacterium. Uptake of an incompatible construct induces its loss, hence resulting in white colonies. Accordingly, we could substantiate the in silico predictions about stable maintenance of dnaA-like plasmids and thereby functionally validate our approach of plasmid classification based on phylogenetic analyses.     

Diversity, biology and evolution of IncQ-family plasmids

Plasmids of IncQ-family are distinguished by having a unique strand-displacement mechanism of replication that is capable of functioning in a wide variety of bacterial hosts. In addition, these plasmids are highly mobilizable and therefore very promiscuous. Common features of the replicons have been used to identify IncQ-family plasmids in DNA sequence databases and in this way several unstudied plasmids have been compared to more well-studied IncQ plasmids. We propose that IncQ plasmids can be divided into four subgroups based on a number of mutually supportive criteria. The most important of these are the amino acid sequences of their three essential replication proteins and the observation that the replicon of each subgroup has become fused to four different lineages of mobilization genes. This review of IncQ-family plasmid diversity has highlighted several events in the evolution of these plasmids and raised several questions for further research.     

Origin and evolution of plasmids

Studies on the origin and evolution of plasmids may provide valuable insights on the promiscuous nature of DNA. The first examples of the selfish nature of nucleic acids are exemplified by primordial oligoribonucleotides which evolved into primitive replicons. The propagation of these molecules were likely patterned after the current viral RNA ribozymes, which have been recently shown to possess RNA synthesizing and template mediated polymerizing capabilities in the absence of proteins. The parasitic nature of nucleic acids is depicted by satellite nucleic acid molecules associated with viruses. The satellites of adenovirus and tobacco ringspot virus serve as established examples: they contain no open reading frames. Comparative analysis of the replication origins of virions and plasmids show them to be conserved, originating from the simplest autocatalytic replicon to highly complex and evolved plasmids, replicating by a rolling circle mechanism. The eventual association of proteins with nucleic acids provided added efficiency and protective advantages for molecular perpetuation. The promiscuous and selfish nature of plasmids is demonstrated by their ability to genetically engineer their host so that the host cell is best able to cope and survive in hostile environments. Survival of the host ensures survival of the plasmid. Sequestering of genes by plasmids occurs when the environmental conditions negatively affect the host. The sequestering mechanism is fundamental and forms the outreach mechanisms to generate and propagate macromolecules of increasing size when necessary for survival. The level of sophistication of plasmids increases with the addition of new genes such as those that allow the host to occupy a specific environment normally inhospitable to the host cell. The vast range of plasmid types which have obtained genes interchangeably reflect the levels of sophistication achieved by these macromolecules. The Ti plasmid in Agrobacterium tumefaciens and the pSym and accessory plasmids in Rhizobium illustrate the level of complexity attained by replicons.     

链霉菌质粒的复制与进化

近年来, 随着大质粒提取和检测技术的发展, 尤其是高通量DNA测序技术的应用, 使得链霉菌大的环型质粒和线型质粒的研究取得了较快的进展。相比于研究透彻的细菌Theta型复制的质粒, 链霉菌Theta型质粒在复制区的结构、复制蛋白和调控蛋白作用的分子机理等方面具有多样性和新颖性。新鉴定的许多线型质粒的中心复制区表明中心复制的起始可以靠近端粒, 一个质粒也可以有2个以上的复制区。新分离的端粒序列显示端粒“折返”不是必需的, 而形成二级结构对于端粒复制是重要的。链霉菌环型和线型质粒的测序分析显示它们之间存在亲缘关系。环型质粒可以与噬菌体共整合, 实验证明它们在一定条件下可以相互转换。这些研究结果表明, 链霉菌环型、线型质粒和噬菌体从结构到功能到进化具有多样性、新颖性和亲缘关系。     

Rhizobium etli CFN42 contains at least three plasmids of the repABC family: a structural and evolutionary analysis

In this paper, we report the identification of replication/partition regions of plasmid p42a and p42b of Rhizobium etli CFN42. Sequence analysis reveals that both replication/partition regions belong to the repABC family. Phylogenetic analysis of all the complete repABC replication/partition regions reported to date, shows that repABC plasmids coexisting in the same strain arose most likely by lateral transfer instead of by duplication followed by divergence. A model explaining how new incompatibility groups originate, is proposed.     

The expression of a novel antisense gene mediates incompatibility within the large repABC family of alpha-proteobacterial plasmids

Large extrachromosomal replicons in many members of the alpha-proteobacteria encode genes that are required for plant or animal pathogenesis or symbiosis. Most of these replicons encode repABC genes that control their replication and faithful segregation during cell division. In addition to its chromosome, the plant endosymbiont Sinorhizobium meliloti also maintains the 1.4 Mb pSymA and 1.7 Mb pSymB symbiotic megaplasmids both of which are repABC-type replicons. In all repABC loci that have been characterized, an apparently untranslated intergenic region between the repB and repC genes encodes a strong incompatibility determinant (referred to as incalpha). Here we report the isolation of mutations within the incalpha regions of pSymA and pSymB that eliminate incompatibility. These mutations map to and inactivate a promoter in the intergenic region that drives the expression of an approximately 56 nucleotide untranslated RNA molecule that mediates incompatibility. This gene, that we have named incA, is transcribed antisense to the repABC genes. Our analysis suggests that the incA gene is conserved in repABC loci from a diverse spectrum of bacteria.     

The evolution of IncP catabolic plasmids

The recent adoption of whole plasmid genome sequencing as a routine analytical technique has provided the basis for cataloging the historical events through which plasmids are assembled from the available families of modular plasmid components. Horizontal gene transfer mediated by plasmids plays an important role in the adaptation of bacteria to the presence of specific metabolizable compounds, including man-made chemicals, in the surrounding environment. Bacterial plasmid genome sequence comparisons indicate that plasmids have complex genetic histories resulting from transposition, homologous recombination, and illegitimate recombinational events. Evidence from IncP plasmid genome sequences indicates that cryptic plasmid backbones acquire diverse catabolic pathways through gene capture and horizontal gene transfer.     

Diversity and evolution of microsporogenesis in Bromeliaceae

In this study, we explore the features of microsporogenesis in Bromeliaceae and, in particular, the diversity and evolution of additional callose deposits. Cytokinesis type, cell wall formation, tetrad form and patterns of additional callose deposition after intersporal wall formation were studied in 12 species of Bromeliaceae (each from a different genus) presenting four different aperture patterns. Microsporogenesis is highly conserved, with successive cytokinesis, centrifugal cell plate formation and predominantly tetragonal and decussate tetrads, as in many monocots, but five different patterns of additional callose deposition were recorded. The optimization of patterns of additional callose deposition on the phylogeny of Bromeliaceae reveals convergences. Additional callose deposition is a variable and labile feature of microsporogenesis in Bromeliaceae and is linked, to some extent, to aperture pattern. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 36–45.     

Diversity and evolution of samara in angiosperm

翅果能够依靠风力进行传播, 可能是被子植物快速散布和物种分化的一个重要因素。狭义的翅果是指果皮延伸成翅且不开裂的干果; 广义的翅果则包括果皮、花被片或苞片形成果翅的所有果实。根据果翅形态及其生长方式的不同, 广义的翅果可分为单侧翅果、周位翅果(圆翅果与蝶翅果)、棱翅果、披针翅果、翼状萼翅果、叶状苞翅果6种类型, 其空中运动方式有自旋式(单侧翅果、翼状萼翅果)、波浪式(周位翅果、叶状苞翅果)、翻滚自旋式(周位翅果)、直升机式(披针翅果、翼状萼翅果)和滚筒式(棱翅果)。棱翅果与圆翅果在被子植物基部类群樟目就有发生, 并同时出现在单子叶植物和双子叶植物中, 可能是最早出现的翅果类型。翅果的演化过程呈现出果翅数量增加、果翅偏向单侧和果翅负荷(果实质量与果翅面积之比)降低的趋势, 以利于适应较小的风并增加传播距离。果翅除了促进果实与种子的风力传播外, 还具有物理防御、调节种子萌发和促进二次传播等作用。泛热带分布的金虎尾科有着极其丰富的翅果类型, 与其多次跨洋长距离扩散密切相关, 可以作为研究翅果适应与演化的一个模式类群。结合生态和演化-发育生物学方法, 研究不同类型翅果在适应风力传播方面的差异、萼片或苞片发育成翅的分子与遗传机制、翅果不同类型的演化历史及其对被子植物物种多样性的影响等是今后值得探讨的重要问题。     

被子植物翅果的多样性及演化

翅果能够依靠风力进行传播, 可能是被子植物快速散布和物种分化的一个重要因素。狭义的翅果是指果皮延伸成翅且不开裂的干果; 广义的翅果则包括果皮、花被片或苞片形成果翅的所有果实。根据果翅形态及其生长方式的不同, 广义的翅果可分为单侧翅果、周位翅果(圆翅果与蝶翅果)、棱翅果、披针翅果、翼状萼翅果、叶状苞翅果6种类型, 其空中运动方式有自旋式(单侧翅果、翼状萼翅果)、波浪式(周位翅果、叶状苞翅果)、翻滚自旋式(周位翅果)、直升机式(披针翅果、翼状萼翅果)和滚筒式(棱翅果)。棱翅果与圆翅果在被子植物基部类群樟目就有发生, 并同时出现在单子叶植物和双子叶植物中, 可能是最早出现的翅果类型。翅果的演化过程呈现出果翅数量增加、果翅偏向单侧和果翅负荷(果实质量与果翅面积之比)降低的趋势, 以利于适应较小的风并增加传播距离。果翅除了促进果实与种子的风力传播外, 还具有物理防御、调节种子萌发和促进二次传播等作用。泛热带分布的金虎尾科有着极其丰富的翅果类型, 与其多次跨洋长距离扩散密切相关, 可以作为研究翅果适应与演化的一个模式类群。结合生态和演化-发育生物学方法, 研究不同类型翅果在适应风力传播方面的差异、萼片或苞片发育成翅的分子与遗传机制、翅果不同类型的演化历史及其对被子植物物种多样性的影响等是今后值得探讨的重要问题。     

Diversity of Pseudomonas plasmids: To what extent?

Results obtained in studies of the biology of Pseudomonas plasmids are presented here as a mini-review. These data indicate that plasmids are ubiquitous in Pseudomonas, but the frequency of their occurrence varies greatly in particular species, or groups of species and in different microbial habitats. Some species of Pseudomonas, for instance P. aeruginosa, possess great diversity of plasmids both from the viewpoint of their incompatibility properties and their ability to endow bacteria with additional features such as resistance to antibiotics or heavy metals, degradation of xenobiotics or inhibition of phage development.     

Diversity and evolution of marine phytoplankton

Marine phytoplankton organisms account for more than 45% of the photosynthetic net primary production on Earth. They are distributed across many of the major clades of the tree of life and include prokaryotes, and eukaryotes that acquired photosynthesis through the process of endosymbiosis. If the number of extant described species is relatively low compared to the diversity of the terrestrial plants, recent insights into the genetic diversity of natural assemblages have revealed a large unsuspected diversity at different taxonomic levels. Wide infra-specific diversity is also being discovered in many widespread and well known morphological species. This review summarizes data obtained in the fields of ecology, evolutionary biology, physiology and genomics that have improved our understanding of the biodiversity and evolution of marine phytoplankton. To cite this article: N. Simon et al., C. R. Biologies 332 (2009).     

Superinfection drives virulence evolution in experimental populations of bacteria and plasmids

A prominent hypothesis proposes that pathogen virulence evolves in large part due to a trade‐off between infectiousness and damage to hosts. Other explanations emphasize how virulence evolves in response to competition among pathogens within hosts. Given the proliferation of theoretical possibilities, what best predicts how virulence evolves in real biological systems? Here, I show that virulence evolution in experimental populations of bacteria and self‐transmissible plasmids is best explained by within‐host competition. Plasmids evolved to severely reduce the fitness of their hosts even in the absence of uninfected cells. This result is inconsistent with the trade‐off hypothesis, which predicts that under these conditions vertically transmitted pathogens would evolve to be less virulent. Plasmid virulence was strongly correlated with the ability to superinfect cells containing competing plasmid genotypes, suggesting a key role for within‐host competition. When virulent genotypes became common, hosts evolved resistance to plasmid infection. These results show that the trade‐off hypothesis can incorrectly predict virulence evolution when within‐host interactions are neglected. They also show that symbioses between bacteria and plasmids can evolve to be surprisingly antagonistic.     

Diversity and evolution of hydrogenase systems in rhizobia

Uptake hydrogenases allow rhizobia to recycle the hydrogen generated in the nitrogen fixation process within the legume nodule. Hydrogenase (hup) systems in Bradyrhizobium japonicum and Rhizobium leguminosarum bv. viciae show highly conserved sequence and gene organization, but important differences exist in regulation and in the presence of specific genes. We have undertaken the characterization of hup gene clusters from Bradyrhizobium sp. (Lupinus), Bradyrhizobium sp. (Vigna), and Rhizobium tropici and Azorhizobium caulinodans strains with the aim of defining the extent of diversity in hup gene composition and regulation in endosymbiotic bacteria. Genomic DNA hybridizations using hupS, hupE, hupUV, hypB, and hoxA probes showed a diversity of intraspecific hup profiles within Bradyrhizobium sp. (Lupinus) and Bradyrhizobium sp. (Vigna) strains and homogeneous intraspecific patterns within R. tropici and A. caulinodans strains. The analysis also revealed differences regarding the possession of hydrogenase regulatory genes. Phylogenetic analyses using partial sequences of hupS and hupL clustered R. leguminosarum and R. tropici hup sequences together with those from B. japonicum and Bradyrhizobium sp. (Lupinus) strains, suggesting a common origin. In contrast, Bradyrhizobium sp. (Vigna) hup sequences diverged from the rest of rhizobial sequences, which might indicate that those organisms have evolved independently and possibly have acquired the sequences by horizontal transfer from an unidentified source.     

苦苣苔科镜像花的多样性及演化

泛热带分布的苦苣苔科(Gesneriaceae)在我国南方具有极高的物种丰富度与特有率,花部特征变化丰富,是研究物种形成与适应演化的代表类群。镜像花(mirror-image flowers)是极为特化的传粉系统,在苦苣苔科中出现了较多的不同类型,可能与苦苣苔科物种多样性形成与维持有关。该研究总结与分析了苦苣苔科镜像花的类型多样性以及系统分布与适应演化等,讨论了镜像花对苦苣苔科物种形成与维持的积极意义。结果表明:镜像花仅分布在亚洲和非洲的苦苣苔亚科(Didymocarpoideae)的7个属,在历史上就至少发生了5次独立起源。长冠苣苔属(Rhabdothamnopsis)、南洋苣苔属(Henckelia)及长蒴苣苔属(Didymocarpus)镜像花的花柱与可育雄蕊分别向左、右两侧偏转,形成互补镜像花;蛛毛苣苔属(Paraboea)、喜鹊苣苔属(Ornithoboea)、非洲堇属(Saintpaulia)镜像花缺乏与花柱对应侧偏的可育雄蕊(非互补镜像花);而海角苣苔属(Streptocarpus)直立堇兰亚属(subg.Streptocarpella Engler)则同时出现了互补、非互补镜像花。不同于其他被子植物(离瓣花、缺乏花冠筒),苦苣苔科中的镜像花大多伴随着明显的花冠筒、内藏的雄蕊、合生的花药,以非互补镜像花为主;传粉者以小型的无垫蜂(Amegilla spp.)和熊蜂(Bombus spp.)为主。这些特殊的花部综合征与特化的传粉机制,提高了传粉精确性,可能促进了传粉隔离与物种适应辐射。今后的一个研究重点应通过分子系统发育方法,进一步揭示苦苣苔亚科互补与非互补镜像花的进化顺序及其在物种分化与长距离扩散过程中的可能作用。     

Diversity and evolution of rice progenitors in Australia

In the thousands of years of rice domestication in Asia, many useful genes have been lost from the gene pool. Wild rice is a key source of diversity for domesticated rice. Genome sequencing has suggested that the wild rice populations in northern Australia may include novel taxa, within the AA genome group of close (interfertile) wild relatives of domesticated rice that have evolved independently due to geographic separation and been isolated from the loss of diversity associated with gene flow from the large populations of domesticated rice in Asia. Australian wild rice was collected from 27 sites from Townsville to the northern tip of Cape York. Whole chloroplast genome sequences and 4,555 nuclear gene sequences (more than 8 Mbp) were used to explore genetic relationships between these populations and other wild and domesticated rices. Analysis of the chloroplast and nuclear data showed very clear evidence of distinctness from other AA genome Oryza species with significant divergence between Australian populations. Phylogenetic analysis suggested the Australian populations represent the earliest‐branching AA genome lineages and may be critical resources for global rice food security. Nuclear genome analysis demonstrated that the diverse O. meridionalis populations were sister to all other AA genome taxa while the Australian O. rufipogon‐like populations were associated with the clade that included domesticated rice. Populations of apparent hybrids between the taxa were also identified suggesting ongoing dynamic evolution of wild rice in Australia. These introgressions model events similar to those likely to have been involved in the domestication of rice.     

Spread and evolution of natural plasmids harboring transposon Tn5

Abstract: The presence of transposon Tn 5 was studied in 730 Enterobacteriaceae strains from clinical and sewage origin. From these strains, twenty-five conjugative plasmids harboring transposon Tn 5 were isolated. These plasmids were compared with pJR67 and pRYC119, the only previously studied plasmids harboring Tn 5 . A phylogenetic tree of the evolution of all different plasmids was proposed. Irrespective of their bacterial host and geographical place of isolation, some of the plasmids were shown to be identical. All of them can be included in only eight different prototypical plasmid species. Twenty-two plasmids (88%) carried an IncI1 incompatibility determinant as judged form DNA hybridization experiments. The presence of some other common resistance genes suggested that these plasmids are descendants of a common ancestor. These IncI1 plasmids could be grouped in six prototypical species. The results presented here suggest that Tn 5 spread in nature may be dependent on the conjugative ability of the IncI plasmids harboring the transposon, rather than on the efficiency of Tn 5 transposition between different replicons.     

Effective removal of a range of Ti/Ri plasmids using a pBBR1-type vector having a repABC operon and a lux reporter system

Ti and Ri plasmids of pathogenic Agrobacterium strains are stably maintained by the function of a repABC operon and have been classified into four incompatibility groups, namely, incRh1, incRh2, incRh3, and incRh4. Removal of these plasmids from their bacterial cells is an important step in determining strain-specific virulence characteristics and to construct strains useful for transformation. Here, we developed two powerful tools to improve this process. We first established a reporter system to detect the presence and absence of Ti/Ri plasmids in cells by using an acetosyringone (AS)-inducible promoter of the Ti2 small RNA and luxAB from Vibrio harveyi. This system distinguished a Ti/Ri plasmid-free cell colony among plasmid-harboring cell colonies by causing the latter colonies to emit light in response to AS. We then constructed new “Ti/Ri eviction plasmids,” each of which carries a repABC from one of four Ti/Ri plasmids that belonged to incRh1, incRh2, incRh3, and incRh4 groups in the suicidal plasmid pK18mobsacB and in a broad-host-range pBBR1 vector. Introduction of the new eviction plasmids into Agrobacterium cells harboring the corresponding Ti/Ri plasmids led to Ti/Ri plasmid-free cells in every incRh group. The Ti/Ri eviction was more effective by plasmids with the pBBR1 backbone than by those with the pK18mobsacB backbone. Furthermore, the highly stable cryptic plasmid pAtC58 in A. tumefaciens C58 was effectively evicted by the introduction of a pBBR1 vector containing the repABC of pAtC58. These results indicate that the set of pBBR1-repABC plasmids is a powerful tool for the removal of stable rhizobial plasmids.