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.     

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。     

Rates of Molecular Evolution in RNA Viruses: A Quantitative Phylogenetic Analysis

The study of rates of nucleotide substitution in RNA viruses is central to our understanding of their evolution. Herein we report a comprehensive analysis of substitution rates in 50 RNA viruses using a recently developed maximum likelihood phylogenetic method. This analysis revealed a significant relationship between genetic divergence and isolation time for an extensive array of RNA viruses, although more rate variation was usually present among lineages than would be expected under the constraints of a molecular clock. Despite the lack of a molecular clock, the range of statistically significant variation in overall substitution rates was surprisingly narrow for those viruses where a significant relationship between genetic divergence and time was found, as was the case when synonymous sites were considered alone, where the molecular clock was rejected less frequently. An analysis of the ecological and genetic factors that might explain this rate variation revealed some evidence of significantly lower substitution rates in vector-borne viruses, as well as a weak correlation between rate and genome length. Finally, a simulation study revealed that our maximum likelihood estimates of substitution rates are valid, even if the molecular clock is rejected, provided that sufficiently large data sets are analyzed. Received: 23 February 2001 / Accepted: 3 July 2001     

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.     

Evaluation of possible horizontal gene transfer from transgenic plants to the soil bacterium Acinetobacter calcoaceticus BD413

 The use of genetically engineered crop plants has raised concerns about the transfer of their engineered DNA to indigenous microbes in soil. We have evaluated possible horizontal gene transfer from transgenic plants by natural transformation to the soil bacterium Acinetobacter calcoaceticus BD413. The transformation frequencies with DNA from two sources of transgenic plant DNA and different forms of plasmid DNA with an inserted kanamycin resistance gene, nptII, were measured. Clear effects of homology were seen on transformation frequencies, and no transformants were ever detected after using transgenic plant DNA. This implied a transformation frequency of less than 10^-13 (transformants per recipient) under optimised conditions, which is expected to drop even further to a minimum of 10^-16 due to soil conditions and a lowered concentration of DNA available to cells. Previous studies have shown that chromosomal DNA released to soil is only available to A. calcoaceticus for limited period of time and that A. calcoaceticus does not maintain detectable competence in soil. Taken together, these results suggest that A. calcoaceticus does not take up non-homologous plant DNA at appreciable frequencies under natural conditions. Received: 1 November 1996 / Accepted: 18 April 1997     

Phylogenetic analysis using parsimony and likelihood methods

The assumptions underlying the maximum-parsimony (MP) method of phylogenetic tree reconstruction were intuitively examined by studying the way the method works. Computer simulations were performed to corroborate the intuitive examination. Parsimony appears to involve very stringent assumptions concerning the process of sequence evolution, such as constancy of substitution rates between nucleotides, constancy of rates across nucleotide sites, and equal branch lengths in the tree. For practical data analysis, the requirement of equal branch lengths means similar substitution rates among lineages (the existence of an approximate molecular clock), relatively long interior branches, and also few species in the data. However, a small amount of evolution is neither a necessary nor a sufficient requirement of the method. The difficulties involved in the application of current statistical estimation theory to tree reconstruction were discussed, and it was suggested that the approach proposed by Felsenstein (1981,J. Mol. Evol. 17: 368–376) for topology estimation, as well as its many variations and extensions, differs fundamentally from the maximum likelihood estimation of a conventional statistical parameter. Evidence was presented showing that the Felsenstein approach does not share the asymptotic efficiency of the maximum likelihood estimator of a statistical parameter. Computer simulations were performed to study the probability that MP recovers the true tree under a hierarchy of models of nucleotide substitution; its performance relative to the likelihood method was especially noted. The results appeared to support the intuitive examination of the assumptions underlying MP. When a simple model of nucleotide substitution was assumed to generate data, the probability that MP recovers the true topology could be as high as, or even higher than, that for the likelihood method. When the assumed model became more complex and realistic, e.g., when substitution rates were allowed to differ between nucleotides or across sites, the probability that MP recovers the true topology, and especially its performance relative to that of the likelihood method, generally deteriorates. As the complexity of the process of nucleotide substitution in real sequences is well recognized, the likelihood method appears preferable to parsimony. However, the development of a statistical methodology for the efficient estimation of the tree topology remains a difficult open problem.     

昆虫的水平基因转移研究

水平基因转移是一种能够在物种间进行基因交流的现象,是生物迅速适应环境的主要驱动力之一.近年来,随着测序技术的进步,昆虫中的水平基因转移现象被大量报道,成为昆虫研究的热点之一.本文总结了水平基因转移研究的常用流程和手段,以及昆虫水平转移基因的供体、受体和功能,讨论水平基因转移与昆虫食性的联系以及研究方法的局限,并展望昆虫水平基因转移研究领域未来的方向.     

Evidence for horizontal transfer from streptococcus to escherichia coli of the kfid gene encoding the K5-specific UDP-glucose dehydrogenase

Capsular polysaccharides are important virulence factors both in Gram-positive and Gram-negative bacteria. A similar cluster organization of the genes involved in the synthesis of bacterial exopolysaccharides has been postulated in both cases, suggesting that these clusters evolved by module assembly. Horizontal gene transfer has been postulated to explain the polymorphism found in these cellular polymers. The cap1K and cap3A genes coding for the pneumococcal type 1 and type 3 UDP-glucose dehydrogenases, respectively, have been compared with other UDP-sugar dehydrogenases. We have observed that the evolutionary distance between Cap1K and Cap3A is approximately equal to that found between Cap1K (or Cap3A) and other UDP-GlcDH of families evolutionarily distant like KfiD, the dehydrogenase from Escherichia coli K5. On the basis of comparisons of G + C content, patterns of synonymous and nonsynonymous substitutions, dinucleotide frequencies, and codon usage bias, we conclude that the kfiD gene has been introduced into E. coli from an exogenous source, probably from a streptococcal species. Received: 26 May 1997 / Accepted: 30 July 1997     

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 Pseudomonas syringae Pathovars Suggests the Horizontal Gene Transfer of argK and the Evolutionary Stability of hrp Gene Cluster

Pseudomonas syringae are differentiated into approximately 50 pathovars with different plant pathogenicities and host specificities. To understand its pathogenicity differentiation and the evolutionary mechanisms of pathogenicity-related genes, phylogenetic analyses were conducted using 56 strains belonging to 19 pathovars. gyrB and rpoD were adopted as the index genes to determine the course of bacterial genome evolution, and hrpL and hrpS were selected as the representatives of the pathogenicity-related genes located on the genome (chromosome). Based on these data, NJ, MP, and ML phylogenetic trees were constructed, and thus 3 trees for each gene and 12 gene trees in total were obtained, all of which showed three distinct monophyletic groups: Groups 1, 2 and 3. The observation that the same set of OTUs constitute each group in all four genes suggests that these genes had not experienced any intergroup horizontal gene transfer within P. syringae but have been stable on and evolved along with the P. syringae genome. These four index genes were then compared with another pathogenicity-related gene, argK (the phaseolotoxin-resistant ornithine carbamoyltransferase gene, which exists within the argK–tox gene cluster). All 13 strains of pv. phaseolicola and pv. actinidiae used had been confirmed to produce phaseolotoxin and to have argK, whose sequences were completely identical, without a single synonymous substitution among the strains used (Sawada et al. 1997a). On the other hand, argK were not present on the genomes of the other 43 strains used other than pv. actinidiae and pv. phaseolicola. Thus, the productivity of phaseolotoxin and the possession of the argK gene were shown at only two points on the phylogenetic tree: Group 1 (pv. actinidiae) and Group 3 (pv. phaseolicola). A t test between these two pathovars for the synonymous distances of argK and the tandemly combined sequence of the four index genes showed a high significance, suggesting that the argK gene (or argK–tox gene cluster) experienced horizontal gene transfer and expanded its distribution over two pathovars after the pathovars had separated, thus showing a base substitution pattern extremely different from that of the noncluster region of the genome. Received: 18 January 1999 / Accepted: 25 May 1999     

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.     

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.     

Maximum-likelihood models for combined analyses of multiple sequence data

Models of nucleotide substitution were constructed for combined analyses of heterogeneous sequence data (such as those of multiple genes) from the same set of species. The models account for different aspects of the heterogeneity in the evolutionary process of different genes, such as differences in nucleotide frequencies, in substitution rate bias (for example, the transition/transversion rate bias), and in the extent of rate variation across sites. Model parameters were estimated by maximum likelihood and the likelihood ratio test was used to test hypotheses concerning sequence evolution, such as rate constancy among lineages (the assumption of a molecular clock) and proportionality of branch lengths for different genes. The example data from a segment of the mitochondrial genome of six hominoid species (human, common and pygmy chimpanzees, gorilla, orangutan, and siamang) were analyzed. Nucleotides at the three codon positions in the protein-coding regions and from the tRNA-coding regions were considered heterogeneous data sets. Statistical tests showed that the amount of evolution in the sequence data reflected in the estimated branch lengths can be explained by the codon-position effect and lineage effect of substitution rates. The assumption of a molecular clock could not be rejected when the data were analyzed separately or when the rate variation among sites was ignored. However, significant differences in substitution rate among lineages were found when the data sets were combined and when the rate variation among sites was accounted for in the models. Under the assumption that the orangutan and African apes diverged 13 million years ago, the combined analysis of the sequence data estimated the times for the human-chimpanzee separation and for the separation of the gorilla as 4.3 and 6.8 million years ago, respectively.     

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。     

Construction and characterization of a Rhizobium leguminosarum biovar viciae strain designed to assess horizontal gene transfer in the environment

Abstract An integration vector was developed which inserts cloned DNA in a non-essential site of the Rhizobium leguminosarum biovar viciae chromosome. The expression of integrated genes is under the control of the constitutive neomycin phosphotransferase II ( npt II) promotor of transposon Tn5. The design of the vector ensures that loss of vector sequences can be detected, enabling selection of progeny containing only the requisite DNA. The newly constructed vector was employed to insert the Escherichia coli gusA gene conferring GUS activity into R. leguminosarum bv. viciae strain LRS39401 which is cured of its symbiotic plasmid (pSym). One GUS-positive transconjugant, strain CT0370, was shown to have lost all vector sequences. Conjugal transfer of pSym2004 (a Tn5-tagged derivative of symbiotic plasmid pRL1JI, which specifies pea nodulation and symbiotic nitrogen fixation) to CT0370, restored the GUS-positive strain's symbiotic proficiency. Strain CT0370 is presently being used in a field release experiment in order to assess the extent of pSym transfer in a natural R. leguminosarum bv. viciae population under environmental conditions.     

Identification of horizontally transferred genes in the genus Colletotrichum reveals a steady tempo of bacterial to fungal gene transfer

Background

Horizontal gene transfer (HGT) is the stable transmission of genetic material between organisms by means other than vertical inheritance. HGT has an important role in the evolution of prokaryotes but is relatively rare in eukaryotes. HGT has been shown to contribute to virulence in eukaryotic pathogens. We studied the importance of HGT in plant pathogenic fungi by identifying horizontally transferred genes in the genomes of three members of the genus Colletotrichum.

Results

We identified eleven HGT events from bacteria into members of the genus Colletotrichum or their ancestors. The HGT events include genes involved in amino acid, lipid and sugar metabolism as well as lytic enzymes. Additionally, the putative minimal dates of transference were calculated using a time calibrated phylogenetic tree. This analysis reveals a constant flux of genes from bacteria to fungi throughout the evolution of subphylum Pezizomycotina.

Conclusions

Genes that are typically transferred by HGT are those that are constantly subject to gene duplication and gene loss. The functions of some of these genes suggest roles in niche adaptation and virulence. We found no evidence of a burst of HGT events coinciding with major geological events. In contrast, HGT appears to be a constant, albeit rare phenomenon in the Pezizomycotina, occurring at a steady rate during their evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-16-2) contains supplementary material, which is available to authorized users.     

Widespread horizontal transfer of the cerato-ulmin gene between Ophiostoma novo-ulmi and Geosmithia species

Previous work had shown that a sequence homologous to the gene encoding class II hydrophobin cerato-ulmin from the fungus Ophiostoma novo-ulmi, the causal agent of Dutch Elm Disease (DED), was present in a strain of the unrelated species Geosmithia species 5 (Ascomycota: Hypocreales) isolated from Ulmus minor affected by DED. As both fungi occupy the same habitat, even if different ecological niches, the occurrence of horizontal gene transfer was proposed. In the present work we have analysed for the presence of the cerato-ulmin gene 70 Geosmithia strains representing 29 species, isolated from different host plants and geographic locations. The gene was found in 52.1 % of the strains derived from elm trees, while none of those isolated from nonelms possessed it. The expression of the gene in Geosmithia was also assessed by real time PCR in different growth conditions (liquid culture, solid culture, elm sawdust, dual culture with O. novo-ulmi), and was found to be extremely low in all conditions tested. On the basis of these results we propose that the cerato-ulmin gene is not functional in Geosmithia, but can be considered instead a marker of more extensive transfers of genetic material as shown in other fungi.     

Detecting horizontal gene transfer with T-REX and RHOM programs

As the Human Genome Project and other genome projects experience remarkable success and a flood of biological data is produced by means of high-throughout sequencing techniques, detection of horizontal gene transfer (HGT) becomes a promising field in bioinformatics. This review describes two freeware programs: T-REX for MS Windows and RHOM for Linux. T-REX is a graphical user interface program that offers functions to reconstruct the HGT network among the donor and receptor hosts from the gene and species distance matrices. RHOM is a set of command-line driven programs used to detect HGT in genomes. While T-REX impresses with a user-friendly interface and drawing of the reticulation network, the strength of RHOM is an extensive statistical framework of genome and the graphical display of the estimated sequence position probabilities for the candidate horizontally transferred genes.     

Bioprospecting the<Emphasis Type="Italic">lat</Emphasis> gene in soil samples

Twenty soil communities from the northeastern forests (Assam) and the Western Ghats (Maharashtra) were screened for the presence of the lysine aminotransferase (lat) gene fromNocardia. Hybridization probes and primers were synthesized in accordance with the reported sequence of theNocardia lat gene from GenBank (number: G1 49355). Seven positives were obtained from the 20 soils. Six of the seven positive were from the Western Ghats and one from the northeast Assam forests. Eighteen actinomycete isolates from the 7 positive soils showed the presence of thelat gene. Only 9 isolates actually produced an antibiotic. These results are discussed.     

苏云金芽胞杆菌标记重组菌株的构建与杀虫基因水平转移

利用SOE法将构建的绿色荧光蛋白基因gfp和苏云金芽胞杆菌的杀虫晶体蛋白基因cry1Ac10的嵌合基因克隆到穿梭载体pAD4412上获得重组质粒pBMBZGC10,再通过电转化法导入苏云金芽胞杆菌无质粒突变株CryB中获得重组菌株CryB(pBMBZGC10).将重组菌株CryB(pBMBZGC10)的发酵液按30、60和90 ml共3个浓度梯度,菌数约为10.7～10.8·ml^-1,分次喷洒供试植株小白菜、蕹菜和番茄,结果表明,cry1Ac10基因没有向供试土壤细菌、真菌和放线菌转移,也未在供试植物根、茎和叶中检测到该基因.