Identification of Horizontal Gene Transfer from Phylogenetic Gene Trees

We suggest a new procedure to search for the genes with horizontal transfer events in their evolutionary history. The search is based on analysis of topology difference between the phylogenetic trees of gene (protein) groups and the corresponding phylogenetic species trees. Numeric values are introduced to measure the discrepancy between the trees. This approach was applied to analyze 40 prokaryotic genomes classified into 132 classes of orthologs. This resulted in a list of the candidate genes for which the hypothesis of horizontal transfer in evolution looks true.     

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。     

Expression of Clostridium thermocellum Endoglucanase Gene in Lactobacillus gasseri and Lactobacillus johnsonii and Characterization of the Genetically Modified Probiotic Lactobacilli

Endoglucanase A from Clostridium thermocellum resistant to pancreatic proteinase was selected out of a range of microbial cellulases expressed in lactobacilli. Two Lactobacillus–E. coli expression vectors, harboring the endoglucanase gene from C. thermocellum under the control of its own promoter (pSD1) and the Lactococcus lactis lac A promoter (pSD2), were constructed separately. Intestinal Lactobacillus strains, L. gasseri and L. johnsonii, were electrotransformed with pSD1 and pSD2, and the stability of each plasmid was evaluated. The endoglucanase activities of 0.722 and 0.759 U/ml were respectively found in culture medium of L. gasseri and L. johnsonii containing pSD1, and of 0.407 U/ml in medium of L. gasseri harboring pSD2. When the probiotic characteristics such as acid-tolerance, bile-salt tolerance, and antibiotic susceptibility were investigated, L. gasseri and L. johnsonii were resistant to low pHs of 2 and 3. Also, L. johnsonii was bile-salt resistant in the presence of 0.5% oxgall and porcine bile extract. L. johnsonii and L. gasseri showed a rather homogeneous resistant pattern against tested antibiotics. Both strains were resistant to amikacin, bacitracin, gentamicin, streptomycin, kanamycin, and colistin. Received: 11 August 1999 / Accepted: 8 November 1999     

Horizontal Gene Transfer in Aminoacyl-tRNA Synthetases Including Leucine-Specific Subtypes

Aminoacyl-tRNA synthetases catalyze a fundamental reaction for the flow of genetic information from RNA to protein. Their presence in all organisms known today highlights their important role in the early evolution of life. We investigated the evolutionary history of aminoacyl-tRNA synthetases on the basis of sequence data from more than 200 Archaea, Bacteria, and Eukaryota. Phylogenetic profiles are in agreement with previous observations that many genes for aminoacyl-tRNA synthetases were transferred horizontally between species from all domains of life. We extended these findings by a detailed analysis of the history of leucyl-tRNA synthetases. Thereby, we identified a previously undetected case of horizontal gene transfer from Bacteria to Archaea based on phylogenetic profiles, trees, and networks. This means that, finally, the last subfamily of aminoacyl-tRNA synthetases has lost its exceptional position as the sole subfamily that is devoid of horizontal gene transfer. Furthermore, the leucyl-tRNA synthetase phylogenetic tree suggests a dichotomy of the archaeal/eukaryotic-cytosolic and bacterial/eukaryotic-mitochondrial proteins. We argue that the traditional division of life into Prokaryota (non-chimeric) and Eukaryota (chimeric) is favorable compared to Woese’s trichotomy into Archaea/Bacteria/Eukaryota. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Yves Van de Peer]     

Chemoreceptor Gene Loss and Acquisition via Horizontal Gene Transfer in Escherichia coli

Chemotaxis allows bacteria to more efficiently colonize optimal microhabitats within their larger environment. Chemotaxis in Escherichia coli is the best-studied model system, and a large number of E. coli strains have been sequenced. The Escherichia/Shigella genus encompasses a great variety of commensal and pathogenic strains, but the role of chemotaxis in their association with the host remains poorly understood. Here we show that the core chemotaxis genes are lost in many, but not all, nonmotile strains but are well preserved in all motile strains. The genes encoding the Tar, Tsr, and Aer chemoreceptors, which mediate chemotaxis to a broad spectrum of chemical and physical cues, are also nearly uniformly conserved in motile strains. In contrast, the clade of extraintestinal pathogenic E. coli strains apparently underwent an ancestral loss of Trg and Tap chemoreceptors, which sense sugars, dipeptides, and pyrimidines. The broad range of time estimated for the loss of these genes (1 to 3 million years ago) corresponds to the appearance of the genus Homo.     

Potential of Lactobacillus gasseri isolated from infant faeces to produce bacteriocin

Thirty strains of Lactobacillus gasseri isolated from infant faeces were examined for production of an antimicrobial agent against 10 strains of the seven species of the genus Lactobacillus. Each of the strains inhibited the growth of at least one of the indicator strains. The agent was sensitive to proteolytic enzymes and stable for 20 min at 120°C. It is a bacteriocin designated as gassericin A.     

Identification and characterization of novel surface proteins in Lactobacillus johnsonii and Lactobacillus gasseri

We have identified and sequenced the genes encoding the aggregation-promoting factor (APF) protein from six different strains of Lactobacillus johnsonii and Lactobacillus gasseri. Both species harbor two apf genes, apf1 and apf2, which are in the same orientation and encode proteins of 257 to 326 amino acids. Multiple alignments of the deduced amino acid sequences of these apf genes demonstrate a very strong sequence conservation of all of the genes with the exception of their central regions. Northern blot analysis showed that both genes are transcribed, reaching their maximum expression during the exponential phase. Primer extension analysis revealed that apf1 and apf2 harbor a putative promoter sequence that is conserved in all of the genes. Western blot analysis of the LiCl cell extracts showed that APF proteins are located on the cell surface. Intact cells of L. johnsonii revealed the typical cell wall architecture of S-layer-carrying gram-positive eubacteria, which could be selectively removed with LiCl treatment. In addition, the amino acid composition, physical properties, and genetic organization were found to be quite similar to those of S-layer proteins. These results suggest that APF is a novel surface protein of the Lactobacillus acidophilus B-homology group which might belong to an S-layer-like family.     

Strand-biased Gene Distribution in Bacteria Is Related to both Horizontal Gene Transfer and Strand-biased Nucleotide Composition

Although strand-biased gene distribution(SGD) was described some two decades ago,the underlying molecular mechanisms and their relationship remain elusive.Its facets include,but are not limited to,the degree of biases,the strand-preference of genes,and the influence of background nucleotide composition variations.Using a dataset composed of 364 non-redundant bacterial genomes,we sought to illustrate our current understanding of SGD.First,when we divided the collection of bacterial genomes into non-polC and polC groups according to their possession of DnaE isoforms that correlate closely with taxonomy,the SGD of the polC group stood out more significantly than that of the non-polC group.Second,when examining horizontal gene transfer,coupled with gene functional conservation(essentiality) and expressivity(level of expression),we realized that they all contributed to SGD.Third,we further demonstrated a weaker G-dominance on the leading strand of the non-polC group but strong purine dominance(both G and A) on the leading strand of the polC group.We propose that strand-biased nucleotide composition plays a decisive role for SGD since the polC-bearing genomes are not only AT-rich but also have pronounced purine-rich leading strands,and we believe that a special mutation spectrum that leads to a strong purine asymmetry and a strong strand-biased nucleotide composition coupled with functional selections for genes and their functions are both at work.     

Interaction between Conjugative and Retrotransposable Elements in Horizontal Gene Transfer

Mobile genetic elements either encode their own mobilization machineries or hijack them from other mobile elements. Multiple classes of mobile elements often coexist within genomes and it is unclear whether they have the capacity to functionally interact and even collaborate. We investigate the possibility that molecular machineries of disparate mobile elements may functionally interact, using the example of a retrotransposon, in the form of a mobile group II intron, found on a conjugative plasmid pRS01 in Lactococcus lactis. This intron resides within the pRS01 ltrB gene encoding relaxase, the enzyme required for nicking the transfer origin (oriT) for conjugal transmission of the plasmid into a recipient cell. Here, we show that relaxase stimulates both the frequency and diversity of retrotransposition events using a retromobility indicator gene (RIG), and by developing a high-throughput genomic retrotransposition detection system called RIG-Seq. We demonstrate that LtrB relaxase not only nicks ssDNA of its cognate oriT in a sequence- and strand-specific manner, but also possesses weak off-target activity. Together, the data support a model in which the two different mobile elements, one using an RNA-based mechanism, the other using DNA-based transfer, do functionally interact. Intron splicing facilitates relaxase expression required for conjugation, whereas relaxase introduces spurious nicks in recipient DNA that stimulate both the frequency of intron mobility and the density of events. We hypothesize that this functional interaction between the mobile elements would promote horizontal conjugal gene transfer while stimulating intron dissemination in the donor and recipient cells.     

Novel recA-Independent Horizontal Gene Transfer in Escherichia coli K-12

In bacteria, mechanisms that incorporate DNA into a genome without strand-transfer proteins such as RecA play a major role in generating novelty by horizontal gene transfer. We describe a new illegitimate recombination event in Escherichia coli K-12: RecA-independent homologous replacements, with very large (megabase-length) donor patches replacing recipient DNA. A previously uncharacterized gene (yjiP) increases the frequency of RecA-independent replacement recombination. To show this, we used conjugal DNA transfer, combining a classical conjugation donor, HfrH, with modern genome engineering methods and whole genome sequencing analysis to enable interrogation of genetic dependence of integration mechanisms and characterization of recombination products. As in classical experiments, genomic DNA transfer begins at a unique position in the donor, entering the recipient via conjugation; antibiotic resistance markers are then used to select recombinant progeny. Different configurations of this system were used to compare known mechanisms for stable DNA incorporation, including homologous recombination, F’-plasmid formation, and genome duplication. A genome island of interest known as the immigration control region was specifically replaced in a minority of recombinants, at a frequency of 3 X 10^-12 CFU/recipient per hour.     

环境中污染物降解基因的水平转移(HGT)及其在生物修复中的作用

水平基因转移是不同于垂直基因转移的遗传物质的交流方式.在污染环境这一特异生态环境中,降解基因的水平转移有着独特的功能与作用.研究环境中污染物降解基因在微生物间的水平转移,更深入地了解微生物种群适应污染环境的机理,对于评价污染物的环境毒理、生物可降解性以及污染环境的可修复潜力具有重要参考价值.在污染物生物修复实践中,可以通过调控降解基因的水平转移,增强污染环境中微生物的降解能力,更有效地发挥生物修复作用.文章将对环境中细菌间基因交流的机制,污染物降解基因的水平转移对微生物适应污染环境的机理、水平基因转移对代谢途径的进化及其对污染物生物修复作用的影响等方面的研究进展做一综述.     

Multiple Phenotypic Changes Associated with Large-Scale Horizontal Gene Transfer

Horizontal gene transfer often leads to phenotypic changes within recipient organisms independent of any immediate evolutionary benefits. While secondary phenotypic effects of horizontal transfer (i.e., changes in growth rates) have been demonstrated and studied across a variety of systems using relatively small plasmids and phage, little is known about the magnitude or number of such costs after the transfer of larger regions. Here we describe numerous phenotypic changes that occur after a large-scale horizontal transfer event (∼1 Mb megaplasmid) within Pseudomonas stutzeri including sensitization to various stresses as well as changes in bacterial behavior. These results highlight the power of horizontal transfer to shift pleiotropic relationships and cellular networks within bacterial genomes. They also provide an important context for how secondary effects of transfer can bias evolutionary trajectories and interactions between species. Lastly, these results and system provide a foundation to investigate evolutionary consequences in real time as newly acquired regions are ameliorated and integrated into new genomic contexts.     

In Planta Horizontal Transfer of a Major Pathogenicity Effector Gene

Xanthomonas citri pv. citri is a clonal group of strains that causes citrus canker disease and appears to have originated in Asia. A phylogenetically distinct clonal group that causes identical disease symptoms on susceptible citrus, X. citri pv. aurantifolii, arose more recently in South America. Genomes of X. citri pv. aurantifolii strains carry two DNA fragments that hybridize to pthA, an X. citri pv. citri gene which encodes a major type III pathogenicity effector protein that is absolutely required to cause citrus canker. Marker interruption mutagenesis and complementation revealed that X. citri pv. aurantifolii strain B69 carried one functional pthA homolog, designated pthB, that was required to cause cankers on citrus. Gene pthB was found among 38 open reading frames on a 37,106-bp plasmid, designated pXcB, which was sequenced and annotated. No additional pathogenicity effectors were found on pXcB, but 11 out of 38 open reading frames appeared to encode a type IV transfer system. pXcB transferred horizontally in planta, without added selection, from B69 to a nonpathogenic X. citri pv. citri (pthA::Tn5) mutant strain, fully restoring canker. In planta transfer efficiencies were very high (>0.1%/recipient) and equivalent to those observed for agar medium with antibiotic selection, indicating that pthB conferred a strong selective advantage to the recipient strain. A single pathogenicity effector that can confer a distinct selective advantage in planta may both facilitate plasmid survival following horizontal gene transfer and account for the origination of phylogenetically distinct groups of strains causing identical disease symptoms.