Analysis Of Horizontal Gene Transfer Research Articles

Phylogeny-guided genome mining of roseocin family lantibiotics to generate improved variants of roseocin

Roseocin, the two-peptide lantibiotic from Streptomyces roseosporus, carries extensive intramolecular (methyl)lanthionine bridging in the peptides and exhibits synergistic antibacterial activity against clinically relevant Gram-positive pathogens. Both peptides have a conserved leader but a diverse core region. The biosynthesis of roseocin involves post-translational modification of the two precursor peptides by a single promiscuous lanthipeptide synthetase, RosM, to install an indispensable disulfide bond in the Rosα core along with four and six thioether rings in Rosα and Rosβ cores, respectively. RosM homologs in the phylum actinobacteria were identified here to reveal twelve other members of the roseocin family which diverged into three types of biosynthetic gene clusters (BGCs). Further, the evolutionary rate among the BGC variants and analysis of variability within the core peptide versus leader peptide revealed a phylum-dependent lanthipeptide evolution. Analysis of horizontal gene transfer revealed its role in the generation of core peptide diversity. The naturally occurring diverse congeners of roseocin peptides identified from the mined novel BGCs were carefully aligned to identify the conserved sites and the substitutions in the core peptide region. These selected sites in the Rosα peptide were mutated for permitted substitutions, expressed heterologously in E. coli, and post-translationally modified by RosM in vivo. Despite a limited number of generated variants, two variants, RosαL8F and RosαL8W exhibited significantly improved inhibitory activity in a species-dependent manner compared to the wild-type roseocin. Our study proves that a natural repository of evolved variants of roseocin is present in nature and the key variations can be used to generate improved variants.

HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer.

Horizontal gene transfer (HGT) is an important driver in genome evolution, gain-of-function, and metabolic adaptation to environmental niches. Genome-wide identification of putative HGT events has become increasingly practical, given the rapid growth of genomic data. However, existing HGT analysis toolboxes are not widely used, limited by their inability to perform phylogenetic reconstruction to explore potential donors, and the detection of HGT from both evolutionarily distant and closely related species. In this study, we have developed HGTphyloDetect, which is a versatile computational toolbox that combines high-throughput analysis with phylogenetic inference, to facilitate comprehensive investigation of HGT events. Two case studies with Saccharomyces cerevisiae and Candida versatilis demonstrate the ability of HGTphyloDetect to identify horizontally acquired genes with high accuracy. In addition, HGTphyloDetect enables phylogenetic analysis to illustrate a likely path of gene transmission among the evolutionarily distant or closely related species. The HGTphyloDetect computational toolbox is designed for ease of use and can accurately find HGT events with a very low false discovery rate in a high-throughput manner. The HGTphyloDetect toolbox and its related user tutorial are freely available at https://github.com/SysBioChalmers/HGTphyloDetect.

Evolution of PE35 and PPE68 Gene Families in Mycobacterium: Roles of Horizontal Gene Transfer and Evolutionary Constraints

Mycobacterium is a genus of bacteria with over a hundred non-pathogenic and pathogenic species, best recognized for certain members known to cause diseases such as tuberculosis and leprosy. Two novel protein families important in the pathogenesis of Mycobacterium species are the PE and PPE families. These two protein families affect the antigenic profiles, disturbing host immunity. To better understand the origin and evolution of these gene families and the differences in their composition between pathogenic and non-pathogenic strains, several bioinformatic analyses were conducted both among Mycobacterium and closely related species that contain PE35 and PPE68 gene homologs. The methods included protein homology searches (BLASTP), horizontal gene transfer analysis (IslandViewer), phylogenetic analysis, gene cluster analysis and structural and functional constraints. Results revealed that PE and PPE gene homologs were not only limited to Mycobacterium, but also existed in three other non-mycobacterial genera, Rhodococcus, Tsukamurella and Segniliparus, and were possibly initially acquired from non-mycobacterial microorganisms by multiple horizontal gene transfers. Results also demonstrated that PE and PPE genes were more diverse and more rapidly evolving in pathogenic Mycobacterium as compared with non-pathogenic Mycobacterium and other non-mycobacterial species. These findings possibly shed light on the diverse functions and origins of the PE/PPE proteins among these organisms.

Assessing the Probability of Detection of Horizontal Gene Transfer Events in Bacterial Populations

Experimental approaches to identify horizontal gene transfer (HGT) events of non-mobile DNA in bacteria have typically relied on detection of the initial transformants or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to be detected in a short time frame. Population genetic modeling of the growth dynamics of bacterial genotypes is therefore necessary to account for natural selection and genetic drift during the time lag and to predict realistic time frames for detection with a given sampling design. Here we draw on statistical approaches to population genetic theory to construct a cohesive probabilistic framework for investigation of HGT of exogenous DNA into bacteria. In particular, the stochastic timing of rare HGT events is accounted for. Integrating over all possible event timings, we provide an equation for the probability of detection, given that HGT actually occurred. Furthermore, we identify the key variables determining the probability of detecting HGT events in four different case scenarios that are representative of bacterial populations in various environments. Our theoretical analysis provides insight into the temporal aspects of dissemination of genetic material, such as antibiotic resistance genes or transgenes present in genetically modified organisms. Due to the long time scales involved and the exponential growth of bacteria with differing fitness, quantitative analyses incorporating bacterial generation time, and levels of selection, such as the one presented here, will be a necessary component of any future experimental design and analysis of HGT as it occurs in natural settings.

Detection and analysis of horizontal gene transfer in herpesvirus

Horizontal gene transfers, where a significant proportion of the coding DNA is contributed by external sources, might give rise to extremely dynamic genomes, which brings impact on the ecological and pathogenic characters of the recipient organisms. Therefore it is important to computationally discriminate between horizontal transferred genes and normal genes. In this paper, we introduce a novel method for identifying horizontal transferred genes. This method, which relies on a gene's nucleotide composition and hence obviates the need for knowledge of codon boundaries, is able to detect the horizontal transferred genes with an accuracy of higher than 90% within a reasonable length of time by using just a common PC. With this method, 141 putative transferred genes in mammalian herpesvirus were identified. Among them, 16 genes had been predicted or reported to have cellular homologues in previous papers, including those involved in immune systems and apoptosis such as GCR in EHV-2, BCL-2 (Bcelllymphoma/leukemia-2) homologue in MuHV-4, etc., and had been suggested being acquired from other organisms. Other 125 genes were identified for the first time. Twelve of the newly identified putative transferred genes had also been reported to participate in immune response, apoptosis, cell proliferation control or virulence determinant. Moreover, 42 of the 141 putative transferred genes were found to have non-virus homologues and so were convincingly revealed as transferred genes. Nine of the 42 transferred genes were phylogenetically analyzed, the origin and the relative origin time of which were discussed.

P-value based visualization of codon usage data

Two important and not yet solved problems in bacterial genome research are the identification of horizontally transferred genes and the prediction of gene expression levels. Both problems can be addressed by multivariate analysis of codon usage data. In particular dimensionality reduction methods for visualization of multivariate data have shown to be effective tools for codon usage analysis. We here propose a multidimensional scaling approach using a novel similarity measure for codon usage tables. Our probabilistic similarity measure is based on P-values derived from the well-known chi-square test for comparison of two distributions. Experimental results on four microbial genomes indicate that the new method is well-suited for the analysis of horizontal gene transfer and translational selection. As compared with the widely-used correspondence analysis, our method did not suffer from outlier sensitivity and showed a better clustering of putative alien genes in most cases.

Analysis of Horizontal Gene Transfer and Clustering of Microbial ORFs by Use of a GRID Environment

Tsunami of biological data and multiple views of the data analysis require an expandable and flexible information environment. GRID computing is expected to be the solution. We prepared a computational environment composed of 5 sites in OBIGrid [6] and succeeded in analyzing horizontal gene transfer and clusters of ORFs of more than 100 microbial genomes that were stored in the Genome Information Broker [1] as of May, 2003. This scheme is being applied to more than 300 thousands ORFs of genomic sequences of 124 microbial species.