Accurate Localization And Analyzing Structural Characteristics Of Mobile Genomic Islands

Genomic islands (GIs), which are often the products of horizontal gene transfers (HGTs), are a result of prokaryotic evolution. GIs have various biological functions, such as pathogenicity, xenobiotic degradation, antibiotic resistance, ion uptake, secretion activities, and so on. Some GIs are'mobile', such as some plasmids, some prophages, integrative and conjugative elements (ICEs), and conjugative transponsons, are able to be excised from and reintegrated into the chromosome. Some mobile GIs can be transfered to an appropriate chromosome by transformation, transduction or conjugation. The mobile GIs were accurately localized and the structural characteristics of GIs were analyzed. Therefore, the big DNA segment transfer and restruction of engineering bacterium that obtained the special biological function will be completed.Current approaches of detecting GIs include: 1) approaches based on sequence composition difference, for example, SIGI-HMM and Alien_Hunter; 2) approaches based on basic structural characteristics of GIs, for example, Islander and GIDetector; 3) approaches based on comparative genomics, for example, IslandPick; 4) mixed approaches, for example, MobilomeFINDER and IslandViewer. The mobility of GIs is required to determine clear and accurate flanking direct repeats and the presence of the mobility gene in GIs. Many approaches are not considered to accurately localize the GIs because the GIs should have reliable flanking direct repeats and the mobility gene exists in GIs.We developed two approaches to accurate localize the mobile GIs that have clear flanking direct repeats and at least a functional integrase, transposase or recombinase in Pseudomonas. Second approach was furthermore developed in Escherichia coli, and Salmonella enterica and was verified to be reliable. First approach was built through analysis of the sequence composition difference between the core chromosome and the GIs and the structural characteristics of GIs. Second approach was built considering three of obvious characteristics of GIs: 1) The presence of the mobility gene, the key selective element in GIs, 2) the feature of the comparative genomics (i.e., a GI is present in a certain strain while it is absent from very close related strains), and 3) the features of horizontal genomic transfer, namely, abnormal GC content, dinucleotide bias, and gene density. The putative functions of GIs in Pseudomonas were determined. Through analysis of matching relationship between flanking direct repeats and the integrase in GIs, the second approach was proved to be reliable. The GIs were not only integrated into the 3′-end of the tRNA gene, but also into the 5′-end of the tRNA gene.The tandem GIs associated with the tmRNA gene were verified in Escherichia coli and Salmonella enterica. The tandem GIs were not only integrated into the tRNA genes and the RyeB RNA gene, but also into the outer membrane protein W gene and the intergenic spacer in Escherichia coli and Salmonella enterica. The chronology of integration of tandem GIs into the chromosome indicated that GIs farther from the tmRNA gene were incorporated into the genome earlier than those nearer from the tmRNA gene because of the pseudogene integrase, imperfection of direct repeats and the presence of remnant variable regions. The cleavage sites of integrases in tandem GIs move from the 3′-end to the 5′-end of the tmRNA gene, namely, the direct repeats in GIs nearer from the tmRNA are longer. If every integrase in tandem GIs is active, the bigger DNA fragment will be transfered into a new chromosome.The putative functional integrases in 34 GIs integrated into GMP synthase gene mainly composed of the P4 integrases that have island-encoding positive transcriptional regulatory factor AlpA. The dependent relationship between the P4 integrase and AlpA are widespread in GIs associated with the various tRNA genes, the tmRNA gene, exodeoxy ribonuclease I gene and the intergenic spacer in Escherichia coli and Salmonella enterica. The deletion frequency of the GI that contains the P4 integrase will be increased using a relative AlpA gene.