title: A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria.
abstract: We devised software tools to systematically investigate the contents and contexts of bacterial tRNA and tmRNA genes, which are known insertion hotspots for genomic islands (GIs). The strategy, based on MAUVE-facilitated multigenome comparisons, was used to examine 87 Escherichia coli MG1655 tRNA and tmRNA genes and their orthologues in E.coli EDL933, E.coli CFT073 and Shigella flexneri Sf301. Our approach identified 49 GIs occupying approximately 1.7 Mb that mapped to 18 tRNA genes, missing 2 but identifying a further 30 GIs as compared with Islander [Y. Mantri and K. P. Williams (2004), Nucleic Acids Res., 32, D55-D58]. All these GIs had many strain-specific CDS, anomalous GC contents and/or significant dinucleotide biases, consistent with foreign origins. Our analysis demonstrated marked conservation of sequences flanking both empty tRNA sites and tRNA-associated GIs across all four genomes. Remarkably, there were only 2 upstream and 5 downstream deletions adjacent to the 328 loci investigated. In silico PCR analysis based on conserved flanking regions was also used to interrogate hotspots in another eight completely or partially sequenced E.coli and Shigella genomes. The tools developed are ideal for the analysis of other bacterial species and will lead to in silico and experimental discovery of new genomic islands.
authors.affiliation: Department of Infection, Immunity and Inflammation, Leicester Medical School, University of Leicester, Leicester LE1 9HN, UK.
authors.forename: Hong-Yu
authors.initials: HY
authors.lastname: Ou
authors.forename: Ling-Ling
authors.initials: LL
authors.lastname: Chen
authors.forename: James
authors.initials: J
authors.lastname: Lonnen
authors.forename: Roy R
authors.initials: RR
authors.lastname: Chaudhuri
authors.forename: Ali Bin
authors.initials: AB
authors.lastname: Thani
authors.forename: Rebecca
authors.initials: R
authors.lastname: Smith
authors.forename: Natalie J
authors.initials: NJ
authors.lastname: Garton
authors.forename: Jay
authors.initials: J
authors.lastname: Hinton
authors.forename: Mark
authors.initials: M
authors.lastname: Pallen
authors.forename: Michael R
authors.initials: MR
authors.lastname: Barer
authors.forename: Kumar
authors.initials: K
authors.lastname: Rajakumar
mesh_terms: D019295:Computational Biology; D004926:Escherichia coli / Q000235:genetics*; D016680:Genome, Bacterial; D044404:Genomic Islands; D023281:Genomics / Q000379:methods; D016133:Polymerase Chain Reaction; D012329:RNA, Bacterial / Q000235:genetics*; D012343:RNA, Transfer / Q000235:genetics*; D012763:Shigella flexneri / Q000235:genetics*; D012984:Software
chemical_list: D012329:RNA, Bacterial; C096222:tmRNA; D012343:RNA, Transfer