Published online 9 January 2006
Methods Online |
A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria
1Department of Infection, Immunity and Inflammation, Leicester Medical School, University of Leicester Leicester LE1 9HN, UK 2Laboratory for Computational Biology, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Shandong University of Technology Zibo, 255049, China 3Bacterial Pathogenesis and Genomics Unit, Division of Immunity and Infection, Medical School, University of Birmingham Birmingham B15 2TT, UK 4Molecular Microbiology Group, Institute of Food Research Norwich Research Park, Norwich NR4 7UA, UK 5Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust Leicester LE1 5WW, UK
*To whom correspondence should be addressed at Department of Infection, Immunity and Inflammation, Leicester Medical School, University of Leicester, Maurice Shock Building, University Road, PO Box 138, Leicester LE1 9HN, UK. Tel: +44 0 116 2231498; Fax: +44 0 116 2525030; Email: kr46{at}le.ac.uk
Received November 2, 2005. Revised December 12, 2005. Accepted December 12, 2005.
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 
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.
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