Genomic Pathogenicity Islands in the Lpneumophila Genomes

Several genomic (pathogenicity) island-like regions have been identified in the three genomes that seem to exhibit a new type of genomic island with a probably Legionella-specific organization. These islands are typically integrated in tRNA or tmRNA genes, are larger than 30kbp, and contain mobile elements and patho-genicity-related genes as previously defined (Hacker et al. 1997). However, comparison of these islands among the three sequenced strains revealed that in Legio-

Fig. 15.2 Alignment of the complete genome sequences of L. pneumophila strains Paris, Lens, and Philadelphia 1, using the ACT (Artemis comparison tool) software (http:// www.sanger.ac.uk/Software/ACT/). Color code: Red blocks represent homologous sequences; blue blocks, homologous sequences, but inverted. 1, Disruption of the synteny by a 260-kbp inversion in strain Lens; 2, cluster encoding several efflux pumps missing in strain Lens; 3, lvh type IV secretion system; 4, 65-kbp pathogenicity island of strain Philadelphia 1. (This figure also appears with the color plates.)

Fig. 15.2 Alignment of the complete genome sequences of L. pneumophila strains Paris, Lens, and Philadelphia 1, using the ACT (Artemis comparison tool) software (http:// www.sanger.ac.uk/Software/ACT/). Color code: Red blocks represent homologous sequences; blue blocks, homologous sequences, but inverted. 1, Disruption of the synteny by a 260-kbp inversion in strain Lens; 2, cluster encoding several efflux pumps missing in strain Lens; 3, lvh type IV secretion system; 4, 65-kbp pathogenicity island of strain Philadelphia 1. (This figure also appears with the color plates.)

nella these islands are composed of a conserved region that is flanked in each isolate by a strain-specific region, suggesting that the same conserved regions might be transferred by different phages or mobilizable plasmids or by yet unknown mechanisms. One example is the Ivh region, which is highly conserved in all three sequenced genomes but the flanking DNA regions are specific to each strain and different from each other (Fig. 15.3). The size of these flanking regions is also different in each strain, as the Ivh region is flanked by 11kbp and 22kbp in strain Paris, by 5.8kbp and 30kbp in strain Lens, and by 14kbp and 30kbp in strain Philadelphia 1. Furthermore, this region is inserted in the same tmRNA in strains Lens and Paris but in an Arg tRNA in another chromosomal location in strain Philadelphia 1. The lvh region has in addition the particular capacity to exist in an integrated as well as an excised form as a multicopy plasmid, which varies in size in each strain. A similar element contributing to phase variation that can also exist in a plasmid as well as integrated form was previously identified in strain OLDA (Luneberg et al. 2001). The identification of the exact mechanism leading to the excision and integration of these elements will help us to understand the adaptation and versatility mechanisms of Legionella.

Another example of the particular structure of these islands in L. pneumophila is a region containing a 40-kbp genomic island encoding several efflux pumps induced in contact with the host cell and apparently dedicated to detoxification and proper metal ion balance within bacteria (Rankin et al. 2002), which is absent in strain Lens. In the two other sequenced strains, this region is located between

Fig. 15.3 The integrative multicopy plasmid carrying the lvh type IV system and comparison of this region in the three strains. The scale on the right indicates the G+C content values in this region. The black curve indicates variations in G+C content along this region in strain Lens. Red bars indicate homologous regions in the three genomes; light blue indicates genes predicted in this region. Arrows and numbers below indicate the insertion position on the chromosome ofeach strain.

Fig. 15.3 The integrative multicopy plasmid carrying the lvh type IV system and comparison of this region in the three strains. The scale on the right indicates the G+C content values in this region. The black curve indicates variations in G+C content along this region in strain Lens. Red bars indicate homologous regions in the three genomes; light blue indicates genes predicted in this region. Arrows and numbers below indicate the insertion position on the chromosome ofeach strain.

specific regions forming a large island of 130 kbp in strain Paris that is flanked by a Met tRNA gene and codes a putative integrase, and one of 100 kbp in strain Philadelphia 1 that is inserted in a different chromosomal location. One region specific to strain Philadelphia 1 and absent from both the others is the 65 kbp pathogenicity island described previously (Brassinga et al. 2003), although the corresponding chromosomal location in strain Paris contains a 19-kbp duplication carrying a gene cluster homologous to prpA-lvrABC present on this island. Interestingly, despite the presence of many regions which seem to have been acquired by horizontal gene transfer via phages, as suggested by the presence of around 10 integrase genes in each L. pneumophila genome, no complete prophage seems to be present.

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