Gene islands integrated into tRNA(Gly) genes confer genome diversity on a Pseudomonas aeruginosa clone

Abstract

Intraclonal genome diversity of Pseudomonas aeruginosa was studied in one of the most diverse mosaic regions of the P. aeruginosa chromosome. The ca. 110-kb large hypervariable region located near the lipH gene in two members of the predominant P. aeruginosa clone C, strain C and strain SG17M, was sequenced. In both strains the region consists of an individual strain-specific gene island of 111 (strain C) or 106 (SG17M) open reading frames (ORFs) and of a 7-kb stretch of clone C-specific sequence of 9 ORFs. The gene islands are integrated into conserved tRNA(Gly) genes and have a bipartite structure. The first part adjacent to the tRNA gene consists of strain-specific ORFs encoding metabolic functions and transporters, the majority of which have homologs of known function in other eubacteria, such as hemophores, cytochrome c biosynthesis, or mercury resistance. The second part is made up mostly of ORFs of yet-unknown function. Forty-seven of these ORFs are mutual homologs with a pairwise amino acid sequence identity of 35 to 88% and are arranged in the same order in the two gene islands. We hypothesize that this novel type of gene island derives from mobile elements which, upon integration, endow the recipient with strain-specific metabolic properties, thus possibly conferring on it a selective advantage in its specific habitat.

FIG. 1.

Organization of the boundaries of the gene islands. The structure of the genomic region around a cluster of three tRNA genes is shown for P. aeruginosa strains PAO1, C, and SG17M. In P. putida F1 (structure adapted from references and 31) and X. fastidiosa (sequence taken from reference 44), the gene islands integrated into a single tRNA^Gly gene. Map positions in the genome sequence are indicated for P. aeruginosa PAO1 and X. fastidiosa. Large inverted repeats (IRs) are shown as loop structures. Numbers above the maps indicate the lengths (in base pairs) of the corresponding sequences. The 84-bp spacer s1 separating the two tRNA^Gly genes differs by only two nucleotide substitutions between P. aeruginosa PAO1 and the two clone C strains. The localization of attachment sites attB, attL, and attR (see text for explanation) is indicated. All sequences flanking inverted repeats were named (s2, s2c, and s2c∗, etc.) and aligned to visualize the high degree of homology among the different gene islands and strains. Additionally, the sequences of the depicted tRNA^Gly genes, highlighted in black, are shown for the three species.

FIG. 2.

Gene maps of the P. aeruginosa strain PAO1, C, and SG17M hypervariable genome regions. Predicted coding regions are shown by arrows indicating the direction of transcription. The tRNA genes and attachment sites are depicted by rectangles. Vertical lines and their connections represent the borders of the gene islands and their sites of integration in comparison to the PAO1 genome. Genes are color coded according to their functional category (adapted from http://www.pseudomonas.com). All genes carry identification numbers (C1 to C111 and SG1 to SG105 in the two strain-specific gene islands and C112 to C120 in the clone C specific region [highlighted in pink]), but some have been omitted because of space limitations. In cases of a high degree of homology to already-characterized proteins, three-letter designations are provided for individual genes. ORFs with mutual homologs in both gene islands are shown with a light-blue background. Additionally, ORFs with equivalents in the detected gene island of X. fastidiosa are marked with blue boxes and the corresponding gene identification numbers of the sequencing project (44). IS elements and transposons are shaded in gray.

FIG. 3.

Comparison of the strain-specific gene islands in P. aeruginosa SG17M (upper line) and C (lower line). Genes are represented by arrows as in Fig. 2. Homologous ORFs are linked by light blue bars. A slightly darker blue line connects the corresponding bphR genes located at the right border of the SG17M gene island and at the left border of the C-specific insertion. Genes with homologs in the X. fastidiosa gene island are highlighted with a dark blue background. Gray boxes above and below the gene maps mark all ORFs that are presumably associated with the mobilization and transfer of the gene islands (called noncargo ORFs in the text; compare with Tables 2 and 3 for the corresponding gene identification numbers). Additionally, a 500-bp sliding window plot of G+C content is displayed for each gene island.