Dynamics of Pseudomonas aeruginosa genome evolution

Abstract

One of the hallmarks of the Gram-negative bacterium Pseudomonas aeruginosa is its ability to thrive in diverse environments that includes humans with a variety of debilitating diseases or immune deficiencies. Here we report the complete sequence and comparative analysis of the genomes of two representative P. aeruginosa strains isolated from cystic fibrosis (CF) patients whose genetic disorder predisposes them to infections by this pathogen. The comparison of the genomes of the two CF strains with those of other P. aeruginosa presents a picture of a mosaic genome, consisting of a conserved core component, interrupted in each strain by combinations of specific blocks of genes. These strain-specific segments of the genome are found in limited chromosomal locations, referred to as regions of genomic plasticity. The ability of P. aeruginosa to shape its genomic composition to favor survival in the widest range of environmental reservoirs, with corresponding enhancement of its metabolic capacity is supported by the identification of a genomic island in one of the sequenced CF isolates, encoding enzymes capable of degrading terpenoids produced by trees. This work suggests that niche adaptation is a major evolutionary force influencing the composition of bacterial genomes. Unlike genome reduction seen in host-adapted bacterial pathogens, the genetic capacity of P. aeruginosa is determined by the ability of individual strains to acquire or discard genomic segments, giving rise to strains with customized genomic repertoires. Consequently, this organism can survive in a wide range of environmental reservoirs that can serve as sources of the infecting organisms.

Fig. 1.

Large inversions in various P. aeruginosa chromosomes. Whole genome alignments for all five strains of P. aeruginosa were generated using an anchor-alignment software Murasaki (http://murasaki.dna.bio.keio.ac.jp/; ref. 27). Scale in Mb is shown at top. Green, vertical arrowheads represent the rRNA operons. All alignments were performed on genomic sequences reset to the location of the origin of replication (see SI Text). PAO1, PACS2, and PA2192 have large inversions that appear to be anchored at rRNA operons [between rrnA and rrnB (PA01) or rrnC (PACS2) or rrnD (PA2192)]. PA2192 is given a color gradient so that corresponding alignment blocks may be easily visualized in the compared genomes.

Fig. 2.

The P. aeruginosa pangenome. Using the core genes from PA14 as the template, all of the accessory genes from PA2192, C3719, PAO1, and PACS2 were integrated. The outer circle (gold) indicates the core genes, the second circle shows the functional annotations. The third circle indicates the position of tRNAs. The accessory genes in the inner circles are from PA14 (blue) PA2192 (green), C3719 (purple), PAO1 (red), and PACS2 (teal). The outer green arrows show the positions of rRNAs.

Fig. 3.

Detection of RGP excision in various P. aeruginosa strains. (A) A generic model for RGP excision. Primers P1and P2 were designed to detect excision of RGPs and primers P3 and P4 to detect the presence of the circular form of the RGP following excision. Gene A and Gene B represent genes located adjacent to the RGP (anchors). The location of att sites is shown in red. (B) Agarose gel electrophoresis of PCR products generated by amplification for RGP5, RGP8, RGP17, RGP41 (PAPI-1) and RGP62 in strains PAO1, PA14, PA2192, C3719, and PACS2, respectively. Lane A shows the results of amplifications with primers P1 and P2 and B with primers P3 and P4.