Genome sequence of Pseudomonas aeruginosa PAO1161, a PAO1 derivative with the ICEPae1161 integrative and conjugative element

Abstract

Pseudomonas aeruginosa is a common cause of nosocomial infections, especially in patients with cystic fibrosis and burn wounds. An attenuated PAO1 strain and its derivatives are widely used to study the biology of this bacterium, however recent studies indicated an ongoing evolution of the laboratory strains, highlighted by changes in the genomes of PAO1 sublines and derivatives used in different laboratories worldwide.\n\nHere we have sequenced the genome of Pseudomonas aeruginosa PAO1161 strain, a leu-, RifR, restriction-modification defective PAO1 derivative. This strain is described as the host of IncP-8 plasmid FP2, conferring the resistance to mercury and used in the past for preparation of genetic map of the P. aeruginosa chromosome. Comparison of PAO1161 genome sequence with PAO1-UW reference genome revealed an inversion of the large genome segment between rrnA and rrnB rRNA operons and more than 100 nucleotide polymorphisms and short insertions-deletions, many of which were also found within the recently re-sequenced PAO1 sublines. The PAO1161 specific sequence variants include E108K mutation in PA3792 (leuA), which we showed is responsible for leucine auxotrophy, H531L in PA4270 (rpoB), likely conferring rifampicin resistance, as well as nonsense mutations in PA2735 encoding a DNA methyltransferase as well as a putative OLD family endonuclease PA1939. Additionally, PAO1161 genome poses a 12 kb RPG42 prophage and a 108 kbp insertion within tRNA-Lys, encompassing a putative mercury resistance and showing similarity to PAPI-1 like integrative conjugative elements (ICE). Our data indicate that the ICE can excise from the bacterial chromosome and can be transferred to Pseudomonas putida cells where it integrates in the genome at three specific sites and confers the cells with mercury resistance. Overall this data provide insight into the genome variation between P. aeruginosa laboratory strains. Moreover, this data indicate that the FP2 element for years described as a IncP-8 plasmid is an integrative conjugative element.