Catabolism of Nucleic Acids by a Cystic Fibrosis Pseudomonas aeruginosa Isolate: An Adaptive Pathway to Cystic Fibrosis Sputum Environment

Abstract

Pseudomonas aeruginosa is a major cause of morbidity and mortality in patients with cystic fibrosis (CF). We undertook Biolog Phenotype Microarray testing of P. aeruginosa CF isolates to investigate their catabolic capabilities compared to P. aeruginosa laboratory strains PAO1 and PA14. One strain, PASS4, displayed an unusual phenotype, only showing strong respiration on adenosine and inosine. Further testing indicated that PASS4 could grow on DNA as a sole carbon source, with a higher biomass production than PAO1. This suggested that PASS4 was specifically adapted to metabolize extracellular DNA, a substrate present at high concentrations in the CF lung. Transcriptomic and proteomic profiling of PASS4 and PAO1 when grown with DNA as a sole carbon source identified a set of upregulated genes, including virulence and host-adaptation genes. PASS4 was unable to utilize N -Acetyl- D -glucosamine, and when we selected PASS4 mutants able to grow on this carbon source, they also displayed a gain in ability to catabolize a broad range of other carbon sources. Genome sequencing of the mutants revealed they all contained mutations within the purK gene, encoding a key protein in the de novo purine biosynthesis pathway. This suggested that PASS4 was a purine auxotroph. Growth assays in the presence of 2 mM adenosine and the complementation of PASS4 with an intact purK gene confirmed this conclusion. Purine auxotrophy may represent a viable microbial strategy for adaptation to DNA-rich environments such as the CF lung.

Pseudomonas aeruginosa: An Audacious Pathogen with an Adaptable Arsenal of Virulence Factors

“…This adaptation may be a double-edged sword because, while it contributes to high fitness in the CF airways, it also limits the potential to move to other environments, where nutrients are scarce [ 285 ]. A recent study showed that a CF isolate was only able to use purines and DNA as carbon sources, likely as an adaptation to the availability of eDNA in the CF environment [ 286 ].…”

From genotype to phenotype: adaptations of Pseudomonas aeruginosa to the cystic fibrosis environment

“…Auxotrophy or reduction of catabolic capacities are frequently observed and arise from either low or high molecule availability in the CF environment. Amino acid auxotrophy often arises in CF-adapted P. aeruginosa due to the high abundance of these molecules in CF sputum [107,[110][111][112]; in addition, purine auxotrophy can be established in DNA-rich sputa [113]. Development of new metabolic capacities can nonetheless arise through enrichment of the accessory genome in metabolic functions [17,28,60].…”

Transcriptomic determinants of the response of ST-111 Pseudomonas aeruginosa AG1 to ciprofloxacin identified by a top-down systems biology approach

“…We detected a concentration-dependent reduction of growth rate as the CIP concentration was increased, similar to another study with CIP in P. aeruginosa 12 . We then employed RNA-Seq analysis to investigate the influence of a sub-inhibitory CIP concentration on the gene expression of PaeAG1 and its relationship with the bacterial growth, similar to recent studies in P. aeruginosa 76 , 77 and other bacteria 16 , 44 , 78 – 81 . Differential expression analysis (Fig.…”

“…This profile is associated with tolerance to oxidative stress, iron availability, biofilms, virulence and killing microbial competitors 109 . Phenazine biosynthesis is regulated by the Rhl 76 and PQS 110 quorum sensing systems in P. aeruginosa . The rhlR gene was found to be up-regulated, suggesting a possible regulation of the phenazines.…”