Genetically and Phenotypically Distinct Pseudomonas aeruginosa Cystic Fibrosis Isolates Share a Core Proteomic Signature

Abstract

The opportunistic pathogen Pseudomonas aeruginosa is among the main colonizers of the lungs of cystic fibrosis (CF) patients. We have isolated and sequenced several P. aeruginosa isolates from the sputum of CF patients and compared them with each other and with the model strain PAO1. Phenotypic analysis of CF isolates showed significant variability in colonization and virulence-related traits suggesting different strategies for adaptation to the CF lung. Genomic analysis indicated these strains shared a large set of core genes with the standard laboratory strain PAO1, and identified the genetic basis for some of the observed phenotypic differences. Proteomics revealed that in a conventional laboratory medium PAO1 expressed 827 proteins that were absent in the CF isolates while the CF isolates shared a distinctive signature set of 703 proteins not detected in PAO1. PAO1 expressed many transporters for the uptake of organic nutrients and relatively few biosynthetic pathways. Conversely, the CF isolates expressed a narrower range of transporters and a broader set of metabolic pathways for the biosynthesis of amino acids, carbohydrates, nucleotides and polyamines. The proteomic data suggests that in a common laboratory medium PAO1 may transport a diverse set of “ready-made” nutrients from the rich medium, whereas the CF isolates may only utilize a limited number of nutrients from the medium relying mainly on their own metabolism for synthesis of essential nutrients. These variations indicate significant differences between the metabolism and physiology of P. aeruginosa CF isolates and PAO1 that cannot be detected at the genome level alone. The widening gap between the increasing genomic data and the lack of phenotypic data means that researchers are increasingly reliant on extrapolating from genomic comparisons using experimentally characterized model organisms such as PAO1. While comparative genomics can provide valuable information, our data suggests that such extrapolations may be fraught with peril.

Virulence adaptations of Pseudomonas aeruginosa isolated from patients with non-cystic fibrosis bronchiectasis

“…As such, the aim of our study was to address this current gap of knowledge with respect to the adaptation of P. aeruginosa in nCFB. Indeed, we found similar adaptation strategies between isolates of P. aeruginosa from nCFB patientswhich, due to the broad range of environmental niches, display a wide spectrum of virulence and motility (Pujana et al, 1999;Penesyan et al, 2015). While differences in airway characteristics exist between CF and nCFB, we have found that P. aeruginosa largely adapts in a similar manner, extending from virulence factor production to motility and biofilm formation, and that virulence tends to decrease over time.…”

Paucimannose-Rich N-glycosylation of Spatiotemporally Regulated Human Neutrophil Elastase Modulates Its Immune Functions*.

“…Bacteriostatic Assay-The clinically relevant Pseudomonas aeruginosa PASS1 strain was isolated and cultured to mid-log growth phase as previously described (60,61). PASS1 was then washed twice in 1ϫ PBS and diluted to an OD 600 nm of 0.1 in Luria Beria broth before use.…”

Pseudomonas aeruginosa Cell Membrane Protein Expression from Phenotypically Diverse Cystic Fibrosis Isolates Demonstrates Host-Specific Adaptations

“…We recently reported whole genome sequences and global proteomic characterisation from four CF isolate strains of P. aeruginosa grown in LB medium 11 . This showed that CF strains had similar sized genomes (ranging 6.1-6.4Mbp) and shared common core features, many of which were different to PAO1.…”