Supporting data for "Genome-scale metabolic modelling of responses to polymyxins in Pseudomonas aeruginosa."
Dataset type: Genomic, Transcriptomic
Data released on February 22, 2018
Zhu Y; Czauderna T; Zhao J; Klapperstueck M; Maifiah MHM; Han ML; Lu J; Sommer B; Velkov T; Lithgow T; Song J; Schreiber F; Li J (2018): Supporting data for "Genome-scale metabolic modelling of responses to polymyxins in Pseudomonas aeruginosa." GigaScience Database. http://dx.doi.org/10.5524/100414
Pseudomonas aeruginosa often causes multidrug-resistant infections in immunocompromised patients and polymyxins are often used as the last-line therapy. Alarmingly, resistance to polymyxins has been increasingly reported worldwide recently. To rescue this last-resort class of antibiotics, it is necessary to systematically understand how P. aeruginosa alters its metabolism in response to polymyxin treatment, thereby facilitating the development of effective therapies. To this end, a genome-scale metabolic model (GSMM) was employed to analyse bacterial metabolic changes at the systems level.
A high-quality GSMM iPAO1 was constructed for P. aeruginosa PAO1 for antimicrobial pharmacological research. Model iPAO1 encompasses an additional periplasmic compartment and contains 3,022 metabolites, 4,265 reactions and 1,458 genes in total. Growth prediction on 190 carbon and 95 nitrogen sources achieved an accuracy of 89.1%, outperforming all reported P. aeruginosa models. Notably, prediction of the essential genes for growth achieved a high accuracy of 87.9%. Metabolic simulation showed that lipid A modifications associated with polymyxin resistance exerted a limited impact on bacterial growth and metabolism, but remarkably changed the physiochemical properties of the outer membrane. Modelling with transcriptomic constraints revealed a broad range of metabolic responses to polymyxin treatment, including reduced biomass synthesis, upregulated amino acids catabolism, induced flux through the tricarboxylic acid cycle, and increased redox turnover.
Overall, iPAO1 represents the most comprehensive GSMM constructed to date for Pseudomonas. It provides a powerful systems pharmacology platform for the elucidation of complex killing mechanisms of antibiotics.
Read the peer-reviewed publication(s):
Zhu, Y., Czauderna, T., Zhao, J., Klapperstueck, M., Maifiah, M. H. M., Han, M.-L., … Li, J. (2018). Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa. GigaScience, 7(4). doi:10.1093/gigascience/giy021
Gioiosa, S., Bolis, M., Flati, T., Massini, A., Garattini, E., Chillemi, G., … Castrignanò, T. (2018). Massive NGS Data Analysis Reveals Hundreds Of Potential Novel Gene Fusions in Human Cell Lines. GigaScience. doi:10.1093/gigascience/giy062
Accessions (data included in GigaDB):
|Sample ID||Taxonomic ID||Common Name||Genbank Name||Scientific Name||Sample Attributes|
|SAMN07807133||208964||Pseudomonas aeruginosa PAO1|| Strain:PAO1|
Description:RNA extract from Pseudomonas aeruginos...
Description:RNA extract from Pseudomonas aeruginosa, isolated from a human host with multiple sclerosis.
Alternative accession-SRA Sample:SRA647946
Geographic location (latitude and longitude):37.8136, 144.963
Geographic location (country and/or sea,region):Australia: Melbourne
Collected by:Mohd Hafidz Mahamad MAIFIAH
Health or disease status of specific host at time of collection:multiple sclerosis [DOID:2377]