Payne2021 - genome-scale metabolic model (iPau21) of Pseudomonas aeruginosa UCBPP-PA14

  public model
Model Identifier
MODEL2106110001
Short description
This model, iPau21, updates and extends the genome-scale metabolic model of the harmful pathogen Pseudomonas aeruginosa UCBPP-PA14, initially published by Bartell et al. (2017). This new model incorporates new information and extensive annotation additions based on manual literature curation. The model was validated using MEMOTE to demonstrate its ability to grow on known carbon sources for this organism, gene essentiality, and additional capabilities. The model was contextualized with transcriptomic data that demonstrate its growth capabilities and differential utilization of fumarate metabolism while also revealing an increased utilization of propionate metabolism upon MUC5B exposure.
Format
COMBINE archive (0.1)
Related Publication
  • An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism
  • Dawson Payne, Alina Renz, Laura J. Dunphy, Taylor Lewis, Andreas Dräger, Papin JA
  • bioRxiv , 3/ 2021 , DOI: 10.1101/2021.03.10.434463
  • University of Virginia
  • Mucins are present in mucosal membranes throughout the body and play a key role in the microbe clearance and infection prevention. Understanding the metabolic responses of pathogens to mucins will further enable the development of protective approaches against infections. We update the genome-scale metabolic network reconstruction (GENRE) of one such pathogen, Pseudomonas aeruginosa PA14, through metabolic coverage expansion, format update, extensive annotation addition, and literature-based curation to produce iPau21. We then validate iPau21 through MEMOTE, growth rate, carbon source utilization, and gene essentiality testing to demonstrate its improved quality and predictive capabilities. We then integrate the GENRE with transcriptomic data in order to generate context-specific models of P. aeruginosa metabolism. The contextualized models recapitulated known phenotypes of unaltered growth and a differential utilization of fumarate metabolism, while also providing a novel insight about an increased utilization of propionate metabolism upon MUC5B exposure. This work serves to validate iPau21 and demonstrate its utility for providing novel biological insights.
Contributors
Andreas Dräger

Metadata information


Curation status
Non-curated

Modelling approach(es)

Name Description Size Actions

Model files

iPau21.omex Payne2021 - genome-scale metabolic model (iPau21) of Pseudomonas aeruginosa UCBPP-PA14 863.66 KB Preview | Download

  • Model originally submitted by : Andreas Dräger
  • Submitted: 11-Jun-2021 16:01:11
  • Last Modified: 11-Jun-2021 16:01:11
Revisions
  • Version: 1 public model Download this version
    • Submitted on: 11-Jun-2021 16:01:11
    • Submitted by: Andreas Dräger
    • With comment: Import of Payne2021 - genome-scale metabolic model (iPau21) of Pseudomonas aeruginosa UCBPP-PA14