%0 Journal Article %A Dawson D. Payne %A Alina Renz %A Laura J. Dunphy %A Taylor Lewis %A Andreas Dräger %A Jason A. Papin %T An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism %D 2021 %R 10.1101/2021.03.10.434463 %J bioRxiv %P 2021.03.10.434463 %X 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 revealing an increased utilization of propionate metabolism upon MUC5B exposure. This work serves to validate iPau21 and demonstrate its utility for providing biological insights.Competing Interest StatementThe authors have declared no competing interest.(ABTGC)Agrobacterium minimal medium with thiamine, glucose, and casamino acids(ADP)Adenosine diphosphate(ATP)Adenosine triphosphate(BiGG)Biochemical Genetic and Genomic(BOF)biomass objective function(DNA)deoxyribonucleic acid(GPR)gene-protein-reaction(FBA)flux balance analysis(FADH2)flavin adenine dinucleotide(GEMs)genome-scale metabolic models(GENREs)genome-scale metabolic network reconstructions(KEGG)Kyoto Encyclopedia of Genes and Genomes(LB),lysogeny broth(MCC)Matthews correlation coefficient(MEMOTE)metabolic model testing(NADH)reduced nicotinamide adenine dinucleotide(NADPH)Nicotinamide adenine dinucleotide phosphate(NMDS)non-metric multidimensional scaling(PA14)UCBPP-PA14(RIPTiDe)Reaction Inclusion by Parsimony and Transcript Distribution(SBO)Systems Biology Ontology(SBML)Systems Biology Markup Language(SCFM)synthetic cystic fibrosis media(RNA)ribonucleic acid(WHO)World Health Organization %U https://www.biorxiv.org/content/biorxiv/early/2021/06/16/2021.03.10.434463.full.pdf