title: An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228.
abstract: Klebsiella pneumoniae is a Gram-negative bacterium of the family Enterobacteriaceae that possesses diverse metabolic capabilities: many strains are leading causes of hospital-acquired infections that are often refractory to multiple antibiotics, yet other strains are metabolically engineered and used for production of commercially valuable chemicals. To study its metabolism, we constructed a genome-scale metabolic model (iYL1228) for strain MGH 78578, experimentally determined its biomass composition, experimentally determined its ability to grow on a broad range of carbon, nitrogen, phosphorus and sulfur sources, and assessed the ability of the model to accurately simulate growth versus no growth on these substrates. The model contains 1,228 genes encoding 1,188 enzymes that catalyze 1,970 reactions and accurately simulates growth on 84% of the substrates tested. Furthermore, quantitative comparison of growth rates between the model and experimental data for nine of the substrates also showed good agreement. The genome-scale metabolic reconstruction for K. pneumoniae presented here thus provides an experimentally validated in silico platform for further studies of this important industrial and biomedical organism.
authors.affiliation: Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan 350, Taiwan.
authors.forename: Yu-Chieh
authors.initials: YC
authors.lastname: Liao
authors.forename: Tzu-Wen
authors.initials: TW
authors.lastname: Huang
authors.forename: Feng-Chi
authors.initials: FC
authors.lastname: Chen
authors.forename: Pep
authors.initials: P
authors.lastname: Charusanti
authors.forename: Jay S J
authors.initials: JS
authors.lastname: Hong
authors.forename: Hwan-You
authors.initials: HY
authors.lastname: Chang
authors.forename: Shih-Feng
authors.initials: SF
authors.lastname: Tsai
authors.forename: Bernhard O
authors.initials: BO
authors.lastname: Palsson
authors.forename: Chao A
authors.initials: CA
authors.lastname: Hsiung
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D005075:Biological Evolution; D015415:Biomarkers; D018533:Biomass; D003470:Culture Media; D004734:Energy Metabolism / Q000235:genetics / Q000502:physiology; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology*; D016680:Genome, Bacterial; D007711:Klebsiella pneumoniae / Q000235:genetics* / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D015415:Biomarkers; D003470:Culture Media