An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228

Yu Chieh Liao, Tzu Wen Huang, Feng Chi Chen, Pep Charusanti, Jay S J Hong, Hwan You Chang, Shih Feng Tsai, Bernhard O. Palsson, Chao A. Hsiung

Research output: Contribution to journalArticle

62 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)1710-1717
Number of pages8
JournalJournal of Bacteriology
Volume193
Issue number7
DOIs
Publication statusPublished - Apr 2011
Externally publishedYes

Fingerprint

Klebsiella pneumoniae
Genome
Growth
Enterobacteriaceae
Cross Infection
Gram-Negative Bacteria
Sulfur
Computer Simulation
Biomass
Phosphorus
Theoretical Models
Nitrogen
Carbon
Anti-Bacterial Agents
Enzymes
Genes

ASJC Scopus subject areas

  • Microbiology
  • Molecular Biology

Cite this

Liao, Y. C., Huang, T. W., Chen, F. C., Charusanti, P., Hong, J. S. J., Chang, H. Y., ... Hsiung, C. A. (2011). An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228. Journal of Bacteriology, 193(7), 1710-1717. https://doi.org/10.1128/JB.01218-10

An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228. / Liao, Yu Chieh; Huang, Tzu Wen; Chen, Feng Chi; Charusanti, Pep; Hong, Jay S J; Chang, Hwan You; Tsai, Shih Feng; Palsson, Bernhard O.; Hsiung, Chao A.

In: Journal of Bacteriology, Vol. 193, No. 7, 04.2011, p. 1710-1717.

Research output: Contribution to journalArticle

Liao, YC, Huang, TW, Chen, FC, Charusanti, P, Hong, JSJ, Chang, HY, Tsai, SF, Palsson, BO & Hsiung, CA 2011, 'An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228', Journal of Bacteriology, vol. 193, no. 7, pp. 1710-1717. https://doi.org/10.1128/JB.01218-10
Liao, Yu Chieh ; Huang, Tzu Wen ; Chen, Feng Chi ; Charusanti, Pep ; Hong, Jay S J ; Chang, Hwan You ; Tsai, Shih Feng ; Palsson, Bernhard O. ; Hsiung, Chao A. / An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228. In: Journal of Bacteriology. 2011 ; Vol. 193, No. 7. pp. 1710-1717.
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