Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling

J.A. Wodke, J. Puchalka, M. Lluch-Senar, J. Marcos, E. Yus, M. Godinho, R. Gutierrez-Gallego, V.A.P. Martins Dos Santos, L. Serrano, E. Klipp, T. Maier

Research output: Contribution to journalArticleAcademicpeer-review

31 Citations (Scopus)

Abstract

Mycoplasma pneumoniae, a threatening pathogen with a minimal genome, is a model organism for bacterial systems biology for which substantial experimental information is available. With the goal of understanding the complex interactions underlying its metabolism, we analyzed and characterized the metabolic network of M. pneumoniae in great detail, integrating data from different omics analyses under a range of conditions into a constraint-based model backbone. Iterating model predictions, hypothesis generation, experimental testing, and model refinement, we accurately curated the network and quantitatively explored the energy metabolism. In contrast to other bacteria, M. pneumoniae uses most of its energy for maintenance tasks instead of growth. We show that in highly linear networks the prediction of flux distributions for different growth times allows analysis of time-dependent changes, albeit using a static model. By performing an in silico knock-out study as well as analyzing flux distributions in single and double mutant phenotypes, we demonstrated that the model accurately represents the metabolism of M. pneumoniae. The experimentally validated model provides a solid basis for understanding its metabolic regulatory mechanisms
Original languageEnglish
Article number653
Number of pages19
JournalMolecular Systems Biology
Volume9
DOIs
Publication statusPublished - 2013

Fingerprint

Mycoplasma pneumoniae
Energy Metabolism
energy metabolism
Genome
Genes
genome
Modeling
Metabolism
Systems Biology
Growth
Metabolic Networks and Pathways
Model
Computer Simulation
Fluxes
Linear networks
Theoretical Models
Metabolic Network
Maintenance
Pathogens
metabolism

Keywords

  • cobra toolbox extension
  • flux balance models
  • escherichia-coli
  • reduced bacterium
  • biochemical networks
  • invivo measurement
  • bacillus-subtilis
  • optimal selection
  • genetic-analysis
  • membrane-lipids

Cite this

Wodke, J. A., Puchalka, J., Lluch-Senar, M., Marcos, J., Yus, E., Godinho, M., ... Maier, T. (2013). Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling. Molecular Systems Biology, 9, [653]. https://doi.org/10.1038/msb.2013.6
Wodke, J.A. ; Puchalka, J. ; Lluch-Senar, M. ; Marcos, J. ; Yus, E. ; Godinho, M. ; Gutierrez-Gallego, R. ; Martins Dos Santos, V.A.P. ; Serrano, L. ; Klipp, E. ; Maier, T. / Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling. In: Molecular Systems Biology. 2013 ; Vol. 9.
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abstract = "Mycoplasma pneumoniae, a threatening pathogen with a minimal genome, is a model organism for bacterial systems biology for which substantial experimental information is available. With the goal of understanding the complex interactions underlying its metabolism, we analyzed and characterized the metabolic network of M. pneumoniae in great detail, integrating data from different omics analyses under a range of conditions into a constraint-based model backbone. Iterating model predictions, hypothesis generation, experimental testing, and model refinement, we accurately curated the network and quantitatively explored the energy metabolism. In contrast to other bacteria, M. pneumoniae uses most of its energy for maintenance tasks instead of growth. We show that in highly linear networks the prediction of flux distributions for different growth times allows analysis of time-dependent changes, albeit using a static model. By performing an in silico knock-out study as well as analyzing flux distributions in single and double mutant phenotypes, we demonstrated that the model accurately represents the metabolism of M. pneumoniae. The experimentally validated model provides a solid basis for understanding its metabolic regulatory mechanisms",
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Wodke, JA, Puchalka, J, Lluch-Senar, M, Marcos, J, Yus, E, Godinho, M, Gutierrez-Gallego, R, Martins Dos Santos, VAP, Serrano, L, Klipp, E & Maier, T 2013, 'Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling', Molecular Systems Biology, vol. 9, 653. https://doi.org/10.1038/msb.2013.6

Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling. / Wodke, J.A.; Puchalka, J.; Lluch-Senar, M.; Marcos, J.; Yus, E.; Godinho, M.; Gutierrez-Gallego, R.; Martins Dos Santos, V.A.P.; Serrano, L.; Klipp, E.; Maier, T.

In: Molecular Systems Biology, Vol. 9, 653, 2013.

Research output: Contribution to journalArticleAcademicpeer-review

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AU - Wodke, J.A.

AU - Puchalka, J.

AU - Lluch-Senar, M.

AU - Marcos, J.

AU - Yus, E.

AU - Godinho, M.

AU - Gutierrez-Gallego, R.

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AU - Serrano, L.

AU - Klipp, E.

AU - Maier, T.

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KW - invivo measurement

KW - bacillus-subtilis

KW - optimal selection

KW - genetic-analysis

KW - membrane-lipids

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