Issue 2, 2008
From the journal:

Molecular BioSystems

Reconstruction, modeling & analysis of Halobacterium salinarum R-1 metabolism†

Orland Gonzalez,*ab   Susanne Gronau,a   Michaela Falb,a   Friedhelm Pfeiffer,a   Eduardo Mendoza,cd   Ralf Zimmerb  and  Dieter Oesterhelta  

* Corresponding authors

a Department of Membrane Biochemistry, Max-Planck Institute of Biochemistry, Martinsried, Germany
E-mail: gonzalez@biochem.mpg.de

b Department of Informatics, Ludwig-Maximilians University Munich, Munich, Germany

c Physics Department & Center for NanoScience, Ludwig-Maximilians University Munich, Munich, Germany

d Computer Science Department, University of the Philippines Diliman, Quezon City, Philippines

Abstract

We present a genome-scale metabolic reconstruction for the extreme halophile Halobacterium salinarum. The reconstruction represents a summary of the knowledge regarding the organism's metabolism, and has already led to new research directions and improved the existing annotation. We used the network for computational analysis and studied the aerobic growth of the organism using dynamic simulations in media with 15 available carbon and energy sources. Simulations resulted in predictions for the internal fluxes, which describe at the molecular level how the organism lives and grows. We found numerous indications that cells maximized energy production even at the cost of longer term concerns such as growth prospects. Simulations showed a very low carbon incorporation rate of only ≈15%. All of the supplied nutrients were simultaneously degraded, unexpectedly including five which are essential. These initially surprising behaviors are likely adaptations of the organism to its natural environment where growth occurs in blooms. In addition, we also examined specific aspects of metabolism, including how each of the supplied carbon and energy sources is utilized. Finally, we investigated the consequences of the model assumptions and the network structure on the quality of the flux predictions.

Graphical abstract: Reconstruction, modeling & analysis of Halobacterium salinarum R-1 metabolism

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Article information

DOI
https://doi.org/10.1039/B715203E
Article type
Paper
Submitted
03 Oct 2007
Accepted
31 Oct 2007
First published
05 Dec 2007

Mol. BioSyst., 2008,4, 148-159

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Reconstruction, modeling & analysis of Halobacterium salinarum R-1 metabolism

O. Gonzalez, S. Gronau, M. Falb, F. Pfeiffer, E. Mendoza, R. Zimmer and D. Oesterhelt, Mol. BioSyst., 2008, 4, 148 DOI: 10.1039/B715203E

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