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Open Access Highly Accessed Research article

Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae

Natalie C Duarte1, Bernhard Ø Palsson1 and Pengcheng Fu2*

Author Affiliations

1 Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA

2 Department of Molecular Biosciences & Bioengineering, University of Hawaii, 1955 East-West Road, Honolulu, HI 96822-2321, USA

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BMC Genomics 2004, 5:63  doi:10.1186/1471-2164-5-63

Published: 8 September 2004

Abstract

Background

The yeast Saccharomyces cerevisiae is an important microorganism for both industrial processes and scientific research. Consequently, there have been extensive efforts to characterize its cellular processes. In order to fully understand the relationship between yeast's genome and its physiology, the stockpiles of diverse biological data sets that describe its cellular components and phenotypic behavior must be integrated at the genome-scale. Genome-scale metabolic networks have been reconstructed for several microorganisms, including S. cerevisiae, and the properties of these networks have been successfully analyzed using a variety of constraint-based methods. Phenotypic phase plane analysis is a constraint-based method which provides a global view of how optimal growth rates are affected by changes in two environmental variables such as a carbon and an oxygen uptake rate. Some applications of phenotypic phase plane analysis include the study of optimal growth rates and of network capacity and function.

Results

In this study, the Saccharomyces cerevisiae genome-scale metabolic network was used to formulate a phenotypic phase plane that displays the maximum allowable growth rate and distinct patterns of metabolic pathway utilization for all combinations of glucose and oxygen uptake rates. In silico predictions of growth rate and secretion rates and in vivo data for three separate growth conditions (aerobic glucose-limited, oxidative-fermentative, and microaerobic) were concordant.

Conclusions

Taken together, this study examines the function and capacity of yeast's metabolic machinery and shows that the phenotypic phase plane can be used to accurately predict metabolic phenotypes and to interpret experimental data in the context of a genome-scale model.