Dataset Information

Predictive potential of flux balance analysis of Saccharomyces cerevisiae using as optimization function combinations of cell compartmental objectives.

ABSTRACT:

Background

The main objective of flux balance analysis (FBA) is to obtain quantitative predictions of metabolic fluxes of an organism, and it is necessary to use an appropriate objective function to guarantee a good estimation of those fluxes.

Methodology

In this study, the predictive performance of FBA was evaluated, using objective functions arising from the linear combination of different cellular objectives. This approach is most suitable for eukaryotic cells, owing to their multiplicity of cellular compartments. For this reason, Saccharomyces cerevisiae was used as model organism, and its metabolic network was represented using the genome-scale metabolic model iMM904. As the objective was to evaluate the predictive performance from the FBA using the kind of objective function previously described, substrate uptake and oxygen consumption were the only input data used for the FBA. Experimental information about microbial growth and exchange of metabolites with the environment was used to assess the quality of the predictions.

Conclusions

The quality of the predictions obtained with the FBA depends greatly on the knowledge of the oxygen uptake rate. For the most of studied classifications, the best predictions were obtained with "maximization of growth", and with some combinations that include this objective. However, in the case of exponential growth with unknown oxygen exchange flux, the objective function "maximization of growth, plus minimization of NADH production in cytosol, plus minimization of NAD(P)H consumption in mitochondrion" gave much more accurate estimations of fluxes than the obtained with any other objective function explored in this study.

SUBMITTER: Garcia Sanchez CE

PROVIDER: S-EPMC3415429 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Publications

Predictive potential of flux balance analysis of Saccharomyces cerevisiae using as optimization function combinations of cell compartmental objectives.

García Sánchez Carlos Eduardo CE Vargas García César Augusto CA Torres Sáez Rodrigo Gonzalo RG

PloS one 20120809 8

<h4>Background</h4>The main objective of flux balance analysis (FBA) is to obtain quantitative predictions of metabolic fluxes of an organism, and it is necessary to use an appropriate objective function to guarantee a good estimation of those fluxes.<h4>Methodology</h4>In this study, the predictive performance of FBA was evaluated, using objective functions arising from the linear combination of different cellular objectives. This approach is most suitable for eukaryotic cells, owing to their m ...[more]

PMID: 22912775

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Project description:BackgroundMannosylglycerate (MG) is one of the most widespread compatible solutes among marine microorganisms adapted to hot environments. This ionic solute holds excellent ability to protect proteins against thermal denaturation, hence a large number of biotechnological and clinical applications have been put forward. However, the current prohibitive production costs impose severe constraints towards large-scale applications. All known microbial producers synthesize MG from GDP-mannose and 3-phosphoglycerate via a two-step pathway in which mannosyl-3-phosphoglycerate is the intermediate metabolite. In an early work, this pathway was expressed in Saccharomyces cerevisiae with the goal to confirm gene function (Empadinhas et al. in J Bacteriol 186:4075-4084, 2004), but the level of MG accumulation was low. Therefore, in view of the potential biotechnological value of this compound, we decided to invest further effort to convert S. cerevisiae into an efficient cell factory for MG production.ResultsTo drive MG production, the pathway for the synthesis of GDP-mannose, one of the MG biosynthetic precursors, was overexpressed in S. cerevisiae along with the MG biosynthetic pathway. MG production was evaluated under different cultivation modes, i.e., flask bottle, batch, and continuous mode with different dilution rates. The genes encoding mannose-6-phosphate isomerase (PMI40) and GDP-mannose pyrophosphorylase (PSA1) were introduced into strain MG01, hosting a plasmid encoding the MG biosynthetic machinery. The resulting engineered strain (MG02) showed around a twofold increase in the activity of PMI40 and PSA1 in comparison to the wild-type. In batch mode, strain MG02 accumulated 15.86 mgMG g DCW -1 , representing a 2.2-fold increase relative to the reference strain (MG01). In continuous culture, at a dilution rate of 0.15 h-1, there was a 1.5-fold improvement in productivity.ConclusionIn the present study, the yield and productivity of MG were increased by overexpression of the GDP-mannose pathway and optimization of the mode of cultivation. A maximum of 15.86 mgMG g DCW -1 was achieved in batch cultivation and maximal productivity of 1.79 mgMG g DCW -1 h-1 in continuous mode. Additionally, a positive correlation between MG productivity and growth rate/dilution rate was established, although this correlation is not observed for MG yield.

Dataset Information

Predictive potential of flux balance analysis of Saccharomyces cerevisiae using as optimization function combinations of cell compartmental objectives.

Background

Methodology

Conclusions

Publications

Predictive potential of flux balance analysis of Saccharomyces cerevisiae using as optimization function combinations of cell compartmental objectives.

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