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Validation of an FBA model for Pichia pastoris in chemostat cultures.

Morales Y, Tortajada M, Picó J, Vehí J, Llaneras F - BMC Syst Biol (2014)

Bottom Line: We conclude that our predictions based on growth maximisation are reasonably accurate, but still far from perfect.However, predictions are much better when glycerol or glucose are used as substrates.In these scenarios, even if our FBA model is small and imposes a strong assumption regarding how cells will regulate their metabolic fluxes, it provides reasonably good predictions in terms of growth, substrate preference, product formation, and respiration rates.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Constraint-based metabolic models and flux balance analysis (FBA) have been extensively used in the last years to investigate the behavior of cells and also as basis for different industrial applications. In this context, this work provides a validation of a small-sized FBA model of the yeast Pichia pastoris. Our main objective is testing how accurate is the hypothesis of maximum growth to predict the behavior of P. pastoris in a range of experimental environments.

Results: A constraint-based model of P. pastoris was previously validated using metabolic flux analysis (MFA). In this paper we have verified the model ability to predict the cells behavior in different conditions without introducing measurements, experimental parameters, or any additional constraint, just by assuming that cells will make the best use of the available resources to maximize its growth. In particular, we have tested FBA model ability to: (a) predict growth yields over single substrates (glucose, glycerol, and methanol); (b) predict growth rate, substrate uptakes, respiration rates, and by-product formation in scenarios where different substrates are available (glucose, glycerol, methanol, or mixes of methanol and glycerol); (c) predict the different behaviors of P. pastoris cultures in aerobic and hypoxic conditions for each single substrate. In every case, experimental data from literature are used as validation.

Conclusions: We conclude that our predictions based on growth maximisation are reasonably accurate, but still far from perfect. The deviations are significant in scenarios where P. pastoris grows on methanol, suggesting that the hypothesis of maximum growth could be not dominating in these situations. However, predictions are much better when glycerol or glucose are used as substrates. In these scenarios, even if our FBA model is small and imposes a strong assumption regarding how cells will regulate their metabolic fluxes, it provides reasonably good predictions in terms of growth, substrate preference, product formation, and respiration rates.

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FBA growth predictions vs. experimental growth. Comparison of predicted growth and experimental growth for each dataset with different substrates as carbon sources: A) glycerol, B) glucose, C) methanol and methanol-glycerol mixtures. Green labels represent consistent datasets, whereas red ones are those classified as inaccurate. Gray represents those in which the carbon balance could not be checked.
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Fig2: FBA growth predictions vs. experimental growth. Comparison of predicted growth and experimental growth for each dataset with different substrates as carbon sources: A) glycerol, B) glucose, C) methanol and methanol-glycerol mixtures. Green labels represent consistent datasets, whereas red ones are those classified as inaccurate. Gray represents those in which the carbon balance could not be checked.

Mentions: Prediction of growth, substrate uptake, respiration rates, and byproduct formation rates are given in Figure 2 and Table 2 for each scenario. As shown in Figure 2 and Table 2, predictions of growth and substrate uptake are remarkably accurate in scenarios growing on glycerol and glucose. It seems clear that growth maximization is a quite reasonable assumption in these scenarios. It seems that substrates tend to be used through pathways that result in almost optimal growth. Notice also that byproduct formation is not predicted in any scenario, which is also in agreement with the experimental evidence.Figure 2


Validation of an FBA model for Pichia pastoris in chemostat cultures.

Morales Y, Tortajada M, Picó J, Vehí J, Llaneras F - BMC Syst Biol (2014)

FBA growth predictions vs. experimental growth. Comparison of predicted growth and experimental growth for each dataset with different substrates as carbon sources: A) glycerol, B) glucose, C) methanol and methanol-glycerol mixtures. Green labels represent consistent datasets, whereas red ones are those classified as inaccurate. Gray represents those in which the carbon balance could not be checked.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4301075&req=5

Fig2: FBA growth predictions vs. experimental growth. Comparison of predicted growth and experimental growth for each dataset with different substrates as carbon sources: A) glycerol, B) glucose, C) methanol and methanol-glycerol mixtures. Green labels represent consistent datasets, whereas red ones are those classified as inaccurate. Gray represents those in which the carbon balance could not be checked.
Mentions: Prediction of growth, substrate uptake, respiration rates, and byproduct formation rates are given in Figure 2 and Table 2 for each scenario. As shown in Figure 2 and Table 2, predictions of growth and substrate uptake are remarkably accurate in scenarios growing on glycerol and glucose. It seems clear that growth maximization is a quite reasonable assumption in these scenarios. It seems that substrates tend to be used through pathways that result in almost optimal growth. Notice also that byproduct formation is not predicted in any scenario, which is also in agreement with the experimental evidence.Figure 2

Bottom Line: We conclude that our predictions based on growth maximisation are reasonably accurate, but still far from perfect.However, predictions are much better when glycerol or glucose are used as substrates.In these scenarios, even if our FBA model is small and imposes a strong assumption regarding how cells will regulate their metabolic fluxes, it provides reasonably good predictions in terms of growth, substrate preference, product formation, and respiration rates.

View Article: PubMed Central - PubMed

ABSTRACT

Background: Constraint-based metabolic models and flux balance analysis (FBA) have been extensively used in the last years to investigate the behavior of cells and also as basis for different industrial applications. In this context, this work provides a validation of a small-sized FBA model of the yeast Pichia pastoris. Our main objective is testing how accurate is the hypothesis of maximum growth to predict the behavior of P. pastoris in a range of experimental environments.

Results: A constraint-based model of P. pastoris was previously validated using metabolic flux analysis (MFA). In this paper we have verified the model ability to predict the cells behavior in different conditions without introducing measurements, experimental parameters, or any additional constraint, just by assuming that cells will make the best use of the available resources to maximize its growth. In particular, we have tested FBA model ability to: (a) predict growth yields over single substrates (glucose, glycerol, and methanol); (b) predict growth rate, substrate uptakes, respiration rates, and by-product formation in scenarios where different substrates are available (glucose, glycerol, methanol, or mixes of methanol and glycerol); (c) predict the different behaviors of P. pastoris cultures in aerobic and hypoxic conditions for each single substrate. In every case, experimental data from literature are used as validation.

Conclusions: We conclude that our predictions based on growth maximisation are reasonably accurate, but still far from perfect. The deviations are significant in scenarios where P. pastoris grows on methanol, suggesting that the hypothesis of maximum growth could be not dominating in these situations. However, predictions are much better when glycerol or glucose are used as substrates. In these scenarios, even if our FBA model is small and imposes a strong assumption regarding how cells will regulate their metabolic fluxes, it provides reasonably good predictions in terms of growth, substrate preference, product formation, and respiration rates.

Show MeSH
Related in: MedlinePlus