Figure 1.
Enzyme turnover numbers and enzyme molecular weights are significantly correlated with metabolic flux rates.
(A) Correlations of enzyme turnover numbers, enzyme molecular weights, gene expression levels, and combinations of the latter via a linear regression model with measured metabolic flux rates. Measured flux rates in E.coli under glucose minimal media in low and high growth rates were taken from Ishii et al. [17], and Schuetz et al. data [18], respectively. Each bar represents a correlation between flux rates and a single or multiple data sources (marked by ‘+’ signs). (B) Enzyme turnover numbers correlate with measured metabolic flux rates in E. coli (both in log10 scale). Linear regression line in red.
Figure 2.
Enzyme turnover rates show higher correlation with average flux across media and with flux under aerobic conditions.
(A) Histogram of Pearson correlations between enzyme turnover numbers and predicted flux rates under different single carbon and energy source media (in blue). The Pearson correlation between enzyme turnover numbers and the averaged flux distribution across conditions (in green) is shown to be markedly higher than those obtained under the different media. (B) Pearson correlations between enzyme turnover numbers and predicted fluxes under a set of single carbon and energy source media under either aerobic versus anaerobic conditions. As shown, under most growth conditions, the correlation between enzyme turnover numbers and fluxes is higher when fluxes are predicted under aerobic conditions.
Figure 3.
Growth rate prediction accuracy by MOMENT versus other approaches.
The prediction of E.coli growth rate under 24 different minimal media based on MOMENT, FBAwMC, and MOMENT with random enzyme turnover rates (with the error bar representing standard deviation over 1000 randomly shuffled turnover numbers). As shown, only MOMENT (with the true turnover rates) achieves a statistically significant Pearson correlation between predicted and measured growth rates (p-values are shown on top of each bar).
Figure 4.
The prediction of growth rates by MOMENT.
MOMENT predicted growth rates achieving a Pearson correlation of 0.47 (p-value = 0.02) with the measured growth rates.
Figure 5.
Metabolic flux and gene expression level predictions via MOMENT versus other approaches.
(A) The prediction of flux rates in E.coli under glucose minimal media based on MOMENT in comparison to FBAwMC, FBA, and MOMENT with random enzyme turnover rates (error bar representing standard deviation over randomly shuffled turnover numbers). (B) The prediction of differential gene expression levels in E.coli under glucose minimal media, between low and high growth rate conditions (with the high growth rate condition involving overflow metabolism). p values are shown above each bar.