A novel approach for determining environment-specific protein costs: the case of Arabidopsis thaliana

Motivation: Comprehensive understanding of cellular processes requires development of approaches which consider the energetic balances in the cell. The existing approaches that address this problem are based on defining energy-equivalent costs which do not include the effects of a changing environment. By incorporating these effects, one could provide a framework for integrating ‘omics’ data from various levels of the system in order to provide interpretations with respect to the energy state and to elicit conclusions about putative global energy-related response mechanisms in the cell

Reactions with highest ranking according to functional centrality.

<p>Rankings are shown for the metabolic functions of lactate production (LAC) and ATP production (ATP) under conditions of aerobic respiration (), nitrate respiration () and fermentation (). Reactions with highest FCs obtain lowest numbering.</p

Pairwise correlation between functional centralities for different metabolic functions.

<p>Examined metabolic functions: biomass production (BM), ATP production (ATP), lactate production (LAC). Significant correlations are marked by ^*.</p

Pairwise correlation between functional centralities under different environmental conditions.

<p>Environmental conditions: aerobic respiration (), nitrate respiration () and fermentation (). Significant correlations are marked by ^*.</p

Algorithm for estimation of functional centralities.

<p> denotes the set of all permutations of a set and the element of the set .</p

KO-reduced functionality of biomass production under conditions of nitrate respiration.

<p>Errorbars are provided for all and indicate 95% confidence intervals. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003368#s2" target="_blank">Results</a> are only depicted for a relative standard error smaller than 10%.</p

Pairwise correlation between measures of structural metabolic control capabilities for the metabolic function of biomass production.

<p>Pairwise correlation of functional centralities (FC), coupling degrees (FCA), reaction participations in biomass producing EFMs unweighted (EFM) and weighted by biomass yield () as well as of control-effective fluxes (CEFs). Significant correlations are marked by ^*.</p

KO-reduced functionality of biomass production under conditions of aerobic respiration.

<p>Errorbars are provided for all and indicate 95% confidence intervals. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003368#s2" target="_blank">Results</a> are only depicted for a relative standard error smaller than 10%.</p

Prediction of gene expression patterns by control-effective fluxes (CEFs).

<p>Calculated ratios between transcript levels during exponential growth on glucose (GLC) and growth on acetate (AC) under conditions of aerobic respiration based on CEFs versus experimentally determined transcript ratios. Lines indicate 95% confidence intervals for experimental data (horizontal lines), linear regression (solid line), perfect match (dashed line) and two-fold deviation (dotted line).</p

Prediction of gene expression patterns by functional centralities (FCs).

<p>Calculated ratios between transcript levels during exponential growth on glucose (GLC) and growth on acetate (AC) under conditions of aerobic respiration based on FCs versus experimentally determined transcript ratios. Lines indicate 95% confidence intervals for experimental data (horizontal lines), linear regression (solid line), perfect match (dashed line) and two-fold deviation (dotted line).</p