Fig. 3

Proteome allocation can explain important biological phenomena. a Illustration of the physiological function of cAMP-dependent carbon catabolite repression (CCR) in allocating proteomic resources to meet growth demand adapted from ref. [3]. Under carbon limitation, catabolic genes (namely mass fraction of catabolic proteins \(\phi_{C}\)) are upregulated while anabolic genes (indicated by the mass fraction of anabolic proteins \(\phi_{A}\)) are downregulated with decreased growth rates. b Illustration of the overflow metabolism in fast-growing E. coli adapted from ref. [4]. The fraction of total proteome allocated to fermentation (\(\phi_{f}\)) and respiration (\(\phi_{r}\)) is different between slow growth (low carbon uptake) and fast growth (high carbon uptake). The key driver of such modulation of proteome resources lies in the much lower protein investment per ATP flux (yellow arrow) of the fermentation pathway compared with respiration. c Illustration of the coarse-grained model of diauxie and co-utilization of carbon sources adapted from ref. [37]. For diauxie, two group A sources (A1 and A2) can both supply precursor pools for biomass production but with different pathway efficiencies (\(\varepsilon_{1}\) and \(\varepsilon_{2}\)). The one with higher efficiency is preferred for maximal growth. If two precursor pools supply the biomass synthesis, each pool derives from an intermediate node M or N. Either intermediate node can draw flux from either of the two sources A and B. Co-utilization occurs under conditions where the efficiency for biomass production is highest when directly drawing carbon flux from source A to precursor Pool 1 and from source B to precursor Pool 2, i.e. the optimal overall efficiency would be \(\varepsilon_{a1} + \varepsilon_{a2} + \varepsilon_{b1} + \varepsilon_{b2}\)