A yield-cost tradeoff governs Escherichia coli’s decision between fermentation and respiration in carbon-limited growth

Schematic view of the proteome allocation problem. a Effect of growth limitation via carbon starvation on proteome composition. An increase in the cost of the catabolic (C) sector reduces the growth rate. Part of the non-catabolic (NC) sector, no longer required at slower growth, is freed and can be reallocated. The decrease in growth can be counteracted by expanding the C-sector (i.e., by increasing ？C) and/or by allocating part of the NC-sector to re-organize metabolism so as to decrease the specific carbon intake q？=？JC/μ. b Proteome sectors considered for E. coli, namely ribosomal (R), enzymatic (E), carbon-import (C), and housekeeping core (Q). Following ref. 30 we assume that all sectors but the core have condition-dependent parts denoted by Δ？j. By normalization, their sums are constrained as in Eq. (3). c A change in the nutrient level affects the cellular metabolism and gene expression. In Constrained Allocation FBA,30 the interplay between metabolic fluxes, protein levels, and growth rate leads to optimal phenotypes with maximum growth rat