Fig. 2
Weiße’s whole-cell modelling framework. a Expression of proteins is carried out in 3 steps; transcription, ribosome binding and translation. Free mRNA, ribosome-bound mRNA and protein are denoted by mx, cx and x respectively, with x being r for ribosomal, q for housekeeping, em for metabolic or et for transport. The substrate, s, is supplied to the cell at a constant rate (sin) controlled by a chemostat and imported into the cell by transport proteins. The imported substrate, si, is converted into energy units, a, by metabolic proteins. b A simplified translation model accounts for ribosome binding and unbinding to mRNA and then an irreversible elongation reaction. Energy units are consumed in translation elongation, with one energy unit consumed for each addition of an amino acid (aa). c Growth rate, λ, is calculated as a function of the rate of translation of all proteins in the cell and the total proteome content of the cell. All intracellular molecules will be lost at a dilution rate equal to the growth rate. d The finite energy pool available to the cell is determined by the balance between energy produced by metabolism of the substrate and consumption of energy required for protein translation. For a full description of these equations, see Weiße et al. [33] and Additional file 1: Table S1. Parameters (in red): x ∈ {r: ribosomal, et: transport, em: metabolic, q: housekeeping}; sin: rate of glucose input; vt: kcat of transport reaction; KMt: Michaelis constant for transport reaction; vm: kcat of metabolic reaction; KMm: Michaelis constant for metabolic reaction; ns: nutrient efficiency; ωx: maximum transcription rate of protein x; θx: “transcription threshold” for protein x; γmax: maximum translation rate; Kγ: “translation threshold”; kb: rate of ribosome binding; ku: rate of ribosome unbinding; nx: length of protein x in amino acids; M: all amino acids in the proteome