Figure 1: Genome-scale modelling of metabolism and expression.
From: In silico method for modelling metabolism and gene product expression at genome scale
(a) Modern stoichiometric models of metabolism (M-models) relate genetic loci to their encoded functions through causal Boolean relationships. The gene and its functions are either present or absent. The dashed arrow signifies incomplete and/or uncertain causal knowledge, whereas blue arrows signify mechanistic coverage. (b) ME-Models provide links between the biological sciences. With an integrated model of metabolism and macromolecular expression, it is possible to explore the relationships between gene products, genetic perturbations and gene functions in the context of cellular physiology. (c) Models of metabolism and expression (ME-Models) explicitly account for the genotype–phenotype relationship with biochemical representations of transcriptional and translational processes. This facilitates quantitative modelling of the relation between genome content, gene expression and cellular physiology. (d) When simulating cellular physiology, the transcriptional, translational and enzymatic activities are coupled to doubling time (Td) using constraints that limit transcription and translation rates as well as enzyme efficiency. τmRNA, mRNA half-life; kcat, catalytic turnover constant; ktranslation, translation rate; ν, reaction flux.
