Table 1.
Summary of published metabolic and macromolecular expression ME models.
Model | Organism | Coverage | Key findings |
---|---|---|---|
T. maritima- ME105 | Thermotoga maritima | Metabolism, macromolecular synthesis, post-transcriptional modification and dilution to daughter cells | Accurately predicted cellular composition and gene expression; Enabled new regulon discovery and genome annotation |
iOL1650-ME124 | Escherichia. coli | 1,650 genes, 1,295 protein complexes accounting for metabolism, gene expression and macromolecular synthesis | Accurate prediction of multi-scale phenotypes; Revealed the importance of proteomic constraints on growth, by-product secretion, metabolic flux, uptake rates and optimal |
iJL1678-ME106 | E. coli | Incorporated four compartments, (cytoplasm, periplasm, inner, and outer membranes) translocation pathways, membrane constraints in previous iOL1650- ME | Enabled prediction of enzyme abundances and their cellular location; Predicted impact of perturbations such as membrane crowding and enzymatic efficiency |
iJL1678b-ME108 | E. coli | Compared to iJL1678- ME: reformulated coupling constraints; groupedlumped major cellular processes; and iIncluded non-equivalent changes | Significantly reduced free variables and solve time; Increased accuracy in model prediction |
iJL965-ME109 | Clostridium ljungdahlii | 965 genes, 735 protein complexes accounting for central metabolism, transcription, translation, macromolecule modifications, and translocation | Produced accurate prediction of fermentation profiles, yielding deep interpretation of overflow metabolism products, gene expression, and usage of cofactors and metals |