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. Author manuscript; available in PMC: 2021 Jul 28.
Published in final edited form as: Nat Rev Microbiol. 2020 Sep 21;18(12):731–743. doi: 10.1038/s41579-020-00440-4

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
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