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SBRG / cobrame

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
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biomass constituents #35

Open weif000 opened 4 years ago

weif000 commented 4 years ago

Hi, when you built Escherichia coli ME-model, why did you divide the iJO1366 biomass equations into several different equations such as biomass_constituent_demand, lipid components and DNA demand requirements.

coltonlloyd commented 4 years ago

Hello,

Since the synthesis and dilution of enzymes (and their prosthetic groups) and RNA is explicitly modeled in the ME-model, portions of the biomass objective function are no longer relevant (amino acids, nucleotides, iron-sulfur clusters, etc.). Other biomass constituents (folates, NADH, etc.) are not components of enzymes. Therefore, the biomass_constituent_demand is needed to drive their synthesis.

Lipid and DNA requirements received their own biomass demand reaction to users to defined their own coupling functions. For example, DNA content in E. coli is not a linear function of growth.

Sorry for the very late response and hope this answers your question! Colton