Mar 23, 2020

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

BioRxiv : the Preprint Server for Biology
Colton J LloydBernhard O Palsson

Abstract

Sustaining a robust metabolic network requires a balanced and fully functioning proteome. In addition to amino acids, many enzymes require cofactors (coenzymes and engrafted prosthetic groups) to function properly. Extensively validated genome-scale models of metabolism and gene expression (ME-models) have the unique ability to compute an optimal proteome composition underlying a metabolic phenotype, including the provision of all required cofactors. Here we use the ME-model for Escherichia coli K-12 MG1655 to computationally examine how environmental conditions change the proteome and its accompanying cofactor usage. We found that: (1) The cofactor requirements computed by the ME model mostly agree with the standard biomass objective function used in models of metabolism alone (M models); (2) ME-model computations reveal non-intuitive variability in cofactor use under different growth conditions; (3) An analysis of ME-model predicted protein use in aerobic and anaerobic conditions suggests an enrichment in the use of prebiotic amino acids in the proteins used to sustain anaerobic growth (4) The ME-model could describe how limitation in key protein components affect the metabolic state of E. coli. Genome-scale models have thus ...Continue Reading

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Mentioned in this Paper

Biochemical Pathway
Microarray Analysis
Regenerative Medicine
Profile (Lab Procedure)
Gene Expression
Cell Differentiation Process
High Throughput Analysis
Fat Cell Differentiation
Tissue Dissection
Gene Expression Profiling

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