Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

Chuankai Cheng, Edward J. O'Brien, Douglas McCloskey, Jose Utrilla, Connor Olson, Ryan A. LaCroix, Troy E. Sandberg, Adam M. Feist, Bernhard O. Palsson, Zachary A. King

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Abstract

Growth rate and yield are fundamental features of microbial growth. However, we lack a mechanistic and quantitative understanding of the rate-yield relationship. Studies pairing computational predictions with experiments have shown the importance of maintenance energy and proteome allocation in explaining rate-yield tradeoffs and overflow metabolism. Recently, adaptive evolution experiments of Escherichia coli reveal a phenotypic diversity beyond what has been explained using simple models of growth rate versus yield. Here, we identify a two-dimensional rate-yield tradeoff in adapted E. coli strains where the dimensions are (A) a tradeoff between growth rate and yield and (B) a tradeoff between substrate (glucose) uptake rate and growth yield. We employ a multi-scale modeling approach, combining a previously reported coarse-grained small-scale proteome allocation model with a fine-grained genome-scale model of metabolism and gene expression (ME-model), to develop a quantitative description of the full rate-yield relationship for E. coli K-12 MG1655. The multi-scale analysis resolves the complexity of ME-model which hindered its practical use in proteome complexity analysis, and provides a mechanistic explanation of the two-dimensional tradeoff. Further, the analysis identifies modifications to the P/O ratio and the flux allocation between glycolysis and pentose phosphate pathway (PPP) as potential mechanisms that enable the tradeoff between glucose uptake rate and growth yield. Thus, the rate-yield tradeoffs that govern microbial adaptation to new environments are more complex than previously reported, and they can be understood in mechanistic detail using a multi-scale modeling approach.

Original languageEnglish
Article numbere1007066
JournalPLOS Computational Biology
Volume15
Issue number6
ISSN1553-7358
DOIs
Publication statusPublished - 2019

Cite this

Cheng, C., O'Brien, E. J., McCloskey, D., Utrilla, J., Olson, C., LaCroix, R. A., Sandberg, T. E., Feist, A. M., Palsson, B. O., & King, Z. A. (2019). Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism. PLOS Computational Biology, 15(6), [e1007066]. https://doi.org/10.1371/journal.pcbi.1007066