Resource allocation accounts for the large variability of rate-yield phenotypes across bacterial strains

Abstract

Different strains of a microorganism growing in the same environment display a wide variety of growth rates and growth yields. We developed a coarse-grained model to test the hypothesis that different resource allocation strategies, corresponding to different compositions of the proteome, can account for the observed rate-yield variability. The model predictions were verified by means of a database of hundreds of published rate-yield and uptake-secretion phenotypes of Escherichia coli strains grown in standard laboratory conditions. We found a very good quantitative agreement between the range of predicted and observed growth rates, growth yields, and glucose uptake and acetate secretion rates. These results support the hypothesis that resource allocation is a major explanatory factor of the observed variability of growth rates and growth yields across different bacterial strains. The model also predicts resource allocation strategies allowing an E. coli strain to grow, at the same time, rapidly and efficiently. A number of salient features of these strategies agree with the experimental data, but in order to exactly reproduce the observed strategies, differences in enzyme activity need to be taken into account as well. Our model allows a fundamental understanding of quantitative bounds on rate and yield in E. coli and other microorganisms. It may also be useful for the rapid screening of strains in metabolic engineering and synthetic biology.