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 flux phenotypes of Escherichia coli strains grown in standard laboratory conditions. We found a very good quantitative agreement between the predicted and observed variability in rates and yields. Moreover, over the entire range of wild-type and mutant strains considered, acetate overflow was predicted not to correlate with the growth rate, in agreement with the experimental data. These results support the hypothesis that resource allocation is a major explanatory factor of the observed variety of growth rates and growth yields across different bacterial strains. We also show, however, that differences in enzyme activity need to be taken into account to explain variations in protein abundance. 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.