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We propose a biophysical model of Escherichia coli that predicts growth rateand an effective cellular composition from an effective, coarse-grainedrepresentation of its genome. We assume that E. coli is in a state of balancedexponential steadystate growth, growing in a temporally and spatially constantenvironment, rich in resources. We apply this model to a series of pastmeasurements, where the growth rate and rRNA-to-protein ratio have beenmeasured for seven E. coli strains with an rRNA operon copy number ranging fromone to seven (the wild-type copy number). These experiments show that growthrate markedly decreases for strains with fewer than six copies. Using themodel, we were able to reproduce these measurements. We show that the modelthat best fits these data suggests that the volume fraction of macromoleculesinside E. coli is not fixed when the rRNA operon copy number is varied.Moreover, the model predicts that increasing the copy number beyond sevenresults in a cytoplasm densely packed with ribosomes and proteins. Assumingthat under such overcrowded conditions prolonged diffusion times tend to weakenbinding affinities, the model predicts that growth rate will not increasesubstantially beyond the wild-type growth rate, as indicated by otherexperiments. Our model therefore suggests that changing the rRNA operon copynumber of wild-type E. coli cells growing in a constant rich environment doesnot substantially increase their growth rate. Other observations regardingstrains with an altered rRNA operon copy number, such as nucleoid compactionand the rRNA operon feedback response, appear to be qualitatively consistentwith this model. In addition, we discuss possible design principles suggestedby the model and propose further experiments to test its validity.

A Coarse-Grained Biophysical Model of E. coli and Its Application to Perturbation of the rRNA Operon Copy Number