A Sensitivity Analysis of Growth Rate to Perturbations in Essential Gene Expression

Cell growth is one of the most fundamental physiological processes that bacteria perform, yet the mechanisms by which cells achieve specific growth rates are unknown. To elucidate the genetic basis for cell growth, we performed an essential genome-wide stability analysis of single-cell growth rate upon CRISPRi-mediated perturbation in gene expression. We used mechanistic mathematical modeling to interpret our data. We found that acute transcriptional inhibition of expression of a ribosomal subunit resulted in a growth rate decay that could be predicted by the linear correlation between ribosome concentration and growth rate previously reported. While this confirms that ribosome concentration is rate-limiting with respect to growth, transcriptional inhibition of several other genes involved in various processes resulted in much more rapid growth decay. Overall, decay times were heterogeneous even among genes in the same metabolic pathway. Genes whose inhibition yields fast growth-rate decay times represent key regulators of cellular growth rate. We found that the proteolysis of these proteins is critical for their ability to efficiently mediate growth-rate kinetics in response to nutrient shifts.