Disentangling the cost of gene expression

Abstract

Gene expression is essential for biological functions but also incurs a fitness cost. Although the fitness cost can be experimentally measured as the relative reduction in growth rate, it remains unclear how the cost quantitatively depends on different limiting factors. In this work, we establish a resource competition model and disentangle the fitness cost into components arising from limiting resources, including ribosomes, RNA polymerases, and transcription factors. Comparing our model predictions with experimental data for Saccharomyces cerevisiae, we demonstrate that ribosome competition dominates the translation cost, and that transcription factor competition dominates the transcription cost. Our model reveals that the fitness costs originate from the processes of transcription and translation, rather than from the products. The model also systematically connects the fitness cost to genetic and environmental properties, making quantitative predictions consistent with various experimental observations. Our work establishes a systematic framework for gene expression cost, guiding synthetic biology to optimize genetic design.