Revisiting Demand Rules for Gene Regulation

Abstract

Starting with Savageaus pioneering work from 1970s, here, we choose the simplest transcription network and ask: How does the cell choose a regulatory topology from the different available possibilities? We study the natural distribution of topologies at genome, systems, and micro-level in E. coli and perform stochastic simulations to help explain the differences in natural distributions. Analyzing regulation of amino acid biosynthesis and carbon utilization in E. coli and B. subtilis, we observe many deviations from the demand rules, and observe an alternate pattern emerging. Overall, our results indicate that choice of topology is drawn randomly from a pool of all networks which satisfy the kinetic requirements of the cell, as dictated by physiology. In short, simply, the cell picks \"whatever works\".