Robustness of DNA Looping Across Multiple Divisions in Individual Bacteria

Abstract

DNA looping has emerged as a central paradigm of transcriptional regulation as it is shared across many living systems. One core property of DNA looping-based regulation is its ability to greatly enhance repression or activation of genes with only a few copies of transcriptional regulators. However, this property based on small number of proteins raises the question of the robustness of such a mechanism with respect to the large intracellular perturbations taking place during growth and division of the cell. Here we address the issue of sensitivity to variations of intracellular parameters of gene regulation by DNA looping. We use the lac system as a prototype to experimentally identify the key features of the robustness of DNA looping in growing E. coli cells. Surprisingly, we observe time intervals of tight repression spanning across division events, which can sometimes exceed ten generations. Remarkably, the distribution of such long time intervals exhibits memoryless statistics that is mostly insensitive to repressor concentration, cell division events, and the number of distinct loops accessible to the system. By contrast, gene regulation becomes highly sensitive to these perturbations when DNA looping is absent. Using stochastic simulations, we propose that the robustness to division events of memoryless distributions emerges from the competition between fast, multiple re-binding events of repressors and slow initiation rate of the RNA-polymerase. We argue that fast re-binding events are a direct consequence of DNA looping that ensures robust gene repression across a range of intracellular perturbations. Significance statementIt is well-established that certain intracellular regulators can stabilize DNA loops to greatly enhance activation or repression of gene transcription. In vitro but also in vivo ensemble measurements have determined that only a few copies of regulators are in fact needed to stably form DNA loops. In view of such a small number, we address the issue of sensitivity of gene regulation by DNA looping to variations of intracellular parameters in individual growing E. coli bacteria. Surprisingly, we find that DNA looping from the lac system is robust to a range of perturbations including divisions during which cells can maintain tight repression over many generations. We propose a mechanism that governs the observed robustness across a range of intracellular perturbations.