Dynamic interactive events in gene regulation using E. coli dehydrogenase as a model

Different approaches in gene expression analysis always provide a snapshot view of cellular events. During the bacterial growth, the decisions are dynamically made with participation of various genes and their interactions with modulating factors. We have selected Escherichia coli dehydrogenases as a model to capture these interactions. We have treated the cells with hydrogen peroxide with very low level and asked the questions how cellular physiology has modulated itself to survive post-shock conditions. We hypothesized that while global regulators and associated gene network dictate the overall cellular intelligence, specific redox-sensitive classes of enzymes like dehydrogenase-mediated modulation could provide the option to cell for survival under peroxide after-effect. To understand the dynamic gene interaction, we used multidimensional scaling of genes and overlaid with minimum spanning tree to understand the clustering patterns under different conditions. Study shows that under peroxide after-effect, it is the interplay of ArcA (global regulator), with ldhA (involved in intermediary metabolism) and ndh (managing co-factor NADH), that emerges as modulating association. Knockout mutants of global regulators confirmed the promoter activity trend through gene expression change for dehydrogenases.