258480 Exploring Bacterial Sugar Consumption At the Single-Cell Level Using An Integrated Computational and Experimental Approach
L-arabinose is a five-carbon monosaccharide, found in hemicelluloses (biomass) and abundant in nature. It has recently received increasing interest as hemicelluloses constitute the raw material for production of commodity chemicals and fuels using microbes and must be broken down in this production process. The most common microorganism used for breaking down L-arabinose and producing fuels and chemicals is E. coli.
E. colipossesses the arabinose system which consists of different operons that are responsible for the uptake and degradation of arabinose. The main operon, called L-arabinose operon, comprises of a regulatory protein, which controls gene expression in an arabinose-dependent fashion, as well as genes that encode proteins involved in the catabolism of arabinose. It has been demonstrated that when the genes important for arabinose degradation are deleted, administration of arabinose results in an all-or-nothing behavior. In particular, the cell population is divided in a subpopulation with saturated arabinose concentrations and a subpopulation with no arabinose at all.
Even though the arabinose consumption mechanism in E. colihas been thoroughly investigated, most of the studies have explored its dynamics in the absence of arabinose consumption, i.e. deleting the genes associated with arabinose degradation. We are using a combination of computational and experimental work to interrogate the dynamic behavior of the arabinose system both in the presence and absence of arabinose consumption proteins. We are developing a detailed stochastic mathematical model accounting for the biomolecular interactions underlying the arabinose system. We monitor the evolution of cell behavior over time using fluorescence microscopy and directly compare the experimental phenotype with the simulation results. The simulations are performed using an algorithm which is a fusion of a stochastic-discrete and a stochastic-continuous approach.
Importantly, we are observing an intriguing dynamic behavior which differs significantly from the well characterized all-or-nothing behavior. Overall, our study provides new insights into arabinose consumption at the single cell level. Therefore, our findings may contribute to reverse-engineering sugar consumption in E. coli or designing complex synthetic biological circuits whose functionality is analogous to arabinose system.