Bacterial sugar utilization gives rise to distinct single‐cell behaviours

Abstract

Inducible utilization pathways reflect widespread microbial strategies to uptake and consume sugars from the environment. Despite their broad importance and extensive characterization, little is known how these pathways naturally respond to their inducing sugar in individual cells. Here, we performed single-cell analyses to probe the behavior of representative pathways in the model bacterium Escherichia coli. We observed diverse single-cell behaviors, including uniform responses (D-lactose, D-galactose, N-acetylglucosamine, N-acetylneuraminic acid), “all-or-none” responses (D-xylose, L-rhamnose), and complex combinations thereof (L-arabinose, D-gluconate). Mathematical modeling and probing of genetically modified pathways revealed that the simple framework underlying these pathways—inducible transport and inducible catabolism—could give rise to most of these behaviors. Sugar catabolism was also an important feature, as disruption of catabolism eliminated tunable induction as well as enhanced memory of previous conditions. For instance, disruption of catabolism in pathways that respond to endogenously synthesized sugars led to full pathway induction even in the absence of exogenous sugar. Our findings demonstrate the remarkable flexibility of this simple biological framework, with direct implications for environmental adaptation and the engineering of synthetic utilization pathways as titratable expression systems and for metabolic engineering.

Rethinking the Hierarchy of Sugar Utilization in Bacteria

“…This "all-ornone" response was initially considered a biological artifact, because TMG circumvents catabolism; accordingly, L-lactose yields uniform, graded induction of the pathway across an isogenic population (11). However, single-cell analyses of other utilization pathways in E. coli (e.g., for L-arabinose, D-xylose, L-rhamnose, D-gluconate) revealed "all-or-none" behaviors and other distinct single-cell responses (12)(13)(14), suggesting more diverse and heterogeneous responses to individual nutrients in the environment.…”

“…These two sugars represent the major constituents of lignocellulosic biomass used for the production of biofuels and other chemical products (16). Both L-arabinose and D-xylose are also known to individually generate "all-or-none"-like responses in E. coli (12)(13)(14)17). Finally, the Rao group had previously shown that an uninduced subpopulation, a subpopulation with only the L-arabinose utilization pathway induced, a subpopulation with only the D-xylose utilization pathway induced, and finally a subpopulation with both pathways induced (Fig.…”

Mathematical modelling of microbes: metabolism, gene expression and growth

“…In all of these cases, protein constitutes the largest mass fraction. Consistent with the decision above to consider the population as a non-segregated volume, we define the concentration c i (g) of each molecular constituent i in a population as [50,56]. An immediate consequence of the above definition is the following relation:…”

Spot 42 Small RNA Regulates Arabinose-Inducible araBAD Promoter Activity by Repressing Synthesis of the High-Affinity Low-Capacity Arabinose Transporter

“…However, for experiments in which levels of Spot 42 are high (early exponential phase or growth in glucose medium), endogenous levels of Spot 42 will reinforce the all-or-none behavior of the ara regulon by repressing basal levels of araFGH expression and thus may confound the interpretation of effects expected from the P BAD -controlled protein. Many other sugar utilization pathways are regulated by Spot 42 (13), and some of them (e.g., D-xylose and L-rhamnose) also show all-or-none responses (30). Thus, it is very likely that Spot 42 also contributes to complex single-cell behaviors in these pathways.…”