Phenotypic bistability in Escherichia coli's central carbon metabolism

Abstract

Fluctuations in intracellular molecule abundance can lead to distinct, coexisting phenotypes in isogenic populations. Although metabolism continuously adapts to unpredictable environmental changes, and although bistability was found in certain substrate-uptake pathways, central carbon metabolism is thought to operate deterministically. Here, we combine experiment and theory to demonstrate that a clonal Escherichia coli population splits into two stochastically generated phenotypic subpopulations after glucose-gluconeogenic substrate shifts. Most cells refrain from growth, entering a dormant persister state that manifests as a lag phase in the population growth curve. The subpopulation-generating mechanism resides at the metabolic core, overarches the metabolic and transcriptional networks, and only allows the growth of cells initially achieving sufficiently high gluconeogenic flux. Thus, central metabolism does not ensure the gluconeogenic growth of individual cells, but uses a population-level adaptation resulting in responsive diversification upon nutrient changes.

Transcription factor levels enable metabolic diversification of single cells of environmental bacteria

“…Our study highlights the importance of cell physiology and internal composition and its impact on phenotypic variability. Also, the model presented here emphasizes the need to understand regulatory complexity under the light of population behaviour (Silva-Rocha et al, 2013) and community function (Ackermann, 2013;Kotte et al, 2014;Gallie et al, 2015;Zimmermann et al, 2015) rather than just individual benefit.…”

“…In other cases, an initially homogeneous population shows phenotypic diversification after a nutritional or physicochemical shift. This situation, known as responsive diversification (Grimbergen et al, 2015), has been recently observed as an adaptation strategy to changes in metabolic conditions (Kotte et al, 2014;New et al, 2014;Venturelli et al, 2015). In this scenario, there is a transition from a single gene expression state to two different stable states driven by a change in substrate.…”

“…In this scenario, there is a transition from a single gene expression state to two different stable states driven by a change in substrate. In all these cases, the presence of positive feedback is required to generate and maintain the different expression states (Acar et al, 2005;Maamar and Dubnau, 2005;Suel et al, 2006;Veening et al, 2008;Kotte et al, 2014;Gallie et al, 2015;Venturelli et al, 2015), while molecular noise may enable phenotype switching. The existence of two simultaneous expression states without positive feedback is a much less-frequent phenomenon, and to the best of our knowledge has never been observed in this context.…”

“…This originates large fluctuations in this transcription factor, which is required to activate the TOL network response, inducing long-lasting random episodes where the Pu promoter remains inactive. This mechanism of phenotypic diversification adds to the repertoire of genetic, regulatory and biochemical devices through which bacteria cope with nutritionally changing environments (Kotte et al, 2014;Ackermann, 2015;Gallie et al, 2015).…”

Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes

“…In general, a small fraction of bacteria is usually observed to survive an antibiotic treatment, after which they are able to regrown and restablish an antibiotic-sensitive population, thus indicating that the origin of the resistance of this "persistent" small subpopulation does not rely on genotype mutations. Persister phenotypes are thus known to coexist in cultures in stressed conditions and show an active, yet no (or very slow) growing, metabolism [15]. It has been quantitatively shown that the fitness landscape of E Coli endows inherent bistability of the growth rate [16] and it has been observed that the central carbon core metabolism shall thus endow a bistable phenotypic landscape where slow and fast growing cells sit on wells separated by a watersheed barrier whose height and positions are ruled by two phenomenological parameters related to the growth rate and the metabolic flux [17].…”