Ratnikava, M. | Search bioRxiv

bioRxiv2024

Experimental evolution of a reduced bacterial chemotaxis network

Chemotaxis allows bacteria to follow chemical gradients by comparing their environment over time and adjusting their swimming behavior accordingly. The chemotaxis signaling pathway is highly conserved among all chemotactic bacteria. The system comprises two modules: one for environmental sensing and signal transduction toward the flagellar motor, and the other for adapting to the constant level of background stimulation and providing short-term memory for temporal comparisons. Previous experimental analysis and mathematical modeling have suggested that all components of the paradigmatic chemotaxis pathways in Escherichia coli are essential. This indicates that it may contain a minimal set of protein components necessary to mediate gradient sensing and behavioral response. To test this assumption, here we subjected strains carrying deletions in chemotaxis genes to experimental laboratory evolution. We observed that the core components of the chemotaxis pathway are indeed essential. However, the absence of individual auxiliary pathway proteins, including the adaptation enzymes that are conserved in a vast majority of bacteria, and the phosphatase, could be compensated for to varying degrees by changes in other pathway components. Our results suggest that the experimental evolution of these deletion strains has led to the emergence of alternative strategies for bacterial chemotaxis, demonstrating the surprisingly rapid evolvability of this signaling network.

microbiology↗

bioRxiv2022

Dynamic bimodality of curli expression in planktonic cultures of Escherichia coli is stabilized by cyclic-di-GMP regulation

Curli amyloid fibers are a major constituent of the extracellular biofilm matrix formed by bacteria of the Enterobacteriaceae family. Within Escherichia coli biofilms, curli gene expression is limited to a subpopulation of bacteria, leading to heterogeneity of extracellular matrix synthesis. Here we show that bimodal activation of curli expression occurs not only in submerged and macrocolony biofilms, but also in well-mixed planktonic cultures of E. coli, resulting in all-or-none stochastic differentiation into distinct subpopulations of curli-positive and curli-negative cells at the entry into the stationary phase of growth. Stochastic curli activation in individual E. coli cells could further be observed during continuous growth in a conditioned medium in a microfluidic device, which further revealed that the curli-positive state is only metastable. In agreement with previous reports, regulation of curli gene expression by c-di-GMP via two pairs of diguanylate cyclase and phosphodiesterase enzymes, DgcE/PdeH and DgcM/PdeR, modulates the fraction of curli-positive cells under all tested growth conditions. Unexpectedly, removal of this regulatory network does not abolish the bimodality of curli gene expression, although it affects dynamics of activation and increases heterogeneity of expression levels among individual cells. Moreover, the fraction of curli-positive cells within an E. coli population shows stronger dependence on growth conditions in the absence of c-di-GMP regulation. We thus conclude that, while not required for the emergence of bimodal curli gene expression in E. coli, this c-di-GMP regulatory network attenuates the frequency and dynamics of gene activation and increases its robustness to cellular heterogeneity and environmental variation.

microbiology↗