Reinders, A. | Search bioRxiv

bioRxiv2022

A Novel Biosensor Reveals Dynamic Changes of C-di-GMP in Differentiating Cells with Ultra-High Temporal Resolution

Cyclic diguanylate (c-di-GMP) is a ubiquitous second messenger that regulates a wide range of biological processes in bacteria, including motility, surface attachment, virulence and persistence. The regulatory networks controlling c-di-GMP are generally complex and understudied. This is largely due to a lack of appropriate tools to monitor dynamic changes of c-di-GMP concentrations in vivo in a non-invasive manner. Here, we develop a genetically-encoded ratiometric c-di-GMP biosensor, called cdGreen2, by applying a powerful directed evolution approach based on iterative fluorescence-activated cell sorting (FACS) under alternating c-di-GMP regimes. We demonstrate that cdGreen2 can robustly track c-di-GMP dynamics in live cells with ultra-high temporal resolution over multiple generations. To validate its exquisite diagnostic power, we utilize cdGreen2 to dissect the regulatory networks driving bimodal developmental programs in the environmental model organism Caulobacter crescentus and the human pathogen Pseudomonas aeruginosa. These studies disclose the molecular determinants governing cell cycle-dependent c-di-GMP oscillations in C. crescentus and surface-induced c-di-GMP asymmetry in P. aeruginosa. The sensitivity and versatility of cdGreen2 will help unveil c-di-GMP dynamics in a wide range of organisms with unprecedented temporal resolution. The simple, yet powerful design principles underlying cdGreen2 will serve as a blueprint for the development of similar, orthogonal biosensors for other signaling molecules, metabolites or antibiotics, paving the way to uncover the complex interplay of small molecule-based networks with unprecedented spatiotemporal resolution.

microbiology↗

bioRxiv2021

Digital control of c-di-GMP in E. coli balances population-wide developmental transitions and phage sensitivity

Nucleotide-based signaling molecules (NSMs) are widespread in bacteria and eukaryotes, where they control important physiological and behavioral processes. In bacteria, NSM-based regulatory networks are highly complex, entailing large numbers of enzymes involved in the synthesis and degradation of active signaling molecules. How the converging input from multiple enzymes is transformed into robust and unambiguous cellular responses has remained unclear. Here we show that Escherichia coli converts dynamic changes of c-di-GMP into discrete binary signaling states, thereby generating heterogeneous populations with either high or low c-di-GMP. This is mediated by an ultrasensitive switch protein, PdeL, which senses the prevailing cellular concentration of the signaling molecule and couples this information to c-di-GMP degradation and transcription feedback boosting its own expression. We demonstrate that PdeL acts as a digital filter that facilitates precise developmental transitions, confers cellular memory, and generates functional heterogeneity in bacterial populations to evade phage predation. Based on our findings, we propose that bacteria apply ultrasensitive regulatory switches to convert dynamic changes of NSMs into binary signaling modes to allow robust decision-making and bet-hedging for improved overall population fitness.

microbiology↗