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C-di-GMP primarily controls motile to sessile transitions in bacteria. Diguanylate cyclases (DGCs) catalyze the synthesis of c-di-GMP from two GTP molecules. Typically, bacteria encode multiple DGCs that are activated by specific environmental signals. Their catalytic activity is modulated by c-di-GMP binding to autoinhibitory sites (I-sites). YfiN is a conserved inner membrane DGC that lacks these sites. Instead, YfiN activity is directly repressed by periplasmic YfiR, which is inactivated by redox stress. In E. coli, an additional envelope stress causes YfiN to relocate to the mid-cell to inhibit cell division by interacting with the division machinery. Here, we report a third activity for YfiN in E. coli, where cell growth is inhibited without YfiN relocating to the division site. This action of YfiN is only observed when the bacteria are cultured on gluconeogenic carbon sources, and is dependent on absence of the autoinhibitory sites. Restoration of I-site function relieves the growth-arrest phenotype, and disabling this function in a heterologous DGC causes acquisition of this phenotype. Arrested cells are tolerant to a wide range of antibiotics. We show that the likely cause of growth arrest is depletion of cellular GTP from run-away synthesis of c-di-GMP, explaining the dependence of growth arrest on gluconeogenic carbon sources that exhaust more GTP during production of glucose. This is the first report of c-di-GMP-mediated growth arrest by altering metabolic flow.

The c-di-GMP signaling network in bacteria not only controls a variety of cellular processes such as motility, biofilms, cell development, and virulence, but does so by a dizzying array of mechanisms. The DGC YfiN singularly represents the versatility of this network in that it not only inhibits motility and promotes biofilms, but also arrests growth in Escherichia coli by relocating to the mid-cell and blocking cell division.

How antibiotic-resistance mutations survive Darwinian forces in the absence of antibiotics is a long-standing question. We report an unexpected evolutionary phenomenon we call phenotype surfing wherein twin phenotypes - high mutation frequencies and high efflux - segregate at the advancing edge of moving E. coli swarms. These phenotypes are linked: high efflux causes downregulation of specific DNA repair pathways, elevating mutations. We uncovered a genetic network connecting efflux and DNA repair, which we corroborated in a clinical 'resistome' database: genomes with mutations that increase efflux exhibit a significant increase in antibiotic-resistance mutations. Consequently, inhibitors that target efflux decreased evolvability to antibiotic resistance. Modeling shows how a mutator phenotype delivered to the edge by faster motility increases genetic drift, enabling survival and range expansion of mutants.

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