A Second Role for the Second Messenger Cyclic-di-GMP inE. coli: Arresting Cell Growth by Altering Metabolic Flow

Abstract

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.

During heat stress in Myxococcus xanthus, the CdbS PilZ domain protein, in concert with two PilZ-DnaK chaperones, perturbs chromosome organization and accelerates cell death

“…C-di-GMP is ubiquitous in bacteria and typically associated with regulation of lifestyle transitions [1,2]. However, it is increasingly recognized that c-di-GMP is also involved in regulating very different types of processes including modification of ribosomal proteins in P. fluorescens [53] and metabolic flux in E. coli [54]. Based on the data presented here, we propose that c-di-GMP might also be involved in regulated cell death.…”

The global regulation of c‐di‐GMP and cAMP in bacteria

“…In bacteria, c-di-GMP is an intracellular nucleotide second messenger that controls a variety of cellular functions, including biofilm formation, cell cycle, and virulence [7][8][9][10][11][12] . c-di-GMP is a "switch molecule" that regulates the "lifestyle transition" from motility to biofilm 9 .…”

Cyclic di‐GMP signaling—Where did you come from and where will you go?

“…Furthermore, the environmental conditions under which distinct biofilms are formed can vary substantially even within a single isolate (Cole et al, 2014). Interference with other associated fundamental traits such as the cell cycle, recombination, and DNA repair and alteration in cell morphology seems to require specific cyclic di-GMP turnover proteins (Fernandez et al, 2018;Gupta et al, 2016;Hwang & Harshey, 2023;Kaczmarczyk et al, 2020;Manikandan et al, 2018). This diversity of biofilm traits and their flexibility to respond to different environmental conditions partly answers the conundrum of the | 567 RÖMLING abundant presence of numerous cyclic di-GMP turnover proteins encoded by bacterial genomes (Amikam & Galperin, 2006;López-Ochoa et al, 2017;Lorite et al, 2022;Roelofs et al, 2015;Römling et al, 2005).…”