Cellulose production is coupled to sensing of the pyrimidine biosynthetic pathway via c‐di‐GMP production by the DgcQ protein of Escherichia coli

Abstract

Production of cellulose, a stress response-mediated process in enterobacteria, is modulated in Escherichia coli by the activity of the two pyrimidine nucleotide biosynthetic pathways, namely, the de novo biosynthetic pathway and the salvage pathway, which relies on the environmental availability of pyrimidine nitrogenous bases. We had previously reported that prevalence of the salvage over the de novo pathway triggers cellulose production via synthesis of the second messenger c-di-GMP by the DgcQ (YedQ) diguanylate cyclase. In this work, we show that DgcQ enzymatic activity is enhanced by UTP, whilst being inhibited by N-carbamoyl-aspartate, an intermediate of the de novo pathway. Thus, direct allosteric control by these ligands allows full DgcQ activity exclusively in cells actively synthesizing pyrimidine nucleotides via the salvage pathway. Inhibition of DgcQ activity by N-carbamoyl-aspartate appears to be favoured by protein-protein interaction between DgcQ and PyrB, a subunit of aspartate transcarbamylase, which synthesizes N-carbamoyl-aspartate. Our results suggest that availability of pyrimidine bases might be sensed, somehow paradoxically, as an environmental stress by E. coli. We hypothesize that this link might have evolved since stress events, leading to extensive DNA/RNA degradation or lysis of neighbouring cells, can result in increased pyrimidine concentrations and activation of the salvage pathway.

Escherichia coli adaptation and response to exposure to heavy atmospheric pollution

“…Interestingly, the most downregulated gene in T56-1 was pyrB , which encodes the aspartate carbamoyltransferase catalytic subunit involved in pyrimidine biosynthesis and amino acid metabolism (Table S9). This enzyme catalyzes the conversion of carbamoyl-phosphate into n-carbomoyl-aspartate, a compound that inhibits the diguanylate cyclase DgcQ, which activates cellulose production via the second messenger c-di-GMP 73 .…”

Exploring the Links between Nucleotide Signaling and Quorum Sensing Pathways in Regulating Bacterial Virulence

“…Furthermore, the polymeric composition of the E. coli biofilm is modulated by the availability of pyrimidine bases; an abundance of pyrimidines favors UMP synthesis through nucleotide salvage and upregulates cellulose production via allosteric activation of DgcQ by UTP. Conversely, reliance on de novo pyrimidine synthesis decreases cellulose biogenesis due to allosteric inhibition of DgcQ by N -carbamoyl l -Asp (an intermediate in de novo pyrimidine synthesis). , These findings illustrate the therapeutic potential of modulating nucleotide metabolism to intercept c-di-GMP signaling and disrupt biofilm formation.…”

“…Conversely, reliance on de novo pyrimidine synthesis decreases cellulose biogenesis due to allosteric inhibition of DgcQ by N-carbamoyl L-Asp (an intermediate in de novo pyrimidine synthesis). 102,103 These findings illustrate the therapeutic potential of modulating nucleotide metabolism to intercept c-di-GMP signaling and disrupt biofilm formation.…”

Inactivation of the Pyrimidine Biosynthesis pyrD Gene Negatively Affects Biofilm Formation and Virulence Determinants in the Crohn’s Disease-Associated Adherent Invasive Escherichia coli LF82 Strain

“…Unlike survival in the macrophage-mimicking medium and adhesion factors’ production, flagellar motility was not fully restored by uracil supplementation ( Figure 2 C), possibly suggesting that accumulation of early intermediates of the de novo pyrimidine biosynthesis, rather than pyrimidine availability, might be involved in this process. Indeed, pyrimidine biosynthesis intermediates such as N-carbamoyl-aspartate can modulate production of c-di-GMP, a signal molecule involved in several processes, including flagellar motility [ 52 ].…”