Abstract
Cyclic diguanylic acid (c-di-GMP; cGpGp) is a global second messenger controlling motility and adhesion in bacterial cells. Intracellular concentrations of c-di-GMP depend on two opposite activities: diguanylate cyclase, recently assigned to the widespread GGDEF domain, and c-di-GMP-specific phosphodiesterase, associated with proteins harboring the EAL domain. To date, little is known about the targets of c-di-GMP in the cell or if it affects transcriptional regulation of certain genes. In order to expand our knowledge of the effect of this molecule on the bacterial metabolism, here we report on the Escherichia coli transcriptional profile under high levels of c-di-GMP. We show that an important number of genes encoding cell surface and membrane-bound proteins are altered in their transcriptional activity. On the other hand, genes encoding several transcriptional factors, such as Fur, RcsA, SoxS, and ZraR, are up-regulated, and others, such as GadE, GadX, GcvA, and MetR, are down-regulated. Transcription of motility and cell division genes were altered, and consistent with this was the physiological analysis of cells overexpressing yddV, a diguanylate cyclase; these cells displayed an abnormal cell division process when high levels of c-di-GMP were present. We also show evidence that the diguanylate cyclase gene yddV is co-transcribed with dos, a heme base oxygen sensor with c-di-GMP-specific phosphodiesterase activity. A delta dos::kan mutation rendered the cells unable to divide properly, suggesting that dos and yddV may be part of a fine-tuning mechanism for regulating the intracellular levels of c-di-GMP.
Highlights
Both prokaryotes and eukaryotes use selected small molecules, commonly referred to as second messengers to regulate cell function
In order to shed light into the regulatory mechanisms where c-di-GMP may be involved in the bacterial metabolism, here we report on the genome wide transcriptional profile of Escherichia coli after an abrupt increase in c -diGMP intracellular levels
Identification of yddV as a diguanylate cyclase-Genomic studies have identified 19 proteins with a GGDEF domain in Escherichia coli [supplementary Table IV; [9]], taking the amino acid sequence of DGC1 from Gluconacetobacter xylinus as template, we found that one of the closest matches (31% identical in the GGDEF domain) to this protein in E. coli was the product of the gene yddV named yhcK or b1490 (Fig. 2A)
Summary
Both prokaryotes and eukaryotes use selected small molecules, commonly referred to as second messengers to regulate cell function. The guanine nucleotide, cyclic dinucleotide GMP (c-di-GMP; 3’, 5’cyclic diguanylic acid, cGpGp; Fig. 1) was identified as a novel intracellular bacterial signaling molecule whose structure is known and consists of two cGMP molecules joined by a 3’, 5’-phosphodiester bond (1, 2; Fig. 1). Increasing evidence has demonstrated that c-diGMP acts as an important signaling molecule in a variety of bacterial species influencing various aspects of physiology and behavior such as motility, biofilm formation, virulence and cellcell interactions (for a review see 5). These findings indicate that c-di-GMP signaling is widespread and that like cAMP and cGMP, is a ubiquitous signaling molecule. The intracellular levels of c-di-GMP are regulated by the opposing activities of two types of enzymes, diguanylate cyclases (DGC) and cdi-GMP phosphodiesterases (PDE) [3, 6, 7]
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