Systemic phylogenetic and transcriptomic analyses reveal diguanylate cyclases and phosphodiesterases required for the basal level of c-di-GMP in Pseudomonas aeruginosa

Cyclic diguanosine monophosphate (c-di-GMP) is an important second messenger involved in bacterial switching from motile to sessile lifestyles. In the opportunistic pathogen Pseudomonas aeruginosa, at least 40 genes are predicted to encode proteins for the making and breaking of this signal molecule. However, there is still paucity of information concerning the systemic expression pattern of those genes and the functions of uncharacterized genes. In this study, we analyzed the phylogenetic distribution of genes from P. aeruginosa that predicted to have a GGDEF domain and found five genes (PA5487, PA0285, PA0290, PA4367 and PA5017) with highly conserved distribution across 52 public complete Pseudomonads genomes. PA5487 was further characterized as a typical diguanylate cyclase (DGC) and was named dgcH. A systemic analysis of the gene expression data revealed that the expression of dgcH is highly invariable and dgcH probably functions as a conserved gene to maintain the basal level of c-di-GMP, as reinforced by gene expression analyses. The other four conserved genes also had similar expression pattern as dgcH. The functional analysis suggested that PA0290 encoded a DGC while the others functioned as phosphodiesterases (PDE). Our data revealed that there are five DGC and PDE genes that maintain the basal level of c-di-GMP in P. aeruginosa. ImportancePseudomonas aeruginosa is an opportunistic pathogen that can cause infections in animals, humans and plants. The formation of biofilms by P. aeruginosa is the central mode of action to persist in hosts and evade immune and antibiotic attacks. Cyclic-di-GMP (c-di-GMP) is an important second messenger involved in the regulation of biofilm formation. In P. aeruginosa PAO1 strain, there are around 40 genes that encode enzymes for the making and breaking this dinucleotide. A major missing information in this field is the phylogeny and expression profile of those genes. Here we took a systemic approach to investigate this mystery. We found that among 40 c-di-GMP metabolizing genes, five of them have well conserved phylogenetic distribution and invariable expression profiles, suggesting there are enzymes required for the basal level of c-di-GMP in P. aeruginosa. This study would thus provide putative therapeutic targets against P. aeruginosa infections.