Pectobacterium versatile (formerly P. carotovorum) is a recently defined species of soft rot enterobacteria capable of infecting many plant hosts and damaging different tissues. Complex transcriptional regulation of virulence properties can be expected for such a versatile pathogen. However, the relevant information is available only for related species and is rather limited. The PhoPQ two-component system, originally described in pectobacteria as PehRS, was previously shown to regulate a single gene, pehA. Using an insertional phoP mutant of Pectobacterium versatile (earlier—P. carotovorum), we demonstrate that PhoP regulates at least 115 genes with a majority of them specific for pectobacteria. The functions performed by PhoP-controlled genes include degradation, transport and metabolism of plant-derived carbon sources (polygalacturonate, arabinose-containing polysaccharides and citrate), modification of bacterial cell envelope and stress resistance. We also demonstrated PhoP involvement in establishing the order of plant cell wall decomposition and utilisation of the corresponding breakdown products. Based on experimental data and in silico analysis, we defined a PhoP binding site motif and provided proof for its universality in enteric bacteria. Scanning P. versatile genome for the locations of this motif suggested a much larger PhoP regulon enriched with the genes important for a plant pathogen, which makes PhoP a global virulence regulator. Potential PhoP targets include many regulatory genes and PhoP control over one of them, expI, was confirmed experimentally, highlighting the link between the PhoPQ two-component and quorum sensing systems. High concentrations of calcium and magnesium ions were found to abolish the PhoPQ-dependent transcription activation but did not relieve repression. Reduced PhoP expression and minimisation of PhoP dependence of regulon members’ expression in P. versatile cells isolated from potato tuber tissues suggest that PhoPQ system is a key switch of expression levels of multiple virulence-related genes fine-tuned to control the development of P. versatile-host plant pathosystem.

RNA-Seq transcriptome data for the wild type and phoP mutant strains of Pectobacterium versatile is described. P. versatile is a recently introduced name for a species of plant pathogenic bacteria that unites a group of strains previously embedded within the Pectobacterium carotovorum clade [ 1 , 2 ]. Little detail is available about how this pathogen adapts to changing environmental conditions, including those within its host plant. The PhoP/PhoQ two-component system is an important sensor responding to several stimuli and is present in most species of enteric bacteria. It usually controls large regulons, which vary greatly even between closely related species [3] . This dataset enables the discovery of the genes under direct or indirect transcriptional control by PhoP in P. versatile and should help to understand the physiology of this plant pathogen.

The PhoPQ two-component system, originally described in pectobacteria as PehRS, was previously shown to regulate a single gene, pehA. Using an insertional phoP mutant of Pectobacterium versatile, we demonstrate that PhoP controls a regulon of at least 116 genes with a large fraction of regulon members specific for pectobacteria. The functions performed by the PhoP controlled genes include transport and metabolism of plant-derived carbon sources (polygalacturonate, arabinose and citrate), modification of bacterial cell envelope and stress resistance. High concentrations of calcium and magnesium ions were found to abolish the PhoPQdependent transcription activation. Reduced PhoP expression and minimisation of PhoP dependence of regulon members' expression in the cells isolated from rotten potato tuber tissues suggest that PhoPQ system may adjust expression levels of multiple virulence-related genes during the course of P. versatile-host plant pathosystem development.PehR was originally described as a transcriptional activator of the pehA gene encoding endopolygalacturonase, a major virulence factor in soft rot bacteria (16). PehR is a response regulator that forms a two-component sensory system (TCS) with the membrane histidine kinase PehS. In the SCC3193 strain, which is currently classified as Pectobacterium parmentieri, inactivation of either pehR or pehS resulted in reduced virulence and Ca 2+ was reported as the ligand detected by the PehS sensor (16,17). It was also suggested that the PehRS system is responsible for the decrease of the polygalacturonase and increase of the pectate lyase activities in response to Ca 2+ released from the degraded cell walls (17).The pectobacterial PehRS two-component system received very little attention since its discovery two decades ago. However, much information has been accumulated about the orthologous system called PhoPQ in other bacteria from the order Enterobacetrales. In Dickeya dadantii, which belongs to the Pectobacteriaceae family together with Pve, PhoPQ TCS was shown to control pellicle formation, motility, resistance to cationic antimicrobial peptides and expression of pectate lyases in response to Mg 2+ concentration (18,19). The PhoPQ system has been thoroughly characterised in Salmonella and to a lesser extent in few more Enterobacteriaceae species including Escherichia coli and Yersinia spp. (see (20) for a review). The PhoQ sensor histidine kinase activates PhoP by phosphorylation in response to several stimuli, including low Mg 2+ concentration (21), cationic peptides (22), acidity (23) and high osmolarity (24). PhoP binds to direct repeats with a consensus gGTTTA which seems to be well conserved in enterobacteria (25,26). The regulon composition nevertheless varies widely even between closely related bacteria. In Salmonella enterica, over a hundred genes are regulated by PhoP, but only three of them (phoP, phoQ and slyB) are always under PhoP control in other enterobacteria. Some regulon members are shared by several species, but most PhoP controlled gene...