Combined transcriptomic and metabolomic analysis of Salmonella in the presence or absence of PhoP–PhoQ system under low Mg 2+ conditions

Introduction Previous reports revealed the role played by Salmonella PhoP–PhoQ system in virulence activation, antimicrobial tolerance and intracellular survival, the impact of PhoP–PhoQ on cell metabolism has been less extensively described. Objectives The aim of this study is to address whether and how the PhoP–PhoQ system affects the cell metabolism of Salmonella. Methods We constructed a Salmonella phoP deletion mutant strain TT-81 (PhoP-OFF), a Salmonella PhoP constitutively expressed strain TT-82 (PhoP-ON) and a wild-type Salmonella PhoP strain TT-80 (PhoP-N), using P22-mediated generalized transduction or λ Red-mediated targeted mutagenesis. We then measured the in vitro growth kinetics of all test strains and determined their metabolomic and transcriptomic profiles using gas chromatography coupled with tandem mass spectrometry (GC–MS/MS) and RNA-seq technique, respectively. Results Low-Mg 2+ conditions impaired the growth of the phoP deletion mutant strain TT-81 (PhoP-OFF) dramatically. 42 metabolites in the wild-type PhoP strain TT-80 (PhoP-N) and 28 metabolites in the PhoP constitutively expressed strain TT-82 (PhoP-ON) changed by the absence of phoP . In contrast, the level of 19 compounds in TT-80 (PhoP-N) changed comparing to the PhoP constitutively expressed strain TT-82 (PhoP-N). The mRNA level of 95 genes in TT-80 (PhoP-N) changed when phoP was disrupted, wherein 78 genes downregulated and 17 genes upregulated. 106 genes were determined to be differentially expressed between TT-81 (PhoP-OFF) and TT-82 (PhoP-ON). While only 16 genes were found to differentially expressed between TT-82 (PhoP-ON) and TT-80 (PhoP-N). Conclusion Our findings confirmed the impact of PhoP–PhoQ system on lipopolysaccharide (LPS) modification, energy metabolism, and the biosynthesis or transport of amino acids. Most importantly, we demonstrated that the turnover of a given metabolite could respond differentially to the level of phoP . Taken together, the present study provided new insights into the adaptation of Salmonella to the host environment and helped to characterize the impact of the PhoP–PhoQ system on the cell metabolism.