Determining the different mechanisms used by Pseudomonas strains to cope with minimal inhibitory concentrations of zinc via comparative transcriptomic and metabolic analyses

Abstract

Background Pseudomonas is one of the most diverse bacterial genera identified in soil, water, plants and clinical samples. Genome sequence analysis has indicated that this genus can be clustered into three lineages and ten groups. Each group can adopt different mechanisms to thrive under zinc-depleted or high-zinc conditions, two environments that are frequently encountered during their environmental propagation. Results The response mechanisms of three prominent Pseudomonas strains (Pseudomonas aeruginosa PAO1, Pseudomonas putida KT2440, and Pseudomonas fluorescence ATCC13525T) under high-zinc condition were compared using RNA-seq and ultra-performance liquid chromatography–tandem mass spectrometry analysis. Results demonstrated that the three strains shared only minimal similarity at the transcriptional level. Only four genes responsible for zinc efflux were commonly upregulated. P. aeruginosa PAO1 specifically downregulated the operons involved in siderophore synthesis and the genes that encode ribosomal protein, while upregulated the genes associated with antibiotic efflux and cell envelope biosynthesis. The membrane transporters in P. putida KT2440 were globally downregulated, indicating changes in cell permeability. Compared with P. aeruginosa PAO1 and P. putida KT2440, the most remarkable transcriptional variation in P. fluorescence ATCC13525 is the significant downregulation of the type VI secretion system. Metabolite quantitative analysis showed that low concentrations of the metabolites involved in central carbon metabolism and amino acid synthesis were detected in the three strains. Dipeptides containing branched-chain amino acids seems played an important role in alleviating stress caused by zinc ions. Conclusion The exclusion of cytoplasmic ions and reducing the intrusion of excess zinc are equally important for P. aeruginosa, P. putida, and P. fluorescence to withstand external zinc stress. Although similar metal efflux systems were commonly upregulated, these three strains apparently used different pathways to reduce zinc entry. In addition, zinc treatment can increase the difficulties of scavenging P. aeruginosa from its colonisation area, and reduce the effectiveness of P. fluorescence as a biocontrol agent.