Summary
Pseudomonas putida strains are generally recognized as solvent tolerant, exhibiting varied sensitivity to organic solvents. Pan‐genome analysis has revealed that 30% of genes belong to the core‐genome of Pseudomonas. Accessory and unique genes confer high degree of adaptability and capabilities for the degradation and synthesis of a wide range of chemicals. For the use of these microbes in bioremediation and biocatalysis, it is critical to understand the mechanisms underlying these phenotypic differences. In this study, RNA‐seq analysis compared the short‐ and long‐term responses of the toluene‐sensitive KT2440 strain and the highly tolerant DOT‐T1E strain. The sensitive strain activates a larger number of genes in a higher magnitude than DOT‐T1E. This is expected because KT2440 bears one toluene tolerant pump, while DOT‐T1E encodes three of these pumps. Both strains activate membrane modifications to reduce toluene membrane permeability. The KT2440 strain activates the TCA cycle to generate energy, while avoiding energy‐intensive processes such as flagellar biosynthesis. This suggests that KT2440 responds to toluene by focusing on survival mechanisms. The DOT‐T1E strain activates toluene degradation pathways, using toluene as source of energy. Among the unique genes encoded by DOT‐T1E is a 70 kb island composed of genes of unknown function induced in response to toluene.