Quantitative proteomic analysis of Rhodococcus ruber responsive to organic solvents

Rhodococcus ruber with organic tolerance has potential applications in biotransformation and bioremediation. To explore the possible organic tolerance mechanism, the response of R. ruber SD3 to toluene and phenol was investigated using a quantitative proteomics approach with isobaric tag for relative and absolute quantification (iTRAQ) and liquid chromatography-tandem mass spectrometry. A total of 362 and 488 differentially expressed proteins were identified in the toluene treatment group and the phenol treatment group as compared to the control group, respectively. Functional annotation and metabolic pathway enrichment showed that transporter, degradation pathway and two-component system were closely related to organic solvent tolerance of R. ruber SD3. The quantitative real-time polymerase chain reaction experiment indicated the mRNA levels of stress proteins with an increased expression of 3.23 times upon toluene stress as compared to the control. The expression of 4-nitrophenol 2-monooxygenase in the phenol treatment group was similar to 123 times higher than the counterpart in the control group. The study revealed the possible tolerance mechanism of R. ruber SD3 to organic solvents stress and provided some potential targets for the engineering of R. ruber SD3 to improve its organic solvent tolerance.