Paradigm in biodegradation using Pseudomonas putida—A review of proteomics studies

Pseudomonas putida has been extensively studied as a paradigm in environmental biotechnology due to its capabilities in catabolizing various aromatic compounds. In addition to the fate of these aromatic compounds, the physiological status of the bacterial cells involved is another important aspect in biodegradation processes. In recent years, proteomics that deals with the high-throughput analysis of gene products directly at the protein level has been shown as a powerful tool to explore bacterial physiology in biodegradation processes. Through proteomics approaches, the understanding of global metabolic and regulatory alterations in response to various environmental stimuli or phenotypic changes after metabolic engineering has been facilitated. In this review, we summarize the proteomics tools in environmental applications and the proteomics studies of P. putida in bioremediation. The technological and methodological advances in P. putida proteome research and the physiological responses to different environmental conditions revealed by proteomics as well as P. putida catabolic pathway elucidation through proteomics are discussed.