Genomic Responses of Pseudomonas putida to Aromatic Hydrocarbons

Abstract

When Pseudomonas putida mt-2 cells face aromatic hydrocarbons, they must make a number of decisions that exemplify virtually every challenge that environmental bacteria need to overcome for thriving in polluted sites. It is thus no surprise that the genome-wide responses of P. putida to a variety conditions have been studied in considerable detail. One long-standing issue is how P. putida handles nutrient choice when a mixture of substrates coexist in the same site. A complex mechanism reminiscent of catabolite repression is in place to ensure that hydrocarbons are tackled only after virtually all other easy nutrients are depleted. Once this occurs, typical components of the lighter aromatic fractions of petroleum (e.g., toluene and xylenes) are not only potential nutrients but also strong stressors for P. putida. For handling this scenario, simultaneous processing of their presence both as an edible carbon source to benefit from and as a detrimental hassle to keep at bay becomes necessary. A second issue is the metabolic jam caused by the coincident presence in the same cells of competing pathways for ortho-cleavage and meta-cleavage of the intermediate catechols that degradation of aromatics must necessarily go through. Availability of a suite of genomic, proteomic and reporter technologies has shed light on these questions and exposed a number of surprising solutions that would otherwise look like intractable biochemical and regulatory problems. These include not only specific biochemical and transcriptional devices that overcome intracellular conflicts but also diversification of the population for acquiring different phenotypic roles.