High-density whole-genome cDNA microarrays were used to investigate substrate-dependent gene expression of Methylibium petroleiphilum PM1, one of the best-characterized aerobic methyl tert-butyl ether (MTBE)-degrading bacteria. Differential gene expression profiling was conducted with PM1 grown on MTBE and ethanol as sole carbon sources. Based on microarray high scores and protein similarity analysis, an MTBE regulon located on the megaplasmid was identified for further investigation. Putative functions for enzymes encoded in this regulon are described with relevance to the predicted MTBE degradation pathway. A new unique dioxygenase enzyme system that carries out the hydroxylation of tert-butyl alcohol to 2-methyl-2-hydroxy-1-propanol in M. petroleiphilum PM1 was discovered. Hypotheses regarding the acquisition and evolution of MTBE genes as well as the involvement of IS elements in these complex processes were formulated. The pathways for toluene, phenol, and alkane oxidation via toluene monooxygenase, phenol hydroxylase, and propane monooxygenase, respectively, were upregulated in MTBE-grown cells compared to ethanol-grown cells. Four out of nine putative cyclohexanone monooxygenases were also upregulated in MTBE-grown cells. The expression data allowed prediction of several hitherto-unknown enzymes of the upper MTBE degradation pathway in M. petroleiphilum PM1 and aided our understanding of the regulation of metabolic processes that may occur in response to pollutant mixtures and perturbations in the environment.Petroleum releases are among the most ubiquitous sources of composite organic contaminants in groundwater. The majority of petroleum-associated contaminants reach aquifers via spills or leaks from underground storage tanks at service stations (49). Over 300,000 releases from underground storage tanks have been confirmed, with more than 150,000 remediation efforts completed in the United States (32). Fuel oxygenates, such as methyl tertiary butyl ether (MTBE), often form extensive, unattenuated "plumes" in groundwater because of their high water solubility and low biodegradation rates under oxygen-limited conditions (24,28,34). MTBE was one of the major oxygenates incorporated into reformulated gasoline to increase the fuel's oxygen content and decrease carbon monoxide and ozone emissions. MTBE and its primary metabolite tert-butyl alcohol (TBA) are suspected and known carcinogens, respectively (1, 7, 31, 57). Recently, alternative oxygenates, such as ethanol, have been substituted for MTBE, but because of the very slow depletion of contaminant mass from spill areas under anoxic conditions, the impacts of MTBE on the subsurface will be felt for many years and likely decades to come (8,29).Methylibium petroleiphilum PM1 is one of the best-characterized aerobic MTBE degraders known to date, and PM1-like bacteria have been shown to be present in several MTBEcontaminated aquifers in California (19,20,25) and Europe (12,33,42). M. petroleiphilum PM1 uses MTBE as a sole carbon source, oxidizing it complete...