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Applied and Environmental Microbiology, November 2007, p. 7347-7357, Vol. 73, No. 22
0099-2240/07/$08.00+0     doi:10.1128/AEM.01604-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Comparative Transcriptome Analysis of Methylibium petroleiphilum PM1 Exposed to the Fuel Oxygenates Methyl tert-Butyl Ether and Ethanol ^,

Department of Land Air and Water Resources, University of California, Davis, Davis, California,¹ Chemistry, Materials and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California,² Microbial Program, Joint Genome Institute, Walnut Creek, California 94598³

Received 13 July 2007/ Accepted 10 September 2007

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.

Published ahead of print on 21 September 2007.

Supplemental material for this article may be found at http://aem.asm.org/.

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