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| Status |
Public on Oct 20, 2007 |
| Title |
Methylibium petroleiphilum PM1 exposed to the fuel-oxygenates methyl-tert-butyl ether and ethanol |
| Organism |
Methylibium petroleiphilum PM1 |
| Experiment type |
Expression profiling by array
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| Summary |
Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel-oxygenates methyl-tert-butyl ether and ethanol
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 TBA to 2-methyl-2-hydroxy-1-propanol in M. petroleiphilum PM1 was discovered. Based on the expression data, 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, alkane monooxygenase as well as 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 global transcriptome response revealed the link between metabolism of MTBE and aromatic compounds (e.g. benzene, toluene) present in gasoline mixtures. The expression data aids our understanding of the regulation of metabolic processes that may occur in response to pollutant mixtures and perturbations in the environment.
Keywords: bacterial metabolism
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| Overall design |
After growth with MTBE or ethanol as sole carbon source under aerobic conditions, cells from three biological replicates for each treatment were harvested at mid-exponential phase. RNA was extracted from each replicate for microarray analysis.
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| Contributor(s) |
Hristova KR, Schmidt R, Chakicherla AY, Legler TC, Wu J, Chain PS, Scow KM, Kane SR |
| Citation(s) |
17890343 |
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| Submission date |
Oct 19, 2007 |
| Last update date |
Mar 17, 2012 |
| Contact name |
Anu Chakicherla |
| E-mail(s) |
chakicherla1@llnl.gov
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| Organization name |
Lawrence Livermore National Lab
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| Street address |
7000 East Avenue, Mail Stop: L-446
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| City |
Livermore |
| State/province |
CA |
| ZIP/Postal code |
94551 |
| Country |
USA |
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| Platforms (1) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA103093 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE9381_RAW.tar |
99.3 Mb |
(http)(custom) |
TAR (of DATA, PAIR, TXT) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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