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Title: Whole-genorne analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1

Abstract

Methylibium petroleiphilum PM1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (MTBE). Strain PM1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain (C, to C,,) hydrocarbons present in petroleum products. Whole-genome analysis of PM1 revealed an similar to 4-Mb circular chromosome and an similar to 600-kb megaplasmid, containing 3,831 and 646 genes, respectively. Aromatic hydrocarbon and alkane degradation, metal resistance, and methylotrophy are encoded on the chromosome. The megaplasmid contains an unusual t-RNA island, numerous insertion sequences, and large repeated elements, including a 40-kb region also present on the chromosome and a 29-kb tandem repeat encoding phosphonate transport and cobalamin biosynthesis. The megaplasmid also codes for alkane degradation and was shown to play an essential role in MTBE degradation through plasmid-curing experiments. Discrepancies between the insertion sequence element distribution patterns, the distributions of best BLASTP hits among major phylogenetic groups, and the G+C contents of the chromosome (69.2%) and plasmid (66%), together with comparative genome hybridization experiments, suggest that the plasmid was recently acquired and apparently carries the genetic information responsible for PM1's ability to degrade MTBE. Comparative genomic hybridization analysis with two PM1-like MTBE-degrading environmental isolates (similar to 99% identicalmore » 16S rRNA gene sequences) showed that the plasmid was highly conserved (ca. 99% identical), whereas the chromosomes were too diverse to conduct resequencing analysis. PM1's genome sequence provides a foundation for investigating MTBE biodegradation and exploring the genetic regulation of multiple biodegradation pathways in M. petroleiphilum and other MTBE-degrading beta-proteobacteria.« less

Authors:
 [1];  [1];  [1];  [2];  [3];  [1];  [2];  [4];  [5];  [3];  [2]
  1. Lawrence Livermore National Laboratory (LLNL)
  2. University of California, Davis
  3. U.S. Department of Energy, Joint Genome Institute
  4. ORNL
  5. Joint Genome Institute, Walnut Creek, California
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
931553
DOE Contract Number:  
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Bacteriology; Journal Volume: 189; Journal Issue: 5
Country of Publication:
United States
Language:
English
Subject:
02 PETROLEUM; ETHERS; PETROLEUM PRODUCTS; PLASMIDS; GENES

Citation Formats

Kane, Staci R., Chakicherla, Anu Y., Chain, Patrick S. G., Schmidt, Radomir, Shin, M, Legler, Tina C., Scow, Kate M., Larimer, Frank W, Lucas, Susan, Richardson, P M, and Hristova, Krassimira R. Whole-genorne analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1. United States: N. p., 2007. Web. doi:10.1128/JB.01259-06.
Kane, Staci R., Chakicherla, Anu Y., Chain, Patrick S. G., Schmidt, Radomir, Shin, M, Legler, Tina C., Scow, Kate M., Larimer, Frank W, Lucas, Susan, Richardson, P M, & Hristova, Krassimira R. Whole-genorne analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1. United States. doi:10.1128/JB.01259-06.
Kane, Staci R., Chakicherla, Anu Y., Chain, Patrick S. G., Schmidt, Radomir, Shin, M, Legler, Tina C., Scow, Kate M., Larimer, Frank W, Lucas, Susan, Richardson, P M, and Hristova, Krassimira R. Thu . "Whole-genorne analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1". United States. doi:10.1128/JB.01259-06.
@article{osti_931553,
title = {Whole-genorne analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1},
author = {Kane, Staci R. and Chakicherla, Anu Y. and Chain, Patrick S. G. and Schmidt, Radomir and Shin, M and Legler, Tina C. and Scow, Kate M. and Larimer, Frank W and Lucas, Susan and Richardson, P M and Hristova, Krassimira R.},
abstractNote = {Methylibium petroleiphilum PM1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (MTBE). Strain PM1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain (C, to C,,) hydrocarbons present in petroleum products. Whole-genome analysis of PM1 revealed an similar to 4-Mb circular chromosome and an similar to 600-kb megaplasmid, containing 3,831 and 646 genes, respectively. Aromatic hydrocarbon and alkane degradation, metal resistance, and methylotrophy are encoded on the chromosome. The megaplasmid contains an unusual t-RNA island, numerous insertion sequences, and large repeated elements, including a 40-kb region also present on the chromosome and a 29-kb tandem repeat encoding phosphonate transport and cobalamin biosynthesis. The megaplasmid also codes for alkane degradation and was shown to play an essential role in MTBE degradation through plasmid-curing experiments. Discrepancies between the insertion sequence element distribution patterns, the distributions of best BLASTP hits among major phylogenetic groups, and the G+C contents of the chromosome (69.2%) and plasmid (66%), together with comparative genome hybridization experiments, suggest that the plasmid was recently acquired and apparently carries the genetic information responsible for PM1's ability to degrade MTBE. Comparative genomic hybridization analysis with two PM1-like MTBE-degrading environmental isolates (similar to 99% identical 16S rRNA gene sequences) showed that the plasmid was highly conserved (ca. 99% identical), whereas the chromosomes were too diverse to conduct resequencing analysis. PM1's genome sequence provides a foundation for investigating MTBE biodegradation and exploring the genetic regulation of multiple biodegradation pathways in M. petroleiphilum and other MTBE-degrading beta-proteobacteria.},
doi = {10.1128/JB.01259-06},
journal = {Journal of Bacteriology},
number = 5,
volume = 189,
place = {United States},
year = {Thu Mar 01 00:00:00 EST 2007},
month = {Thu Mar 01 00:00:00 EST 2007}
}