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Applied and Environmental Microbiology, June 2009, p. 3733-3744, Vol. 75, No. 11
0099-2240/09/$08.00+0     doi:10.1128/AEM.00031-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Proteomic and Transcriptomic Analyses Reveal Genes Upregulated by cis-Dichloroethene in Polaromonas sp. Strain JS666

Laura K. Jennings,^1, Michelle M. G. Chartrand,^2, Georges Lacrampe-Couloume,² Barbara Sherwood Lollar,² Jim C. Spain,³ and James M. Gossett^1*

School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, 14853,¹ Stable Isotope Laboratory, Department of Geology, University of Toronto, Toronto, Ontario, Canada M5S 3B1,² School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332³

Received 24 December 2008/ Accepted 30 March 2009

Polaromonas sp. strain JS666 is the only bacterial isolate capable of using cis-dichloroethene (cDCE) as a sole carbon and energy source. Studies of cDCE degradation in this novel organism are of interest because of potential bioremediation and biocatalysis applications. The primary cellular responses of JS666 to growth on cDCE were explored using proteomics and transcriptomics to identify the genes upregulated by cDCE. Two-dimensional gel electrophoresis revealed upregulation of genes annotated as encoding glutathione S-transferase, cyclohexanone monooxygenase, and haloacid dehalogenase. DNA microarray experiments confirmed the proteomics findings that the genes indicated above were among the most highly upregulated by cDCE. The upregulation of genes with antioxidant functions and the inhibition of cDCE degradation by elevated oxygen levels suggest that cDCE induces an oxidative stress response. Furthermore, the upregulation of a predicted ABC transporter and two sodium/solute symporters suggests that transport is important in cDCE degradation. The omics data were integrated with data from compound-specific isotope analysis (CSIA) and biochemical experiments to develop a hypothesis for cDCE degradation pathways in JS666. The CSIA results indicate that the measured isotope enrichment factors for aerobic cDCE degradation ranged from –17.4 to –22.4. Evidence suggests that cDCE degradation via monooxygenase-catalyzed epoxidation (CC cleavage) may be only a minor degradation pathway under the conditions of these experiments and that the major degradation pathway involves carbon-chloride cleavage as the initial step, a novel mechanism. The results provide a significant step toward elucidation of cDCE degradation pathways and enhanced understanding of cDCE degradation in JS666.

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* Corresponding author. Mailing address: School of Civil and Environmental Engineering, Cornell University, 220 Hollister Hall, Ithaca, NY 14853. Phone: (607) 257-4170. Fax: (607) 255-9004. E-mail: jmg18{at}cornell.edu

Published ahead of print on 10 April 2009.

Present address: Center for Biofilm Engineering, Montana State University, 366 EPS Building, Bozeman, MT 59717.

Present address: G. G. Hatch Isotope Laboratory, Earth Sciences Department, University of Ottawa, Ottawa, Ontario, Canada KIN 6N5.

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Applied and Environmental Microbiology, June 2009, p. 3733-3744, Vol. 75, No. 11
0099-2240/09/$08.00+0     doi:10.1128/AEM.00031-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.