This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Denef, V. J.
Right arrow Articles by Tiedje, J. M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Denef, V. J.
Right arrow Articles by Tiedje, J. M.
Agricola
Right arrow Articles by Denef, V. J.
Right arrow Articles by Tiedje, J. M.

 Previous Article  |  Next Article 

Applied and Environmental Microbiology, August 2004, p. 4961-4970, Vol. 70, No. 8
0099-2240/04/$08.00+0     DOI: 10.1128/AEM.70.8.4961-4970.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Biphenyl and Benzoate Metabolism in a Genomic Context: Outlining Genome-Wide Metabolic Networks in Burkholderia xenovorans LB400

V. J. Denef,1,2 J. Park,1 T. V. Tsoi,1 J.-M. Rouillard,3 H. Zhang,4 J. A. Wibbenmeyer,4 W. Verstraete,2 E. Gulari,3 S. A. Hashsham,1,5 and J. M. Tiedje1*

Center for Microbial Ecology,1 Department of Civil and Environmental Engineering, Michigan State University, East Lansing, Michigan 48824,5 Laboratory of Microbial Ecology and Technology, Ghent University, Ghent, Belgium,2 Chemical Engineering Department, University of Michigan, Ann Arbor, Michigan 48109,3 Xeotron Corporation, Houston, Texas 770544

Received 15 January 2004/ Accepted 22 April 2004

We designed and successfully implemented the use of in situ-synthesized 45-mer oligonucleotide DNA microarrays (XeoChips) for genome-wide expression profiling of Burkholderia xenovorans LB400, which is among the best aerobic polychlorinated biphenyl degraders known so far. We conducted differential gene expression profiling during exponential growth on succinate, benzoate, and biphenyl as sole carbon sources and investigated the transcriptome of early-stationary-phase cells grown on biphenyl. Based on these experiments, we outlined metabolic pathways and summarized other cellular functions in the organism relevant for biphenyl and benzoate degradation. All genes previously identified as being directly involved in biphenyl degradation were up-regulated when cells were grown on biphenyl compared to expression in succinate-grown cells. For benzoate degradation, however, genes for an aerobic coenzyme A activation pathway were up-regulated in biphenyl-grown cells, while the pathway for benzoate degradation via hydroxylation was up-regulated in benzoate-grown cells. The early-stationary-phase biphenyl-grown cells showed similar expression of biphenyl pathway genes, but a surprising up-regulation of C1 metabolic pathway genes was observed. The microarray results were validated by quantitative reverse transcription PCR with a subset of genes of interest. The XeoChips showed a chip-to-chip variation of 13.9%, compared to the 21.6% variation for spotted oligonucleotide microarrays, which is less variation than that typically reported for PCR product microarrays.

* Corresponding author. Mailing address: Center for Microbial Ecology, 540 Plant and Soil Sciences Building, East Lansing, MI 48824. Phone: (517) 353-9021. Fax: (517) 353-2917. E-mail: tiedjej{at}msu.edu.

Applied and Environmental Microbiology, August 2004, p. 4961-4970, Vol. 70, No. 8
0099-2240/04/$08.00+0     DOI: 10.1128/AEM.70.8.4961-4970.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Bains, J., Leon, R., Boulanger, M. J. (2009). Structural and Biophysical Characterization of BoxC from Burkholderia xenovorans LB400: A NOVEL RING-CLEAVING ENZYME IN THE CROTONASE SUPERFAMILY. J. Biol. Chem. 284: 16377-16385 [Abstract] [Full Text]  
  • Johnson, D. R., Brodie, E. L., Hubbard, A. E., Andersen, G. L., Zinder, S. H., Alvarez-Cohen, L. (2008). Temporal Transcriptomic Microarray Analysis of "Dehalococcoides ethenogenes" Strain 195 during the Transition into Stationary Phase. Appl. Environ. Microbiol. 74: 2864-2872 [Abstract] [Full Text]  
  • Smith, D. J., Patrauchan, M. A., Florizone, C., Eltis, L. D., Mohn, W. W. (2008). Distinct Roles for Two CYP226 Family Cytochromes P450 in Abietane Diterpenoid Catabolism by Burkholderia xenovorans LB400. J. Bacteriol. 190: 1575-1583 [Abstract] [Full Text]  
  • Smith, D. J., Park, J., Tiedje, J. M., Mohn, W. W. (2007). A Large Gene Cluster in Burkholderia xenovorans Encoding Abietane Diterpenoid Catabolism. J. Bacteriol. 189: 6195-6204 [Abstract] [Full Text]  
  • Nogales, J., Macchi, R., Franchi, F., Barzaghi, D., Fernandez, C., Garcia, J. L., Bertoni, G., Diaz, E. (2007). Characterization of the last step of the aerobic phenylacetic acid degradation pathway. Microbiology 153: 357-365 [Abstract] [Full Text]  
  • Chain, P. S. G., Denef, V. J., Konstantinidis, K. T., Vergez, L. M., Agullo, L., Reyes, V. L., Hauser, L., Cordova, M., Gomez, L., Gonzalez, M., Land, M., Lao, V., Larimer, F., LiPuma, J. J., Mahenthiralingam, E., Malfatti, S. A., Marx, C. J., Parnell, J. J., Ramette, A., Richardson, P., Seeger, M., Smith, D., Spilker, T., Sul, W. J., Tsoi, T. V., Ulrich, L. E., Zhulin, I. B., Tiedje, J. M. (2006). Inaugural Article: Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc. Natl. Acad. Sci. USA 103: 15280-15287 [Abstract] [Full Text]  
  • Parnell, J. J., Park, J., Denef, V., Tsoi, T., Hashsham, S., Quensen, J. III, Tiedje, J. M. (2006). Coping with Polychlorinated Biphenyl (PCB) Toxicity: Physiological and Genome-Wide Responses of Burkholderia xenovorans LB400 to PCB-Mediated Stress. Appl. Environ. Microbiol. 72: 6607-6614 [Abstract] [Full Text]  
  • Goncalves, E. R., Hara, H., Miyazawa, D., Davies, J. E., Eltis, L. D., Mohn, W. W. (2006). Transcriptomic Assessment of Isozymes in the Biphenyl Pathway of Rhodococcus sp. Strain RHA1. Appl. Environ. Microbiol. 72: 6183-6193 [Abstract] [Full Text]  
  • Wu, L., Liu, X., Schadt, C. W., Zhou, J. (2006). Microarray-Based Analysis of Subnanogram Quantities of Microbial Community DNAs by Using Whole-Community Genome Amplification.. Appl. Environ. Microbiol. 72: 4931-4941 [Abstract] [Full Text]  
  • Shimomura, Y., Ohno, R., Kawai, F., Kimbara, K. (2006). Method for assessment of viability and morphological changes of bacteria in the early stage of colony formation on a simulated natural environment.. Appl. Environ. Microbiol. 72: 5037-5042 [Abstract] [Full Text]  
  • Fujihara, H., Yoshida, H., Matsunaga, T., Goto, M., Furukawa, K. (2006). Cross-Regulation of Biphenyl- and Salicylate-Catabolic Genes by Two Regulatory Systems in Pseudomonas pseudoalcaligenes KF707. J. Bacteriol. 188: 4690-4697 [Abstract] [Full Text]  
  • Fortin, P. D., Horsman, G. P., Yang, H. M., Eltis, L. D. (2006). A glutathione s-transferase catalyzes the dehalogenation of inhibitory metabolites of polychlorinated biphenyls.. J. Bacteriol. 188: 4424-4430 [Abstract] [Full Text]  
  • Gao, H., Yang, Z. K., Wu, L., Thompson, D. K., Zhou, J. (2006). Global Transcriptome Analysis of the Cold Shock Response of Shewanella oneidensis MR-1 and Mutational Analysis of Its Classical Cold Shock Proteins.. J. Bacteriol. 188: 4560-4569 [Abstract] [Full Text]  
  • Denef, V. J., Klappenbach, J. A., Patrauchan, M. A., Florizone, C., Rodrigues, J. L. M., Tsoi, T. V., Verstraete, W., Eltis, L. D., Tiedje, J. M. (2006). Genetic and Genomic Insights into the Role of Benzoate-Catabolic Pathway Redundancy in Burkholderia xenovorans LB400. Appl. Environ. Microbiol. 72: 585-595 [Abstract] [Full Text]  
  • Kalyuzhnaya, M. G., Bowerman, S., Nercessian, O., Lidstrom, M. E., Chistoserdova, L. (2005). Highly Divergent Genes for Methanopterin-Linked C1 Transfer Reactions in Lake Washington, Assessed via Metagenomic Analysis and mRNA Detection. Appl. Environ. Microbiol. 71: 8846-8854 [Abstract] [Full Text]  
  • Denef, V. J., Patrauchan, M. A., Florizone, C., Park, J., Tsoi, T. V., Verstraete, W., Tiedje, J. M., Eltis, L. D. (2005). Growth Substrate- and Phase-Specific Expression of Biphenyl, Benzoate, and C1 Metabolic Pathways in Burkholderia xenovorans LB400. J. Bacteriol. 187: 7996-8005 [Abstract] [Full Text]  
  • Johnson, D. R., Lee, P. K. H., Holmes, V. F., Alvarez-Cohen, L. (2005). An Internal Reference Technique for Accurately Quantifying Specific mRNAs by Real-Time PCR with Application to the tceA Reductive Dehalogenase Gene. Appl. Environ. Microbiol. 71: 3866-3871 [Abstract] [Full Text]  
  • Navarro-Llorens, J. M., Patrauchan, M. A., Stewart, G. R., Davies, J. E., Eltis, L. D., Mohn, W. W. (2005). Phenylacetate Catabolism in Rhodococcus sp. Strain RHA1: a Central Pathway for Degradation of Aromatic Compounds. J. Bacteriol. 187: 4497-4504 [Abstract] [Full Text]  
  • Barriault, D., Sylvestre, M. (2004). Evolution of the Biphenyl Dioxygenase BphA from Burkholderia xenovorans LB400 by Random Mutagenesis of Multiple Sites in Region III. J. Biol. Chem. 279: 47480-47488 [Abstract] [Full Text]  
  • Barriault, D., Lepine, F., Mohammadi, M., Milot, S., Leberre, N., Sylvestre, M. (2004). Revisiting the Regiospecificity of Burkholderia xenovorans LB400 Biphenyl Dioxygenase toward 2,2'-Dichlorobiphenyl and 2,3,2',3'-Tetrachlorobiphenyl. J. Biol. Chem. 279: 47489-47496 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»