Biodegradation

, Volume 21, Issue 1, pp 147–156 | Cite as

Environmentally relevant parameters affecting PCB degradation: carbon source- and growth phase-mitigated effects of the expression of the biphenyl pathway and associated genes in Burkholderia xenovorans LB400

  • J. Jacob Parnell
  • Vincent J. Denef
  • Joonhong Park
  • Tamara Tsoi
  • James M. Tiedje
Original Paper

Abstract

The principal means for microbial degradation of polychlorinated biphenyls (PCBs) is through the biphenyl pathway. Although molecular aspects of the regulation of the biphenyl pathway have been studied, information on environmental facets such as the effect of alternative carbon sources on (polychlorinated) biphenyl degradation is limited. Here we explore the effect of environmental conditions (e.g., carbon source and growth phase) on the variation in PCB degradation profiles of Burkholderia xenovorans LB400. Genome-wide expression patterns reveal 25 genes commonly up-regulated during PCB degradation and growth on biphenyl to be upregulated in the transition to stationary phase (relative to growth on succinate) including two putative detoxification pathways. Quantitative reverse transcription PCR (Q-RT-PCR) analysis of the upper biphenyl pathway (bphA, bphD, and bphR1), and detoxification genes in response to environmental conditions suggest associated regulation of the biphenyl pathway and chloroacetaldehyde dehydrogenase. The response of genes in the upper biphenyl pathway to carbon source competition and growth phase reveals inhibition of the biphenyl pathway by PCBs. Although PCBs are not degraded during growth on succinate with PCBs, expression data indicate that the biphenyl pathway is induced, suggesting that post-transcriptional regulation or active transport of biphenyl maybe limiting PCB degradation. Identification of the involvement of peripheral pathways in degradation of PCBs is crucial to understanding PCB degradation in an environmental context as bacteria capable of biodegradation experience a range of carbon sources and growth phases.

Keywords

Polychlorinated biphenyl degradation Cometabolism Biphenyl degradation pathway Burkholderia xenovorans LB400 

Notes

Acknowledgments

This work was supported by the Superfund Basic Research Program grant P42 ES 04911-12 from the U.S. National Institute of Environmental Health Sciences. We acknowledge John Quensen for assistance with PCB degradation analyses and Christopher Bradley and Jeff Landgraff for Q-RT-PCR assistance.

References

  1. Ahmed M, Focht DD (1973) Degradation of polychlorinated biphenyls by two species of Achromobacter. Can J Microbiol 19:47–52PubMedCrossRefGoogle Scholar
  2. Barriault D, Durand J, Maaroufi H, Eltis LD, Sylvestre M (1998) Degradation of polychlorinated biphenyl metabolites by naphthalene-catabolizing enzymes. Appl Environ Microbiol 64:4637–4642PubMedGoogle Scholar
  3. Bedard DL, Quensen JF III (1995) Microbial reductive dechlorination of polychlorinated biphenyls. In: Young LY, Cerniglia C (eds) Microbial transformation and degradation of toxic organic chemicals. Wiley-Liss Division, John Wiley & Sons, Inc., New York, pp 127–216Google Scholar
  4. Bedard DL, Unterman R, Bopp LH, Brennan MJ, Haberl ML, Johnson C (1986) Rapid assay for screening and characterizing microorganisms for the ability to degrade polychlorinated biphenyls. Appl Environ Microbiol 51:761–768PubMedGoogle Scholar
  5. Bedard DL, Haberl ML, May RJ, Brennan MJ (1987) Evidence for novel mechanisms of polychlorinated biphenyl metabolism in Alcaligenes eutrophus H850. Appl Environ Microbiol 53:1103–1112PubMedGoogle Scholar
  6. Beltrametti F, Reniero D, Backhaus S, Hofer B (2001) Analysis of transcription of the bph locus of Burkholderia sp. strain LB400 and evidence that the ORF0 gene product acts as a regulator of the bphA1 promotor. Microbiology 147:2169–2182PubMedGoogle Scholar
  7. Billingsley KA, Backus SM, Juneson C, Ward OP (1997) Comparison of the degradation patterns of polychlorinated biphenyl congeners in Aroclors by Pseudomonas strain LB400 after growth on various carbon sources. Can J Microbiol 43:1172–1179PubMedCrossRefGoogle Scholar
  8. Bopp LH (1986) Degradation of highly chlorinated PCBs by Pseudomonas strain LB400. J Ind Microbiol 1:23–29CrossRefGoogle Scholar
  9. Chain PSG, Denef VJ, Konstantinidis K, Vergez LM, Agulló L, Reyes VL, Hauser L, Córdova M, Gómez L, González M, Land M, Lao V, Larimer F, LiPuma JJ, Mahenthiralingam E, Malfatti SA, Marx CJ, Parnell JJ, Ramette A, Richardson P, Seeger M, Smith D, Spilker T, Sul W-J, Tsoi TV, Ulrich LE, Zhulin IB, Tiedje JM (2006) Burkholderia xenovorans LB400 harbors a multi-replicon, 9.7 M bp genome shaped for versatility. Proc Natl Acad Sci 103:15280–15287CrossRefPubMedGoogle Scholar
  10. Denef VJ, Park J, Tsoi TV, Rouillard J-M, Zhang H, Wibbenmeyer JA, Verstraete W, Gulari E, Hashsham SA, Tiedje JM (2004) Biphenyl and benzoate metabolism in a genomic context: outlining genome-wide metabolic networks in Burkholderia xenovorans LB400. Appl Environ Microbiol 70:4961–4970CrossRefPubMedGoogle Scholar
  11. Denef VJ, Patrauchan MA, Florizone C, Park J, Tsoi TV, Verstraete W, Tiedje JM, Eltis LD (2005) Growth substrate- and phase-specific expression of biphenyl, benzoate, and C1 metabolic pathways in Burkholderia xenovorans LB400. J Bacteriol 187:7996–8005CrossRefPubMedGoogle Scholar
  12. Erickson BD, Mondello FJ (1993) Enhanced biodegradation of polychlorinated biphenyls after site-directed mutagenesis of a biphenyl dioxygenase gene. Appl Environ Microbiol 59:3858–3862PubMedGoogle Scholar
  13. Furukawa K, Simon JR, Chakrabarty AM (1983) Common Induction and regulation of biphenyl, xylene/toluene, and salicylate catabolism in Pseudomonas paucimobilis. J Bacteriol 154:1356–1362PubMedGoogle Scholar
  14. Gibson DT, Cruden DL, Haddock JD, Zylstra GJ, Brand JM (1993) Oxidation of polychlorinated biphenyls by Pseudomonas sp. strain LB400 and Pseudomonas pseudoalcaligenes KF707. J Bacteriol 175:4561–4564PubMedGoogle Scholar
  15. Goris J, De Vos P, Caballero-Mellado J, Park J, Falsen E, Quensen JF III, Tiedje JM, Vandamme P (2004) Classification of the PCB-and biphenyl degrading strain LB400 and relatives as Burkholderia xenovorans sp. nov. Int J Syst Evol Microbiol 54:1677–1681CrossRefPubMedGoogle Scholar
  16. Kohler H-PE, Kohler-Staub D, Focht DD (1988) Cometabolism of polychlorinated biphenyls: enhanced transformation of Aroclor 1254 by growing bacterial cells. Appl Environ Microbiol 54:1940–1945PubMedGoogle Scholar
  17. Maltseva OV, Tsoi TV, Quensen JF III, Fukuda M, Tiedje JM (1999) Degradation of anaerobic reductive dechlorination products of Aroclor 1242 by four aerobic bacteria. Biodegradation 10:363–371CrossRefPubMedGoogle Scholar
  18. Marx CJ, Miller JA, Chistoserdova L, Lidstrom ME (2004) Multiple formaldehyde oxidation/detoxification pathways in Burkholderia fungorum LB400. J Bacteriol 186:2173–2178CrossRefPubMedGoogle Scholar
  19. Master ER, Mohn WW (2001) Induction of bphA, encoding biphenyl dioxygenase, in two polychlorinated biphenyl-degrading bacteria, psychrotolerant Pseudomonasstrain Cam-1 and mesophilic Burkholderia strain LB400. Appl Environ Microbiol 67:2669–2676CrossRefPubMedGoogle Scholar
  20. Master ER, McKinlay JJ, Stewart GR, Mohn WW (2005) Biphenyl uptake by psychrotolerant Pseudomonas sp. strain Cam-1 and mesophilic Burkholderia sp. strain LB400. Can J Microbiol 51:399–404CrossRefPubMedGoogle Scholar
  21. Mondello FJ, Turcich MP, Lobos JH, Erickson BD (1997) Identification and modification of biphenyl dioxygenase sequences that determine the specificity of polychlorinated biphenyl degradation. Appl Environ Microbiol 63:3096–3103PubMedGoogle Scholar
  22. Mouz S, Merlin C, Springael D, Toussaint A (1999) A GntR-like negative regulator of the biphenyl degradation genes of the transposon Tn4371. Mol Gen Genet 262:790–799CrossRefPubMedGoogle Scholar
  23. Ohtsubo Y, Nagata Y, Kimbara K, Takagi M, Ohta A (2000) Expression of the bph genes involved in biphenyl/PCB degradation in Pseudomonas sp KKS102 induced by the biphenyl degradation intermediate, 2-hydroxy-6-oxo-6-phenylhexa-2, 4-dienoic acid. Gene 256:223–228CrossRefPubMedGoogle Scholar
  24. Ohtsubo Y, Kudo T, Tsuda M, Nagata Y (2004) Strategies for bioremediation of polychlorinated biphenyls. Appl Microbiol Biotechnol 65:250–258CrossRefPubMedGoogle Scholar
  25. Parnell JJ, Park J, Denef V, Tsoi T, Hashsham S, Quensen J III, Tiedje JM (2006) Coping with PCB toxicity: the physiological and genome-wide response of Burkholderia xenovorans LB400 to PCB (polychlorinated biphenyl)-mediated stress. Appl Environ Microbiol 72:6607–6614CrossRefPubMedGoogle Scholar
  26. Pieper DH, Seeger M (2008) Bacterial metabolism of polychlorinated biphenyls. J Mol Microbiol Biotechnol 15:121–138PubMedGoogle Scholar
  27. Quensen JF III, Boyd SA, Tiedje JM (1990) Dechlorination of four commercial polychlorinated biphenyl mixtures (Aroclors) by anaerobic microorganisms from sediments. Appl Environ Microbiol 56:2360–2369PubMedGoogle Scholar
  28. Seeger M, Timmis KN, Hofer B (1995) Conversion of chlorobiphenyls into phenylhexadienoates and benzoates by the enzymes of the upper pathway for polychlorobiphenyl degradation encoded by the bph locus of Pseudomonas sp. strain LB400. Appl Environ Microbiol 61:2654–2658PubMedGoogle Scholar
  29. Watanabe T, Fujihara H, Furukawa K (2003) Characterization of the second LysRtype regulator in the biphenyl-catabolic gene cluster of Pseudomonas pseudoalcaligenes KF707. J Bacteriol 185:3575–3582CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • J. Jacob Parnell
    • 1
    • 4
  • Vincent J. Denef
    • 2
  • Joonhong Park
    • 3
  • Tamara Tsoi
    • 1
  • James M. Tiedje
    • 1
  1. 1.Center for Microbial Ecology and Crop and Soil ScienceMichigan State UniversityEast LansingUSA
  2. 2.Department of Earth and Planetary SciencesUniversity of California BerkeleyBerkeleyUSA
  3. 3.School of Civil and Environmental EngineeringYonsei UniversitySeoulRepublic of Korea
  4. 4.Center for Integrated BioSystems and Department of BiologyUtah State UniversityLoganUSA

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