scholarly journals Degradation of Aroclor 1242 Dechlorination Products in Sediments by Burkholderia xenovorans LB400(ohb) and Rhodococcus sp. Strain RHA1(fcb)

2006 ◽  
Vol 72 (4) ◽  
pp. 2476-2482 ◽  
Author(s):  
Jorge L. M. Rodrigues ◽  
C. Alan Kachel ◽  
Michael R. Aiello ◽  
John F. Quensen ◽  
Olga V. Maltseva ◽  
...  
Keyword(s):  
Population Dynamics ◽  
Polychlorinated Biphenyl ◽  
Contaminated Sediment ◽  
Burkholderia Xenovorans ◽  
Burkholderia Xenovorans Lb400 ◽  
Aroclor 1242 ◽  
Selective Plating ◽  
Cell Densities ◽  
Pcb Biodegradation ◽  
Rhodococcus Sp

ABSTRACT Burkholderia xenovorans strain LB400, which possesses the biphenyl pathway, was engineered to contain the oxygenolytic ortho dehalogenation (ohb) operon, allowing it to grow on 2-chlorobenzoate and to completely mineralize 2-chlorobiphenyl. A two-stage anaerobic/aerobic biotreatment process for Aroclor 1242-contaminated sediment was simulated, and the degradation activities and genetic stabilities of LB400(ohb) and the previously constructed strain RHA1(fcb), capable of growth on 4-chlorobenzoate, were monitored during the aerobic phase. The population dynamics of both strains were also followed by selective plating and real-time PCR, with comparable results; populations of both recombinants increased in the contaminated sediment. Inoculation at different cell densities (104 or 106 cells g−1 sediment) did not affect the extent of polychlorinated biphenyl (PCB) biodegradation. After 30 days, PCB removal rates for high and low inoculation densities were 57% and 54%, respectively, during the aerobic phase.

scholarly journals Genetic and Genomic Insights into the Role of Benzoate-Catabolic Pathway Redundancy in Burkholderia xenovorans LB400

2006 ◽  
Vol 72 (1) ◽  
pp. 585-595 ◽  
Author(s):  
V. J. Denef ◽  
J. A. Klappenbach ◽  
M. A. Patrauchan ◽  
C. Florizone ◽  
J. L. M. Rodrigues ◽  
...  
Keyword(s):  
Polychlorinated Biphenyl ◽  
Gene Clusters ◽  
Large Chromosome ◽  
Wild Type ◽  
Burkholderia Xenovorans ◽  
Burkholderia Xenovorans Lb400 ◽  
Cell Assays ◽  
Aromatic Degradation ◽  
Proteomic Analyses

ABSTRACT Transcriptomic and proteomic analyses of Burkholderia xenovorans LB400, a potent polychlorinated biphenyl (PCB) degrader, have implicated growth substrate- and phase-dependent expression of three benzoate-catabolizing pathways: a catechol ortho cleavage (ben-cat) pathway and two benzoyl-coenzyme A pathways, encoded by gene clusters on the large chromosome (boxC ) and the megaplasmid (boxM ). To elucidate the significance of this apparent redundancy, we constructed mutants with deletions of the ben-cat pathway (the ΔbenABCD::kan mutant), the boxC pathway (the ΔboxABC ::kan mutant), and both pathways (the ΔbenABCDΔ boxABC ::kan mutant). All three mutants oxidized benzoate in resting-cell assays. However, the ΔbenABCD::kan and ΔbenABCD ΔboxABC ::kan mutants grew at reduced rates on benzoate and displayed increased lag phases. By contrast, growth on succinate, on 4-hydroxybenzoate, and on biphenyl was unaffected. Microarray and proteomic analyses revealed that cells of the ΔbenABCD::kan mutant growing on benzoate expressed both box pathways. Overall, these results indicate that all three pathways catabolize benzoate. Deletion of benABCD abolished the ability of LB400 to grow using 3-chlorobenzoate. None of the benzoate pathways could degrade 2- or 4-chlorobenzoate, indicating that the pathway redundancy does not directly contribute to LB400's PCB-degrading capacities. Finally, an extensive sigmaE-regulated oxidative stress response not present in wild-type LB400 grown on benzoate was detected in these deletion mutants, supporting our earlier suggestion that the box pathways are preferentially active under reduced oxygen tension. Our data further substantiate the expansive network of tightly interconnected and complexly regulated aromatic degradation pathways in LB400.

scholarly journals Coping with Polychlorinated Biphenyl (PCB) Toxicity: Physiological and Genome-Wide Responses of Burkholderia xenovorans LB400 to PCB-Mediated Stress

2006 ◽  
Vol 72 (10) ◽  
pp. 6607-6614 ◽  
Author(s):  
J. Jacob Parnell ◽  
Joonhong Park ◽  
Vincent Denef ◽  
Tamara Tsoi ◽  
Syed Hashsham ◽  
...  
Keyword(s):  
Protein Function ◽  
Polychlorinated Biphenyl ◽  
Membrane Separation ◽  
Expression Patterns ◽  
Burkholderia Xenovorans ◽  
Inhibition Of Growth ◽  
Burkholderia Xenovorans Lb400 ◽  
Genome Wide ◽  
Differential Gene ◽  
Genome Wide Expression

ABSTRACT The biodegradation of polychlorinated biphenyls (PCBs) relies on the ability of aerobic microorganisms such as Burkholderia xenovorans sp. LB400 to tolerate two potential modes of toxicity presented by PCB degradation: passive toxicity, as hydrophobic PCBs potentially disrupt membrane and protein function, and degradation-dependent toxicity from intermediates of incomplete degradation. We monitored the physiological characteristics and genome-wide expression patterns of LB400 in response to the presence of Aroclor 1242 (500 ppm) under low expression of the structural biphenyl pathway (succinate and benzoate growth) and under induction by biphenyl. We found no inhibition of growth or change in fatty acid profile due to PCBs under nondegrading conditions. Moreover, we observed no differential gene expression due to PCBs themselves. However, PCBs did have a slight effect on the biosurface area of LB400 cells and caused slight membrane separation. Upon activation of the biphenyl pathway, we found growth inhibition from PCBs beginning after exponential-phase growth suggestive of the accumulation of toxic compounds. Genome-wide expression profiling revealed 47 differentially expressed genes (0.56% of all genes) under these conditions. The biphenyl and catechol pathways were induced as expected, but the quinoprotein methanol metabolic pathway and a putative chloroacetaldehyde dehydrogenase were also highly expressed. As the latter protein is essential to conversion of toxic metabolites in dichloroethane degradation, it may play a similar role in the degradation of chlorinated aliphatic compounds resulting from PCB degradation.

scholarly journals Family Shuffling of Soil DNA To Change the Regiospecificity of Burkholderia xenovorans LB400 Biphenyl Dioxygenase

2006 ◽  
Vol 189 (3) ◽  
pp. 779-788 ◽  
Author(s):  
Julie Vézina ◽  
Diane Barriault ◽  
Michel Sylvestre
Keyword(s):  
Amino Acid ◽  
Polychlorinated Biphenyl ◽  
Ethyl Benzene ◽  
Amino Acid Residues ◽  
Terminal Portion ◽  
Degenerate Primers ◽  
Biphenyl Dioxygenase ◽  
Soil Dna ◽  
Burkholderia Xenovorans ◽  
Burkholderia Xenovorans Lb400

ABSTRACT Previous work has shown that the C-terminal portion of BphA, especially two amino acid segments designated region III and region IV, influence the regiospecificity of the biphenyl dioxygenase (BPDO) toward 2,2′-dichlorobiphenyl (2,2′-CB). In this work, we evolved BPDO by shuffling bphA genes amplified from polychlorinated biphenyl-contaminated soil DNA. Sets of approximately 1-kb DNA fragments were amplified with degenerate primers designed to amplify the C-terminal portion of bphA. These fragments were shuffled, and the resulting library was used to replace the corresponding fragment of Burkholderia xenovorans LB400 bphA. Variants were screened for their ability to oxygenate 2,2′-CB onto carbons 5 and 6, which are positions that LB400 BPDO is unable to attack. Variants S100, S149, and S151 were obtained and exhibited this feature. Variant S100 BPDO produced exclusively cis-5,6-dihydro-5,6-dihydroxy-2,2′-dichlorobiphenyl from 2,2′-CB. Moreover, unlike LB400 BPDO, S100 BphA catalyzed the oxygenation of 2,2′,3,3′-tetrachlorobiphenyl onto carbons 5 and 6 exclusively and it was unable to oxygenate 2,2′,5,5′-tetrachlorobiphenyl. Based on oxygen consumption measurements, variant S100 oxygenated 2,2′-CB at a rate of 16 ± 1 nmol min−1 per nmol enzyme, which was similar to the value observed for LB400 BPDO. cis-5,6-Dihydro-5,6-dihydroxy-2,2′-dichlorobiphenyl was further oxidized by 2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase (BphB) and 2,3-dihydroxybiphenyl dioxygenase (BphC). Variant S100 was, in addition, able to oxygenate benzene, toluene, and ethyl benzene. Sequence analysis identified amino acid residues M237S238 and S283 outside regions III and IV that influence the activity toward doubly ortho-substituted chlorobiphenyls.

scholarly journals Growth Substrate- and Phase-Specific Expression of Biphenyl, Benzoate, and C1 Metabolic Pathways in Burkholderia xenovorans LB400

2005 ◽  
Vol 187 (23) ◽  
pp. 7996-8005 ◽  
Author(s):  
V. J. Denef ◽  
M. A. Patrauchan ◽  
C. Florizone ◽  
J. Park ◽  
T. V. Tsoi ◽  
...  
Keyword(s):  
Polychlorinated Biphenyl ◽  
Transition Phase ◽  
Growth Substrate ◽  
Specific Expression ◽  
General Stress Response ◽  
Burkholderia Xenovorans ◽  
Degrading Bacterium ◽  
Burkholderia Xenovorans Lb400 ◽  
Regulated Expression ◽  
Order Of Magnitude

ABSTRACT Recent microarray experiments suggested that Burkholderia xenovorans LB400, a potent polychlorinated biphenyl (PCB)-degrading bacterium, utilizes up to three apparently redundant benzoate pathways and a C1 metabolic pathway during biphenyl and benzoate metabolism. To better characterize the roles of these pathways, we performed quantitative proteome profiling of cells grown on succinate, benzoate, or biphenyl and harvested during either mid-logarithmic growth or the transition between the logarithmic and stationary growth phases. The Bph enzymes, catabolizing biphenyl, were ∼16-fold more abundant in biphenyl- versus succinate-grown cells. Moreover, the upper and lower bph pathways were independently regulated. Expression of each benzoate pathway depended on growth substrate and phase. Proteins specifying catabolism via benzoate dihydroxylation and catechol ortho-cleavage (ben-cat pathway) were approximately an order of magnitude more abundant in benzoate- versus biphenyl-grown cells at the same growth phase. The chromosomal copy of the benzoyl-coenzyme A (CoA) (box C) pathway was also expressed during growth on biphenyl: BoxC proteins were approximately twice as abundant as Ben and Cat proteins under these conditions. By contrast, proteins of the megaplasmid copy of the benzoyl-CoA (box M) pathway were only detected in transition-phase benzoate-grown cells. Other proteins detected at increased levels in benzoate- and biphenyl-grown cells included general stress response proteins potentially induced by reactive oxygen species formed during aerobic aromatic catabolism. Finally, C1 metabolic enzymes were present in biphenyl-grown cells during transition phase. This study provides insights into the physiological roles and integration of apparently redundant catabolic pathways in large-genome bacteria and establishes a basis for investigating the PCB-degrading abilities of this strain.

scholarly journals Enhanced polychlorinated biphenyl removal in a switchgrass rhizosphere by bioaugmentation with Burkholderia xenovorans LB400

2014 ◽  
Vol 71 ◽  
pp. 215-222 ◽  
Author(s):  
Yi Liang ◽  
Richard Meggo ◽  
Dingfei Hu ◽  
Jerald L. Schnoor ◽  
Timothy E. Mattes
Keyword(s):  
Polychlorinated Biphenyl ◽  
Burkholderia Xenovorans ◽  
Burkholderia Xenovorans Lb400

Genomic analysis of the phenylacetyl-CoA pathway in Burkholderia xenovorans LB400

2011 ◽  
Vol 193 (9) ◽  
pp. 641-650 ◽  
Author(s):  
Marianna A. Patrauchan ◽  
J. Jacob Parnell ◽  
Michael P. McLeod ◽  
Christine Florizone ◽  
James M. Tiedje ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Burkholderia Xenovorans ◽  
Burkholderia Xenovorans Lb400

scholarly journals Complete Genome Sequence of the Polychlorinated Biphenyl Degrader Rhodococcus sp. WB1

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Yuxin Xu ◽  
Man Yu ◽  
Alin Shen
Keyword(s):  
Gene Cluster ◽  
Genome Sequence ◽  
Contaminated Soil ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Polychlorinated Biphenyl ◽  
Xenobiotic Metabolism ◽  
Rhodococcus Sp

Rhodococcus sp. WB1 is a polychlorinated biphenyl degrader which was isolated from contaminated soil in Zhejiang, China. Here, we present the complete genome sequence. The analysis of this genome indicated that a biphenyl-degrading gene cluster and several xenobiotic metabolism pathways are harbored.

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