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 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 Genome-wide expression patterns of invasion front, inner tumor mass and surrounding normal epithelium of colorectal tumors

2007 ◽  
Vol 6 (1) ◽  
pp. 79 ◽  
Author(s):  
Eike Staub ◽  
Joern Groene ◽  
Maya Heinze ◽  
Detlev Mennerich ◽  
Stefan Roepcke ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Colorectal Tumors ◽  
Normal Epithelium ◽  
Tumor Mass ◽  
Invasion Front ◽  
Genome Wide ◽  
Genome Wide Expression

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 Meta-analysis of genome-wide expression patterns associated with behavioral maturation in honey bees

BMC Genomics ◽  
2008 ◽  
Vol 9 (1) ◽  
pp. 503 ◽  
Author(s):  
Heather A Adams ◽  
Bruce R Southey ◽  
Gene E Robinson ◽  
Sandra L Rodriguez-Zas
Keyword(s):  
Honey Bees ◽  
Meta Analysis ◽  
Expression Patterns ◽  
Genome Wide ◽  
Behavioral Maturation ◽  
Genome Wide Expression

scholarly journals Genome-wide expression patterns associated with oncogenesis and sarcomatous transdifferentation of cholangiocarcinoma

BMC Cancer ◽  
2011 ◽  
Vol 11 (1) ◽  
Author(s):  
Min-A Seol ◽  
In-Sun Chu ◽  
Mi-Jin Lee ◽  
Goung-Ran Yu ◽  
Xiang-Dan Cui ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Genome Wide ◽  
Genome Wide Expression

Abstract T P240: Sex-specific Differential Gene Expression in a Murine Model of Experimental Intracerebral Hemorrhage

Stroke ◽  
2014 ◽  
Vol 45 (suppl_1) ◽  
Author(s):  
Sankalp Gokhale ◽  
Dawn Kernagis ◽  
Beilei Lei ◽  
Yi-Ju Li ◽  
David Warner ◽  
...  
Keyword(s):  
Gene Expression ◽  
Intracerebral Hemorrhage ◽  
Differential Gene Expression ◽  
Mouse Genome ◽  
Differential Analysis ◽  
Genome Wide ◽  
Collagenase Injection ◽  
Differential Gene ◽  
Males And Females ◽  
Genome Wide Expression

Introduction: Decreased mortality and improved functional outcome in female compared to male mice after experimental intracerebral hemorrhage (ICH) has been demonstrated. We postulate that sex-specific differences in post-ICH gene expression may provide mechanistic insight. Methods: Ten to 12 week old C57/Bl6 male (M) and female in low estrus (LE-F) or high estrous state (HE-F) mice (n=3/group) underwent ICH induction via left intrastriatal collagenase injection. Whole brain samples were collected at baseline, immediately after sham injury and 6 hours after injury. Genome-wide expression profiling was performed with Affymetrix GeneChip Mouse Genome 2.0 to identify genes differentially expressed between baseline and 6 hours in males and females. Probes showing expression levels greater than log2 (10) for all samples were selected for differential analysis. Comparisons were made between baseline and 6-hour time points to determine significant differential gene expression in both sexes. An adjusted p < 0.05 was considered significant. Results: A total of 12136 probes qualified for our filtering criteria, representing 9830 genes. Of the genes tested, 119 in M, 76 in LE-F, and 420 in HE-F were expressed differently at 6 hours as compared to baseline. Of these genes, a total of 37 were shared in M and HE-F groups, 32 in M and LE-F groups, and 42 in HE-F and LE-F groups. Several pathways were identified based on the top list of genes in each group comparison, including coagulation and inflammatory mediator signaling. Conclusions: Sex-specific differential gene expression exists at 6 hours after experimental ICH. Further experiments will be designed to test whether these observed differences in gene expression are associated with outcome after experimental ICH and, thus, may yield novel therapeutic targets for translation into the human disease.

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