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

2009 ◽  
Vol 21 (1) ◽  
pp. 147-156 ◽  
Author(s):  
J. Jacob Parnell ◽  
Vincent J. Denef ◽  
Joonhong Park ◽  
Tamara Tsoi ◽  
James M. Tiedje
Keyword(s):  
Carbon Source ◽  
Growth Phase ◽  
Burkholderia Xenovorans ◽  
Burkholderia Xenovorans Lb400

Morphological Characterization of Mycobacteriophage R1

1974 ◽  
Vol 32 ◽  
pp. 254-255
Author(s):  
B. L. Soloff ◽  
T. A. Rado
Keyword(s):  
Carbon Source ◽  
Stationary Phase ◽  
Growth Phase ◽  
Minimal Medium ◽  
Morphological Characterization ◽  
Logarithmic Growth Phase ◽  
Complete Lysis ◽  
Lysogenic Culture ◽  
Logarithmic Growth

Mycobacteriophage R1 was originally isolated from a lysogenic culture of M. butyricum. The virus was propagated on a leucine-requiring derivative of M. smegmatis, 607 leu−, isolated by nitrosoguanidine mutagenesis of typestrain ATCC 607. Growth was accomplished in a minimal medium containing glycerol and glucose as carbon source and enriched by the addition of 80 μg/ ml L-leucine. Bacteria in early logarithmic growth phase were infected with virus at a multiplicity of 5, and incubated with aeration for 8 hours. The partially lysed suspension was diluted 1:10 in growth medium and incubated for a further 8 hours. This permitted stationary phase cells to re-enter logarithmic growth and resulted in complete lysis of the culture.

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 Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility

2006 ◽  
Vol 103 (42) ◽  
pp. 15280-15287 ◽  
Author(s):  
P. S. G. Chain ◽  
V. J. Denef ◽  
K. T. Konstantinidis ◽  
L. M. Vergez ◽  
L. Agullo ◽  
...  
Keyword(s):  
Burkholderia Xenovorans ◽  
Burkholderia Xenovorans Lb400

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 Poly-β-Hydroxybutyrate Production by the Cyanobacterium Scytonema geitleri Bharadwaja under Varying Environmental Conditions

Biomolecules ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 198 ◽  
Author(s):  
Manoj K. Singh ◽  
Pradeep K. Rai ◽  
Anuradha Rai ◽  
Surendra Singh ◽  
Jay Shankar Singh
Keyword(s):  
Carbon Source ◽  
Growth Phase ◽  
Environmental Conditions ◽  
Carbon Sources ◽  
Stationary Growth Phase ◽  
Stationary Growth ◽  
Cell Weight ◽  
Dry Cell Weight ◽  
Phb Production ◽  
Dry Cell

The production of poly-β-hydroxybutyrate (PHB) under varying environmental conditions (pH, temperature and carbon sources) was examined in the cyanobacterium Scytonema geitleri Bharadwaja isolated from the roof-top of a building. The S. geitleri produced PHB and the production of PHB was linear with the growth of cyanobacterium. The maximum PHB production (7.12% of dry cell weight) was recorded when the cells of S. geitleri were at their stationary growth phase. The production of PHB was optimum at pH 8.5 and 30 °C, and acetate (30 mM) was the preferred carbon source.

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.

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