ArticleApplied and environmental microbiology2004
Biphenyl and benzoate metabolism in a genomic context: outlining genome-wide metabolic networks in Burkholderia xenovorans LB400.
Article in Applied and environmental microbiology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed, 116 citations in OpenAlex.
- Genomic analyses ofFrontiers in microbiology · 2023Article
- Evolution of genetic architecture and gene regulation in biphenyl/PCB-degrading bacteria.Frontiers in microbiology · 2023Review
- Genetic characterization of the cyclohexane carboxylate degradation pathway in the denitrifying bacterium Aromatoleum sp. CIB.Environmental microbiology · 2022Article
- Zeimonas arvi gen. nov., sp. nov., of the family Burkholderiaceae, harboring biphenyl- and phenolic acid-metabolizing genes, isolated from a long-term ecological research field.Antonie van Leeuwenhoek · 2021Article
- Structure and diversity of native bacterial communities in soils contaminated with polychlorinated biphenyls.AMB Express · 2020Article
- Whole genome sequence analysis of Cupriavidus campinensis S14E4C, a heavy metal resistant bacterium.Molecular biology reports · 2020Article
- Functional genomic analysis of bacterial lignin degraders: diversity in mechanisms of lignin oxidation and metabolism.Applied microbiology and biotechnology · 2020Review
- Complete Genome Sequence and Biodegradation Characteristics of Benzoic Acid-Degrading BacteriumBioMed research international · 2020Article
- Article
- Metabolic pathway and cell adaptation mechanisms revealed through genomic, proteomic and transcription analysis of a Sphingomonas haloaromaticamans strain degrading ortho-phenylphenol.Scientific reports · 2017Article
- Lanthanides: New life metals?World journal of microbiology & biotechnology · 2016Review
- Genetic and Functional Analysis of the Biosynthesis of a Non-Ribosomal Peptide Siderophore in Burkholderia xenovorans LB400.PloS one · 2016Article
- Genome-Wide Analysis of Host Responses to Four Different Types of Microorganisms in Bombyx Mori (Lepidoptera: Bombycidae).Journal of insect science (Online) · 2016Article
- Characterization of the molecular degradation mechanism of diphenyl ethers by Cupriavidus sp. WS.Environmental science and pollution research international · 2015Article
- Article
- Spatial distribution of an uranium-respiring betaproteobacterium at the Rifle, CO field research site.PloS one · 2015Article
- Transformation of hydroxylated derivatives of 2,5-dichlorobiphenyl and 2,4,6-trichlorobiphenyl by Burkholderia xenovorans LB400.Environmental science and pollution research international · 2014Article
- Identification of 3-sulfinopropionyl coenzyme A (CoA) desulfinases within the Acyl-CoA dehydrogenase superfamily.Journal of bacteriology · 2014Article
- Metabolomic and proteomic insights into carbaryl catabolism by Burkholderia sp. C3 and degradation of ten N-methylcarbamates.Biodegradation · 2013Article
- Regulon studies and in planta role of the BraI/R quorum-sensing system in the plant-beneficial Burkholderia cluster.Applied and environmental microbiology · 2013Article
Corrections and comments
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Authors and funding
10 authors at 4 institutions in 3 countries.
Funding
Abstract
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 C(1) 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.
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