Biphenyl and benzoate metabolism in a genomic context: Outlining genome-wide metabolic networks in Burkholderia xenovorans LB400

V. J. Denef, J. Park, T. V. Tsoi, J. M. Rouillard, H. Zhang, J. A. Wibbenmeyer, W. Verstraete, E. Gulari, S. A. Hashsham, J. M. Tiedje

Research output: Contribution to journalArticle

85 Citations (Scopus)

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 C1 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.

Original languageEnglish
Pages (from-to)4961-4970
Number of pages10
JournalApplied and Environmental Microbiology
Volume70
Issue number8
DOIs
Publication statusPublished - 2004 Aug 1

Fingerprint

Burkholderia
Benzoates
benzoates
Metabolic Networks and Pathways
biphenyl
genomics
genome
metabolism
Genome
gene
degradation
Oligonucleotide Array Sequence Analysis
Genes
Succinic Acid
cells
succinic acid
oligonucleotides
genes
biochemical pathways
gene expression

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Food Science
  • Applied Microbiology and Biotechnology
  • Ecology

Cite this

Denef, V. J. ; Park, J. ; Tsoi, T. V. ; Rouillard, J. M. ; Zhang, H. ; Wibbenmeyer, J. A. ; Verstraete, W. ; Gulari, E. ; Hashsham, S. A. ; Tiedje, J. M. / Biphenyl and benzoate metabolism in a genomic context : Outlining genome-wide metabolic networks in Burkholderia xenovorans LB400. In: Applied and Environmental Microbiology. 2004 ; Vol. 70, No. 8. pp. 4961-4970.
@article{f65a7a6f436342b0a36daa76c156c0a8,
title = "Biphenyl and benzoate metabolism in a genomic context: Outlining genome-wide metabolic networks in Burkholderia xenovorans LB400",
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 C1 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.",
author = "Denef, {V. J.} and J. Park and Tsoi, {T. V.} and Rouillard, {J. M.} and H. Zhang and Wibbenmeyer, {J. A.} and W. Verstraete and E. Gulari and Hashsham, {S. A.} and Tiedje, {J. M.}",
year = "2004",
month = "8",
day = "1",
doi = "10.1128/AEM.70.8.4961-4970.2004",
language = "English",
volume = "70",
pages = "4961--4970",
journal = "Applied and Environmental Microbiology",
issn = "0099-2240",
publisher = "American Society for Microbiology",
number = "8",

}

Denef, VJ, Park, J, Tsoi, TV, Rouillard, JM, 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', Applied and Environmental Microbiology, vol. 70, no. 8, pp. 4961-4970. https://doi.org/10.1128/AEM.70.8.4961-4970.2004

Biphenyl and benzoate metabolism in a genomic context : Outlining genome-wide metabolic networks in Burkholderia xenovorans LB400. / Denef, V. J.; Park, J.; Tsoi, T. V.; Rouillard, J. M.; Zhang, H.; Wibbenmeyer, J. A.; Verstraete, W.; Gulari, E.; Hashsham, S. A.; Tiedje, J. M.

In: Applied and Environmental Microbiology, Vol. 70, No. 8, 01.08.2004, p. 4961-4970.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Biphenyl and benzoate metabolism in a genomic context

T2 - Outlining genome-wide metabolic networks in Burkholderia xenovorans LB400

AU - Denef, V. J.

AU - Park, J.

AU - Tsoi, T. V.

AU - Rouillard, J. M.

AU - Zhang, H.

AU - Wibbenmeyer, J. A.

AU - Verstraete, W.

AU - Gulari, E.

AU - Hashsham, S. A.

AU - Tiedje, J. M.

PY - 2004/8/1

Y1 - 2004/8/1

N2 - 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 C1 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.

AB - 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 C1 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.

UR - http://www.scopus.com/inward/record.url?scp=4143056119&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=4143056119&partnerID=8YFLogxK

U2 - 10.1128/AEM.70.8.4961-4970.2004

DO - 10.1128/AEM.70.8.4961-4970.2004

M3 - Article

C2 - 15294836

AN - SCOPUS:4143056119

VL - 70

SP - 4961

EP - 4970

JO - Applied and Environmental Microbiology

JF - Applied and Environmental Microbiology

SN - 0099-2240

IS - 8

ER -