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Aromatics Degradation in Geobacter metallireducens


ABSTRACT: Geobacter metallireducens serves as the model for Geobacter species that anaerobically oxidize aromatic contaminants with the reduction of Fe(III) oxides in contaminated sediments. Analysis of the complete G. metallireducens genome sequence revealed a 307 kb region, designated the aromatics island, not found in closely related species that do not degrade aromatics. This region encoded enzymes for the degradation of benzoate and other aromatic compounds with the exception of the genes for the conversion of toluene to benzyol-CoA which were in a different region of the genome. Predicted aromatic degradation pathways were similar to those described in more well-studied organisms except that no genes encoding a benzoyl-CoA reductase were present. A genome-wide comparison of gene transcript levels during growth on benzoate versus growth on acetate demonstrated that the majority of the most significant increases in transcript levels were among genes within the aromatics island. Of particular interest were highly expressed genes that encode redox proteins of unknown function, one of which had a homolog outside the aromatics island that was also highly expressed. There was also an apparent shift in the acetyl-CoA oxidation pathway to the use of a putative ATP-yielding succinyl-CoA synthase during growth on benzoate. These results provide new insights into the pathways for the degradation of aromatic compounds in G. metallireducens, indicate genes whose role in benzoate metabolism need to be evaluated further, and suggest target genes whose expression may be monitored in order to better assess the degradation of aromatic compounds in contaminated environments. Keywords: Metabolism Overall design: G. metallireducens GS-15 from our laboratory culture collection was cultured at 30°C in electron donor limited chemostats. The dilution rate was 0.05 h-1 with acetate (5 mM) or benzoate (1.25 mM) provided as the electron donor and ferric citrate (55mM) as the electron acceptor. Cells were harvested from three replicate chemostats for each of the electron donors. RNA extraction, purification, and labeling were performed independently on each cell sample.Two samples of each total RNA preparation were labeled, one with Cy3-dUTP and another with Cy5-dUTP for microarray hybridization (Dye swap) The dye swap hybridization was repeated for all samples, yielding 12 hybridizations in total.

INSTRUMENT(S): ORNL-ESD Geobacter metallireducens 70mer oligo-array

ORGANISM(S): Geobacter Metallireducens Gs-15

SUBMITTER: Qiang He  

PROVIDER: GSE5401 | GEO | 2007-07-03

SECONDARY ACCESSION(S): PRJNA96299

REPOSITORIES: GEO

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Publications

Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site.

Butler Jessica E JE   He Qiang Q   Nevin Kelly P KP   He Zhili Z   Zhou Jizhong J   Lovley Derek R DR  

BMC genomics 20070619


<h4>Background</h4>Groundwater and subsurface environments contaminated with aromatic compounds can be remediated in situ by Geobacter species that couple oxidation of these compounds to reduction of Fe(III)-oxides. Geobacter metallireducens metabolizes many aromatic compounds, but the enzymes involved are not well known.<h4>Results</h4>The complete G. metallireducens genome contained a 300 kb island predicted to encode enzymes for the degradation of phenol, p-cresol, 4-hydroxybenzaldehyde, 4-hy  ...[more]

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